for Journals by Title or ISSN
for Articles by Keywords
help
  Subjects -> BIOLOGY (Total: 3153 journals)
    - BIOCHEMISTRY (243 journals)
    - BIOENGINEERING (119 journals)
    - BIOLOGY (1504 journals)
    - BIOPHYSICS (48 journals)
    - BIOTECHNOLOGY (240 journals)
    - BOTANY (229 journals)
    - CYTOLOGY AND HISTOLOGY (30 journals)
    - ENTOMOLOGY (69 journals)
    - GENETICS (164 journals)
    - MICROBIOLOGY (259 journals)
    - MICROSCOPY (10 journals)
    - ORNITHOLOGY (26 journals)
    - PHYSIOLOGY (73 journals)
    - ZOOLOGY (139 journals)

BIOLOGY (1504 journals)                  1 2 3 4 5 6 7 8 | Last

Showing 1 - 200 of 1720 Journals sorted alphabetically
AAPS Journal     Hybrid Journal   (Followers: 22)
Achievements in the Life Sciences     Open Access   (Followers: 5)
ACS Synthetic Biology     Hybrid Journal   (Followers: 25)
Acta Biologica Colombiana     Open Access   (Followers: 7)
Acta Biologica Hungarica     Full-text available via subscription   (Followers: 4)
Acta Biologica Sibirica     Open Access   (Followers: 1)
Acta Biomaterialia     Hybrid Journal   (Followers: 27)
Acta Biotheoretica     Hybrid Journal   (Followers: 4)
Acta Chiropterologica     Full-text available via subscription   (Followers: 6)
acta ethologica     Hybrid Journal   (Followers: 4)
Acta Fytotechnica et Zootechnica     Open Access   (Followers: 1)
Acta Limnologica Brasiliensia     Open Access   (Followers: 3)
Acta Médica Costarricense     Open Access   (Followers: 2)
Acta Musei Silesiae, Scientiae Naturales     Open Access  
Acta Neurobiologiae Experimentalis     Open Access  
Acta Parasitologica     Hybrid Journal   (Followers: 10)
Acta Scientiarum. Biological Sciences     Open Access   (Followers: 2)
Acta Scientifica Naturalis     Open Access   (Followers: 3)
Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis     Open Access  
Actualidades Biológicas     Open Access   (Followers: 1)
Advanced Health Care Technologies     Open Access   (Followers: 4)
Advanced Journal of Graduate Research     Open Access  
Advanced Studies in Biology     Open Access  
Advances in Antiviral Drug Design     Full-text available via subscription   (Followers: 2)
Advances in Bioinformatics     Open Access   (Followers: 17)
Advances in Biological Regulation     Hybrid Journal   (Followers: 4)
Advances in Biology     Open Access   (Followers: 9)
Advances in Biosensors and Bioelectronics     Open Access   (Followers: 7)
Advances in Cell Biology/ Medical Journal of Cell Biology     Open Access   (Followers: 25)
Advances in Cellular and Molecular Biology of Membranes and Organelles     Full-text available via subscription   (Followers: 12)
Advances in Developmental Biology     Full-text available via subscription   (Followers: 12)
Advances in DNA Sequence-Specific Agents     Full-text available via subscription   (Followers: 5)
Advances in Ecological Research     Full-text available via subscription   (Followers: 44)
Advances in Environmental Sciences - International Journal of the Bioflux Society     Open Access   (Followers: 17)
Advances in Enzyme Research     Open Access   (Followers: 10)
Advances in Experimental Biology     Full-text available via subscription   (Followers: 7)
Advances in Genome Biology     Full-text available via subscription   (Followers: 8)
Advances in High Energy Physics     Open Access   (Followers: 19)
Advances in Human Biology     Open Access   (Followers: 3)
Advances in Life Science and Technology     Open Access   (Followers: 16)
Advances in Life Sciences     Open Access   (Followers: 6)
Advances in Marine Biology     Full-text available via subscription   (Followers: 17)
Advances in Molecular and Cell Biology     Full-text available via subscription   (Followers: 22)
Advances in Organ Biology     Full-text available via subscription   (Followers: 1)
Advances in Planar Lipid Bilayers and Liposomes     Full-text available via subscription   (Followers: 3)
Advances in Regenerative Biology     Open Access   (Followers: 1)
Advances in Space Biology and Medicine     Full-text available via subscription   (Followers: 6)
Advances in Structural Biology     Full-text available via subscription   (Followers: 5)
Advances in Virus Research     Full-text available via subscription   (Followers: 5)
African Journal of Range & Forage Science     Hybrid Journal   (Followers: 6)
AFRREV STECH : An International Journal of Science and Technology     Open Access   (Followers: 1)
Ageing Research Reviews     Hybrid Journal   (Followers: 11)
Aging Cell     Open Access   (Followers: 16)
Agrokémia és Talajtan     Full-text available via subscription   (Followers: 2)
Agrokreatif Jurnal Ilmiah Pengabdian kepada Masyarakat     Open Access  
AJP Cell Physiology     Hybrid Journal   (Followers: 15)
AJP Endocrinology and Metabolism     Hybrid Journal   (Followers: 24)
AJP Lung Cellular and Molecular Physiology     Hybrid Journal   (Followers: 3)
Al-Kauniyah : Jurnal Biologi     Open Access  
Alasbimn Journal     Open Access   (Followers: 1)
Alces : A Journal Devoted to the Biology and Management of Moose     Open Access  
AMB Express     Open Access   (Followers: 1)
Ambix     Hybrid Journal   (Followers: 3)
American Biology Teacher     Full-text available via subscription   (Followers: 14)
American Fern Journal     Full-text available via subscription   (Followers: 1)
American Journal of Agricultural and Biological Sciences     Open Access   (Followers: 8)
American Journal of Bioethics     Hybrid Journal   (Followers: 12)
American Journal of Human Biology     Hybrid Journal   (Followers: 14)
American Journal of Medical and Biological Research     Open Access   (Followers: 8)
American Journal of Plant Sciences     Open Access   (Followers: 19)
American Journal of Primatology     Hybrid Journal   (Followers: 15)
American Malacological Bulletin     Full-text available via subscription   (Followers: 3)
American Naturalist     Full-text available via subscription   (Followers: 74)
Amphibia-Reptilia     Hybrid Journal   (Followers: 6)
Anadolu University Journal of Science and Technology : C Life Sciences and Biotechnology     Open Access  
Anaerobe     Hybrid Journal   (Followers: 4)
Analytical Methods     Full-text available via subscription   (Followers: 11)
Anatomical Science International     Hybrid Journal   (Followers: 3)
Animal Cells and Systems     Hybrid Journal   (Followers: 4)
Animal Models and Experimental Medicine     Open Access  
Annales de Limnologie - International Journal of Limnology     Hybrid Journal   (Followers: 1)
Annales françaises d'Oto-rhino-laryngologie et de Pathologie Cervico-faciale     Full-text available via subscription   (Followers: 3)
Annales Henri Poincaré     Hybrid Journal   (Followers: 3)
Annals of Applied Biology     Hybrid Journal   (Followers: 7)
Annals of Biomedical Engineering     Hybrid Journal   (Followers: 18)
Annals of Human Biology     Hybrid Journal   (Followers: 5)
Annals of Science and Technology     Open Access  
Annual Review of Biomedical Engineering     Full-text available via subscription   (Followers: 14)
Annual Review of Biophysics     Full-text available via subscription   (Followers: 23)
Annual Review of Cancer Biology     Full-text available via subscription   (Followers: 2)
Annual Review of Cell and Developmental Biology     Full-text available via subscription   (Followers: 37)
Annual Review of Food Science and Technology     Full-text available via subscription   (Followers: 13)
Annual Review of Genomics and Human Genetics     Full-text available via subscription   (Followers: 23)
Annual Review of Phytopathology     Full-text available via subscription   (Followers: 12)
Anthropological Review     Open Access   (Followers: 23)
Anti-Infective Agents     Hybrid Journal   (Followers: 3)
Antibiotics     Open Access   (Followers: 9)
Antioxidants     Open Access   (Followers: 4)
Antioxidants & Redox Signaling     Hybrid Journal   (Followers: 8)
Antonie van Leeuwenhoek     Hybrid Journal   (Followers: 5)
Anzeiger für Schädlingskunde     Hybrid Journal   (Followers: 1)
Apidologie     Hybrid Journal   (Followers: 4)
Apmis     Hybrid Journal   (Followers: 1)
APOPTOSIS     Hybrid Journal   (Followers: 8)
Applied Bionics and Biomechanics     Open Access   (Followers: 8)
Applied Vegetation Science     Full-text available via subscription   (Followers: 10)
Aquaculture Environment Interactions     Open Access   (Followers: 3)
Aquaculture International     Hybrid Journal   (Followers: 24)
Aquaculture Reports     Open Access   (Followers: 3)
Aquaculture, Aquarium, Conservation & Legislation - International Journal of the Bioflux Society     Open Access   (Followers: 7)
Aquatic Biology     Open Access   (Followers: 5)
Aquatic Ecology     Hybrid Journal   (Followers: 34)
Aquatic Ecosystem Health & Management     Hybrid Journal   (Followers: 15)
Aquatic Science and Technology     Open Access   (Followers: 3)
Aquatic Toxicology     Hybrid Journal   (Followers: 23)
Archaea     Open Access   (Followers: 3)
Archiv für Molluskenkunde: International Journal of Malacology     Full-text available via subscription   (Followers: 3)
Archives of Biological Sciences     Open Access  
Archives of Microbiology     Hybrid Journal   (Followers: 8)
Archives of Natural History     Hybrid Journal   (Followers: 6)
Archives of Oral Biology     Hybrid Journal   (Followers: 2)
Archives of Virology     Hybrid Journal   (Followers: 5)
Archivum Immunologiae et Therapiae Experimentalis     Hybrid Journal   (Followers: 2)
Arid Ecosystems     Hybrid Journal   (Followers: 2)
Arquivos do Instituto Biológico     Open Access   (Followers: 1)
Arquivos do Museu Dinâmico Interdisciplinar     Open Access  
Arthropod Structure & Development     Hybrid Journal   (Followers: 2)
Arthropods     Open Access   (Followers: 1)
Artificial DNA: PNA & XNA     Hybrid Journal   (Followers: 3)
Asian Bioethics Review     Full-text available via subscription   (Followers: 3)
Asian Journal of Biodiversity     Open Access   (Followers: 4)
Asian Journal of Biological Sciences     Open Access   (Followers: 3)
Asian Journal of Cell Biology     Open Access   (Followers: 5)
Asian Journal of Developmental Biology     Open Access   (Followers: 2)
Asian Journal of Medical and Biological Research     Open Access   (Followers: 4)
Asian Journal of Nematology     Open Access   (Followers: 4)
Asian Journal of Poultry Science     Open Access   (Followers: 4)
Atti della Accademia Peloritana dei Pericolanti - Classe di Scienze Medico-Biologiche     Open Access  
Australian Life Scientist     Full-text available via subscription   (Followers: 2)
Australian Mammalogy     Hybrid Journal   (Followers: 6)
Autophagy     Hybrid Journal   (Followers: 2)
Avian Biology Research     Full-text available via subscription   (Followers: 4)
Avian Conservation and Ecology     Open Access   (Followers: 11)
Bacteriology Journal     Open Access   (Followers: 1)
Bacteriophage     Full-text available via subscription   (Followers: 3)
Bangladesh Journal of Bioethics     Open Access  
Bangladesh Journal of Plant Taxonomy     Open Access  
Bangladesh Journal of Scientific Research     Open Access   (Followers: 1)
Batman Üniversitesi Yaşam Bilimleri Dergisi     Open Access  
Berita Biologi     Open Access   (Followers: 1)
Between the Species     Open Access   (Followers: 1)
Bio Tribune Magazine     Hybrid Journal  
BIO Web of Conferences     Open Access  
BIO-Complexity     Open Access  
Bio-Grafía. Escritos sobre la Biología y su enseñanza     Open Access  
Bioanalytical Reviews     Hybrid Journal   (Followers: 2)
Biocatalysis and Biotransformation     Hybrid Journal   (Followers: 6)
BioCentury Innovations     Full-text available via subscription   (Followers: 1)
Biochemistry and Cell Biology     Hybrid Journal   (Followers: 15)
Biochimie     Hybrid Journal   (Followers: 7)
BioControl     Hybrid Journal   (Followers: 5)
Biocontrol Science and Technology     Hybrid Journal   (Followers: 5)
Biodemography and Social Biology     Hybrid Journal  
BioDiscovery     Open Access   (Followers: 2)
Biodiversitas : Journal of Biological Diversity     Open Access  
Biodiversity Data Journal     Open Access   (Followers: 4)
Biodiversity Informatics     Open Access   (Followers: 1)
Biodiversity Information Science and Standards     Open Access  
Biodiversity: Research and Conservation     Open Access   (Followers: 26)
Bioedukasi : Jurnal Pendidikan Biologi FKIP UM Metro     Open Access  
Bioeksperimen : Jurnal Penelitian Biologi     Open Access  
Bioelectrochemistry     Hybrid Journal   (Followers: 2)
Bioelectromagnetics     Hybrid Journal   (Followers: 1)
Bioenergy Research     Hybrid Journal   (Followers: 2)
Bioengineering and Bioscience     Open Access   (Followers: 1)
BioEssays     Hybrid Journal   (Followers: 10)
Bioethics     Hybrid Journal   (Followers: 15)
BioéthiqueOnline     Open Access  
Biofabrication     Hybrid Journal   (Followers: 5)
Biofilms     Full-text available via subscription   (Followers: 1)
Biogeosciences (BG)     Open Access   (Followers: 10)
Biogeosciences Discussions (BGD)     Open Access   (Followers: 2)
Bioinformatics     Hybrid Journal   (Followers: 305)
Bioinformatics and Biology Insights     Open Access   (Followers: 11)
Bioinspiration & Biomimetics     Hybrid Journal   (Followers: 7)
Biointerphases     Open Access   (Followers: 1)
Biojournal of Science and Technology     Open Access  
BioLink : Jurnal Biologi Lingkungan, Industri, Kesehatan     Open Access  
Biologia     Hybrid Journal  
Biologia on-line : Revista de divulgació de la Facultat de Biologia     Open Access  
Biological Bulletin     Partially Free   (Followers: 6)
Biological Control     Hybrid Journal   (Followers: 4)
Biological Invasions     Hybrid Journal   (Followers: 20)
Biological Journal of the Linnean Society     Hybrid Journal   (Followers: 18)
Biological Letters     Open Access   (Followers: 5)
Biological Procedures Online     Open Access  
Biological Psychiatry     Hybrid Journal   (Followers: 48)
Biological Psychology     Hybrid Journal   (Followers: 6)
Biological Research     Open Access  
Biological Rhythm Research     Hybrid Journal   (Followers: 2)

        1 2 3 4 5 6 7 8 | Last

Journal Cover
Anaerobe
Journal Prestige (SJR): 1.144
Citation Impact (citeScore): 3
Number of Followers: 4  
 
  Hybrid Journal Hybrid journal (It can contain Open Access articles)
ISSN (Print) 1075-9964 - ISSN (Online) 1095-8274
Published by Elsevier Homepage  [3162 journals]
  • Identification of an early stage biofilm inhibitor from Veillonella
           tobetsuensis
    • Abstract: Publication date: August 2018Source: Anaerobe, Volume 52Author(s): Izumi Mashima, Hiroshi Miyakawa, Frank A. Scannapieco, Futoshi Nakazawa Oral biofilm, the cause of dental caries and periodontal diseases, consists of multiple bacterial species. Streptococcus spp. and Veillonella spp. have been reported as to be initial and early colonizers of oral biofilms. Our previous studies showed that Veillonella tobetsuensis may play an important role on the development of S. gordonii biofilms without coaggregation involving extracellular biomolecules. In this study, the effect of a cyclic dipeptide autoinducer from culture supernatants from V. tobetsuensis at late-exponential growth phase on S. gordonii biofilm was examined. The cyclic dipeptide, identified as cyclo (-L-Leu-L-Pro) by gas chromatography/mass spectrometry, inhibited the development of S. gordonii biofilm. Furthermore, cyclo (-L-Leu-L-Pro) appeared not to cause bactericidal effects on planktonic cells of S. gordonii. This is the first report that oral Veillonella produces cyclo (-L-Leu-L-Pro) in their culture supernatants. Moreover, the results of this study suggest that cyclo (-L-Leu-L-Pro) may have an application to inhibit early stage development of oral biofilms.Graphical abstractImage 1
       
  • Comparative diversity analysis of ruminal methanogens in Murrah buffaloes
           (Bubalus bubalis) in four states of North India
    • Abstract: Publication date: August 2018Source: Anaerobe, Volume 52Author(s): Sanjay Kumar, Sumit Singh Dagar, Ravi Kant Agrawal, Anil Kumar Puniya We compared the community structure of methanogens in Murrah breed of buffaloes of four states of north India using 16S rRNA gene clone library method. The results revealed the dominance of methanogens related to Methanobrevibacter in three states, while Methanomicrobium-related methanogens were abundant in one state.
       
  • Diversity of multidrug-resistant epidemic Clostridium difficile
           NAP1/RT027/ST01 strains in tertiary hospitals from Honduras
    • Abstract: Publication date: August 2018Source: Anaerobe, Volume 52Author(s): Fanny Hidalgo-Villeda, Edgardo Tzoc, Luque Torres, Efraín Bu, César Rodríguez, Carlos Quesada-Gómez In recent years, reports of NAP1/RT027/ST01 epidemic strains of Clostridium difficile producing outbreaks of healthcare-associated diarrhea have increased in America and Europe. We cultivated multidrug-resistant NAP1/RT027/ST01 strains from the FQR2 linage from TcdA/TcdB+ stool samples obtained from patients in two Honduran hospitals. The PFGE macrorestriction patterns of two of the isolates were new. These bacteria were toxigenic and induced with different magnitude classical cytopathic effects on HeLa cells. Besides their resistance to twelve antibiotics, including to clindamycin, fluoroquinolones, linezolid and tigecycline. In this regard, they show the gyrA mutation that typifies epidemic C. difficile genotypes and carry cfr-like genes in different molecular contexts, respectively. These results confirm the spread of multidrug-resistant NAP1/RT027/ST01 strains in Central America with potential idiosyncratic adaptations.
       
  • Multidrug resistant Clostridium difficile ribotype 027 in southwestern
           Virginia, 2007 to 2013
    • Abstract: Publication date: August 2018Source: Anaerobe, Volume 52Author(s): R.J. Carman, H.M. Daskalovitz, M.W. Lyerly, M.Y. Davis, M.V. Goodykoontz, J.H. Boone The excess from fecal samples submitted to a centralized laboratory in Roanoke, Virginia for routine C. difficile testing was used for this research study. We tested all samples, including any formed samples usually not assayed in diagnostic laboratories. Our first aim was to rank ribotypes by their frequency. Between 2007 and 2013, fluoroquinolone resistant 027 (027FQR), a multi-drug resistant ribotype, was 32% of 3118 Clostridium difficile isolates and the most common of 128 ribotypes. 027FQR was in 45% of cytotoxin positive but only 17% of cytotoxin negative fecal samples (p = 0.001) and 34% of unformed but only 21% of formed stool samples (p = 0.001), strong associations with features of symptomatic infection. Conversely, 014/020 (10% of isolates, third most common ribotype) was more often in unformed than formed stools (14% versus 9%; p = 0.002) and in cytotoxin negative than cytotoxin positive samples (11% versus 8%, p = 0.01). Fecal lactoferrin levels, an indication of intestinal inflammation, were significantly higher with 027FQR than with 014/020 infections (median 308 versus 26 ng/mL, p = 0.02). 027FQR fecal bioburdens and toxin levels were significantly higher than their 014/020 equivalents (median 104.1 versus 103.2/g feces, p = 0.01; median TcdA 58.7 versus 1.3 ng/g feces, p = 0.04; median TcdB 43.4 versus 0.3 ng/g feces, p = 0.001). Binary toxin was present in 40% of 027FQR positive samples but none of the 014/020 or non-toxigenic C. difficile positive samples. 027FQR made no more TcdA/cell than did 014/020 (p = 0.7) but did make close to significantly more TcdB/cell (p = 0.08).
       
  • In-vitro investigation of anti-acne properties of Mangifera indica L.
           kernel extract and its mechanism of action against Propionibacterium acnes
           
    • Abstract: Publication date: August 2018Source: Anaerobe, Volume 52Author(s): Worrapan Poomanee, Wantida Chaiyana, Monika Mueller, Helmut Viernstein, Watcharee Khunkitti, Pimporn Leelapornpisid Propionibacterium acnes has been recognized as a main target for medical treatment of acne since this bacterium promotes acne inflammation by inducing upregulation of pro-inflammatory cytokines production, resulting in an accumulation of neutrophils and oxygen-free radicals produced by neutrophils within acne lesion. The aims of this study were to evaluate the biological activities of Mangifera indica kernel extracts grown in Northern Thailand (Kaew-Moragot cultivar), related to anti-acne properties including antimicrobial effect against acne-inducing bacteria together with the first elucidation of the mechanism of action against Propionibacterium acnes, anti-oxidation, and anti-inflammation. The kernels of M. indica, obtained from raw and ripe fruits, were macerated using various solvents. Agar diffusion and broth microdilution methods were performed to investigate the antibacterial activities of the extracts against P. acnes, Staphylococcus aureus, and Staphylococcus epidermidis. The ethanolic fractions exhibited the strongest antimicrobial effect against P. acnes with minimum inhibitory concentration and minimum bactericidal concentration of 1.56 mg/mL and 12.50 mg/mL, respectively. Bactericidal effect against P. acnes of these extracts could be observed after 3 h of incubation from time-kill curve. The chromatograms of high-performance liquid chromatography showed that the extracts existed gallic acid with high total phenolic content. These extracts additionally showed strong free radical scavenging properties on 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) as well as a notable inhibitory effect on linoleic acid peroxidation, which highly correlated to their antimicrobial effect, total phenolic, and gallic acid contents. The images, studied through using transmission electron microscopy, revealed that the extract certainly disrupted P. acnes cell membrane after exposure for 1 h as well as induced the consequent leakage of cytoplasmic materials. The inhibitory effects of the extracts on IL-8 secretion from LPS-inducing RAW 264.7 cells were also presented. In conclusion, the kernel extracts of raw M. indica fruit were effective against aerobic and anaerobic acne-inducing bacteria particularly P. acnes and exerted antioxidant along with anti-inflammatory activities. Therefore, the extracts might be potential agents for inflammatory acne treatment. However, clinical study is needed for further investigation.Graphical abstractImage
       
  • A multicenter survey of antimicrobial susceptibility of Prevotella species
           as determined by Etest methodology
    • Abstract: Publication date: August 2018Source: Anaerobe, Volume 52Author(s): Nurver Ulger Toprak, Alida C.M. Veloo, Edit Urban, Ingrid Wybo, Ulrik S. Justesen, Helene Jean-Pierre, Trefor Morris, Oncu Akgul, Guven Kulekci, Guner Soyletir, Elisabeth Nagy, ESCMID Study Group for Anaerobic Infections (ESGAI) Knowledge about the antimicrobial susceptibility patterns of different Prevotella species is limited. The aim of this study was to determine the current antimicrobial susceptibility of clinical isolates of Prevotella species from different parts of Europe, Kuwait and Turkey. Activity of 12 antimicrobials against 508 Prevotella isolates, representing 19 species, were tested according to Etest methodology. EUCAST, CLSI and FDA guidelines were used for susceptibility interpretations. All Prevotella species were susceptible to piperacillin/tazobactam, imipenem, meropenem, tigecycline and metronidazole. Ampicillin/sulbactam and cefoxitin also showed good activity. Ampicillin, clindamycin, tetracycline and moxifloxacin were less active; 51.2%, 33.7%, 36.8% and 18.3% of isolates were non-susceptible, respectively. A total of 49 (9.6%) isolates were resistant to three or more antimicrobials. Prevotella bivia was the most prevalent species (n = 118) and accounted for most of the multidrug-resistant isolates. In conclusion, the level of non-susceptibility to antimicrobials, which may be used for treatment of infections involving Prevotella species, are a cause of concern. This data emphasizes the need for species level identification of clinical Prevotella isolates and periodic monitoring of their susceptibility to guide empirical treatment.
       
  • ent-Copalic acid antibacterial and anti-biofilm properties against
           Actinomyces naeslundii and Peptostreptococcus anaerobius
    • Abstract: Publication date: August 2018Source: Anaerobe, Volume 52Author(s): Maria Gorete Mendes de Souza, Luís Fernando Leandro, Thaís da Silva Moraes, Fariza Abrão, Rodrigo Cassio Sola Veneziani, Sergio Ricardo Ambrosio, Carlos Henrique Gomes Martins Diterpenes are an important class of plant metabolites that can be used in the search for new antibacterial agents. ent-Copalic acid (CA), the major diterpene in Copaifera species exudates, displays several pharmacological properties. This study evaluates the CA antibacterial potential against the anaerobic bacteria Peptostreptococcus anaerobius and Actinomyces naeslundii. Antimicrobial assays included time-kill and biofilm inhibition and eradication assays. Time-kill assays conducted for CA concentrations between 6.25 and 12.5 μg/mL evidenced bactericidal activity within 72 h. CA combined with chlorhexidine dihydrochloride (CHD) exhibited bactericidal action against P. anaerobius within 6 h of incubation. As for A. naeslundii, the same combination reduced the number of microorganisms by over 3 log10 at 24 h and exerted a bactericidal effect at 48 h of incubation. CA at 500 and 2000 μg/mL inhibited P. anaerobius and A. naeslundii biofilm formation by at least 50%, respectively. CA at 62.5 and 1.000 μg/mL eradicated 99.9% of pre-formed P. anaerobius and A. naeslundii biofilms, respectively. These results indicated that CA presents in vitro antibacterial activity and is a potential biofilm inhibitory agent. This diterpene may play an important role in the search for novel sources of agents that can act against anaerobic bacteria.
       
  • In vitro stability of three oral vancomycin preparations stored at 2-
           5 °C and ambient room temperature for up to 60 days against 100
           Clostridioides (Clostridium) difficile and 51Staphylococcus aureus strains
           
    • Abstract: Publication date: August 2018Source: Anaerobe, Volume 52Author(s): Ellie J.C. Goldstein, Diane M. Citron, Kerin L. Tyrrell, Eliza Leoncio Oral vancomycin is used to treat Clostridioides (Clostridium) difficile infection. Several different preparations are available including reconstituted IV solutions, vancomycin capsules, and grape flavored vancomycin oral solution kit (CutisPharma). The shelf life for IV after reconstitution varies between 7 and 14 days under refrigeration, and a standard 30 days for vancomycin oral solution kit (CutisPharma). The impact of storage on the in vitro potency was determined in 3 different vancomycin preparations by measuring MICs for 100 strains of C. difficile and 25 strains of Staphylococcus aureus, at T0, 14, 30, and 60 days, stored at ambient (RT) and refrigerated (2–5 °C) temperatures. All vancomycin preparations showed potency over a period of 60 days regardless of storage conditions. However, the capsule preparation showed mold after 60 days at room temperature, but unlike vancomycin oral solution kit, which retained a clear appearance, the IV and capsule preps showed evidence of crystallization.
       
  • Qualitative, quantitative and genotypic evaluation of Aggregatibacter
           actinomycetemcomitans and Fusobacterium nucleatum isolated from
           individuals with different periodontal clinical conditions
    • Abstract: Publication date: August 2018Source: Anaerobe, Volume 52Author(s): Viviane Aparecida Arenas Rodrigues, Erica Dorigatti de Avila, Viviane Nakano, Mario Julio Avila-Campos Aggregatibacter actinomycetemcomitans and Fusobacterium nucleatum are strongly associated with periodontitis, and their evaluations are relevant to understand their role in the etiology and progression of periodontal diseases. In this study, the qualitative and quantitative detection of A. actinomycetemcomitans and F. nucleatum, as well as their genetic diversity, were evaluated in individuals with gingivitis, chronic periodontitis and periodontally healthy. In addition, the biotyping, serotyping, and prevalence of the ltx and cdt genes in A. actinomycetemcomitans were also determined. Subgingival biofilms obtained from gingivitis (70), periodontitis (75) and healthy (95) individuals were analyzed by cultures and PCR. Bacterial typing and presence of ltx and cdt genes in A. actinomycetemcomitans were also verified. DNA from A. actinomycetemcomitans and F. nucleatum was detected respectively, in 65.7% and 57.1% of gingivitis, 80% and 68% of periodontitis, and 57.8% and 37.8% of healthy. A. actinomycetemcomitans from gingivitis were biotypes I, II, IV, V, and X, and serotypes a, c, and e. In periodontitis, biotypes II, VI, and X, and serotypes a, b, and c were found. In healthy subjects, biotypes II and X, and serotypes b and c were found. The LTX and ltxA were observed in strains from gingivitis and periodontitis pockets. Subsequently, our data also showed no direct relationship between ltxA gene expression and leukotoxin gene 530-bp presence. On the other hand, cdt gene predominated during the inflammatory disease process. Our results strongly support a role of A. actinomycetemcomitans and F. nucleatum in advanced stage of periodontal disease.
       
  • Composition and metabolism of fecal microbiota from normal and overweight
           children are differentially affected by melibiose, raffinose and
           raffinose-derived fructans
    • Abstract: Publication date: August 2018Source: Anaerobe, Volume 52Author(s): Kaarel Adamberg, Signe Adamberg, Karin Ernits, Anneli Larionova, Tiia Voor, Madis Jaagura, Triinu Visnapuu, Tiina Alamäe The aim of the study was to investigate the metabolism of non-digestible oligo- and polysaccharides by fecal microbiota, using isothermal microcalorimetry. The five tested substrates were raffinose, melibiose, a mixture of oligo- and polysaccharides produced from raffinose by levansucrase, levan synthesized from raffinose, and levan from timothy grass. Two inocula were comprised of pooled fecal samples from overweight or normal-weight children, from healthy adult volunteers and a pure culture of Bacteroides thetaiotaomicron as a reference bacterium for colon microbiota. The growth was analyzed based on the heat evolution curves, and the production of organic acids and gases. Taxonomic profiles of the microbiota were assessed by 16S rDNA sequencing.Raffinose and melibiose promoted the growth of bifidobacteria in all fecal pools. Several pool-specific substrate-related responses to raffinose and melibiose were revealed. Lactate-producing bacteria (Streptococcus and Enterococcus) became enriched in the pool of overweight children resulting in lactic acid as the major fermentation product on short saccharides. Acetic and butyric acids were prevalent at fermentation in the normal-weight pool coinciding with the enrichment of Catenibacterium. In the adult pool, the specific promotion of Bacteroides and Lachnospiraceae by levans was disclosed. In the fecal pool of normal-weight children, levans stimulated the growth of Senegalimassilia and Lachnoclostridium and this particular pool also showed the highest maximum heat production rate at levan fermentation. Levans and raffinose-derived oligosaccharides, but not raffinose and melibiose were completely fermented by a pure culture of Bacteroides thetaiotaomicron.The main conclusion from the study is that fecal microbiota of normal and overweight children have different compositions and they respond in specific manners to non-digestible oligo- and polysaccharides: raffinose, melibiose, raffinose-derived oligosaccharides and levans. The potential of the tested saccharides to support a healthy balance of colon microbiota requires further studies.Graphical abstractImage 1
       
  • Smokeless tobacco impacts oral microbiota in a Syrian Golden hamster cheek
           pouch carcinogenesis model
    • Abstract: Publication date: August 2018Source: Anaerobe, Volume 52Author(s): Jinshan Jin, Lei Guo, Linda VonTungeln, Michelle Vanlandingham, Carl E. Cerniglia, Huizhong Chen The use of smokeless tobacco products (STPs) can cause many serious health problems. The oral microbiota plays important roles in oral and systemic health, and the disruption in the oral microbial population is linked to periodontal disease and other health problems. To assess the impact of smokeless tobacco on oral microbiota in vivo, high-throughput sequencing was used to examine the oral microbiota present in Syrian Golden hamster cheek pouches. Sixteen hamsters were divided into four groups and treated with the STP Grizzly snuff (0, 2.5, 25, or 250 mg) twice daily for 4 weeks. After 0, 1, 2, 3, and 4 weeks of treatment, bacterial genomic DNA was extracted from oral swabs sampled from the cheek pouches of the hamsters. The oral bacterial communities present in different hamster groups were characterized by sequencing the hypervariable regions V1-V2 and V4 of 16S rRNA using the Illumina MiSeq platform. Fifteen phyla, 27 classes, 59 orders, 123 families, and 250 genera were identified from 4,962,673 sequence reads from the cheek pouch samples. The bacterial diversity and taxonomic abundances for the different treatment groups were compared to the non–treated hamsters. Bacterial diversity was significantly decreased after 4 weeks of exposure to 2.5 mg, and significantly increased by exposure to 250 mg STP. Treatment with 250 mg STP significantly increased Firmicutes, transiently increased Cyanobacteria and TM7, and decreased Bacteroidetes and Fusobacteria compared to the control group. At the genus level, 4 weeks of administration of 250 mg STP significantly increased Granulicatella, Streptococcus, Oribacterium, Anaerococcus, Acidaminococcus, Actinomyces, Eubacterium, Negativicoccus, and Staphylococcus, and decreased Bacteroides, Buleidia, Dialister, and Leptotrichia, and transiently decreased Arcanobacterium compared to the control group. For the first time, an animal model was used for evaluating the effects of STP on oral microbiota by metagenomic sequencing. Our results provide a view of the shift of the oral microbiota in response to STP exposure in Syrian Golden hamster. Our findings indicate that the use of smokeless tobacco significantly disrupts the oral microbiota.
       
  • Two extracellular sialidases from Bifidobacterium bifidum promote the
           degradation of sialyl-oligosaccharides and support the growth of
           Bifidobacterium breve
    • Abstract: Publication date: August 2018Source: Anaerobe, Volume 52Author(s): Keita Nishiyama, Aki Nagai, Kazuya Uribayashi, Yuji Yamamoto, Takao Mukai, Nobuhiko Okada We investigated the roles of extracellular sialidases (SiaBb1 and SiaBb2) in cross-feeding between sialidase-carrying Bifidobacterium bifidum and sialic acid-utilizing Bifidobacterium breve. Using 6ʹ sialyllactose (6ʹSL) as a carbon source, the number of wild-type B. bifidum cells increased while that of a siabb2-inactivated strain (Δsiabb2) did not. Coculture of these two strains in the presence of 6ʹSL resulted in similar increase in cell numbers. Coculture of wild-type B. bifidum, but not the Δsiabb2 strain, with sialic acid-utilizing Bifidobacterium breve, which cannot release sialic acids from carbohydrates, in the presence of 6ʹSL increased the number of B. breve cells. Moreover, when mucin was used as a carbon source, B. breve growth was increased in cocultures with B. bifidum wild-type and Δsiabb2 strains, suggesting that SiaBb1 may be involved. Additionally, B. breve cell numbers increased during cultivation with recombinant SiaBb1-and SiaBb2-treated mucin as the sole carbon source. These results indicated that B. bifidum SiaBb2 liberated sialic acid from sialyl-human milk oligosaccharides and -mucin glycans, supporting the growth of B. breve through sialic acid cross-feeding. SiaBb1 may assist in the degradation of mucin glycan. Collectively, our results revealed that both the B. bifidum extracellular sialidases promote the utilization of sialylated carbohydrates and supply free sialic acid to other Bifidobacterium strains.
       
  • Characterization of quorum sensing system in Clostridium chauvoei
    • Abstract: Publication date: August 2018Source: Anaerobe, Volume 52Author(s): Sujeet Kumar, Mohmad Mashooq, Ravi Kumar Gandham, S.V. Alavandi, Viswas Konasagara Nagaleekar Clostridium chauvoei causes fatal black quarter infection in cattle and buffaloes. The quorum sensing (QS) system, a bacterial cell to cell communication process, of the pathogen was characterized in the current study. The results indicated that C. chauvoei lacked luxS (autoinducer-2) based quorum sensing as detected by the sensor strain Vibrio harveyi BB170. This was supported by absence of luxS gene in C. chauvoei genome. However, the genomic analysis indicated the presence of agrBD system in all three genomes of C. chauvoei available at the NCBI database. The AgrD, which synthesizes QS messenger auto-inducing peptide, was a 44 amino acid protein which shared 59% identity and 75% similarity with AgrD of C. perfringens strain 13 and 56% identity (20% coverage) with Staphylococcus aureus N315. The functional cysteine amino acid was conserved in all the strains. The genomic organisation further suggests the presence of diguanylate cyclase, a gene responsible for synthesis of secondary messenger cyclic di-GMP, at 3’ immediate downstream of agrD gene. The real time expression analysis for agrD gene indicated that expression was better at 37 °C (1.9–3.7 fold increase) compared to a higher temperature of 40 °C. However, stable expression was observed at different growth stages (log and early stationary phase) with 0.8–1.4 fold changes in expression pattern. The results indicate the presence of a constitutively expressed agrBD quorum sensing system in C. chauvoei.
       
  • Evaluation of a novel molecular assay to diagnose toxigenic strains of
           Clostridium difficile
    • Abstract: Publication date: August 2018Source: Anaerobe, Volume 52Author(s): Catherine Eckert, Thomas Devallière, Rabab Syed-Zaidi, Valérie Lalande, Frédéric Barbut The objective of this study was to evaluate the Amplidiag C. difficile+027® assay, a new molecular method that detects toxin B gene in stool samples and identifies the hypervirulent 027 strain, to diagnose Clostridium difficile infections. The assay was compared to the reference method i.e. toxigenic culture. Amplidiag C. difficile+027® assay was prospectively evaluated from 309 diarrheal stool specimens of patients suspected of C. difficile infection. Forty-five (14.6%) stools were positive by toxigenic culture and 11 (3.6%) stools gave discordant results with the molecular method. PR027 was not recovered during the study. After resolving the discrepant results, the sensitivity, specificity, positive and negative predictive values of Amplidiag C. difficile+027® assay were 91.1% [CI 95% 77.9–97.1], 99.6% [CI 95% 97.6–100], 97.6% [CI 95% 85.9–99.9] and 98.5% [CI 95% 96–99.5], respectively compared to toxigenic culture. This assay is sensitive compared to the toxigenic culture.
       
  • Establishment of a species-specific primer pair for detecting Veillonella
           infantium based on the 70 kDa heat shock protein gene dnaK
    • Abstract: Publication date: August 2018Source: Anaerobe, Volume 52Author(s): Izumi Mashima, Ariadna A. Djais, Elaine M. Haase, Frank A. Scannapieco, Maiko Otomo, Masato Saitoh, Futoshi Nakazawa Recently, Veillonella infantium was isolated from tongue biofilm of a Thai child and established as a novel Veillonella species. In this study, a species-specific primer was designed to identify V. infantium on the basis of the sequence of the 70 kDa heat shock protein (dnaK) gene of Veillonella infantium JCM 31738T (= TSD-88T). The primer pair generated a specific PCR (Polymerase Chain Reaction) product specific for V. infantium, but not for other oral Veillonella species. This specific primer pair could detect dnaK even from 1 pg of genomic DNA extracted from the V. infantium type strain. To validate the primer pair, a number of strains of Veillonella species were isolated from tongue biofilm of 3 Japanese children, DNA was isolated from each strain, and PCR was performed using species-specific primers. All oral Veillonella species except V. infantium were identified by one-step PCR method reported previously. Four kinds of Veillonella species were detected in these subjects. V. rogosae was detected in all subjects and the most predominant species with an average prevalence of 82%. However, V. infantium was detected in 2 of 3 subjects and it was the second most predominant species of oral Veillonella detected in these subjects with an average prevalence of 9.4%. V. infantium appears to coexist with other oral Veillonella species in tongue biofilm. This species-specific primer pair established in this study could be useful to detect V. infantium and support the study of Veillonella for oral health in the future.
       
  • Anaerobic gaseous biofuel production using microalgal biomass – A
           review
    • Abstract: Publication date: August 2018Source: Anaerobe, Volume 52Author(s): Roland Wirth, Gergely Lakatos, Tamás Böjti, Gergely Maróti, Zoltán Bagi, Gábor Rákhely, Kornél L. Kovács Most photosynthetic organisms store and convert solar energy in an aerobic process and produce biomass for various uses. Utilization of biomass for the production of renewable energy carriers employs anaerobic conditions. This review focuses on microalgal biomass and its use for biological hydrogen and methane production. Microalgae offer several advantages compared to terrestrial plants. Strategies to maintain anaerobic environment for biohydrogen production are summarized. Efficient biogas production via anaerobic digestion is significantly affected by the biomass composition, pretreatment strategies and the parameters of the digestion process. Coupled biohydrogen and biogas production increases the efficiency and sustainability of renewable energy production.Graphical abstractImage 1
       
  • Molecular genotyping, biofilm formation and antibiotic resistance of
           enterotoxigenic Clostridium perfringens isolated from meat supplied to
           school cafeterias in South Korea
    • Abstract: Publication date: August 2018Source: Anaerobe, Volume 52Author(s): Wen-Si Hu, Hun Kim, Ok Kyung Koo Clostridium perfringens is one of the leading causes of food poisoning worldwide. The aims of this study were to investigate the presence of C. perfringens in food supplied to school cafeterias, to assess the presence of toxin genes in the isolates, and to investigate the biofilm formation and antibiotic susceptibility of the isolates. A total of 30 C. perfringens strains (12.9%) from 232 samples of beef, pork, chicken, and duck meat were isolated. Toxin genes, including cpa, cpe, cpb2, and netB, were detected, while the cpb, etx, iap and tpeL genes were absent. Biofilm formation was analyzed, and all the isolates were able to form biofilm. Antibiotic resistance was observed against penicillin (97%), lincomycin (20%), bacitracin (97%), oxytetracycline (73%), trimethoprim (7%), gentamicin (10%), tetracycline (93%), erythromycin (83%), ampicillin (100%), amikacin (7%), and streptomycin (3%). In conclusion, the results showed that students are exposed to a potentially high risk of food poisoning by C. perfringens; therefore, precaution is required for these types of catering services.
       
  • Characterization of Clostridium difficile Isolates Collected during a
           Phase 2b Clinical Study with SYN-004 (ribaxamase) for the Prevention of C.
           difficile Infection
    • Abstract: Publication date: Available online 5 July 2018Source: AnaerobeAuthor(s): John F. Kokai-Kun, J. Lauren Sarver, Robert J. Carman During a Phase 2b study with SYN-004 (ribaxamase) for prevention of Clostridium difficile infection (CDI) conducted in North America and Eastern Europe, 45 C. difficile isolates from subjects with laboratory-confirmed CDI and or colonized with C. difficile were collected and characterized. Several C. difficile PCR ribotypes, including 027 and 198, were identified.
       
  • In Vitro Activity of Eravacycline and Comparator Antimicrobials Against
           143 Recent Strains of Bacteroides and Parabacteroides Species
    • Abstract: Publication date: Available online 4 July 2018Source: AnaerobeAuthor(s): Ellie.J.C. Goldstein, Diane M. Citron, Kerin L. Tyrrell Eravacycline, a novel fluorocycline antibiotic, has been evaluated against complicated mixed aerobic/anaerobic intra-abdominal infections but scant supporting in vitro data against anaerobes has been published. We found that eravacycline had good anaerobic in vitro activity with MICs of 4 μg/ml or less against all Bacteroides and Parabacteroides strains tested, except for two B. ovatus strains that had MICs of 8 μg/ml and one strain that had an MIC of 16 μg/ml. Eravacycline was four-to-eight fold more active than tigecycline
       
  • Routine use of MALDI-TOF MS for anaerobic bacterial identification in
           clinical microbiology
    • Abstract: Publication date: Available online 3 July 2018Source: AnaerobeAuthor(s): Samantha Shannon, Daniel Kronemann, Robin Patel, Audrey N. Schuetz In 2013, we adopted MALDI-TOF MS using the Bruker Biotyper system for identification of anaerobic bacteria into our routine clinical practice. Here, we describe our experience with the use of MALDI-TOF MS for anaerobic bacterial identification, highlighting its value in replacing the more costly and time-consuming 16S ribosomal RNA gene PCR plus sequencing-based approach as the primary method of anaerobic bacterial identification. We also describe our more recent experience with the use of early/rapid MALDI-TOF MS for identification of anaerobic bacteria performed on short incubation (4–6 h) plated aerobic media from anaerobic blood culture bottles positive for Gram-negative bacilli.
       
  • Identification of Porphyromonas isolates from clinical origin using
           MALDI-TOF Mass Spectrometry
    • Abstract: Publication date: Available online 2 July 2018Source: AnaerobeAuthor(s): Maribel Zamora-Cintas, Mercedes Marín, Lidia Quiroga, Andrea Martínez, María Antonia Fernández-Chico, Emilio Bouza, Belén Rodríguez-Sánchez, Luis Alcalá Despite the wide implementation of MALDI-TOF MS for the rapid and reliable identification of most microorganisms, some taxonomic groups such as the Porphyromonas genus remain largely untested.In this study we evaluated the performance of MALDI-TOF MS on this genus using a collection of 39 isolates sent for routine identification to our institution over a 16-year period. All of them were identified by DNA-sequencing analysis of the 16S rRNA gene plus the hsp60 gene when the previous one did not yield species-level assignment. MALDI-TOF MS provided correct identification at least at the genus level of 21/39 isolates (53.9%). Twelve isolates were correctly identified at the species level with a score value ≥ 2.0 and 9 more with score values 
       
  • Neutralization of macrophage migration inhibitory factor improves host
           survival after Clostridium difficile infection
    • Abstract: Publication date: Available online 23 June 2018Source: AnaerobeAuthor(s): Shinsmon Jose, Anindita Mukherjee, Mayuresh M. Abhyankar, Lin Leng, Richard Bucala, Divya Sharma, Rajat Madan Clostridium difficile is an important cause of nosocomial diarrhea in the western world. Toxins (A, B, and binary toxins) generated by C. difficile bacteria damage intestinal epithelial cells. Hallmarks of host response to C. difficile infection (CDI) include upregulation of inflammatory mediators and tissue infiltration by immune cells. Macrophage migration inhibitory factor (MIF) is an inflammatory cytokine that is known to enhance the host immune response to infectious pathogens. Additionally, MIF can adversely impact host survival to numerous infections. The role of MIF in the pathogenesis of CDI remains poorly understood. Here, we show that patients with CDI had significantly higher circulating MIF compared to patients who had diarrhea but tested negative for C. difficile (non-CDI controls). Similarly, in a mouse model, C. difficile challenge significantly increased levels of plasma and tissue MIF. Antibody-mediated depletion of MIF decreased C. difficile-induced inflammatory responses, clinical disease, and mortality. Together, these results uncover a potential role for MIF in exacerbating CDI and suggest that use of anti-MIF antibodies may represent a therapeutic strategy to curb host inflammatory responses and improve disease outcomes in CDI.
       
  • Examination of the Clostridioides (Clostridium) difficile VanZ
           ortholog, CD1240
    • Abstract: Publication date: Available online 22 June 2018Source: AnaerobeAuthor(s): Emily C. Woods, Daniela Wetzel, Monjori Mukerjee, Shonna M. McBride Clostridioides (Clostridium) difficile causes severe diarrheal disease that is directly associated with antibiotic use and resistance. Although C. difficile demonstrates intrinsic resistance to many antimicrobials, few genetic mechanisms of resistance have been characterized in this pathogen. In this study, we investigated the putative resistance factor, CD1240 (VanZ1), an ortholog of the teicoplanin resistance factor, VanZ, of Enterococcus faecium. In C. difficile, the vanZ1 gene is located within the skin element of the sporulation factor σK, which is excised from the mother cell compartment during sporulation. This unique localization enabled us to create a vanZ1 deletion mutant by inducing excision of the skin element. The Δskin mutant exhibited moderately decreased resistance to teicoplanin and had small effects on growth in some other cell-surface antimicrobials tested. Examination of vanZ1 expression revealed induction of vanZ1 transcription by the antimicrobial peptide LL-37; however, LL-37 resistance was not impacted by VanZ1, and none of the other tested antimicrobials induced vanZ1 expression. Further, expression of vanZ1 via an inducible promoter in the Δskin mutant restored growth in teicoplanin. These results demonstrate that like the E. faecium VanZ, C. difficile VanZ1 contributes to low-level teicoplanin resistance through an undefined mechanism.
       
  • Phenotypic identification of periodontal Prevotella intermedia/nigrescens
           group isolates validated by MALDI-TOF mass spectrometry.
    • Abstract: Publication date: Available online 18 June 2018Source: AnaerobeAuthor(s): Thomas E. Rams, Jacqueline D. Sautter, Chinhua Y. Hsiao, Arie J. van Winkelhoff The accuracy of a phenotypic scheme to recognize periodontal Prevotella intermedia/nigrescens group clinical isolates on primary isolation culture plates was assessed with matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS). A total of 84 fresh subgingival isolates from 23 chronic periodontitis patients were presumptively recognized on anaerobically-incubated enriched Brucella blood agar primary isolation plates as P. intermedia/nigrescens based on their dark-pigmented colony morphology, brick-red autofluorescence under long-wave ultraviolet light, and a negative fluorescence test for lactose production. The presumptive P. intermedia/nigrescens clinical isolates were subjected to MALDI-TOF MS analysis using Bruker MALDI Biotyper analytic software containing mass spectra for P. intermedia and Prevotella nigrescens in its reference library of bacterial protein profiles. Using a ≥ 1.7 log score agreement threshold, 60 (71.4%) of the presumptive P. intermedia/nigrescens clinical isolates were confirmed as either P. intermedia (25 isolates) or P. nigrescens (35 isolates). All isolates with a < 1.7 log score were also identified as P. intermedia or P. nigrescens from the top choice designated on the MALDI Biotyper most likely species identification list. These MALDI-TOF MS findings document the ability of the phenotypic scheme to correctly recognize most periodontal P. intermedia/nigrescens group clinical isolates on primary isolation culture plates.
       
  • Synthesis of peptide based epsilon toxin vaccine by covalent anchoring to
           tetanus toxoid
    • Abstract: Publication date: Available online 18 June 2018Source: AnaerobeAuthor(s): Himani Kaushik, Aparna Dixit, Lalit C. Garg The epsilon toxin (Etx) produced by Clostridium perfringens type B and D causes severe enterotoxaemia associated with a general edema and neurological alterations, leading to subsequent death and is listed as one of the most lethal toxins. Currently employed vaccines against C. perfringens epsilon toxin include toxoid based vaccines. Use of peptide vaccines has become an interesting approach for vaccination after the successful licensing of peptide vaccines against Haemophilus influenza, Neisseria meningitides and Streptococcus pneumonia that have demonstrated the potential and effectiveness of these vaccines. Therefore, the present study was undertaken to develop a peptide based vaccine against epsilon toxin. Peptides were selected on the basis of epitope mapping by making 35 overlapping peptides of 15 amino acid residues in length specific to the primary amino acid sequence of the toxin, with a 7 amino acid residues overlaps between sequential peptides. Chemically synthesized peptides that were recognised by the antibody against the full length epsilon toxin were further assessed for vaccine potential. The selected peptides were chemically conjugated to partially reduced tetanus toxoid (TT) using of N-succinimidyl-3(2-pyridyldithio) propionate. Immunization of BALB/c mice with TT-peptide conjugates by sub-cutaneous route induced sustained high level mixed immune response as analyzed by antibody isotyping. Immunoblot analysis and ELISA clearly indicated generation of Etx-specific antibodies. Further, neutralization studies with the antisera generated against the TT-conjugated peptide(s) demonstrated that the antisera were able to neutralize the lethal dose of epsilon toxin in vitro demonstrating its potential as a promising vaccine candidate against enterotoxaemia.
       
  • Comparative pathogenesis of enteric clostridial infections in humans and
           animals
    • Abstract: Publication date: Available online 5 June 2018Source: AnaerobeAuthor(s): Francisco A. Uzal, Mauricio A. Navarro, Jihong Li, John C. Freedman, Archana Shrestha, Bruce A. McClane Several enteric clostridial diseases can affect humans and animals. Of these, the enteric infections caused by Clostridium perfringens and Clostridium difficile are amongst the most prevalent and they are reviewed here. C. perfringens type A strains encoding alpha toxin (CPA) are frequently associated with enteric disease of many animal mammalian species, but their role in these diseased mammals remains to be clarified. C. perfringens type B encoding CPA, beta (CPB) and epsilon (ETX) toxins causes necro-hemorrhagic enteritis, mostly in sheep, and these strains have been recently suggested to be involved in multiple sclerosis in humans, although evidence of this involvement is lacking. C. perfringens type C strains encode CPA and CPB and cause necrotizing enteritis in humans and animals, while CPA and ETX producing type D strains of C. perfringens produce enterotoxemia in sheep, goats and cattle, but are not known to cause spontaneous disease in humans. The role of C. perfringens type E in animal or human disease remains poorly defined. The newly revised toxinotype F encodes CPA and enterotoxin (CPE), the latter being responsible for food poisoning in humans, and the less prevalent antibiotic associated and sporadic diarrhea. The role of these strains in animal disease has not been fully described and remains controversial. Another newly created toxinotype, G, encodes CPA and necrotic enteritis toxin B-like (NetB), and is responsible for avian necrotic enteritis, but has not been associated with human disease. C. difficile produces colitis and/or enterocolitis in humans and multiple animal species. The main virulence factors of this microorganism are toxins A, B and an ADP-ribosyltransferase (CDT). Other clostridia causing enteric diseases in humans and/or animals are Clostridium spiroforme, Clostridium piliforme, Clostridium colinum, Clostridium sordellii, Clostridium chauvoei, Clostridium septicum, Clostridium botulinum, Clostridium butyricum and Clostridium neonatale. The zoonotic transmission of some, but not all these clostridsial species, has been demonstrated.
       
  • High prevalence of Clostridium difficile PCR ribotype 078 in pigs
           in Korea
    • Abstract: Publication date: June 2018Source: Anaerobe, Volume 51Author(s): Ha-Young Kim, Ara Cho, Jong Wan Kim, Heejung Kim, Bumseok Kim Clostridium difficile can cause neonatal enteritis, but has been isolated from both diseased and healthy pigs. C. difficile shedding by pigs is a potential source of zoonotic transmission to humans. The objectives of this study were to characterize the prevalence and genotype of C. difficile with respect to age and health status in the pig industry for the first time in Korea. Fecal samples of 910 pigs were analyzed for the presence of C. difficile. In total, 176 (19.3%) C. difficile strains were isolated. The prevalence was significantly higher (p 
       
  • Evaluation of the Cepheid® Xpert® C. difficile binary toxin (BT)
           diagnostic assay
    • Abstract: Publication date: June 2018Source: Anaerobe, Volume 51Author(s): Alan M. McGovern, Grace O. Androga, Peter Moono, Deirdre A. Collins, Niki F. Foster, Barbara J. Chang, Thomas V. Riley Strains of Clostridium difficile producing only binary toxin (CDT) are found commonly in animals but not humans. However, human diagnostic tests rarely look for CDT. The Cepheid Xpert C. difficile BT assay detects CDT with equal sensitivity (≥92%) in human and animal faecal samples.
       
  • Improving culture media for the isolation of Clostridium
           difficile
    from compost
    • Abstract: Publication date: June 2018Source: Anaerobe, Volume 51Author(s): Muthu Dharmasena, Xiuping Jiang This study was to optimize the detection methods for Clostridium difficile from the animal manure-based composts. Both autoclaved and unautoclaved dairy composts were inoculated with a 12-h old suspension of a non-toxigenic C. difficile strain (ATCC 43593) and then plated on selected agar for vegetative cells and endospores. Six types of enrichment broths supplemented with taurocholate and l-cysteine were assessed for detecting a low level of artificially inoculated C. difficile (ca. 5 spores/g) from dairy composts. The efficacy of selected enrichment broths was further evaluated by isolating C. difficile from 29 commercial compost samples. Our results revealed that using heat-shock was more effective than using ethanol-shock for inducing endospore germination, and the highest endospore count (p 
       
  • The detection and prevalence of leukotoxin gene variant strains of
           Fusobacterium necrophorum in footrot lesions of sheep in Kashmir, India
    • Abstract: Publication date: June 2018Source: Anaerobe, Volume 51Author(s): S. Farooq, S.A. Wani, M.N. Hassan, S. Aalamgeer, Z.A. Kashoo, S.N. Magray, M.A. Bhat The objective of this study was to determine the prevalence and identification of leukotoxin gene, lktA, variant strains of Fusobacterium necrophorum in the footrot lesions of sheep. The detection of F. necrophorum was carried out by PCR targeting the lktA gene fragment and identification of lktA variant strains was done by PCR–single stranded conformational polymorphism (PCR-SSCP) and gene sequencing. Of the 450 swabs collected from footrot lesions of sheep, 117 were lktA-positive for F. necrophorum. Of the 50 swabs collected from apparently asymptomatic sheep, only one was lktA-positive for F. necrophorum. The overall prevalence of F. necrophorum in footrot affected sheep in Kashmir valley was 26%, and ranged from 20 to 34.8%, respectively. PCR-SSCP of lktA gene fragment analysis revealed three lktA variants, designated as JKS-F1/F2/F3, while two samples (1.7%) showed multiple lktA variant strains of F. necrophorum in a single footrot-affected sheep hoof. This appears to be the first report on the presence of more than one lktA variant of F. necrophorum in a footrot lesion of sheep. The JKS-F3 lktA variant was the most frequent (75.4%), followed by JKS-F2 (14.4%) and JKS-F1 (8.4%), respectively. Among the three lktA variants identified, JKS-F3 was detected in 74 (86.0%) samples from severe footrot affected sheep with a lesion score of 4. The data suggest that JKS-F3 is the predominant lktA variant of F. necrophorum and is associated with severe footrot in sheep. Hence, JKS-F3 may be a significant variant contributing to the severity and duration of the disease in sheep.
       
  • The ability of human intestinal anaerobes to metabolize different
           oligosaccharides: Novel means for microbiota modulation'
    • Abstract: Publication date: June 2018Source: Anaerobe, Volume 51Author(s): Riichi Ose, Katsuaki Hirano, Shintaro Maeno, Junichi Nakagawa, Seppo Salminen, Takumi Tochio, Akihito Endo Prebiotic oligosaccharides are known to have significant impacts on gut microbiota and are thus widely used to program healthy microbiota composition and activity from infants to the elderly. Bifidobacteria and lactobacilli are among the major target microorganisms of oligosaccharides, but the metabolic properties of oligosaccharides in other predominant gut microbes have not been well characterized. In the present study, we demonstrated the metabolic properties of six oligosaccharides in 31 key gut anaerobes. Bifidobacteria readily metabolized fructooligosaccharide (FOSs) with degree of polymerization (DP) 3, i.e. 1-kestose, but several strains used did not actively metabolize FOSs with DP4 and DP5, i.e. nystose and fructosylnystose. Akkermansia muciniphila, a potential new probiotic against obesity, did not show significant growth with any of the oligosaccharides tested. The butyrate producer Anaerostipes caccae grew well on 1-kestose but poorly on FOS mixtures, whereas it contained 1-kestose at 30%. Bacteroides-Parabacteroides group species were separated into two groups based on oligosaccharide metabolic properties. One group metabolized well most of the oligosaccharides tested, but the others metabolized only 1 or 2 selected oligosaccharides. Oligosaccharide profiles after culturing revealed that Bifidobacterium spp. preferentially metabolized shorter oligosaccharides (DP3) in the mixtures, whereas Bacteroides-Parabacteroides spp. did not show oligosaccharide selectivity for metabolism or rather preferred longer oligosaccharides (>DP4). The fermentation profiles indicated specific links between the microbial end-products and specific gut microbes. Available carbohydrates had a significant impact on the accumulation of amino acid-derived bacterial metabolites (i.e. phenol, p-cresol, indole and skatole) and short chain fatty acids. The results assist in predicting the impact of oligosaccharides in human intervention and gut microbiota modulation.
       
  • Toxin profile of fecal Clostridium perfringens strains isolated from
           children with autism spectrum disorders
    • Abstract: Publication date: June 2018Source: Anaerobe, Volume 51Author(s): Bartłomiej Góra, Zygmunt Gofron, Magdalena Grosiak, Małgorzata Aptekorz, Beata Kazek, Piotr Kocelak, Halina Radosz-Komoniewska, Jerzy Chudek, Gayane Martirosian Infectious factors are taken into consideration in pathophysiology of autism spectrum disorders (ASD). ASD patients often suffer from gastrointestinal disorders. The intestinal microbiota of autistic patients significantly differs from that in healthy individuals. The aim of the study was to compare the profile of toxins produced by C. perfringens strains isolated from feces of children with ASD, with healthy individuals and obese subjects.This study included 111 strains of C. perfringens: 49 isolates from 29 children with ASD, 30 - from 17 healthy individuals and 32 - from 24 young obese subjects. Alpha, beta, beta2, epsilon, iota and enterotoxin genes were detected using appropriate PCRs.The alpha toxin gene (cpa) was present in all 111 examined strains (100%). The beta2 gene (cpb2) was detected in 45/49 strains (91.8%) isolated from children with ASD, 17/30 (56.7%) isolates from healthy subjects, and 12 of 32 (37.5%) isolates from obese subjects. C. perfringens strains with cpb2 gene were detected in 27/29 ASD patients (93.1%), 10/17 healthy subjects (58.8%) and 11/24 (45.8%) obese subjects.Beta2 toxin encoding cpb2 gene was significantly more common in strains isolated from ASD patients, with no significant difference between control subjects regardless of diet. Further research to explain observed phenomena and pathomechanism of beta2 toxin is required.
       
  • Effect of DS-2969b, a novel GyrB inhibitor, on rat and monkey intestinal
           microbiota
    • Abstract: Publication date: June 2018Source: Anaerobe, Volume 51Author(s): Manoj Kumar, Tarun Mathur, Vattan Joshi, Dilip J. Upadhyay, Shin-ichi Inoue, Nobuhisa Masuda DS-2969b, a novel GyrB inhibitor, transiently and reversibly altered the counts of limited intestinal microbiota at around 10 μg/g of faecal levels in rats and monkeys. Considering the high activity of DS-2969b against Clostridium difficile, 10 μg/g of faecal levels would be sufficient for clearing C. difficile from the intestine.
       
  • Effects of supplementing corn silage with different nitrogen sources on
           ruminal fermentation and microbial populations in vitro
    • Abstract: Publication date: June 2018Source: Anaerobe, Volume 51Author(s): Maren Witzig, Melanie B. Lengowski, Karin H.R. Zuber, Jens Möhring, Markus Rodehutscord Compared to grass silage (GS)-, corn silage (CS)-based diets appear to increase the efficiency of microbial protein synthesis (EMPS) in the rumen. Opposite results for the EMPS obtained in vitro have raised the question of whether an inadequate supply of amino N for microbes might explain the low EMPS. We examined the effects of supplementation with different N sources in CS on the EMPS and microbial populations in vitro. GS and CS were used as substrates for in vitro incubation. CS was non-supplemented or supplemented with urea, mixed amino acids (AA), peptone, or protein to adjust the N content to that of GS. Degradation of organic matter (OM) and crude protein (CP) revealed a positive effect of all N supplements, except protein. Additionally, N supplementation increased fiber degradation of CS. Peptone primarily stimulated hemicellulolytic activity and urea stimulated cellulolytic activity. The EMPS of CS was improved by all N supplements, with peptone and urea exhibiting the highest increase (57% and 54%, respectively), followed by AA mix (40%) and protein (11%) compared to that of CS alone (111 g microbial CP kg−1 fermented OM). However, the level of EMPS detected with GS (200 g microbial CP kg−1 fermented OM) was not achieved. Protozoal 18S rRNA gene copy numbers were negatively correlated with the EMPS, whereas no correlation was found between total bacteria and the EMPS. A stimulating effect of urea, AA mix, and peptone was detected for Ruminococcus albus and Prevotella bryantii, whereas Fibrobacter succinogenes was inhibited by N supplementation. This indicated that neither the amount of available N nor the N source was the only limiting factor in the low EMPS values of CS in vitro. Information is also provided on the stimulating effects of different N sources on several microbial species in mixed rumen culture.
       
  • Species-specific serine-threonine protein kinase Pkb2 of Bifidobacterium
           longum subsp. longum: Genetic environment and substrate specificity
    • Abstract: Publication date: June 2018Source: Anaerobe, Volume 51Author(s): V.Z. Nezametdinova, D.A. Mavletova, M.G. Alekseeva, M.S. Chekalina, N.V. Zakharevich, V.N. Danilenko The objective of this study was to determine for phosphorylated substrates of the species-specific serine-threonine protein kinase (STPK) Pkb2 from Bifidobacterium longum subsp. longum GT15. Two approaches were employed: analyses of phosphorylated membrane vesicles protein spectra following kinase reactions and analyses of the genes surrounding pkb2.A bioinformatics analysis of the genes surrounding pkb2 found a species-specific gene cluster PFNA in the genomes of 34 different bifidobacterial species. The identified cluster consisted of 5–8 genes depending on the species. The first five genes are characteristic for all considered species.These are the following genes encoding serine-threonine protein kinase (pkb2), fibronectin type III domain-containing protein (fn3), AAA-ATPase (aaa-atp), hypothetical protein with DUF58 domain (duf58) and transglutaminase (tgm). The sixth (protein phosphatase, prpC), seventh (hypothetical protein, BLGT_RS02790), and eighth (FHA domain-containing protein, fha) genes are included in this cluster, but they are not found in all species. The operon organization of the PFNA gene cluster was confirmed with transcriptional analysis. AAA-ATPase, which is encoded by a gene of the PFNA gene cluster, was found to be a substrate of the STPK Pkb2. Fourteen AAA-ATPase sites (seven serine, six threonine, and one tyrosine) phosphorylated by STPK Pkb2 were revealed.Analysis of the spectra of phosphorylated membrane vesicles proteins allowed us to identify eleven proteins that were considered as possible Pkb2 substrates. They belong to several functional classes: proteins involved in transcription and translation; proteins of the F1-domain of the FoF1–ATPase; ABC-transporters; molecular chaperone GroEL; and glutamine synthase, GlnA1. All identified proteins were considered moonlighting proteins. Three out of 11 proteins (glutamine synthetase GlnA1 and FoF1-ATPase alpha and beta subunits) were selected for further in vitro phosphorylation assays and were shown to be phosphorylated by Pkb2.Four phosphorylated substrates of the species-specific STPK Pkb2 from B. longum subsp. longum GT15 were identified for the first time. They included the moonlighting protein glutamine synthase GlnA, FoF1-ATPase alpha and beta subunits, and the chaperone MoxR family of AAA-ATPase. The ability of bifidobacterial STPK to phosphorylate the substrate on serine, threonine, and tyrosine residues was shown for the first time.
       
  • Rodents are carriers of Clostridioides difficile strains similar to those
           isolated from piglets
    • Abstract: Publication date: June 2018Source: Anaerobe, Volume 51Author(s): Carlos Augusto de Oliveira, Michelle de Paula Gabardo, Roberto Maurício Carvalho Guedes, Fabrice Poncet, Dominique S. Blanc, Francisco Carlos Faria Lobato, Rodrigo Otávio Silveira Silva Features of Clostridioides difficile transmission in swine and the role of rodents as C. difficile reservoir are not clear. To investigate if rodents can carry strains of C. difficile that are genetically similar to those isolated from swine, 97 fecal samples from neonatal piglets and 41 intestinal contents from rodents were collected in two farms. All samples were subjected to C. difficile culture and the presence of A/B toxins in piglet feces were accessed by commercial enzyme imunoassay (EIA). C. difficile isolates were typed by double- (DLST) and multi-locus sequence typing (MLST). C. difficile was isolated from 15.5% of piglets and 31.7% of rodents. Most isolates were identified as DLST type 4-4 and 17-5 (both are ST11), which were found in both rodents and piglets. Results of this study suggested that rodents may have a role on the transmission and spread of C. difficile strains to swine.
       
  • Clostridioides difficile infection in dogs with chronic-recurring diarrhea
           responsive to dietary changes
    • Abstract: Publication date: June 2018Source: Anaerobe, Volume 51Author(s): Rodrigo Otávio Silveira Silva, Carlos Augusto de Oliveira Júnior, Dominique S. Blanc, Silvia Trindade Pereira, Mário Cesar Rennó de Araujo, Artur Vasconcelos, Francisco Carlos Faria Lobato Five dogs with chronic-recurring diarrhea were positive for Clostridioides difficile infection (CDI), but were unresponsive to treatment with metronidazole. One of these animals was subjected to a colonoscopy, which revealed eosinophilic infiltration of the colon. All five animals completely recovered after dietary changes. The present work suggests that CDI might occur in dogs with other intestinal alterations. In addition, this report suggests that dysbiosis should be considered in animals that have chronic-recurring diarrhea and test positive for C. difficile.
       
  • Type C botulism in domestic chickens, dogs and black-pencilled marmoset
           (Callithrix penicillata) in Minas Gerais, Brazil
    • Abstract: Publication date: June 2018Source: Anaerobe, Volume 51Author(s): Rodrigo Otávio Silveira Silva, Ronaldo Alves Martins, Ronnie Antunes Assis, Carlos Augusto Oliveira Junior, Francisco Carlos Faria Lobato Botulism is a well-known intoxication that affects humans and animals. The disease is endemic in cattle in Brazil and recently emerged as an important disease in commercial laying hens and broiler chickens in Europe. Dogs and other animal species can also be affected. Although antitoxins are commonly administered to humans diagnosed with botulism, in animals this is rarely the case and the treatment of botulism is still based only on support therapy. In the present work, we report an outbreak of type C botulism in Brazil that simultaneously affected domestic chickens, dogs and a black-pencilled marmoset (Callithrix penicillata). The successful use of Clostridium botulinum types C and D antitoxin for the treatment of an affected dog is also described.
       
  • Presence of Clostridium difficile in poultry and poultry meat in
           Egypt
    • Abstract: Publication date: June 2018Source: Anaerobe, Volume 51Author(s): Mostafa Y. Abdel-Glil, Prasad Thomas, Gernot Schmoock, Kamel Abou-El-Azm, Lothar H. Wieler, Heinrich Neubauer, Christian Seyboldt C. difficile has been recognized as a potential zoonotic agent encouraging investigations of C. difficile prevalence and ribotypes in animals. Here we report the prevalence and diversity of Egyptian C. difficile in I) samples from healthy poultry (n = 50), II) samples from diseased poultry (n = 54), and III) poultry meat (n = 150). Thirteen isolates were obtained from seven healthy and five diseased animals, but no C. difficile was cultured from poultry meat. The isolated C. difficile strains belonged to 3 different PCR-ribotypes (039/2, 205 and 001/FLI01). The detection of strains related to RT 001 known for its ability to cause disease in humans makes poultry a potential reservoir for pathogenic C. difficile.
       
  • A repeat offender: Recurrent extraintestinal Clostridium difficile
           infection following fecal microbiota transplantation
    • Abstract: Publication date: June 2018Source: Anaerobe, Volume 51Author(s): Bradley J. Gardiner, Cheleste M. Thorpe, Nicholas V. Pinkham, Laura A. McDermott, Seth T. Walk, David R. Snydman Extraintestinal infection with Clostridium difficile has been reported but remains uncommon. Treatment of this unusual complication is complex given the limitations of current therapeutic options. Here we report a novel case of recurrent extraintestinal C. difficile infection that occurred following fecal microbiota transplantation. Using whole genome sequencing, we confirmed recrudescence rather than reinfection was responsible. The patient ultimately responded to prolonged, targeted antimicrobial therapy informed by susceptibility testing.
       
  • Acute septic arthritis of the knee: A rare case report of infection with
           Parvimonas micra after an intra-articular corticosteroid injection for
           osteoarthritis
    • Abstract: Publication date: June 2018Source: Anaerobe, Volume 51Author(s): Assem A. Sultan, William A. Cantrell, Anton Khlopas, Connor Cole, Nicolas S. Piuzzi, Nipun Sodhi, Peter Brooks, Michael A. Mont Acute bacterial mono-articular septic arthritis affects most commonly the lower extremity joints in adult population and most commonly caused by Staphylococcus aureus. Various risk factors determine susceptibility to infection including host immunity, medical co-morbidity and joint structural abnormality and other organisms may be involved. Parvimonas micra (P. micra) is among the rare organisms that may be associated with atypical septic arthritis and primarily affects the native knee joint. Only 3 case reports in the literature have reported on pyogenic pyogenic joint infection caused by this organism. We hereby present our experience with a case of knee septic arthritis caused by P. micra in a patient with knee osteoarthritis following a recent intra-articular injection with corticosteroids. In susceptible patients, Intra-articular corticosteroid injection and crystal induced arthritis may propose a potential risk of contracting infection with P. micra.
       
  • Bioethanol production by a xylan fermenting thermophilic isolate
           Clostridium strain DBT-IOC-DC21
    • Abstract: Publication date: June 2018Source: Anaerobe, Volume 51Author(s): Nisha Singh, Munish Puri, Deepak K. Tuli, Ravi P. Gupta, Colin J. Barrow, Anshu S. Mathur To overcome the challenges associated with combined bioprocessing of lignocellulosic biomass to biofuel, finding good organisms is essential. An ethanol producing bacteria DBT-IOC-DC21 was isolated from a compost site via preliminary enrichment culture on a pure hemicellulosic substrate and identified as a Clostridium strain by 16S rRNA analysis. This strain presented broad substrate spectrum with ethanol, acetate, lactate, and hydrogen as the primary metabolic end products. The optimum conditions for ethanol production were found to be an initial pH of 7.0, a temperature of 70 °C and an L-G ratio of 0.67. Strain presented preferential hemicellulose fermentation when compared to various substrates and maximum ethanol concentration of 26.61 mM and 43.63 mM was produced from xylan and xylose, respectively. During the fermentation of varying concentration of xylan, a substantial amount of ethanol ranging from 25.27 mM to 67.29 mM was produced. An increased ethanol concentration of 40.22 mM was produced from a mixture of cellulose and xylan, with a significant effect observed on metabolic flux distribution. The optimum conditions were used to produce ethanol from 28 g L−1 rice straw biomass (RSB) (equivalent to 5.7 g L−1 of the xylose equivalents) in which 19.48 mM ethanol production was achieved. Thus, Clostridium strain DBT-IOC-DC21 has the potential to perform direct microbial conversion of untreated RSB to ethanol at a yield comparative to xylan fermentation.
       
  • Expression of glyceraldehyde-3-phosphate dehydrogenase on the surface of
           Clostridium perfringens cells
    • Abstract: Publication date: June 2018Source: Anaerobe, Volume 51Author(s): Nozomu Matsunaga, Haruka Shimizu, Kanako Fujimoto, Kanako Watanabe, Tsutomu Yamasaki, Naoya Hatano, Eiji Tamai, Seiichi Katayama, Yasuo Hitsumoto During research to identify fibronectin (Fn)-binding proteins (Fbps) on the surface of Clostridium perfringens cells, we identified glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as a candidate Fbp. GAPDH is a glycolytic enzyme found in a wide range of prokaryotes and eukaryotes. The Fn-binding activity of recombinant C. perfringens GAPDH (rGAPDH) was investigated using both ligand blotting analysis and enzyme-linked immunosorbent assay (ELISA). rGAPDH strongly bound plasminogen but not laminin or gelatin. Although GAPDH has no signal sequence, it is expressed on the cell surface of many microorganisms. The presence of GAPDH on the surface of C. perfringens cells was analyzed using ELISA and flow cytometry analyses; purified rGAPDH bound to the surface of C. perfringens cells. As autolysin is reportedly involved in the binding of GAPDH to the cell surface, we evaluated the interaction between rGAPDH and the C. perfringens autolysin Acp by both ELISA and ligand blotting assay. These assays revealed that rGAPDH binds to the catalytic domain of Acp but not the cell wall binding domains. These results suggest that autolysin mediates expression of GAPDH on the surface of C. perfringens cells and indicate a possible moonlighting function for GAPDH in binding both Fn and plasminogen.
       
  • Occurrence of Clostridium difficile infections in Serbia and high
           proportion of PCR ribotype 027 strains in two hospitals in Belgrade
    • Abstract: Publication date: June 2018Source: Anaerobe, Volume 51Author(s): Milica Jovanović, Mitra Drakulović, Tanja Tošić, Rajica Stošović, Snežana Jovanović BackgroundThe incidence of Clostridium difficile infections (CDI) in the Clinical Center of Serbia (CCS) and the entire Serbia has been constantly rising in the previous 5 years. We aimed to study C. difficile PCR-ribotypes isolated from patients hospitalized at two healthcare institutions: CCS and Specialized Hospital for Cerebrovascular Diseases “Sveti Sava” (SS), both of them from Belgrade, and to investigate the incidence rates of CDI in hospital settings in Serbia, from 2009 to 2013.MethodsThe Bacteriology laboratory database at Clinic for Infectious and Tropical Diseases of CCS was queried from January 1, 2009 to December 31, 2013 for all patients who underwent immunochromatographic toxin A and/or toxin B stool testing and C. difficile stool culture for suspected infection caused by this bacterium. Toxigenic culture was not performed. Ninety- six C. difficile isolates were then selected and characterized by PCR-ribotyping. These were obtained from 94 patients hospitalized in different clinics of CCS and SS from November 2011 to December 2013.ResultsAmong 6164 stool samples sent to Bacteriology laboratory for culture of C. difficile and toxin detection during the study period, 1775 (28.8%) were positive, displaying linear trend of growth. From 96 isolates, typed by PCR-ribotyping, majority (85; 88.54%) belonged to PCR-ribotype 027. The remaining 11 isolates belonged to PCR-ribotypes 014/020 (3 isolates), 015, SLO 191 (two isolates each), 017, 018, 070 and 001/072 (one isolate each).ConclusionOur results demonstrated that C. difficile PCR-ribotype 027 is by far predominant in two hospital settings in Belgrade, at least since 2011.
       
  • Tracking gene expression and oxidative damage of O2-stressed
           Clostridioides difficile by a multi-omics approach
    • Abstract: Publication date: Available online 31 May 2018Source: AnaerobeAuthor(s): Meina Neumann-Schaal, Nicole G. Metzendorf, Daniel Troitzsch, Aaron Mischa Nuss, Julia Danielle Hofmann, Michael Beckstette, Petra Dersch, Andreas Otto, Susanne Sievers Clostridioides difficile is the major pathogen causing diarrhea following antibiotic treatment. It is considered to be a strictly anaerobic bacterium, however, previous studies have shown a certain and strain-dependent oxygen tolerance. In this study, the model strain C. difficile 630Δerm was shifted to micro-aerobiosis and was found to stay growing to the same extent as anaerobically growing cells with only few changes in the metabolite pattern. However, an extensive change in gene expression was determined by RNA-Seq. The most striking adaptation strategies involve a change in the reductive fermentation pathways of the amino acids proline, glycine and leucine. But also a far-reaching restructuring in the carbohydrate metabolism was detected with changes in the phosphotransferase system (PTS) facilitated uptake of sugars and a repression of enzymes of glycolysis and butyrate fermentation. Furthermore, a temporary induction in the synthesis of cofactor riboflavin was detected possibly due to an increased demand for flavin mononucleotid (FMN) and flavin adenine dinucleotide (FAD) in redox reactions. However, biosynthesis of the cofactors thiamin pyrophosphate and cobalamin were repressed deducing oxidation-prone enzymes and intermediates in these pathways.Micro-aerobically shocked cells were characterized by an increased demand for cysteine and a thiol redox proteomics approach revealed a dramatic increase in the oxidative state of cysteine in more than 800 peptides after 15 min of micro-aerobic shock. This provides not only a catalogue of oxidation-prone cysteine residues in the C. difficile proteome but also puts the amino acid cysteine into a key position in the oxidative stress response.Our study suggests that tolerance of C. difficile towards O2 is based on a complex and far-reaching adjustment of global gene expression which leads to only a slight change in phenotype.
       
  • Presence of multiple Clostridium difficile strains at primary infection is
           associated with development of recurrent disease
    • Abstract: Publication date: Available online 31 May 2018Source: AnaerobeAuthor(s): Anna M. Seekatz, Emily Wolfrum, Christopher M. DeWald, Rosemary K.B. Putler, Kimberly C. Vendrov, Krishna Rao, Vincent B. Young Recurrence of Clostridium difficile infection (CDI) places a major burden on the healthcare system. Previous studies have suggested that specific C. difficile strains, or ribotypes, are associated with severe disease and/or recurrence. However, in some patients a new strain is detected in subsequent infections, complicating longitudinal studies focused on strain differences that may contribute to disease outcome. We examined ribotype composition over time in patients who did or did not develop recurrence to examine infection with multiple C. difficile ribotypes (mixed infection), during the course of infection. Using a retrospective patient cohort, we isolated and ribotyped a median of 36 C. difficile colonies from 61 patients (105 total samples) at initial infection, recurrence (a second case of CDI within 15–56 days of initial infection), and reinfection (a second case of CDI after 56 days of initial infection). We observed mixed infection in 78.6% of samples at initial infection in patients who went on to develop recurrence compared to 18.1% of patients who did not, and mixed infection remained associated with subsequent recurrence after adjusting for gender and prior antibiotic exposure (OR 3.5, 95% CI 1.3–9.4, P = .015). In patients who were sampled longitudinally (44 consecutive events in 32 patients), the dominant ribotype changed in 31.8% of consecutive samples and the newly dominant ribotype was not detected in prior samples from that patient. Our results suggest that mixed C. difficile infection is more prevalent than previously demonstrated and potentially a marker of susceptibility to recurrence.
       
  • Evaluation of the Vitek MS and the MALDI Biotyper systems for the
           identification of less commonly isolated but clinically relevant anaerobes
           and facultative anaerobes
    • Abstract: Publication date: Available online 30 May 2018Source: AnaerobeAuthor(s): Janina Ferrand, Isabelle Bonnet, Corentine Alauzet, Alain Lozniewski The Vitek MS and MALDI Biotyper systems were evaluated for the identification of 221 strains belonging to less commonly isolated anaerobes and facultative anaerobes. Identifications were performed using direct deposit (DD), on-target extraction (FA) and full extraction (EXT). After DD, 29.9% and 34.3% of Gram-positive isolates (n = 137) as well as 36.9% and 58.3% of Gram-negative isolates (n = 84) were identified at the species-level with the Vitek-MS and the Biotyper system, respectively. The rates of correct species identification with the Biotyper system were significantly increased after extraction for Gram-positive isolates (FA: 75.2%, EXT: 78.1%) and Gram-negative isolates (FA: 72.6%, EXT: 78.6%). Extraction permitted to achieve higher correct species identification rates only for Gram-positive isolates (FA: 35.8%, EXT: 36.5%) with the Vitek MS. Thus, the accuracy of both systems needs to be further increased by expanding the databases. In the meantime, we recommend using a preliminary extraction step to obtain reliable results at least for the identification of Gram positive anaerobic bacteria with both systems.
       
  • Epsilon toxin from Clostridium perfringens induces cytotoxicity in FRT
           thyroid epithelial cells
    • Abstract: Publication date: Available online 28 May 2018Source: AnaerobeAuthor(s): Jonatan Dorca-Arévalo, Marta Blanch, Marina Pradas, Juan Blasi Epsilon toxin (Etx) is produced by Clostridium perfringens and induces enterotoxemia in ruminants. Etx crosses the blood-brain barrier, binds to myelin structures, and kills oligodendrocytes, inducing central nervous system demyelination. In addition, Etx has a cytotoxic effect on distal and collecting kidney tubules. There are few cell lines sensitive to Etx. At present, the most sensitive in vitro model for Etx is the Madin-Darby canine kidney (MDCK) cell line, where Etx oligomerizes and forms a pore with consequent ion efflux and cell death. Although the Etx receptor has not yet been fully clarified, it is known that caveolin 1 and 2 potentiate Etx cytotoxicity and oligomerization, and more recently, the myelin and lymphocyte (MAL) protein has been implicated in Etx binding and activity. Here, we studied the effect of Etx on Fischer rat thyroid cells (FRT) and observed similar effects as those seen in MDCK cells. Etx incubated with FRT cells showed binding to the plasma membrane, and western blotting assays revealed oligomeric complex formation. Moreover, cytotoxic assays on FRT cells after Etx incubation indicated cell death at a similar level as in MDCK cells. In addition, a luminescent ATP detection assay revealed ATP depletion in FRT cells after Etx exposure. Previous studies have reported that FRT cells do not express caveolins and do not form caveolae but express MAL protein in glycolipid-enriched membrane microdomains. Our results indicate that caveolins are not directly implicated in Etx cytotoxicity, supporting the notion that the MAL protein is involved in Etx action. In addition, a cell line of thyroid origin is described for the first time as a good model to study Etx action.
       
  • Clostridium difficile forms variable biofilms on abiotic surface
    • Abstract: Publication date: Available online 18 May 2018Source: AnaerobeAuthor(s): V. Pantaléon, M. Monot, C. Eckert, S. Hoys, A. Collignon, C. Janoir, T. Candela Clostridium difficile can form biofilms. Thirty-seven strains were characterized for their ability to form a biofilm, adhesion on an inert surface and hydrophobicity. No correlation between the ability to form a biofilm and the strain virulence was highlighted. However, non-motile strains were not able to form a high biofilm.
       
  • Sample preparation method influences direct identification of anaerobic
           bacteria from positive blood culture bottles using MALDI-TOF MS
    • Abstract: Publication date: Available online 15 May 2018Source: AnaerobeAuthor(s): Samo Jeverica, Elisabeth Nagy, Manica Mueller-Premru, Lea Papst Rapid detection and identification of anaerobic bacteria from blood is important to adjust antimicrobial therapy by including antibiotics with activity against anaerobic bacteria. Limited data is available about direct identification of anaerobes from positive blood culture bottles using MALDI-TOF mass spectrometry (MS). In this study, we evaluated the performance of two sample preparation protocols for direct identification of anaerobes from positive blood culture bottles, the MALDI Sepsityper kit (Sepsityper) and the in-house saponin (saponin) method. Additionally, we compared two blood culture bottle types designed to support the growth of anaerobic bacteria, the BacT/ALERT-FN Plus (FN Plus) and the BACTEC-Lytic (Lytic), and their influence on direct identification. A selection of 30 anaerobe strains belonging to 22 different anaerobic species (11 reference strains and 19 clinical isolates) were inoculated to 2 blood culture bottle types in duplicate. In total, 120 bottles were inoculated and 99.2% (n = 119) signalled growth within 5 days of incubation. The Sepsityper method correctly identified 56.3% (n = 67) of anaerobes, while the saponin method correctly identified 84.9% (n = 101) of anaerobes with at least log(score) ≥1.6 (low confidence correct identification), (p 
       
  • The evolving epidemic of Clostridium difficile 630
    • Abstract: Publication date: Available online 27 April 2018Source: AnaerobeAuthor(s): Adam P. Roberts, Wiep Klaas Smits Clostridium difficile is a major pathogen responsible for a range of diseases in humans and animals. The genetic tools used to explore C. difficile biology are a relatively recent development in comparison to those used to investigate some other pathogens. Consequently, a rapid and haphazard dispersal of strains throughout the scientific community has led to the evolution of different C. difficile lineages within strains in different geographical locations and these genotypic differences are likely to affect the phenotype of the organism. Here we review the history of C. difficile 630, the first genome-sequenced C. difficile isolate and the most widely distributed reference strain, and its derivatives. We also invite researchers to take part in a community wide genome sequencing study to trace the evolution of these strains as they have travelled between laboratories around the world.
       
  • Distinct consequences of amoxicillin and ertapenem exposure in the porcine
           gut microbiome
    • Abstract: Publication date: Available online 22 April 2018Source: AnaerobeAuthor(s): Sheila Connelly, Poorani Subramanian, Nur A. Hasan, Rita R. Colwell, Michael Kaleko The gut microbiome influences many, if not all, aspects of human health. Antibiotics, while lifesaving, have the unintended consequence of killing commensal microbiota inhabiting the gastrointestinal (GI) tract, which can lead to overgrowth of opportunistic pathogens such as Clostridium difficile and emergence of antibiotic-resistant organisms. Here, porcine models were developed to evaluate changes to the gut microbiome caused by two distinct types of beta-lactam antibiotics delivered via common administration routes, oral amoxicillin and intravenous ertapenem. Amoxicillin is one of the most often used broad-spectrum antibiotics, frequently prescribed to young children. Ertapenem, a carbapenem considered a last resort antibiotic, is used sparingly in humans and prohibited for use in animals. Cohorts of normal pigs (n = 5) were treated with amoxicillin (20 mg/kg, PO, BID) or ertapenem (30 mg/kg, IV, SID) for seven days. Microbiomes were evaluated using whole genome shotgun metagenomics analyses of fecal DNA collected prior to, during, and after antibiotic treatment. Each antibiotic resulted in significant and distinct changes in the microbiome, causing elimination of key commensal bacterial species and overgrowth of other, potentially pathogenic taxa. In addition, amoxicillin promoted propagation of a broad range of antibiotic resistance genes, many encoding efflux pump components and beta-lactamases, while ertapenem triggered emergence of genes encoding vancomycin resistance, and beta-lactamases, including the carbapenemase, IMP-27. Notably, microbiota alterations and antibiotic resistance gene propagation displayed unique patterns following exposure to amoxicillin or ertapenem. These data underscore the importance of understanding consequences of individual antibiotic use to predict and potentially mitigate adverse outcomes. The porcine models developed here can facilitate evaluation of therapeutic interventions to prevent antibiotic-mediated microbiome disruption.
       
  • Expansion of the Clostridium perfringens toxin-based typing
           scheme
    • Abstract: Publication date: Available online 20 April 2018Source: AnaerobeAuthor(s): Julian I. Rood, Vicki Adams, Jake Lacey, Dena Lyras, Bruce A. McClane, Stephen B. Melville, Robert J. Moore, Michel R. Popoff, Mahfuzur R. Sarker, J. Glenn Songer, Francisco A. Uzal, Filip Van Immerseel Clostridium perfringens causes many different histotoxic and enterotoxic diseases in humans and animals as a result of its ability to produce potent protein toxins, many of which are extracellular. The current scheme for the classification of isolates was finalized in the 1960s and is based on their ability to produce a combination of four typing toxins - α-toxin, β-toxin, ε-toxin and ι-toxin – to divide C. perfringens strains into toxinotypes A to E. However, this scheme is now outdated since it does not take into account the discovery of other toxins that have been shown to be required for specific C. perfringens-mediated diseases. We present a long overdue revision of this toxinotyping scheme. The principles for the expansion of the typing system are described, as is a mechanism by which new toxinotypes can be proposed and subsequently approved. Based on these criteria two new toxinotypes have been established. C. perfringens type F consists of isolates that produce C. perfringens enterotoxin (CPE), but not β-toxin, ε-toxin or ι-toxin. Type F strains will include strains responsible for C. perfringens-mediated human food poisoning and antibiotic associated diarrhea. C. perfringens type G comprises isolates that produce NetB toxin and thereby cause necrotic enteritis in chickens. There are at least two candidates for future C. perfringens toxinotypes, but further experimental work is required before these toxinotypes can formally be proposed and accepted.Graphical abstractImage
       
  • Erratum to “Investigation of Clostridium botulinum group III's mobilome
           content” [Anaerobe 49 (2018) 71–77]
    • Abstract: Publication date: Available online 18 April 2018Source: AnaerobeAuthor(s): Cédric Woudstra, Caroline Le Maréchal, Rozenn Souillard, Fabrizio Anniballi, Bruna Auricchio, Luca Bano, Marie-Hélène Bayon-Auboyer, Miriam Koene, Isabelle Mermoud, Roseane B. Brito, Francisco C.F. Lobato, Rodrigo O.S. Silva, Martin B. Dorner, Patrick Fach
       
  • In vitro activity of DS-2969b and comparator antimicrobial agents against
           Clostridioides (Clostridium) difficile, methicillin-resistant
           Staphylococcus aureus, and other anaerobic bacteria
    • Abstract: Publication date: Available online 13 April 2018Source: AnaerobeAuthor(s): K.L. Tyrrell, D.M. Citron, C.V. Merriam, E. Leoncio, E.J.C. Goldstein The in vitro activity of DS-2969b, a novel GyrB inhibitor, and six comparator agents was studied against 101 recent North American Clostridioides difficile isolates, 46 other intestinal anaerobes and 51 strains of methicillin-resistant Staphylococcus aureus. The MIC ranges (MIC90s) of DS-2969b against C. difficile and S. aureus were 0.03–0.125 (0.125) µg/ml and 0.125–1 (0.5) µg/ml, respectively. DS-2969b showed the greatest activity of the agents tested. There was no difference in MICs of DS-2969b among different ribotypes.
       
  • Restoration of short chain fatty acid and bile acid metabolism following
           fecal microbiota transplantation in patients with recurrent Clostridium
           difficile infection
    • Abstract: Publication date: Available online 12 April 2018Source: AnaerobeAuthor(s): Anna M. Seekatz, Casey M. Theriot, Krishna Rao, Yu-Ming Chang, Alison E. Freeman, John Y. Kao, Vincent B. Young A significant proportion of individuals develop recurrent Clostridium difficile infection (CDI) following initial disease. Fecal microbiota transplantation (FMT), a highly effective treatment method for recurrent CDI, has been demonstrated to induce microbiota recovery. One of the proposed functions associated with restoration of colonization resistance against C. difficile has been recovery of bile acid metabolism. In this study, we aimed to assess recovery of short chain fatty acids (SCFAs) in addition to bile acids alongside microbial community structure in six patients with recurrent CDI following treatment with FMT over time. Using 16S rRNA gene-based sequencing, we observed marked similarity of the microbiota between recipients following FMT (n = 6, sampling up to 6 months post-FMT) and their respective donors. Sustained increases in the levels of the SCFAs butyrate, acetate, and propionate were observed post-FMT, and variable recovery over time was observed in the secondary bile acids deoxycholate and lithocholate. To correlate these changes with specific microbial taxa at an individual level, we applied a generalized estimating equation approach to model metabolite concentrations with the presence of specific members of the microbiota. Metabolites that increased following FMT were associated with bacteria classified within the Lachnospiraceae, Ruminococcaceae, and unclassified Clostridiales families. In contrast, members of these taxa were inversely associated with primary bile acids. The longitudinal aspect of this study allowed us to characterize individualized patterns of recovery, revealing variability between and within patients following FMT.
       
  • Bacteroides fragilis: A whole MALDI-based workflow from identification to
           confirmation of carbapenemase production for routine laboratories
    • Abstract: Publication date: Available online 4 April 2018Source: AnaerobeAuthor(s): M. Cordovana, M. Kostrzewa, J. Sóki, E. Witt, S. Ambretti, A.B. Pranada Bacteroides fragilis is a frequent anaerobic pathogen and can cause severe infections. Resistance to carbapenems, associated with the cfiA gene encoded carbapenemase, represents an emerging problem. To date, no rapid methods are available to detect and confirm this resistance mechanism in routine laboratories, and the missed recognition of carbapenemase-producing strains can lead to therapeutic failures. In this study we have investigated a whole MALDI-TOF MS-based workflow to detect carbapenemase-producing B. fragilis, using the largest set of B. fragilis clinical isolates ever tested. The presence of the cfiA gene was predicted by MALDI subtyping into Division I (cfiA-negative) or Division II (cfiA-positive). The carbapenemase activity in cfiA-positive strains was confirmed by a MALDI-TOF MS imipenem hydrolysis assay (MBT STAR-Carba, Bruker Daltonik, Germany), that was further used for a characterization of the strains in terms of cfiA expression level.The validity of MALDI subtyping was verified by PCR for the cfiA gene, while results of MALDI hydrolysis assay were compared to conventional methods for susceptibility testing and carbapenemase detection (Carba-NP and disk diffusion synergy test). A genetic analysis of the IS elements upstream cfiA was performed, for the evaluations regarding the expression level of cfiA. A total of 5300 B. fragilis isolates (406 from Bologna, Italy, and 4894 from Dortmund, Germany) were identified and subtyped by MALDI-TOF MS, yielding 41/406 (10.1%) strains from Bologna and 374/4894 (7.6%) from Dortmund to belong to Division II. Molecular verification by PCR for the cfiA gene on a subset of strains confirmed the MALDI typing results in all cases (sensitivity and specificity of 100%). MBT STAR-Carba assay detected the carbapenemase activity in all of the 70 cfiA-carrying strains tested. Moreover, it allowed distinct separation into slow (59) and fast (11) imipenem hydrolyzers corresponding to cfiA expression levels as well as to low or high MICs for carbapenems, respectively. Among the 11 cfiA-positive strains with high carbapenem MIC, only 7 harboured IS elements upstream the carbapenemase gene showing low expression level as well.The MALDI-TOF MS-based workflow was superior to the currently available phenotypic methods for carbapenemase detection as it proved to be more sensitive and accurate than Carba NP and disk diffusion synergy test. The whole MALDI-TOF MS-based workflow allows an accurate identification of B. fragilis clinical strains with reliable classification into Division I/II, and confirmation of the carbapenemase-production, together with estimation of carbapenemase activity, within less than 2 h. This may be of particular interest for early therapeutical decisions in life-threatening infections.
       
  • MALDI-TOF MS in Anaerobiospirillum succiniciproducens bacteremia: A report
           of 4 cases in different hosts
    • Abstract: Publication date: Available online 4 April 2018Source: AnaerobeAuthor(s): B. Fox, M.A. Berger, M. Roncallo, L. Pinoche, M.E. Ibáñez, S. Gonzalez-Fraga, L. Fernández-Canigia Anaerobiospirillum succiniciproducens is known as an uncommon cause of diarrhea and bacteremia in humans, usually in immunocompromised hosts. We report four cases of A. succiniciproducens bloodstream infection in different hosts, including a previously healthy man. We describe clinical features, antibiotics susceptibility profile, treatment and outcomes. Strains were identified by 16S rRNA gene sequences which contributed to the extension of our MALDI-TOF MS database.
       
  • Assessing the clinical relevance of Fenollaria massiliensis in human
           infections, using MALDI-TOF MS
    • Abstract: Publication date: Available online 17 March 2018Source: AnaerobeAuthor(s): K.E. Boiten, H. Jean-Pierre, A.C.M. Veloo Within the European Network for the Rapid Identification of Anaerobes (ENRIA) project eight clinical isolates of Fenollaria massiliensis were encountered. In this study a more extensive description of this species is given and the MALDI-TOF MS database is optimized for its identification.F. massiliensis is an anaerobic Gram positive rod with the tendency to decolorize quickly. It is mostly encountered in clinical samples from the groin region.Less common and non-valid species are not represented in the MALDI-TOF MS database. Therefore, F. massiliensis can only be identified by laboratories performing 16S rDNA gene sequencing. The addition of less common and non-valid species to the database will give insight in their clinical relevance.
       
  • Validation of a for anaerobic bacteria optimized MALDI-TOF MS biotyper
           database: The ENRIA project
    • Abstract: Publication date: Available online 12 March 2018Source: AnaerobeAuthor(s): A.C.M. Veloo, H. Jean-Pierre, U.S. Justesen, T. Morris, E. Urban, I. Wybo, M. Kostrzewa, A.W. Friedrich, T. Morris, H. Shah, H. Jean-Pierre, U.S. Justesen, I. Wybo, E. Nagy, E. Urban, M. Kostrzewa, A. Veloo, A.W. Friedrich Within the ENRIA project, several ‘expertise laboratories’ collaborated in order to optimize the identification of clinical anaerobic isolates by using a widely available platform, the Biotyper Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). Main Spectral Profiles (MSPs) of well characterized anaerobic strains were added to one of the latest updates of the Biotyper database db6903; (V6 database) for common use. MSPs of anaerobic strains nominated for addition to the Biotyper database are included in this validation. In this study, we validated the optimized database (db5989 [V5 database] + ENRIA MSPs) using 6309 anaerobic isolates.Using the V5 database 71.1% of the isolates could be identified with high confidence, 16.9% with low confidence and 12.0% could not be identified. Including the MSPs added to the V6 database and all MSPs created within the ENRIA project, the amount of strains identified with high confidence increased to 74.8% and 79.2%, respectively. Strains that could not be identified using MALDI-TOF MS decreased to 10.4% and 7.3%, respectively. The observed increase in high confidence identifications differed per genus. For Bilophila wadsworthia, Prevotella spp., gram-positive anaerobic cocci and other less commonly encountered species more strains were identified with higher confidence. A subset of the non-identified strains (42.1%) were identified using 16S rDNA gene sequencing. The obtained identities demonstrated that strains could not be identified either due to the generation of spectra of insufficient quality or due to the fact that no MSP of the encountered species was present in the database. Undoubtedly, the ENRIA project has successfully increased the number of anaerobic isolates that can be identified with high confidence. We therefore recommend further expansion of the database to include less frequently isolated species as this would also allow us to gain valuable insight into the clinical relevance of these less common anaerobic bacteria.
       
  • Binary Clostridium difficile toxin (CDT) - A virulence factor
           disturbing the cytoskeleton
    • Abstract: Publication date: Available online 7 March 2018Source: AnaerobeAuthor(s): Klaus Aktories, Panagiotis Papatheodorou, Carsten Schwan Clostridium difficile infection causes antibiotics-associated diarrhea and pseudomembranous colitis. Major virulence factors of C. difficile are the Rho-glucosylating toxins TcdA and TcdB. In addition, many, so-called hypervirulent C. difficile strains produce the binary actin-ADP-ribosylating toxin CDT. CDT causes depolymerization of F-actin and rearrangement of the actin cytoskeleton. Thereby, many cellular functions, which depend on actin, are altered. CDT disturbs the dynamic balance between actin and microtubules in target cells. The toxin increases microtubule polymerization and induces the formation of microtubule-based protrusions at the plasma membrane of target cells. Moreover, CDT causes a redistribution of vesicles from the basolateral side to the apical side, where extracellular matrix proteins are released. These processes may increase the adherence of clostridia to target cells. Here, we review the effects of the action of CDT on the actin cytoskeleton and on the microtubule system.
       
  • Antimicrobial susceptibility testing of Bacteroides fragilis using the
           MALDI Biotyper antibiotic susceptibility test rapid assay (MBT-ASTRA)
    • Abstract: Publication date: Available online 2 March 2018Source: AnaerobeAuthor(s): Ulrik Stenz Justesen, Ziyap Acar, Thomas Vognbjerg Sydenham, Åsa Johansson, ESGAI (ESCMID Study Group on Anaerobic Infections) This study evaluated the MBT-ASTRA for antimicrobial susceptibility testing of Bacteroides fragilis with different classes of antibiotics. MALDI-TOF MS peak AUCs from suspensions with B. fragilis with and without an antibiotic were used to calculate the relative growth (AUC “with antibiotic” divided by “without antibiotic”). Antimicrobial susceptibility testing of B. fragilis ATCC 25285 (susceptible) and B. fragilis O18 (resistant) was demonstrated with a clear difference of the relative growth between susceptible and resistant. The MBT-ASTRA needs further development and assessment but could be a relatively easy and inexpensive method for rapid antimicrobial susceptibility testing in specific cases of infection with B. fragilis.
       
  • Polymicrobial anaerobic bacteremia due to Atopobium rimae and Parvimonas
           micra in a patient with cancer
    • Abstract: Publication date: Available online 6 February 2018Source: AnaerobeAuthor(s): Fernando Cobo, Jaime Borrego, Mª Dolores Rojo, José María Navarro-Marí Atopobium rimae and Parvimonas micra are both Gram-positive anaerobes involved infrequently in human infections. We report a polymicrobial anaerobic bacteremia caused by these microorganisms. A 43-year-old woman receiving coadjuvant chemotherapy due to a retroperitoneal leiomiosarcoma presented with nausea, vomiting, abdominal pain and fever (38 °C). The two blood cultures resulted in isolation of A. rimae and P. micra, being identified at species level by matrix assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF MS) technology with high log scores. The microorganisms were susceptible to penicilllin, amoxicillin-clavulanate, piperacillin-tazobactam, clindamycin, metronidazole, imipenem, and moxifloxacin. Treatment with levofloxacin was started and subsequently it was changed to piperacillin/tazobactam plus metronidazole and completed for 10 days, but the patient died days later due to her underlying disease.
       
  • Identification of Clostridium species using the
           VITEK® MS
    • Abstract: Publication date: Available online 31 January 2018Source: AnaerobeAuthor(s): Lucia Sanchez Ramos, Arne C. Rodloff The genus Clostridium is of high clinical relevance, as some species may cause rapid and even lethal infections. Thus, a timely identification of these anaerobic bacteria is desirable. Conventional identification methods rely on biochemical properties of these organisms, however, establishing these is time-consuming and not always reliable. Alternatively, 16S rRNA gene sequence based diagnostic methods may be used, but they are expensive and not ubiquitously available. This study was designed to assess the possibility to identify Clostridium species employing the matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). For this purpose, 848 Clostridium strains representing 42 species were analyzed with the VITEK® MS instrument (bioMérieux, Marcy l’Etoile, France), comparing mass spectra derived from these organisms with the spectra provided in the available database. 90.3% of the strains were correctly identified at species level and another 3.6% at genus level. Since the number of Clostridium species included in the database was rather limited (21 altogether), the spectra obtained were also analyzed employing the Shimadzu Pro Series software. Thus, it became possible to create a dendrogram of the species included in this study.
       
 
 
JournalTOCs
School of Mathematical and Computer Sciences
Heriot-Watt University
Edinburgh, EH14 4AS, UK
Email: journaltocs@hw.ac.uk
Tel: +00 44 (0)131 4513762
Fax: +00 44 (0)131 4513327
 
Home (Search)
Subjects A-Z
Publishers A-Z
Customise
APIs
Your IP address: 54.224.247.42
 
About JournalTOCs
API
Help
News (blog, publications)
JournalTOCs on Twitter   JournalTOCs on Facebook

JournalTOCs © 2009-