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International Journal of Systematic and... May 2022A Gram-stain-positive coccus was isolated from the blood of a paediatric patient suffering from gastroenteritis. The taxonomic position of this catalase-positive,...
A Gram-stain-positive coccus was isolated from the blood of a paediatric patient suffering from gastroenteritis. The taxonomic position of this catalase-positive, non-motile, non-spore-forming facultative anaerobe designated as strain MKL-02 was investigated using a polyphasic approach. Colonies grown on tryptic soy agar with 10 % sheep blood were circular, creamy yellow, and convex. Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences revealed that this strain was most closely related to CCUG 47306 within the cluster of the genus . Average nucleotide identity and digital DNA-DNA hybridization values between strain MKL-02 and DSM 15745, DSM 25571 and DSM 22760 were 89.5 and 37.0 %, 79.6 and 22.4 %, and 75.9 and 21.0 %, respectively. The genomic size of strain MKL-02 was 3 423 857 bp with a 72.7 mol% G+C content. Growth was observed at 10-45 °C (optimum, 37-40 °C) and pH 6.0-10.0 (optimum, pH 7.0), in the presence of 0-10 % (w/v) NaCl (optimum, 0.5 %). Cells of strain MKL-02 were non-motile cocci and 0.50-0.60 µm long, as determined by transmission electron microscopy. The strain was catalase-positive and oxidase-negative. The major fatty acid type (>10 % of total) was C. The polar lipid profile consisted of two unidentified phospholipids, three unidentified lipids and an unidentified aminophospholipid. The strain contained MK-8 (H) as the predominant menaquinone. Based on phylogenetic and phenotypic considerations, it is proposed that strain MKL-02 be classified as a new species, named sp. nov. The type strain is MKL-02 (=NCCP 16967=JCM 34624).
Topics: Actinomycetales; Actinomycetales Infections; Animals; Bacterial Typing Techniques; Base Composition; Catalase; Child; DNA, Bacterial; Fatty Acids; Gastroenteritis; Humans; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sheep
PubMed: 35580017
DOI: 10.1099/ijsem.0.005381 -
Archives of Microbiology Jul 2022Strains Marseille-Q5893 (= CSUR Q5893 = CECT 30496) and Marseille-Q5883 (= CSUR Q5883 = CECT 30497) were isolated from vaginal samples using the culturomics...
Strains Marseille-Q5893 (= CSUR Q5893 = CECT 30496) and Marseille-Q5883 (= CSUR Q5883 = CECT 30497) were isolated from vaginal samples using the culturomics approach. The 16S rRNA gene sequences of each strain were sequenced and then compared by BLASTn to the NCBI database. Strains Marseille-Q5893 and Marseille-Q5883 were most closely related to Anaerococcus obesiensis and Finegoldia magna, with identities of 98.5% and 90.0%, respectively. Strain Marseille-Q5893 is strictly anaerobic, while strain Marseille-Q5883 is facultative anaerobic. Both strains are Gram-positive, coccus-shaped, oxidase- and catalase-negative. The most abundant fatty acid for both strains is hexadecanoic acid, followed by 9-octadecenoic acid and tetradecanoic acid. Strain Marseille-Q5893 has a genome size of 1,831,271 bp with a G+C content of 29.4 mol%, whereas strain Marseille-Q5883 has a genome of 1,997,945 bp with a 33.6 mol% G+C content. The genomic comparison of closely related species with strains Marseille-Q5893 and Marseille-Q5883 showed that all digital DNA-DNA hybridization (dDDH) and orthologous average nucleotide identity (OrthoANI) values were lower than the published species thresholds (70% and 95-96%, respectively). Based on these data, we conclude that strain Marseille-Q5893 belongs to a new species in the family Peptoniphilaceae and strain Marseille-Q5883 belongs to a new genus in the family Peptostreptococcaceae. For these two new bacterial species, the names Anaerococcus ihuae sp. nov. and Mediannikoviicoccus vaginalis gen. nov., sp. nov., were proposed.
Topics: Base Composition; Clostridiales; DNA, Bacterial; Fatty Acids; Female; Humans; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 35859139
DOI: 10.1007/s00203-022-03082-7 -
Current Microbiology Jul 2021Strain Marseille-P2012 was described to represent a new bacterial genus belonging to the phylum Firmicutes using the taxonogenomics concept. It was isolated from stool...
Strain Marseille-P2012 was described to represent a new bacterial genus belonging to the phylum Firmicutes using the taxonogenomics concept. It was isolated from stool samples of a healthy 2-year-old Senegalese boy in a study of the human gut microbiota. This strain is a Gram-positive, anaerobic, non-motile and coccus-shaped bacterium. The 16S rRNA gene sequence of strain Marseille-P2012 exhibited 90.5% similarity with Finegoldia magna strain ATCC 29,328, the phylogenetically closest species with standing in nomenclature. The genome of strain Marseille-P2012 is 1,832,315 bp-long with 32.46 mol% of G + C content. With regard to its phenotypic, biochemical and genomic characteristics, this bacterium was classified as a new bacterial genus and species, Lagierella massiliensis gen. nov., sp. nov., with strain Marseille-P2012 (= CSUR P2012 = DSM100854) as type strain.
Topics: Child, Preschool; DNA, Bacterial; Feces; Firmicutes; Humans; Male; Phylogeny; RNA, Ribosomal, 16S
PubMed: 34043027
DOI: 10.1007/s00284-021-02539-0 -
Pediatrics and Neonatology Mar 2024In recent years, some studies have found that acute uncomplicated appendicitis can be treated with antibiotics alone. Because of the lack of relevant research on...
BACKGROUND
In recent years, some studies have found that acute uncomplicated appendicitis can be treated with antibiotics alone. Because of the lack of relevant research on treating acute appendicitis in Taiwan, this study investigated the microbiological characteristics of acute appendicitis to permit accurate empirical antibiotic use for uncomplicated appendicitis.
METHODS
In this single-center retrospective cohort study, patients listed in the Taiwan National Health Insurance Research Database with a discharge diagnosis of acute appendicitis were identified. Data for bacterial specimens and antibiotic susceptibility tests among patients treated at Tri-Service General Hospital between January 2016 and December 2021 were analyzed.
RESULTS
Among 2805 patients diagnosed with acute appendicitis, 167 (6%) were <18 years old. The culture positivity rates among children and adults were 33% and 18%, respectively. In total, 367 aerobes and 207 anaerobes were isolated. The predominant aerobic gram-positive coccus was viridans group streptococci (8.9%), the most common aerobic gram-negative bacillus was Escherichia coli (27.9%), and the most common anaerobic microorganism was Bacteroides spp. (27.7%). The results of antibiotic susceptibility testing of the predominant microorganisms revealed that 86.3% of gram-positive aerobes were susceptible to ampicillin, 76.3% of gram-negative aerobes were susceptible to gentamicin, and all anaerobic isolates were susceptible to metronidazole.
CONCLUSION
Triple first-line antibiotic combination therapy, including ampicillin, gentamicin, and metronidazole, remains highly effective against the pathogens that cause acute appendicitis.
Topics: Child; Adult; Humans; Adolescent; Metronidazole; Appendicitis; Retrospective Studies; Anti-Bacterial Agents; Ampicillin; Gentamicins; Bacteria, Aerobic; Escherichia coli; Microbial Sensitivity Tests
PubMed: 37741758
DOI: 10.1016/j.pedneo.2023.08.003 -
Emerging Infectious Diseases Sep 2020Leuconostoc lactis is a glycopeptide-resistant, gram-positive, facultative anaerobic coccus isolated from dairy products, whereas Staphylococcus nepalensis is...
Leuconostoc lactis is a glycopeptide-resistant, gram-positive, facultative anaerobic coccus isolated from dairy products, whereas Staphylococcus nepalensis is coagulase-negative coccus that has not been identified as human pathogen. We report an instructive case of L. lactis and S. nepalensis bacteremia in a 71-year-old man who experienced Boerhaave syndrome after a meal.
Topics: Aged; Anti-Bacterial Agents; Bacteremia; Gram-Positive Bacterial Infections; Humans; Japan; Leuconostoc; Male; Staphylococcus
PubMed: 32818417
DOI: 10.3201/eid2609.191123 -
International Journal of Systematic and... Jan 2016A bacterial strain, THG-S15-4T, was isolated from garden soil taken from the Guro-gu district of Seoul, Republic of Korea. Strain THG-S15-4T was Gram-stain-positive,...
A bacterial strain, THG-S15-4T, was isolated from garden soil taken from the Guro-gu district of Seoul, Republic of Korea. Strain THG-S15-4T was Gram-stain-positive, facultatively anaerobic, coccus-shaped and non-motile, forming white colonies. The strain grew optimally at 25-37 °C, at pH 7.0 and in the presence of 0-2.0 % (w/v) NaCl. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain THG-S15-4T was affiliated to species of the genus Brachybacterium, and the most closely related species were Brachybacterium rhamnosum KCTC 9917 T (98.5 % sequence similarity) and Brachybacterium squillarum KCTC 19899T (96.9 % sequence similarity). The DNA-DNA relatedness between strain THG-S15-4T and B. rhamnosum KCTC 9917 T was found to be below 20.0 %. The DNA G+C content was determined to be 69.5 mol%. The major isoprenoid quinone detected was MK-7. Strain THG-S15-4T was characterized chemotaxonomically as having meso-diaminopimelic acid in the cell-wall peptidoglycan. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, unidentified glycolipids and an unidentified polar lipid. The major fatty acids were found to be iso-C16 : 0 and anteiso-C15 : 0. The results of physiological and biochemical tests enabled strain THG-S15-4T to be differentiated phenotypically from species of the genus Brachybacterium with validly published names. Therefore, it is suggested that this newly isolated organism represents a novel species, for which the name Brachybacterium horti sp. nov. is proposed. The type strain is THG-S15-4T ( = KCTC 39563T = CCTCC AB 2015116T).
Topics: Actinomycetales; Agriculture; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Diaminopimelic Acid; Fatty Acids; Glycolipids; Molecular Sequence Data; Nucleic Acid Hybridization; Peptidoglycan; Phylogeny; RNA, Ribosomal, 16S; Republic of Korea; Sequence Analysis, DNA; Soil Microbiology; Vitamin K 2
PubMed: 26476895
DOI: 10.1099/ijsem.0.000696 -
International Journal of Systematic and... Aug 2019A Gram-stain-positive and catalase negative coccus, designated strain Gos25-1, isolated from a cotton flower (Gossypium hirsutum L.) collected from Khao Wong district,...
A Gram-stain-positive and catalase negative coccus, designated strain Gos25-1, isolated from a cotton flower (Gossypium hirsutum L.) collected from Khao Wong district, Kalasin province, Thailand. The taxonomic position of this strain was systematically studied based upon polyphasic taxonomic methods. The strain was facultatively anaerobic and produced l-lactic acid from glucose. The predominant cellular fatty acids were the straight-chain fatty acids C18 : 1ω9c and C16 : 0. According to 16S rRNA and phenylalanyl-tRNA synthase alpha subunit (pheS) gene sequence similarity, this strain was closely related to Enterococcus pallens NBRC 100697, E. hermanniensis CIP 108559, E. avium NBRC 100477 and E. raffinosus NBRC 100492 with 98.9-99.1 % and 77.0-82.0 % sequence similarities, respectively. Phylogenetic analysis indicated that strain Gos25-1 was clearly distinguished from closely related species of the genus Enterococcus. Draft genome of Gos25-1 had a size of 3.99 Mb which was contained 3788 coding sequences with in silico G+C content of 42.4 mol%. The ANIb and a digital DNA-DNA hybridisation (dDDH) values between strain Gos25-1 and the closest related species, E. pallens NBRC 100697 were 73.65 and 21.10 %, respectively. According to polyphasic characterisation, this strain represents a novel species of the genus Enterococcus, for which the name Enterococcus florum sp. nov. is proposed. The type strain is Gos25-1 (=CIP 110956=LMG 29007=NBRC 111461=TISTR 2382).
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Enterococcus; Fatty Acids; Flowers; Genes, Bacterial; Gossypium; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Thailand
PubMed: 31204971
DOI: 10.1099/ijsem.0.003524 -
IDCases 2022
PubMed: 35127449
DOI: 10.1016/j.idcr.2022.e01417 -
Current Microbiology Jul 2019A novel facultative anaerobic and Gram-stain-positive coccus, designated strain ChDC F135, was isolated from human subgingival dental plaque of periodontitis lesion and...
A novel facultative anaerobic and Gram-stain-positive coccus, designated strain ChDC F135, was isolated from human subgingival dental plaque of periodontitis lesion and was characterized by polyphasic taxonomic analysis. The 16S rRNA gene (16S rDNA) sequence of strain ChDC F135 was closest to that of Streptococcus sinensis HKU4 (98.2%), followed by Streptococcus intermedia SK54 (97.0%), Streptococcus constellatus NCTC11325 (96.0%), and Streptococcus anginosus NCTC 10713 (95.7%). In contrast, phylogenetic analysis based on the superoxide dismutase gene (sodA) and the RNA polymerase beta-subunit gene (rpoB) showed that the nucleotide sequence similarities of strain ChDC F135 were highly similar to the corresponding genes of S. anginosus NCTC 10713 (99.2% and 97.6%, respectively), S. constellatus NCTC11325 (87.8% and 91.4%, respectively), and S. intermedia SK54 (85.8% and 91.2%, respectively) rather than those of S. sinensis HKU4 (80.5% and 82.6%). The complete genome of strain ChDC F135 consisted of 1,901,251 bp and the G+C content was 38.9 mol %. Average nucleotide identity value between strain ChDC F135 and S. sinensis HKU4 or S. anginosus NCTC 10713 were 75.7% and 95.6%, respectively. The C composition of the cellular fatty acids of strain ChDC F135 (32.8%) was different from that of S. intermedia (6-8%), S. constellatus (6-13%), and S. anginosus (13-20%). Based on the results of phylogenetic and phenotypic analysis, strain ChDC F135 (= KCOM 2412 = JCM 33300) was classified as a type strain of a novel species of the genus Streptococcus, for which we proposed the name Streptococcus periodonticum sp. nov.
Topics: Bacteria, Anaerobic; Bacterial Proteins; Base Composition; DNA, Bacterial; DNA-Directed RNA Polymerases; Dental Plaque; Fatty Acids; Genome, Bacterial; Humans; Periodontitis; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Species Specificity; Streptococcus; Superoxide Dismutase
PubMed: 31053905
DOI: 10.1007/s00284-019-01695-8 -
MicrobiologyOpen Jun 2018Strain Marseille-P2341 , a nonmotile, nonspore-forming, Gram-stain-positive anaerobic coccus, was isolated in the vaginal specimen of a patient with bacterial vaginosis...
Characterization of a novel Gram-stain-positive anaerobic coccus isolated from the female genital tract: Genome sequence and description of Murdochiella vaginalis sp. nov.
Strain Marseille-P2341 , a nonmotile, nonspore-forming, Gram-stain-positive anaerobic coccus, was isolated in the vaginal specimen of a patient with bacterial vaginosis using culturomics. Its growth occurred at temperatures ranging from 25 to 42°C, with pH between 6.5 and 8.5, and at NaCl concentrations lower than 5%. The major fatty acids were C (27.7%) and C (24.4%). Its genome is 1,671,491 bp long with 49.48 mol% of G+C content. It is composed of 1,501 genes: 1,446 were protein-coding genes and 55 were RNAs. Strain Marseille-P2341 shared 97.3% of 16S rRNA gene sequence similarity with Murdochiella asaccharolytica, the phylogenetically closest species. These results enabled the classification of strain Marseille-P2341 as a new species of the genus Murdochiella for which we proposed the name Murdochiella vaginalis sp. nov. The type strain is strain Marseille-P2341 (=DSM 102237, =CSUR P2341).
Topics: Adult; Anaerobiosis; Bacteria, Anaerobic; Base Composition; Cluster Analysis; Cytosol; DNA, Bacterial; DNA, Ribosomal; Fatty Acids; Female; Firmicutes; Gram-Positive Cocci; Humans; Hydrogen-Ion Concentration; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sodium Chloride; Temperature; Vagina; Vaginosis, Bacterial
PubMed: 29745065
DOI: 10.1002/mbo3.570