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Enfermedades Infecciosas Y... 2021An increase in recent years in the isolation of Vagococcus spp. is suggestive of emerging infection by this pathogen in our hospital. (Review)
Review
INTRODUCTION
An increase in recent years in the isolation of Vagococcus spp. is suggestive of emerging infection by this pathogen in our hospital.
METHODS
Prospective, descriptive study.
PERIOD
July 2014-January 2019. Phenotypic identification of 15 isolates of Vagococcus spp. was performed by conventional biochemical tests, automated methodology and mass spectrometry (MALDI-TOF MS). Molecular identification was achieved by sequencing the 16S rRNA gene. The Vitek™ 2C automated system was used to test antibiotic susceptibility.
RESULTS
The molecular method identified 11 Vagococcus fluvialis, one Vagococcus lutrae and three Vagococcus spp. MALDI-TOF MS facilitated the rapid recognition of the genus. The most active antibiotics were ampicillin, trimethoprim/sulfamethoxazole, vancomycin, teicoplanin and linezolid. Most of the cases of isolation were associated with skin and soft tissue or osteoarticular infections in patients with diabetes.
CONCLUSION
This article is the most extensive review of cases of Vagococcus spp. infection reported in the literature and highlights the microbiological and clinical aspects of this pathogen.
Topics: Enterococcaceae; Humans; Prospective Studies; RNA, Ribosomal, 16S
PubMed: 34353510
DOI: 10.1016/j.eimce.2021.05.002 -
Journal of Microbiology (Seoul, Korea) Jan 2021Two unknown Gram-stain-positive, catalase- and oxidasenegative, non-motile, and coccus-shaped bacteria, designated MN-17 and MN-09, were isolated from yaks faeces (Bos...
Two unknown Gram-stain-positive, catalase- and oxidasenegative, non-motile, and coccus-shaped bacteria, designated MN-17 and MN-09, were isolated from yaks faeces (Bos grunniens) in the Qinghai-Tibet Plateau of China. 16S rRNA gene sequence-based comparative analyses revealed that the two strains were grouped within the genus Vagococcus, displaying the highest similarity with Vagococcus xieshaowenii CGMCC 1.16436 (98.6%) and Vagococcus elongatus CCUG 51432 (96.4%). Both strains grew optimally at 37°C and pH 7.0 in the presence of 0.5% (w/v) NaCl. The complete genome of MN-17 comprises 2,085 putative genes with a total of 2,190,262 bp and an average G + C content of 36.7 mol%. The major fatty acids were C (31.2%), C (28.5%), and Cω9c (13.0%); the predominant respiratory quinone was MK-7 (68.8%); the peptidoglycan type was A4α(L-Lys-D-Asp); and the major polar lipid was diphosphatidylglycerol. Together, these supported the affiliation of strain MN-17 to the genus Vagococcus. In silico DNA-DNA hybridization and the average nucleotide identity values between MN-17 and all recognized species in the genus were 21.6-26.1% and 70.7-83.0%, respectively. MN-17 produced acid from D-cellobiose, D-fructose, glycerol, D-glucose, N-acetyl-glucosamine, gentiobiose, D-mannose, D-maltose, D-ribose, D-saccharose, salicin, D-trehalose, and D-xylose. These results distinguished MN-17 and MN-09 from closely related species in Vagococcus. Thus, we propose that strains MN-17 and MN-09 represent a novel species in the genus Vagococcus, with the name Vagococcus zengguangii sp. The type strain is MN-17 (= CGMCC 1.16726 = GDMCC 1.1589 = JCM 33478).
Topics: Animals; Bacterial Typing Techniques; Base Composition; Cattle; DNA, Bacterial; Enterococcaceae; Fatty Acids; Feces; Genome, Bacterial; RNA, Ribosomal, 16S
PubMed: 33355894
DOI: 10.1007/s12275-021-0406-3 -
International Journal of Systematic and... Jul 2023During our studies on spoilage microbiomes of modified atmosphere packaged broiler meat, we isolated three strains (PNs007, STAA11 and STAA25) of unknown identity. In...
During our studies on spoilage microbiomes of modified atmosphere packaged broiler meat, we isolated three strains (PNs007, STAA11 and STAA25) of unknown identity. In this present polyphasic taxonomy study, including genome-based analyses, we discovered that these isolates represent two novel species belonging to the genus . In all phylogenetic analyses, PNs007 was positioned very close to but both the average nucleotide identity (ANI; 89.5 %) and digital DNA-DNA hybridization (dDDH; 38.3 %) values distinguished it as a novel vagococcal species. STAA11 and STAA25 were genetically highly similar (16S rRNA, ANI and dDDH 100 %). The phylogenetic position of STAA11 was adjacent to but out of the cluster containing , and PNs007. According to the ANI (76.2-76.4 %) and dDDH (<22.6 %) values it also represented a novel vagococcal species. Phenotypic characteristics and chemotaxonomic properties of both novel species were typical for vagococci and they contained C (25.5-30.1 %) and C ω9 (67.3-73.0 %) as the major cellular fatty acids. The streptomycin-resistant genotype of STAA11 and STAA25 allowing the growth on streptomycin thallous acetate actidione medium was considered to result from a modification in codon 104 of the gene leading to P104A substitution. The ability of STAA11 and STAA25 to produce ammonia from arginine separated them from PNs007, which did not show arginine deiminase activity. We propose the names sp. nov. (type strain PNs007=DSM 115185=CCUG 76696) and sp. nov. (type strain STAA11=DSM 115183=CCUG 76697) for these novel species.
Topics: Animals; Fatty Acids; Phylogeny; RNA, Ribosomal, 16S; Base Composition; Sequence Analysis, DNA; DNA, Bacterial; Bacterial Typing Techniques; Chickens; Meat; Enterococcaceae; Nucleic Acid Hybridization; Atmosphere
PubMed: 37462470
DOI: 10.1099/ijsem.0.005963 -
International Journal of Systematic and... Mar 2023The genus belongs to the family (order Lactobacillales) and is closely related to the genus . Currently, 19 species of the genus have been validly named. In this...
The genus belongs to the family (order Lactobacillales) and is closely related to the genus . Currently, 19 species of the genus have been validly named. In this study, we isolated strain G314F from the common green bottle fly collected in Germany. Sequencing of its almost-complete 16S rRNA gene revealed that the isolate belongs to the genus , being closely related to SS1994 with high sequence identity (99.50 %), followed by D7T301 (98.86 %), SS1995 (98.71 %), DSM 21459 (98.64 %), 2B-2 (98.64 %) and CD276 (98.64 %). Genome sequencing of strain G314F was performed by a combination of Illumina and Oxford Nanopore technology, yielding a circular genome with a size of 2 139 468 bp and an 11 kb plasmid. Average nucleotide identity and digital DNA-DNA hybridization values were calculated between G314F and its closest-related taxa, and found to be <91 % and <40 %, respectively, thus strongly supporting that strain G314F represents a novel species of the genus . Phylogenetic and core protein-based phylogenomic trees revealed that G314F was closely related to a group of three species, SS1994, D7T301 and DSM 21459. Comparatively, the genome of G314F is the smallest in the group of the four related species, and the biochemical pathway comparison using BlastKOALA revealed that G314F has lost some amino acid biosynthetic proteins; however, it has gained enzymes for carbohydrate metabolism. Phenotypically, G314F was consistent with other species of the genus including a negative catalase reaction and non-motility. Using the polyphasic approach, our data supports that the isolate represents a new species, for which we propose the name G314F (=DSM 112651= CCM 9164).
Topics: Fatty Acids; Phylogeny; RNA, Ribosomal, 16S; DNA, Bacterial; Sequence Analysis, DNA; Bacterial Typing Techniques; Base Composition; Enterococcaceae; Gram-Positive Cocci; Nucleic Acid Hybridization
PubMed: 37000169
DOI: 10.1099/ijsem.0.005787 -
International Journal of Systematic and... Aug 2019Two unusual catalase-negative, Gram-stain-positive, Vagococcus-like isolates that were referred to the CDC Streptococcus Laboratory for identification are described....
Two unusual catalase-negative, Gram-stain-positive, Vagococcus-like isolates that were referred to the CDC Streptococcus Laboratory for identification are described. Strain SS1994 was isolated from ground beef and strain SS1995 was isolated from a human foot wound. Comparative 16S rRNA gene sequence analysis of isolates SS1994 and SS1995 against Vagococcus type strain sequences supported their inclusion in the genus Vagococcus. Strain SS1994 showed high sequence similarity (>97.0 %) to the two most recently proposed species, Vagococcus martis (99.2 %) and Vagococcus teuberi (99.0 %) followed by Vagococcus penaei (98.8 %), strain SS1995 (98.6 %), Vagococcus carniphilus (98.0 %), Vagococcus acidifermentans (98.0 %) and Vagococcus fluvialis (97.9 %). The 16S rRNA gene sequence of strain SS1995 was most similar to V. penaei (99.1 %), followed by SS1994 (98.6 %), V. martis (98.4 %), V. teuberi (98.1 %), V. acidifermentans (97.8 %), and both V. carniphilus and V. fluvialis (97.5 %). A polyphasic taxonomic study using conventional biochemical and the rapid ID 32 STREP system, MALDI-TOF MS, cell fatty acid analysis, pairwise sequence comparisons of the 16S rRNA, rpoA, rpoB, pheS and groL genes, and comparative core and whole genome sequence analyses revealed that strains SS1994 and SS1995 were two novel Vagococcus species. The novel taxonomic status of the two isolates was confirmed with core genome phylogeny, average nucleotide identity <84 % and in silico DNA-DNA hybridization <28 % to any other Vagococcus species. The names Vagococcusbubulae SS1994=(CCUG 70831=LMG 30164) and Vagococcusvulneris SS1995=(CCUG 70832=LMG 30165) are proposed.
Topics: Animals; Bacterial Typing Techniques; Base Composition; Cattle; DNA, Bacterial; Enterococcaceae; Fatty Acids; Foot; Genes, Bacterial; Humans; Male; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Red Meat; Sequence Analysis, DNA; Wounds and Injuries
PubMed: 31125302
DOI: 10.1099/ijsem.0.003459 -
G3 (Bethesda, Md.) Jan 2021While the gram-positive bacterium Vagococcus fluvialis has been isolated from the environment as well as fish, birds, and mammals, very little is known about the...
While the gram-positive bacterium Vagococcus fluvialis has been isolated from the environment as well as fish, birds, and mammals, very little is known about the species. V. fluvialis is believed to be a probiotic in fishes. However, within mammals, it is more frequently isolated from infectious tissue, including on rare occasions human and livestock lesions. Prior to the study described here, V. fluvialis had never been found in healthy bovine animals. Here, we present the complete genomes of V. fluvialis UFMG-H6, UFMG-H6B, and UFMG-H7, novel strains isolated from urine samples from healthy bovine females. These are the first genomes of mammalian isolates and the first description of V. fluvialis from urine. The genomes did not encode for any known virulence genes, suggesting that they may be commensal members of the urine microbiota.
Topics: Animals; Cattle; Enterococcaceae; Female; Fishes; Virulence
PubMed: 33561240
DOI: 10.1093/g3journal/jkaa034 -
Journal of Microbiology (Seoul, Korea) Feb 2021A polyphasic taxonomic approach was used to characterize two novel bacterial strains, HDW17A and HDW17B, isolated from the intestine of the diving beetle Cybister...
Description of Vagococcus coleopterorum sp. nov., isolated from the intestine of the diving beetle, Cybister lewisianus, and Vagococcus hydrophili sp. nov., isolated from the intestine of the dark diving beetle, Hydrophilus acuminatus, and emended description of the genus Vagococcus.
A polyphasic taxonomic approach was used to characterize two novel bacterial strains, HDW17A and HDW17B, isolated from the intestine of the diving beetle Cybister lewisianus, and the dark diving beetle Hydrophilus acuminatus, respectively. Both strains were Gram-positive and facultative anaerobic cocci forming cream-colored colonies. The isolates grew optimally at 25°C, pH 7, in the presence of 0.3% (wt/vol) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences and genome sequences showed that the isolates were members of the genus Vagococcus, and strain HDW17A was closely related to Vagococcus fessus CCUG 41755 (98.9% of 16S rRNA gene sequence similarity and 74.3% of average nucleotide identity [ANI]), whereas strain HDW17B was closely related to Vagococcus fluvialis NCFB 2497 (98.9% of 16S rRNA gene sequence similarity and 76.6% of ANI). Both strains contained C, and Cω9c as the major cellular fatty acids, but Cω9c was also observed only in strain HDW17B as the major cellular fatty acid. The respiratory quinone of the isolates was MK-7. The major polar lipid components were phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. The genomic DNA G + C content of strains HDW17A and HDW17B were 36.6 and 34.4%, respectively. Both strains had cell wall peptidoglycan composed of the amino acids L-alanine, glycine, D-glutamic acid, L-tryptophan, L-lysine, and L-aspartic acid, and the sugars ribose, glucose, and galactose. Based on phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses, strains HDW17A and HDW17B represent two novel species in the genus Vagococcus. We propose the name Vagococcus coleopterorum sp. nov. for strain HDW17A (= KACC 21348 = KCTC 49324 = JCM 33674) and the name Vagococcus hydrophili sp. nov. for strain HDW17B (= KACC 21349 = KCTC 49325 = JCM 33675).
Topics: Animals; Bacterial Typing Techniques; Base Composition; Coleoptera; Enterococcaceae; Fatty Acids; Intestines; Phylogeny
PubMed: 33355892
DOI: 10.1007/s12275-021-0485-1 -
Journal of Fish Diseases May 2022In November 2018, Vagococcus salmoninarum was identified as the causative agent of a chronic coldwater streptococcosis epizootic in broodstock brook trout (Salvelinus...
In November 2018, Vagococcus salmoninarum was identified as the causative agent of a chronic coldwater streptococcosis epizootic in broodstock brook trout (Salvelinus fontinalis) at the Iron River National Fish Hatchery in Wisconsin, USA. By February 2019, the epizootic spread to adjacent raceways containing broodstock lake trout (Salvelinus namaycush), whereby fish were found to be coinfected with Carnobacterium maltaromaticum and V. salmoninarum. To differentiate these two pathogens and determine the primary cause of the lake trout morbidity, a quantitative real-time PCR (qPCR) was developed targeting the C. maltaromaticum phenylalanyl-tRNA synthase alpha subunit (pheS) gene. The qPCR was combined with a V. salmoninarum qPCR, creating a duplex qPCR assay that simultaneously quantitates C. maltaromaticum and V. salmoninarum concentrations in individual lake trout tissues, and screens presumptive isolates from hatchery inspections and wild fish from national fish hatchery source waters throughout the Great Lakes basin. Vagococcus salmoninarum and C. maltaromaticum were co-detected in broodstock brook trout from two tribal hatcheries and C. maltaromaticum was present in wild fish in source waters of several national fish hatcheries. This study provides a powerful new tool to differentiate and diagnose two emerging Gram-positive bacterial pathogens.
Topics: Animals; Carnobacterium; Enterococcaceae; Fish Diseases; Real-Time Polymerase Chain Reaction
PubMed: 35195301
DOI: 10.1111/jfd.13592 -
Journal of Fish Diseases Mar 2020Vagococcus salmoninarum was identified as the causative agent of a chronic epizootic in broodstock "coaster" brook trout (Salvelinus fontinalis) at the Iron River...
Vagococcus salmoninarum was identified as the causative agent of a chronic epizootic in broodstock "coaster" brook trout (Salvelinus fontinalis) at the Iron River National Fish Hatchery. The epizootic spanned more than a year, was unresponsive to multiple florfenicol treatments, and resulted in >50% mortality of the affected fish. The decision was made to cull the remaining fish during spawning, which presented an opportunity to more thoroughly examine V. salmoninarum sampling methods, organ tropism and vertical transmission. A newly developed qPCR targeting the pheS gene was used in concert with bacterial culture to show that V. salmoninarum indeed disproportionately affects females and has a tropism for female reproductive tissues. The study demonstrates that some female reproductive tissues (e.g. ovarian fluid, unfertilized eggs) are also an effective option for non-lethal detection. Despite the widespread presence of V. salmoninarum in ovarian fluid and on egg surfaces, we found no evidence of intra-ova transmission.
Topics: Animals; Aquaculture; Enterococcaceae; Female; Fish Diseases; Gram-Positive Bacterial Infections; Male; Ovum; Polymerase Chain Reaction; Prevalence; Trout; Viral Tropism; Wisconsin
PubMed: 32030787
DOI: 10.1111/jfd.13125 -
International Journal of Systematic and... Mar 2020A Gram-stain-positive, coccus- or oval-shaped, non-motile, haemolytic, asporogenous, catalase- and oxidase-negative, and facultatively anaerobic strain, 2B-2, was...
A Gram-stain-positive, coccus- or oval-shaped, non-motile, haemolytic, asporogenous, catalase- and oxidase-negative, and facultatively anaerobic strain, 2B-2, was isolated from a brewer's grain used to make silage in Taiwan. Comparative analyses of 16S rRNA, and gene sequences demonstrated that strain 2B-2 was a member of the genus . On the basis of 16S rRNA gene sequence similarity, the type strains of (98.4 % similarity), (98.4 %), (98.2 %), (98.2 %) and (98.0 %) were the closest neighbours to this novel strain. The similarity levels of concatenated housekeeping gene sequences ( and ) between strain 2B-2 and these closely related species ranged from 84.5 to 88.0 %. The average nucleotide identity and DNA-DNA hybridization values between strain 2B-2 and its closest relatives were lower than 72.9 and 21.6 %, respectively. The DNA G+C content was 34.7 mol%. Phenotypic and genotypic features demonstrated that strain 2B-2 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is 2B-2 (=BCRC 81132=NBRC 113536).
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Edible Grain; Enterococcaceae; Fatty Acids; Genes, Bacterial; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Silage; Taiwan
PubMed: 32003713
DOI: 10.1099/ijsem.0.003999