RESUMO
Rhodococcus sp. strain W8901 is a Gram-positive, aerobic, mycolic acid-containing coccobacillus obtained from a patient with acute lymphocytic leukemia. Here, we report on the complete, circular genome sequence obtained using Illumina MiSeq and Oxford Nanopore Technologies MinION reads in order to better resolve the phylogeny of a rare pathogen.
RESUMO
Rat bite fever and Haverhill fever are often difficult to diagnose in a clinical setting. This difficulty results in part from clinicians and laboratory professionals not being able to reliably recover the causative agent Streptobacillus moniliformis using culture-based methods. After utilizing an automated continuous-monitoring blood culture bottle system, we showed that the organism can be reliably cultured when a blood volume inoculum of 10 mL is used. Further, we showed that when the above recommendation is followed, sodium polyanethole sulfonate (up to a concentration of 0.05% w/v) in commercially purchased blood culture bottle formulations seems to be inactivated, allowing for the growth and detection of S. moniliformis. Herein, we offer data and methods used to overcome these clinical limitations. This is a comprehensive study of the historical collection of S. moniliformis isolates maintained by our facility and believed to be the largest of its kind to date.
Assuntos
Streptobacillus , Animais , Automação Laboratorial , Hemocultura , Febre por Mordedura de Rato , Ratos , Estudos RetrospectivosRESUMO
Rat bite fever (RBF) caused by Streptobacillus moniliformis has been described as a diagnostic challenge. While it has a favorable prognosis with treatment, timely diagnosis is hindered by the lack of culture-free identification methods. Here we present a multiplex real-time PCR assay that detects the zoonotic Streptobacillus spp. as well as differentiate the primary causative agent of RBF, Streptobacillus moniliformis. The performance of this assay was evaluated using mock clinical specimens for blood, serum, and urine. Analytical sensitivity was determined to be 3-4 genome equivalents (GE)/µl for the zoonotic Streptobacillus spp. target, and 1-2 GE/µl for the S. moniliformis specific target. The assay correctly detected only the intended targets with no cross-reactivity identified. The pathogen was detected in all spiked matrices and not detected in the negative non-spiked specimens. This rapid diagnostic assay may permit quicker diagnosis of RBF patients.
Assuntos
Zoonoses Bacterianas/microbiologia , Febre por Mordedura de Rato/microbiologia , Reação em Cadeia da Polimerase em Tempo Real/métodos , Streptobacillus/classificação , Streptobacillus/isolamento & purificação , Animais , Clonagem Molecular , Humanos , Reprodutibilidade dos Testes , Especificidade da EspécieRESUMO
Kroppenstedtia eburnea DSM 45196T and Kroppenstedtia pulmonis W9323T are aerobic, Gram-positive, filamentous, chemoorganotrophic thermoactinomycetes. Here, we report on the complete and circular genome assemblies generated using Illumina MiSeq and Oxford Nanopore Technologies MinION reads. Putative gene clusters predicted to be involved in the production of secondary metabolites were also identified.
RESUMO
The genus Chryseobacterium in the family Weeksellaceae is known to be polyphyletic. Amino acid identity (AAI) values were calculated from whole-genome sequences of species of the genus Chryseobacterium, and their distribution was found to be multi-modal. These naturally-occurring non-continuities were leveraged to standardise genus assignment of these species. We speculate that this multi-modal distribution is a consequence of loss of biodiversity during major extinction events, leading to the concept that a bacterial genus corresponds to a set of species that diversified since the Permian extinction. Transfer of nine species (Chryseobacterium arachidiradicis, Chryseobacterium bovis, Chryseobacterium caeni, Chryseobacterium hispanicum, Chryseobacterium hominis, Chryseobacterium hungaricum,, Chryseobacterium pallidum and Chryseobacterium zeae) to the genus Epilithonimonas and eleven (Chryseobacterium anthropi, Chryseobacterium antarcticum, Chryseobacterium carnis, Chryseobacterium chaponense, Chryseobacterium haifense, Chryseobacterium jeonii, Chryseobacterium montanum, Chryseobacterium palustre, Chryseobacterium solincola, Chryseobacterium treverense and Chryseobacterium yonginense) to the genus Kaistella is proposed. Two novel species are described: Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. Evidence is presented to support the assignment of Planobacterium taklimakanense to a genus apart from Chryseobacterium, to which Planobacterium salipaludis comb nov. also belongs. The novel genus Halpernia is proposed, to contain the type species Halpernia frigidisoli comb. nov., along with Halpernia humi comb. nov., and Halpernia marina comb. nov.
Assuntos
Chryseobacterium/classificação , Filogenia , Aminoácidos/química , Extinção BiológicaRESUMO
Kroppenstedtia sanguinis X0209T, a thermoactinomycete, was isolated from the blood of a patient in Sweden. We report on the draft genome sequence obtained with an Illumina MiSeq instrument. The assembled genome totaled 3.73 Mb and encoded 3,583 proteins. Putative genes for virulence, transposons, and biosynthetic gene clusters have been identified.
RESUMO
Two unusual catalase-negative, Gram-stain-positive, Vagococcus-like isolates that were referred to the CDC Streptococcus Laboratory for identification are described. Strain SS1994T was isolated from ground beef and strain SS1995T was isolated from a human foot wound. Comparative 16S rRNA gene sequence analysis of isolates SS1994T and SS1995T against Vagococcus type strain sequences supported their inclusion in the genus Vagococcus. Strain SS1994T showed high sequence similarity (>97.0â%) to the two most recently proposed species, Vagococcus martis (99.2â%) and Vagococcus teuberi (99.0â%) followed by Vagococcus penaei (98.8â%), strain SS1995T (98.6â%), Vagococcus carniphilus (98.0â%), Vagococcus acidifermentans (98.0â%) and Vagococcus fluvialis (97.9â%). The 16S rRNA gene sequence of strain SS1995T was most similar to V. penaei (99.1â%), followed by SS1994T (98.6â%), V. martis (98.4â%), V. teuberi (98.1â%), V. acidifermentans (97.8â%), and both V. carniphilus and V. fluvialis (97.5â%). 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 SS1994T and SS1995T were two novel Vagococcus species. The novel taxonomic status of the two isolates was confirmed with core genome phylogeny, average nucleotide identity <84â% and in silico DNA-DNA hybridization <28â% to any other Vagococcus species. The names Vagococcusbubulae SS1994T=(CCUG 70831T=LMG 30164T) and Vagococcusvulneris SS1995T=(CCUG 70832T=LMG 30165T) are proposed.
Assuntos
Enterococcaceae/classificação , Pé/microbiologia , Filogenia , Carne Vermelha/microbiologia , Ferimentos e Lesões/microbiologia , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , Bovinos , DNA Bacteriano/genética , Enterococcaceae/isolamento & purificação , Ácidos Graxos/química , Genes Bacterianos , Humanos , Masculino , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNARESUMO
The complete genome sequence of the Nocardia farcinica type strain was obtained by combining Illumina HiSeq and PacBio reads, producing a single 6.29-Mb chromosome and 2 circular plasmids. Bioinformatic analysis identified 5,991 coding sequences, including putative genes for virulence, microbial resistance, transposons, and biosynthesis gene clusters.
RESUMO
Nosocomial infections of Elizabethkingia species can have fatal outcomes if not identified and treated properly. The current diagnostic tools available require culture and isolation, which can extend the reporting time and delay treatment. Using comparative genomics, we developed an efficient multiplex real-time PCR for the simultaneous detection of all known species of Elizabethkingia, as well as differentiating the two most commonly reported species, Elizabethkingia anophelis and Elizabethkingia meningoseptica.
Assuntos
Flavobacteriaceae/classificação , Flavobacteriaceae/isolamento & purificação , Genômica , Técnicas de Diagnóstico Molecular/métodos , Reação em Cadeia da Polimerase Multiplex/métodos , DNA Bacteriano/isolamento & purificação , Infecções por Flavobacteriaceae/microbiologia , Genoma Bacteriano , Humanos , Filogenia , Sensibilidade e Especificidade , Análise de Sequência de DNARESUMO
Corynebacterium bovis is an opportunistic bacterial pathogen shown to cause eye and prosthetic joint infections as well as abscesses in humans, mastitis in dairy cattle, and skin disease in laboratory mice and rats. Little is known about the genetic characteristics and genomic diversity of C. bovis because only a single draft genome is available for the species. The overall aim of this study was to sequence and compare the genome of C. bovis isolates obtained from different species, locations, and time points. Whole-genome sequencing was conducted on 20 C. bovis isolates (six human, four bovine, nine mouse and one rat) using the Illumina MiSeq platform and submitted to various comparative analysis tools. Sequencing generated high-quality contigs (over 2.53 Mbp) that were comparable to the only reported assembly using C. bovis DSM 20582T (97.8 ± 0.36% completeness). The number of protein-coding DNA sequences (2,174 ± 12.4) was similar among all isolates. A Corynebacterium genus neighbor-joining tree was created, which revealed Corynebacterium falsenii as the nearest neighbor to C. bovis (95.87% similarity), although the reciprocal comparison shows Corynebacterium jeikeium as closest neighbor to C. falsenii. Interestingly, the average nucleotide identity demonstrated that the C. bovis isolates clustered by host, with human and bovine isolates clustering together, and the mouse and rat isolates forming a separate group. The average number of genomic islands and putative virulence factors were significantly higher (p<0.001) in the mouse and rat isolates as compared to human/bovine isolates. Corynebacterium bovis' pan-genome contained a total of 3,067 genes of which 1,354 represented core genes. The known core genes of all isolates were primarily related to ''metabolism" and ''information storage/processing." However, most genes were classified as ''function unknown" or "unclassified". Surprisingly, no intact prophages were found in any isolate; however, almost all isolates had at least one complete CRISPR-Cas system.
Assuntos
Corynebacterium/genética , Corynebacterium/isolamento & purificação , Animais , Bovinos , Corynebacterium/patogenicidade , Infecções por Corynebacterium/microbiologia , Infecções por Corynebacterium/veterinária , DNA Circular , Feminino , Genoma Bacteriano , Genótipo , Humanos , Camundongos Nus , Infecções Oportunistas/microbiologia , Infecções Oportunistas/veterinária , Filogenia , RNA Bacteriano , RNA Ribossômico 16S , Ratos , Fatores de Virulência/genéticaRESUMO
Streptacidiphilus sp. strain 15-057A was isolated from a bronchial lavage sample and represents the only member of the genus not isolated from acidic soils. A single circular chromosome of 7.01 Mb was obtained by combining Illumina and PacBio sequencing data. Bioinformatic analysis detected 63 putative secondary biosynthetic gene clusters and recognized 43 transposons.
RESUMO
We report the isolation and characterization of two Elizabethkingia anophelis strains (OSUVM-1 and OSUVM-2) isolated from sources associated with horses in Oklahoma. Both strains appeared susceptible to fluoroquinolones and demonstrated high MICs to all cell wall active antimicrobials including vancomycin, along with aminoglycosides, fusidic acid, chloramphenicol, and tetracycline. Typical of the Elizabethkingia, both draft genomes contained multiple copies of ß-lactamase genes as well as genes predicted to function in antimicrobial efflux. Phylogenetic analysis of the draft genomes revealed that OSUVM-1 and OSUVM-2 differ by only 6 SNPs and are in a clade with 3 strains of Elizabethkingia anophelis that were responsible for human infections. These findings therefore raise the possibility that Elizabethkingia might have the potential to move between humans and animals in a manner similar to known zoonotic pathogens.
Assuntos
Flavobacteriaceae/genética , Genes Bacterianos/genética , Variação Genética , Genoma Bacteriano/genética , Animais , Antibacterianos/farmacologia , Flavobacteriaceae/classificação , Flavobacteriaceae/fisiologia , Infecções por Flavobacteriaceae/microbiologia , Infecções por Flavobacteriaceae/veterinária , Doenças dos Cavalos/microbiologia , Cavalos , Especificidade de Hospedeiro , Humanos , Testes de Sensibilidade Microbiana , Filogenia , Análise de Sequência de DNA , Especificidade da EspécieRESUMO
We report here a nearly complete draft genome sequence for a Corynebacterium mastitidis isolate from a mouse. The total read coverage is 198×, and the genome size is 2,264,319 bp with a 69.04% GC content. This genome complements the only other genome available for C. mastitidis, which was obtained from a sheep.
RESUMO
The genus Elizabethkingia is genetically heterogeneous, and the phenotypic similarities between recognized species pose challenges in correct identification of clinically derived isolates. In addition to the type species Elizabethkingia meningoseptica, and more recently proposed Elizabethkingia miricola, Elizabethkingia anophelis and Elizabethkingia endophytica, four genomospecies have long been recognized. By comparing historic DNA-DNA hybridization results with whole genome sequences, optical maps, and MALDI-TOF mass spectra on a large and diverse set of strains, we propose a comprehensive taxonomic revision of this genus. Genomospecies 1 and 2 contain the type strains E. anophelis and E. miricola, respectively. Genomospecies 3 and 4 are herein proposed as novel species named as Elizabethkingia bruuniana sp. nov. (type strain, G0146T = DSM 2975T = CCUG 69503T = CIP 111191T) and Elizabethkingia ursingii sp. nov. (type strain, G4122T = DSM 2974T = CCUG 69496T = CIP 111192T), respectively. Finally, the new species Elizabethkingia occulta sp. nov. (type strain G4070T = DSM 2976T = CCUG 69505T = CIP 111193T), is proposed.
Assuntos
Flavobacteriaceae/classificação , Flavobacteriaceae/genética , Genoma Bacteriano , Genômica , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Sequenciamento Completo do Genoma , Técnicas de Tipagem Bacteriana , Biologia Computacional/métodos , Código de Barras de DNA Taxonômico , DNA Bacteriano , Evolução Molecular , Flavobacteriaceae/química , Genômica/métodos , Hibridização de Ácido Nucleico , Fenótipo , FilogeniaRESUMO
A facultatively anaerobic, Gram-stain-positive bacterium, designated ETRF1T, was found in faecal material of a timber rattlesnake (Crotalus horridus). Based on a comparative 16S rRNA gene sequence analysis, the isolate was assigned to the genus Enterococcus. The 16S rRNA gene sequence of strain ETRF1T showed >97â% similarity to that of the type strains of Enterococcus rotai, E. caccae, E. silesiacus, E haemoperoxidus, E. ureasiticus, E. moraviensis, E. plantarum, E. quebecensis, E. ureilyticus, E. termitis, E. rivorum and E. faecalis. The organism could be distinguished from these 12 phylogenetically related enterococci using conventional biochemical testing, the Rapid ID32 Strep system, comparative pheS and rpoA gene sequence analysis, and comparative whole genome sequence analysis. The estimated in silico DNA-DNA hybridization values were <70â%, and average nucleotide identity values were <96â%, when compared to these 12 species, further validating that ETRF1T represents a unique species within the genus Enterococcus. On the basis of these analyses, strain ETRF1T (=CCUG 65857T=LMG 28312T) is proposed as the type strain of a novel species, Enterococcus crotali sp. nov.
Assuntos
Crotalus/microbiologia , Enterococcus/classificação , Fezes/microbiologia , Filogenia , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Enterococcus/genética , Enterococcus/isolamento & purificação , Minnesota , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNARESUMO
The inclusion of molecular methods in the characterization of the novel species Enterococcus horridus necessitated the sequencing and assembly of the genomes of the closely related Enterococcus rotai and Enterococcus silesiacus Sequencing using Illumina technology in combination with optical mapping led to the generation of closed genomes for both isolates.
RESUMO
The complete circularized genome sequences of selected specimens from the largest known Elizabethkingia anophelis outbreak to date are described here. Genomic rearrangements observed among the outbreak strains are discussed.
RESUMO
Draft genome sequences of Elizabethkingia meningoseptica and representatives of each of its four historically described genomospecies were sequenced here. Preliminary analysis suggests that Elizabethkingia miricola belongs to genomospecies 2, and both Elizabethkingia anophelis and Elizabethkingia endophytica are most similar to genomospecies 1.
RESUMO
Results obtained through 16S rRNA gene sequencing and phenotypic testing of eight related, but unidentified, isolates located in a historical collection at the Centers for Disease Control and Prevention suggested that these isolates belong to a novel genera of bacteria. The genomes of the bacteria, to be named Oblitimonas alkaphilia gen. nov. sp. nov., were sequenced using Illumina technology. Closed genomes were produced for all eight isolates.
RESUMO
Here we report the complete genome sequences of two strains of the novel fastidious, partially acid-fast, Gram-positive bacillus "Lawsonella clevelandensis" (proposed). Their clinical relevance and unusual growth characteristics make them intriguing candidates for whole-genome sequencing.