scholarly journals Coagulase-Negative Staphylococci Pathogenomics

2019 ◽  
Vol 20 (5) ◽  
pp. 1215 ◽  
Author(s):  
Xavier Argemi ◽  
Yves Hansmann ◽  
Kevin Prola ◽  
Gilles Prévost
Keyword(s):  
Staphylococcus Aureus ◽  
Virulence Factors ◽  
Molecular Basis ◽  
Sequence Data ◽  
Commensal Bacteria ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
Coagulase Negative Staphylococci ◽  
Major Pathogens

Coagulase-negative Staphylococci (CoNS) are skin commensal bacteria. Besides their role in maintaining homeostasis, CoNS have emerged as major pathogens in nosocomial settings. Several studies have investigated the molecular basis for this emergence and identified multiple putative virulence factors with regards to Staphylococcus aureus pathogenicity. In the last decade, numerous CoNS whole-genome sequences have been released, leading to the identification of numerous putative virulence factors. Koch’s postulates and the molecular rendition of these postulates, established by Stanley Falkow in 1988, do not explain the microbial pathogenicity of CoNS. However, whole-genome sequence data has shed new light on CoNS pathogenicity. In this review, we analyzed the contribution of genomics in defining CoNS virulence, focusing on the most frequent and pathogenic CoNS species: S. epidermidis, S. haemolyticus, S. saprophyticus, S. capitis, and S. lugdunensis.

scholarly journals Whole genome characterization of strains belonging to the Ralstonia solanacearum species complex and in silico analysis of TaqMan assays for detection in this heterogenous species complex

2021 ◽  
Author(s):  
Viola Kurm ◽  
Ilse Houwers ◽  
Claudia E. Coipan ◽  
Peter Bonants ◽  
Cees Waalwijk ◽  
...  
Keyword(s):  
Ralstonia Solanacearum ◽  
In Silico ◽  
Species Complex ◽  
Sequence Data ◽  
In Silico Analysis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
Pcr Assays

AbstractIdentification and classification of members of the Ralstonia solanacearum species complex (RSSC) is challenging due to the heterogeneity of this complex. Whole genome sequence data of 225 strains were used to classify strains based on average nucleotide identity (ANI) and multilocus sequence analysis (MLSA). Based on the ANI score (>95%), 191 out of 192(99.5%) RSSC strains could be grouped into the three species R. solanacearum, R. pseudosolanacearum, and R. syzygii, and into the four phylotypes within the RSSC (I,II, III, and IV). R. solanacearum phylotype II could be split in two groups (IIA and IIB), from which IIB clustered in three subgroups (IIBa, IIBb and IIBc). This division by ANI was in accordance with MLSA. The IIB subgroups found by ANI and MLSA also differed in the number of SNPs in the primer and probe sites of various assays. An in-silico analysis of eight TaqMan and 11 conventional PCR assays was performed using the whole genome sequences. Based on this analysis several cases of potential false positives or false negatives can be expected upon the use of these assays for their intended target organisms. Two TaqMan assays and two PCR assays targeting the 16S rDNA sequence should be able to detect all phylotypes of the RSSC. We conclude that the increasing availability of whole genome sequences is not only useful for classification of strains, but also shows potential for selection and evaluation of clade specific nucleic acid-based amplification methods within the RSSC.

Taxonomic revision of Harveyi clade bacteria (family Vibrionaceae) based on analysis of whole genome sequences

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2742-2751 ◽  
Author(s):  
Henryk Urbanczyk ◽  
Yoshitoshi Ogura ◽  
Tetsuya Hayashi
Keyword(s):  
Genome Sequence ◽  
Sequence Data ◽  
Draft Genome ◽  
Taxonomic Revision ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
Genome Sequence Data ◽  
The Family

Use of inadequate methods for classification of bacteria in the so-called Harveyi clade (family Vibrionaceae, Gammaproteobacteria) has led to incorrect assignment of strains and proliferation of synonymous species. In order to resolve taxonomic ambiguities within the Harveyi clade and to test usefulness of whole genome sequence data for classification of Vibrionaceae, draft genome sequences of 12 strains were determined and analysed. The sequencing included type strains of seven species: Vibrio sagamiensis NBRC 104589T, Vibrio azureus NBRC 104587T, Vibrio harveyi NBRC 15634T, Vibrio rotiferianus LMG 21460T, Vibrio campbellii NBRC 15631T, Vibrio jasicida LMG 25398T, and Vibrio owensii LMG 25443T. Draft genome sequences of strain LMG 25430, previously designated the type strain of [Vibrio communis], and two strains (MWB 21 and 090810c) from the ‘beijerinckii’ lineage were also determined. Whole genomes of two additional strains (ATCC 25919 and 200612B) that previously could not be assigned to any Harveyi clade species were also sequenced. Analysis of the genome sequence data revealed a clear case of synonymy between V. owensii and [V. communis], confirming an earlier proposal to synonymize both species. Both strains from the ‘beijerinckii’ lineage were classified as V. jasicida, while the strains ATCC 25919 and 200612B were classified as V. owensii and V. campbellii, respectively. We also found that two strains, AND4 and Ex25, are closely related to Harveyi clade bacteria, but could not be assigned to any species of the family Vibrionaceae. The use of whole genome sequence data for the taxonomic classification of the Harveyi clade bacteria and other members of the family Vibrionaceae is also discussed.

scholarly journals Whole-genome sequence data and analysis of a Staphylococcus aureus strain SJTUF_J27 isolated from seaweed

Data in Brief ◽  
2018 ◽  
Vol 20 ◽  
pp. 894-898
Author(s):  
Yanping Xie ◽  
Yiping He ◽  
Sandeep Ghatak ◽  
Peter Irwin ◽  
Xianghe Yan ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Genome Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Aureus Strain ◽  
Whole Genome ◽  
Genome Sequence Data

scholarly journals Complete Genome Sequences of Four Staphylococcus aureus Sequence Type 398 Isolates from Four Goats with Osteomyelitis

2018 ◽  
Vol 7 (12) ◽  
Author(s):  
Mohamed A. Abouelkhair ◽  
Rebecca E. Rifkin ◽  
Remiqiusz M. Grzeskowiak ◽  
Alexandru S. Biris ◽  
David E. Anderson ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Orthopedic Surgery ◽  
Sequence Type ◽  
Whole Genome Sequence ◽  
Multiple Infections ◽  
Whole Genome ◽  
Genome Sequences ◽  
Prosthetic Device ◽  
Content Type ◽  
History Of

Staphylococcus aureus is the causative agent of multiple infections, including bacteremia, infective endocarditis, osteomyelitis, septic arthritis, and prosthetic device infections. We report here the first whole-genome sequence for four S. aureus sequence type 398 isolates from clinical cases of osteomyelitis in four goats with a history of orthopedic surgery.

scholarly journals Genomic insights into the host specific adaptation of the Pneumocystis genus

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Ousmane H. Cissé ◽  
Liang Ma ◽  
John P. Dekker ◽  
Pavel P. Khil ◽  
Jung-Ho Youn ◽  
...  
Keyword(s):  
Host Specificity ◽  
Genome Sequence ◽  
Molecular Basis ◽  
Sequence Data ◽  
Host Adaptation ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Specific Adaptation ◽  
Genetic Features

AbstractPneumocystis jirovecii, the fungal agent of human Pneumocystis pneumonia, is closely related to macaque Pneumocystis. Little is known about other Pneumocystis species in distantly related mammals, none of which are capable of establishing infection in humans. The molecular basis of host specificity in Pneumocystis remains unknown as experiments are limited due to an inability to culture any species in vitro. To explore Pneumocystis evolutionary adaptations, we have sequenced the genomes of species infecting macaques, rabbits, dogs and rats and compared them to available genomes of species infecting humans, mice and rats. Complete whole genome sequence data enables analysis and robust phylogeny, identification of important genetic features of the host adaptation, and estimation of speciation timing relative to the rise of their mammalian hosts. Our data reveals insights into the evolution of P. jirovecii, the sole member of the genus able to infect humans.

scholarly journals Genomic insights into the host specific adaptation of the Pneumocystis genus and emergence of the human pathogen Pneumocystis jirovecii

2020 ◽  
Author(s):  
Ousmane H. Cissé ◽  
Liang Ma ◽  
John P. Dekker ◽  
Pavel P. Khil ◽  
Jung-Ho Youn ◽  
...  
Keyword(s):  
Molecular Basis ◽  
Sequence Data ◽  
Host Adaptation ◽  
Pneumocystis Jirovecii ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Human Pathogen ◽  
Specific Adaptation ◽  
Genetic Features

AbstractPneumocystis jirovecii, the fungal agent of human Pneumocystis pneumonia, is closely related to macaque Pneumocystis. Little is known about other Pneumocystis species in distantly related mammals, none of which are capable of establishing infection in humans. The molecular basis of host specificity in Pneumocystis remains unknown as experiments are limited due to an inability to culture any species in vitro. To explore Pneumocystis evolutionary adaptations, we have sequenced the genomes of species infecting macaques, rabbits, dogs and rats and compared them to available genomes of species infecting humans, mice and rats. Complete whole genome sequence data enables analysis and robust phylogeny, identification of important genetic features of the host adaptation, and estimation of speciation timing relative to the rise of their mammalian hosts. Our data reveals novel insights into the evolution of P. jirovecii, the sole member of the genus able to infect humans.

scholarly journals UK circulating strains of human parainfluenza 3: an amplicon based next generation sequencing method and phylogenetic analysis

2018 ◽  
Vol 3 ◽  
pp. 118
Author(s):  
Anna Smielewska ◽  
Edward Emmott ◽  
Kyriaki Ranellou ◽  
Ashley Popay ◽  
Ian Goodfellow ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genome Sequence ◽  
Sequence Data ◽  
Hypervariable Region ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Full Genome ◽  
Genome Sequences ◽  
Genome Data ◽  
The Uk

Background:Human parainfluenza viruses type 3 (HPIV3) are a prominent cause of respiratory infection with a significant impact in both pediatric and transplant patient cohorts.  Currently there is a paucity of whole genome sequence data that would allow for detailed epidemiological and phylogenetic analysis of circulating strains in the UK. Although it is known that HPIV3 peaks annually in the UK, to date there are no whole genome sequences of HPIV3 UK strains available. Methods:Clinical strains were obtained from HPIV3 positive respiratory patient samples collected between 2011 and 2015.  These were then amplified using an amplicon based method, sequenced on the Illumina platform and assembled using a new robust bioinformatics pipeline. Phylogenetic analysis was carried out in the context of other epidemiological studies and whole genome sequence data currently available with stringent exclusion of significantly culture-adapted strains of HPIV3.Results:In the current paper we have presented twenty full genome sequences of UK circulating strains of HPIV3 and a detailed phylogenetic analysis thereof.  We have analysed the variability along the HPIV3 genome and identified a short hypervariable region in the non-coding segment between the M (matrix) and F (fusion) genes. The epidemiological classifications obtained by using this region and whole genome data were then compared and found to be identical.Conclusions:The majority of HPIV3 strains were observed at different geographical locations and with a wide temporal spread, reflecting the global distribution of HPIV3. Consistent with previous data, a particular subcluster or strain was not identified as specific to the UK, suggesting that a number of genetically diverse strains circulate at any one time. A small hypervariable region in the HPIV3 genome was identified and it was shown that, in the absence of full genome data, this region could be used for epidemiological surveillance of HPIV3.

scholarly journals Identification ofKlebsiellacapsule synthesis loci from whole genome data

2016 ◽  
Author(s):  
Kelly L. Wyres ◽  
Ryan R. Wick ◽  
Claire Gorrie ◽  
Adam Jenney ◽  
Rainer Follador ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Multi Drug Resistance ◽  
Reference Database ◽  
Whole Genome ◽  
Genome Sequences ◽  
Protein Coding ◽  
Genome Data

AbstractBackgroundKlebsiella pneumoniaeand close relatives are a growing cause of healthcare-associated infections for which increasing rates of multi-drug resistance are a major concern. TheKlebsiellapolysaccharide capsule is a major virulence determinant and epidemiological marker. However, little is known about capsule epidemiology since serological typing is not widely accessible, and many isolates are serologically non-typeable. Molecular methods for capsular typing are needed, but existing methods lack sensitivity and specificity and fail to take advantage of the information available in whole-genome sequence data, which is increasingly being generated for surveillance and investigation ofKlebsiella.MethodsWe investigated the diversity of capsule synthesis loci (K loci) among a large, diverse collection of 2503 genome sequences ofK. pneumoniaeand closely related species. We incorporated analyses of both full-length K locus DNA sequences and clustered protein coding sequences to identify, annotate and compare K locus structures, and we propose a novel method for identifying K loci based on full locus information extracted from whole genome sequences.ResultsA total of 134 distinct K loci were identified, including 31 novel types. Comparative analysis of K locus gene content detected 508 unique protein coding gene clusters that appear to reassort via homologous recombination, generating novel K locus types. Extensive nucleotide diversity was detected among thewziandwzcgenes, both within and between K loci, indicating that current typing schemes based on these genes are inadequate. As a solution, we introduceKaptive, a novel software tool that automates the process of identifying K loci from large sets ofKlebsiellagenomes based on full locus information.ConclusionsThis work highlights the extensive diversity ofKlebsiellaK loci and the proteins that they encode. We propose a standardised K locus nomenclature forKlebsiella, present a curated reference database of all known K loci, and introduce a tool for identifying K loci from genome data (https://github.com/katholt/Kaptive). These developments constitute important new resources for theKlebsiellacommunity for use in genomic surveillance and epidemiology.

scholarly journals SCCmecFinder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome mec in Staphylococcus aureus Using Whole-Genome Sequence Data

mSphere ◽  
2018 ◽  
Vol 3 (1) ◽  
Author(s):  
Hülya Kaya ◽  
Henrik Hasman ◽  
Jesper Larsen ◽  
Marc Stegger ◽  
Thor Bech Johannesen ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Web Based ◽  
Bioinformatic Tools ◽  
Bioinformatic Tool ◽  
Pcr Techniques ◽  
Staphylococcal Cassette Chromosome

SCCmec in MRSA is acknowledged to be of importance not only because it contains the mecA or mecC gene but also for staphylococcal adaptation to different environments, e.g., in hospitals, the community, and livestock. Typing of SCCmec by PCR techniques has, because of its heterogeneity, been challenging, and whole-genome sequencing has only partially solved this since no good bioinformatic tools have been available. In this article, we describe the development of a new bioinformatic tool, SCCmecFinder, that includes most of the needs for infection control professionals and researchers regarding the interpretation of SCCmec elements. The software detects all of the SCCmec elements accepted by the International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements, and users will be prompted if diverging and potential new elements are uploaded. Furthermore, SCCmecFinder will be curated and updated as new elements are found and it is easy to use and freely accessible.

scholarly journals Comparison of Whole-Genome Sequences for Three Species of the Elizabethkingia Genus

2020 ◽  
Author(s):  
Chen Yang ◽  
Zhe Liu ◽  
Shuai Yu ◽  
Kun Ye ◽  
Xin Li ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Virulence Factors ◽  
Gc Content ◽  
Antibiotic Resistance Genes ◽  
Severe Infection ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
New Genes ◽  
Associated Proteins

Abstract Background: There are increasing researches on whole-genome sequences for clinical strains of Elizabethkingia genus which can cause severe infection in humans, while few studies on the comparative genomics of species in the Elizabethkingia genus in China have been conducted. Methods: The Elizabethkingia genus, isolated in a tertiary hospital of Beijing, China, were re-identified and analyzed through in silico DNA-DNA hybridization (DDH), whole-genome sequence-based phylogeny. Antibiotic resistance genes, antimicrobial resistance-associated proteins, virulence factors were identified, and clusters of orthologous groups were evaluated by Kyoto Encyclopedia of Genes and Genomes (KEGG). The clinical information of patients infected by these organisms was collected and the characteristics were analyzed. Results: There were three species among 20 clinical isolates of Elizabethkingia genus: E. meningoseptica, E. anophelis and E. miricola. E. anophelis accounted for the majority. E. meningoseptica exhibited higher GC content and possessed carbapenemase-encoding genes of blaGOB-16 and blaB-12 while E. anophelis carried genes of blaCME-1. Multiple kinds of antimicrobial resistance-associated proteins were predicted and the virulence factors about adherence, biofilm formation, iron and magnesium uptake, stress adaptation, and immune evasion were discovered. Among 2622 clusters of core genomes identified from the three species of the Elizabethkingia genus, the majority of genes were metabolism-related. Pan genome displayed an upregulation, while the core genome displayed a downregulation with the addition of new genes for the 20 Elizabethkingia strains. Conclusions: The composition was different in antimicrobial resistance-related, virulence-related and metabolism-related genes depending upon species of Elizabethkingia. An adaptive evolution of Elizabethkingia to environmental change including hospital settings has been developed.

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