In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing
Alessandra Carattoli,Ea Zankari,Aurora García-Fernández,Mette Voldby Larsen,Ole Lund,Laura Villa,Frank Møller Aarestrup,Henrik Hasman +7 more
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TLDR
Two easy-to-use Web tools for in silico detection and characterization of whole-genome sequence (WGS) and whole-plasmid sequence data from members of the family Enterobacteriaceae are designed and developed.Abstract:
In the work presented here, we designed and developed two easy-to-use Web tools for in silico detection and characterization of whole-genome sequence (WGS) and whole-plasmid sequence data from members of the family Enterobacteriaceae. These tools will facilitate bacterial typing based on draft genomes of multidrug-resistant Enterobacteriaceae species by the rapid detection of known plasmid types. Replicon sequences from 559 fully sequenced plasmids associated with the family Enterobacteriaceae in the NCBI nucleotide database were collected to build a consensus database for integration into a Web tool called PlasmidFinder that can be used for replicon sequence analysis of raw, contig group, or completely assembled and closed plasmid sequencing data. The PlasmidFinder database currently consists of 116 replicon sequences that match with at least at 80% nucleotide identity all replicon sequences identified in the 559 fully sequenced plasmids. For plasmid multilocus sequence typing (pMLST) analysis, a database that is updated weekly was generated from www.pubmlst.org and integrated into a Web tool called pMLST. Both databases were evaluated using draft genomes from a collection of Salmonella enterica serovar Typhimurium isolates. PlasmidFinder identified a total of 103 replicons and between zero and five different plasmid replicons within each of 49 S . Typhimurium draft genomes tested. The pMLST Web tool was able to subtype genomic sequencing data of plasmids, revealing both known plasmid sequence types (STs) and new alleles and ST variants. In conclusion, testing of the two Web tools using both fully assembled plasmid sequences and WGS-generated draft genomes showed them to be able to detect a broad variety of plasmids that are often associated with antimicrobial resistance in clinically relevant bacterial pathogens.read more
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Journal ArticleDOI
Genomic comparison of diverse Salmonella serovars isolated from swine.
Sushim K. Gupta,Poonam Sharma,Elizabeth A. McMillan,Elizabeth A. McMillan,Charlene R. Jackson,Lari M. Hiott,Tiffanie A. Woodley,Shaheen B. Humayoun,John B. Barrett,Jonathan G. Frye,Michael McClelland +10 more
TL;DR: Overall genomic analysis revealed a great deal of diversity among Salmonella serovars due to acquired genes that enable them to thrive and survive during infection.
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Characterization of the Complete Nucleotide Sequences of mcr-1-Encoding Plasmids From Enterobacterales Isolates in Retailed Raw Meat Products From the Czech Republic.
Marketa Zelendova,Costas C. Papagiannitsis,Adam Valcek,Adam Valcek,Matej Medvecky,Matej Medvecky,Ibrahim Bitar,Jaroslav Hrabak,Tereza Gelbíčová,Alzbeta Barakova,Iva Kutilova,Renata Karpíšková,Monika Dolejska,Monika Dolejska +13 more
TL;DR: In this paper, the authors determined complete nucleotide sequence of mcr-1-carrying plasmids from Enterobacterales isolates recovered from domestic and imported raw retailed meat and compare them with plasmid available at the GenBank sequence database.
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Piperacillin-Tazobactam-Resistant/Third-Generation Cephalosporin-Susceptible Escherichia coli and Klebsiella pneumoniae Isolates: Resistance Mechanisms and In vitro-In vivo Discordance
Kamilia Abdelraouf,Kalyan D. Chavda,Michael J. Satlin,Stephen G. Jenkins,Barry N. Kreiswirth,David P. Nicolau +5 more
TL;DR: TZP resulted in remarkable in vivo activity against TZP-R/Ceph3-S E. coli and K. pneumoniae, despite the observed in vitro resistance.
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Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides.
Zhiqiu Yin,Si Zhang,Yi Wei,Meng Wang,Shuangshuang Ma,Shuang Yang,Jingting Wang,Chao Yuan,Lingyan Jiang,Yuhui Du +9 more
TL;DR: Pan-genome analysis indicated extensive genetic diversity and the presence of large and variable gene repertoires, and discordance between the core genome phylogeny and the pan- genome phylogeny indicated that flexible accessory genomes account for an important proportion of the evolution of P. shigelloides.
Journal ArticleDOI
Evaluation of Incompatibility Group I1 (IncI1) Plasmid-Containing Salmonella enterica and Assessment of the Plasmids in Bacteriocin Production and Biofilm Development.
Pravin R. Kaldhone,Ashlyn Carlton,Ashlyn Carlton,Nesreen H. Aljahdali,Nesreen H. Aljahdali,Bijay K. Khajanchi,Yasser M. Sanad,Yasser M. Sanad,Jing Han,Joanna Deck,Steven C. Ricke,Steven L. Foley,Steven L. Foley +12 more
TL;DR: The study characterized IncI 1 positive Salmonella isolates and provided evidence about the potential contributions of IncI1 plasmids virulence phenotypes and areas where they do not, and should allow for more focused efforts to assess the impact of plasmIDS on bacterial pathophysiology and human health.
References
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