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
Genotypic and Phenotypic Characterization of Incompatibility Group FIB Positive Salmonella enterica Serovar Typhimurium Isolates from Food Animal Sources.
Nesreen H. Aljahdali,Bijay K. Khajanchi,Kennedi Weston,Joanna Deck,Justin Cox,Ruby Singh,Jeffrey M. Gilbert,Yasser M. Sanad,Jing Han,Rajesh Nayak,Steven L. Foley +10 more
TL;DR: It is confirmed that IncFIB plasmids can play a potential role in disseminating antimicrobial resistance and virulence genes amongst bacteria from several food animal species.
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Potentially conjugative plasmids harboring Tn6636, a multidrug-resistant and composite mobile element, in Staphylococcus aureus
TL;DR: In this paper , a detailed characterization of Tn6636, a multidrug-resistant and composite mobile element, in clinical isolates of Staphylococcus aureus was performed by S1 nuclease digestion pulsed-field gel electrophoresis (PFGE) analysis, conjugation test, and whole genome sequencing.
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Genome sequence of Shigella flexneri strain SP1, a diarrheal isolate that encodes an extended-spectrum β-lactamase (ESBL).
Ping Shen,Jianzhong Fan,Lihua Guo,Jiahua Li,Ang Li,Jing Zhang,Chaoqun Ying,Jinru Ji,Hao Xu,Beiwen Zheng,Yonghong Xiao +10 more
TL;DR: Wang et al. as mentioned in this paper reported the whole genome sequence of a blaCTX-M-14-encoding S. flexneri strain SP1, which was recovered from the patient with diarrhea, was subjected to whole genome sequencing.
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Genome Sequences of Two NDM-1 Metallo-β-Lactamase-Producing Multidrug-Resistant Strains of Klebsiella pneumoniae with a High Degree of Similarity, One of Which Contains Prophage.
Nikolay V. Volozhantsev,Angelina A. Kislichkina,Anastasia I. Lev,Tatiana N. Mukhina,Alexander A. Bogun,O.N. Ershova,Irina Alexandrova,Nadezhda K. Fursova +7 more
TL;DR: The genomes of two NDM-1 metallo-β-lactamase-producing multidrug-resistant Klebsiella pneumoniae isolates of sequence type 147 (ST147) are reported from one hospital and differ in prophage located in the chromosome of K. pneumoniae.
Journal ArticleDOI
Genomic Analysis of Multidrug-Resistant Escherichia coli from Surface Water in Northeast Georgia, United States: Presence of an ST131 Epidemic Strain Containing blaCTX-M-15 on a Phage-Like Plasmid.
Sohyun Cho,Sushim K. Gupta,Elizabeth A. McMillan,Poonam Sharma,Hazem Ramadan,Thomas Jové,Charlene R. Jackson,Jonathan G. Frye +7 more
TL;DR: This study is the first report on genomic characterization of MDR E. coli from environmental water in the United States through a whole-genome sequence (WGS) analysis, and the presence of an ST131 epidemic strain suggests a new emerging mechanism of AR gene transmission.
References
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