ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes
Sushim K. Gupta,Babu Roshan Padmanabhan,Seydina M. Diene,Rafael López-Rojas,Marie Kempf,Luce Landraud,Jean-Marc Rolain +6 more
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TLDR
A concise database for BLAST using a Bio-Edit interface that can detect AR genetic determinants in bacterial genomes and can rapidly and easily discover putative new AR geneticeterminants is created.Abstract:
ARG-ANNOT (Antibiotic Resistance Gene-ANNOTation) is a new bioinformatic tool that was created to detect existing and putative new antibiotic resistance (AR) genes in bacterial genomes. ARG-ANNOT uses a local BLAST program in Bio-Edit software that allows the user to analyze sequences without a Web interface. All AR genetic determinants were collected from published works and online resources; nucleotide and protein sequences were retrieved from the NCBI GenBank database. After building a database that includes 1,689 antibiotic resistance genes, the software was tested in a blind manner using 100 random sequences selected from the database to verify that the sensitivity and specificity were at 100% even when partial sequences were queried. Notably, BLAST analysis results obtained using the rmtF gene sequence (a new aminoglycoside-modifying enzyme gene sequence that is not included in the database) as a query revealed that the tool was able to link this sequence to short sequences (17 to 40 bp) found in other genes of the rmt family with significant E values. Finally, the analysis of 178 Acinetobacter baumannii and 20 Staphylococcus aureus genomes allowed the detection of a significantly higher number of AR genes than the Resfinder gene analyzer and 11 point mutations in target genes known to be associated with AR. The average time for the analysis of a genome was 3.35 ± 0.13 min. We have created a concise database for BLAST using a Bio-Edit interface that can detect AR genetic determinants in bacterial genomes and can rapidly and easily discover putative new AR genetic determinants.read more
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Epidemic Clostridioides difficile Ribotype 027 Lineages: Comparisons of Texas Versus Worldwide Strains.
Bradley T. Endres,Khurshida Begum,Hua Sun,Seth T. Walk,Ali Memariani,Chris Lancaster,Anne J Gonzales-Luna,Kierra M Dotson,Eugénie Bassères,Charlene Offiong,Shawn Tupy,Kristi Kuper,Edward Septimus,Raouf Arafat,M. Jahangir Alam,Zhongming Zhao,Julian G Hurdle,Tor C. Savidge,Tor C. Savidge,Kevin W. Garey +19 more
TL;DR: Phylogeny demonstrated unique clustering and resistance genes in Texas strains indicating that spatiotemporal bias has defined the microevolution of ribotype 027 genetics, which emerged earlier than previously reported, coinciding with increased use of fluoroquinolones.
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Role of Plasmids in Plant-Bacteria Interactions.
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Occurrence and clonal diversity of multidrug-resistant Klebsiella pneumoniae recovered from inanimate surfaces in Algerian hospital environment: First report of armA, qnrB and aac(6')-Ib-cr genes.
Karima Zenati,Farida Sahli,Vincent Garcia,Sofiane Bakour,D. Belhadi,Jean-Marc Rolain,Abdelaziz Touati +6 more
TL;DR: The detection of the ESBLs encoding gene linked with plasmid-mediated quinolone resistance (PMQR) and aminoglycosides resistance recovered from inanimate surfaces in hospital environment is reported.
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Zi Xin Peng,Alexandre Maciel-Guerra,Michelle Baker,Xibin Zhang,Yue Hu,Wei Wang,Jia Rong,Ping Zhang,Ning Xue,Paul A. Barrow,David Renney,Dov J. Stekel,Paul Williams,Longhai Liu,Junshi Chen,Fengqin Li,Tania Dottorini +16 more
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Whole genome-based characterisation of antimicrobial resistance and genetic diversity in Campylobacter jejuni and Campylobacter coli from ruminants.
TL;DR: In this article, the authors used Illumina whole-genome sequencing (WGS) to characterize the mechanisms of resistance in Campylobacter jejuni and C. coli recovered from beef cattle, dairy cattle, and sheep in northern Spain.
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