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
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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Carbapenemase-producing Enterobacterales causing secondary infections during the COVID-19 crisis at a New York City hospital.
Angela Gomez-Simmonds,Medini K. Annavajhala,Thomas H. McConville,Donald Dietz,Sherif Shoucri,Justin C Laracy,Felix D Rozenberg,Brian Nelson,William G. Greendyke,E. Yoko Furuya,Susan Whittier,Anne-Catrin Uhlemann +11 more
TL;DR: While CPE prevalence has declined substantially in New York City in recent years, increased detection in patients with COVID-19 may signal a re-emergence of these highly resistant pathogens in the wake of the global pandemic.
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Genomics and the evolution of antibiotic resistance
TL;DR: How DNA analysis has helped reconstruct the origins of the mosaic, multiresistant mobile elements that have spread through pathogens in the last 60 years is reviewed.
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Microbial macroecology: In search of mechanisms governing microbial biogeographic patterns
Xiaofeng Xu,Nannan Wang,Nannan Wang,David A. Lipson,Robert L. Sinsabaugh,Josh Schimel,Liyuan He,Nadejda A. Soudzilovskaia,Leho Tedersoo +8 more
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Antibiotic Resistant Pseudomonas Spp. Spoilers in Fresh Dairy Products: An Underestimated Risk and the Control Strategies.
TL;DR: Light is shed on the resistome of cheese-related pseudomonads and their genomic background, current methods and advances in the prediction tools for MDR detection based on genomic sequences, possible implications for human health, and the affordable strategies to counteract MDR spread.
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Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection.
Jane Hawkey,David B. Ascher,Louise M. Judd,Ryan R. Wick,Xenia Kostoulias,Heather Cleland,Heather Cleland,Denis Spelman,Denis Spelman,Alex Padiglione,Anton Y. Peleg,Anton Y. Peleg,Anton Y. Peleg,Kathryn E. Holt +13 more
TL;DR: Structural modelling of AdeB and FtsI showed that these mutations affected their drug-binding sites and revealed mechanisms for meropenem resistance, suggesting exposure to one drug whose resistance is mediated by the efflux pump can induce collateral resistance to other drugs to which the bacterium has not yet been exposed.
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