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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Mobilization of antibiotic resistance genes differ by resistance mechanism
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Draft Genome Sequence of Multidrug-Resistant Vibrio parahaemolyticus Strain PH698, Infecting Penaeid Shrimp in the Philippines.
Cynthia P. Saloma,Sarah Mae U. Penir,Joseph Matthew R. Azanza,Leobert D. de la Peña,Roselyn C. Usero,Nikko Alvin R. Cabillon,Angela Denise P. Bilbao,Edgar C. Amar +7 more
TL;DR: The draft genome of Vibrio parahaemolyticus PH698, a multidrug-resistant strain isolated from a Philippine shrimp farm is reported.
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Paradoxical β-lactamase activity of archaeal encoding enzymes
Seydina M. Diene,Lucile Pinault,Nicholas Armstrong,Vivek Keshri,Saber Khelaifia,Eric Chabrière,Gustavo Caetano-Anollés,Jean-Marc Rolain,Pierre Pontarotti,Pierre Pontarotti,Didier Raoult +10 more
TL;DR: The class B {beta}-lactamase appears to be highly conserved in archaea and to has been transferred in the bacterial genus Elizabethkingia and the use of these very conserved genes in this domain cannot be explored as a defense system against {beta}, but may be used to feed { beta}- lactams as a source of carbon as shown in bacteria.
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Comparison of Antimicrobial Resistance Profiles in Salmonella spp. from Swine Upon Arrival and Postslaughter at the Abattoir
Feng Qi,Timothy S. Frana,Catherine M. Logue,James D. McKean,Scott H. Hurd,Annette M. O'Connor,Annette M. O'Connor,James S. Dickson,Shanyuan Zhu,Ganwu Li +9 more
TL;DR: The AMR developed by Salmonella within animals used for food products is a major global issue as mentioned in this paper, and monitoring AMR in animals destined for slaughter is therefore, critical.
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