ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

Gupta, Sushim K.; Padmanabhan, Roshan; Diène, Seydina M.; López-Rojas, Rafael; Kempf, Marie; Landraud, Luce; Rolain, Jean‐Marc

doi:10.1128/aac.01310-13

Cited by 1,190 publications

(949 citation statements)

References 29 publications

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“…Assembled contigs were analyzed as described below. Acquired antimicrobial resistance genes were detected using the ResFinder web server (35) and the ARG-ANNOT database (58). The E. coli MLST website (http://mlst.ucc.ie/mlst/dbs/Ecoli) and EnteroBase were used for MLST.…”

Section: Methodsmentioning

confidence: 99%

Whole-Genome Analysis of Antimicrobial-Resistant and Extraintestinal Pathogenic Escherichia coli in River Water

Gomi

Matsuda

Matsumura

et al. 2017

Appl Environ Microbiol

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Contamination of surface waters by antimicrobial-resistant bacteria and pathogenic bacteria is a great concern. In this study, 531 Escherichia coli isolates obtained from the Yamato River in Japan were evaluated phenotypically for resistance to 25 antimicrobials. Seventy-six isolates (14.3%) were multidrug resistant (MDR), 66 (12.4%) were nonsusceptible to one or two classes of agents, and 389 (73.3%) were susceptible. We performed whole-genome sequencing of selected strains by using Illumina technology. In total, the genome sequences of 155 strains were analyzed for antibiotic resistance determinants and phylogenetic characteristics. More than 50 different resistance determinants, including acquired resistance genes and chromosomal resistance mutations, were detected. Among the sequenced MDR strains (n ϭ 66), sequence type 155 (ST155) complex (n ϭ 9), ST10 complex (n ϭ 9), and ST69 complex (n ϭ 7) were prevalent. Among extraintestinal pathogenic E. coli (ExPEC) strains (n ϭ 58), clinically important clonal groups, namely, ST95 complex (n ϭ 18), ST127 complex (n ϭ 8), ST12 complex (n ϭ 6), ST14 complex (n ϭ 6), and ST131 complex (n ϭ 6), were prevalent, demonstrating the clonal distribution of environmental ExPEC strains. Typing of the fimH (type 1 fimbrial adhesin) gene revealed that ST131 complex strains carried fimH22 or fimH41, and no strains belonging to the fimH30 subgroup were detected. Fine-scale phylogenetic analysis and virulence gene content analysis of strains belonging to the ST95 complex (one of the major clonal ExPEC groups causing community-onset infections) revealed no significant differences between environmental and clinical strains. The results indicate contamination of surface waters by E. coli strains belonging to clinically important clonal groups.IMPORTANCE The prevalence of antimicrobial-resistant and pathogenic E. coli strains in surface waters is a concern because surface waters are used as sources for drinking water, irrigation, and recreational purposes. In this study, MDR and ExPEC strains in river water were characterized by genomic sequencing and analysis. We detected more than 50 resistance determinants and identified clonal groups specific to MDR and ExPEC strains. This study showed contamination of surface waters by E. coli strains belonging to clinically important clonal groups. Overall, this study advances our understanding of environmental MDR and ExPEC strains.KEYWORDS antimicrobial resistance, Escherichia coli, ExPEC, whole-genome sequencing E scherichia coli is a commensal member of the gastrointestinal tract of humans and other warm-blooded animals. Consequently, E. coli, as well as Enterococcus spp., has long been used as an indicator of fecal contamination to assess the microbial quality of surface waters. Although most E. coli strains are harmless, some strains are pathogenic

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Section: Methodsmentioning

confidence: 99%

Whole-Genome Analysis of Antimicrobial-Resistant and Extraintestinal Pathogenic Escherichia coli in River Water

Gomi

Matsuda

Matsumura

et al. 2017

Appl Environ Microbiol

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“…Employing continually enhanced bioinformatic pipelines for querying WGS data will greatly expand the depth of laboratory-based strain surveillance efforts. For example, ARG-ANNOT (antibiotic resistance gene annotation) is a very useful bioinformatics tool that provides a periodically updated database (http://en.mediterranee-infection.com/article .php?larefϭ283&titerϭarg-annot-) of known accessory resistance genes to screen bacterial whole-genome sequence data (51).…”

Section: Detection Of Antibiotic Resistancementioning

confidence: 99%

Biological and Epidemiological Features of Antibiotic-Resistant Streptococcus pneumoniae in Pre- and Post-Conjugate Vaccine Eras: a United States Perspective

et al. 2016

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SUMMARYStreptococcus pneumoniaeinflicts a huge disease burden as the leading cause of community-acquired pneumonia and meningitis. Soon after mainstream antibiotic usage, multiresistant pneumococcal clones emerged and disseminated worldwide. Resistant clones are generated through adaptation to antibiotic pressures imposed while naturally residing within the human upper respiratory tract. Here, a huge array of related commensal streptococcal strains transfers core genomic and accessory resistance determinants to the highly transformable pneumococcus. β-Lactam resistance is the hallmark of pneumococcal adaptability, requiring multiple independent recombination events that are traceable to nonpneumococcal origins and stably perpetuated in multiresistant clonal complexes. Pneumococcal strains with elevated MICs of β-lactams are most often resistant to additional antibiotics. Basic underlying mechanisms of most pneumococcal resistances have been identified, although new insights that increase our understanding are continually provided. Although all pneumococcal infections can be successfully treated with antibiotics, the available choices are limited for some strains. Invasive pneumococcal disease data compiled during 1998 to 2013 through the population-based Active Bacterial Core surveillance program (U.S. population base of 30,600,000) demonstrate that targeting prevalent capsular serotypes with conjugate vaccines (7-valent and 13-valent vaccines implemented in 2000 and 2010, respectively) is extremely effective in reducing resistant infections. Nonetheless, resistant non-vaccine-serotype clones continue to emerge and expand.

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“…ARG-ANNOT also provides data relating to point mutations. In another study, the tool was tested for its enhanced sensitivity and specificity for both complete and partial gene sequences (30).…”

Section: Antibiotic Resistance Gene Databasesmentioning

confidence: 99%

Consolidating and Exploring Antibiotic Resistance Gene Data Resources

et al. 2016

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The unrestricted use of antibiotics has resulted in rapid acquisition of antibiotic resistance (AR) and spread of multidrug-resistant (MDR) bacterial pathogens. With the advent of next-generation sequencing technologies and their application in understanding MDR pathogen dynamics, it has become imperative to unify AR gene data resources for easy accessibility for researchers. However, due to the absence of a centralized platform for AR gene resources, availability, consistency, and accuracy of information vary considerably across different databases. In this article, we explore existing AR gene data resources in order to make them more visible to the clinical microbiology community, to identify their limitations, and to propose potential solutions.

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ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

Cited by 1,190 publications

References 29 publications

Whole-Genome Analysis of Antimicrobial-Resistant and Extraintestinal Pathogenic Escherichia coli in River Water

Whole-Genome Analysis of Antimicrobial-Resistant and Extraintestinal Pathogenic Escherichia coli in River Water

Biological and Epidemiological Features of Antibiotic-Resistant Streptococcus pneumoniae in Pre- and Post-Conjugate Vaccine Eras: a United States Perspective

Consolidating and Exploring Antibiotic Resistance Gene Data Resources

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