ResFinder 4.0 for predictions of phenotypes from genotypes

Bortolaia, Valeria; Kaas, Rolf Sommer; Ruppé, Étienne; Roberts, Marilyn C.; Schwarz, Štefan; Cattoir, Vincent; Philippon, A.; Allesøe, Rosa Lundbye; Rebelo, Ana Rita; Florensa, Alfred Ferrer; Fagelhauer, Linda; Chakraborty, Trinad; Neumann, Bernd; Werner, Guido; Bender, Jennifer K.; Stingl, Kerstin; Nguyen, Minh N. H.; Coppens, Jasmine; Xavier, Basil Britto; Malhotra-Kumar, Surbhi; Westh, Henrik; Pinholt, Mette; Anjum, Muna F.; Duggett, Nicholas; Kempf, Isabelle; Nykäsenoja, Suvi; Olkkola, Satu; Wieczorek, Kinga; Amaro, Ana; Clemente, Lurdes; Mossong, Joël; Losch, Serge; Ragimbeau, Catherine; Lund, Ole; Aarestrup, Frank Møller

doi:10.1093/jac/dkaa345

Cited by 1,980 publications

(1,467 citation statements)

References 42 publications

Supporting

Mentioning

1,453

Contrasting

Unclassified

Order By: Relevance

“…All complete A. non- baumannii genome nucleotide sequences were downloaded from GenBank NCBI. Predictive identification of antibiotic resistance genes (ARGs) was performed using the BLASTp, the CARD-RGI [ 22 ], ARG-ANNOT [ 23 ] and ResFinder [ 24 ] software databases. For ARGs prediction, 70% coverage, 95% amino acid identity and <10 −6 e-value were used as the BLASTp parameters.…”

Section: Methodsmentioning

confidence: 99%

An Acinetobacter non-baumannii Population Study: Antimicrobial Resistance Genes (ARGs)

et al. 2020

View full text Add to dashboard Cite

Acinetobacter non-baumannii species are becoming common etiologic agents of nosocomial infections. Furthermore, clinical isolates belonging to this group of bacteria are usually resistant to one or more antibiotics. The current information about antibiotic resistance genes in the different A. non-baumannii species has not yet been studied as a whole. Therefore, we did a comparative study of the resistomes of A. non-baumannii pathogens based on information available in published articles and genome sequences. We searched the available literature and sequences deposited in GenBank to identify the resistance gene content of A. calcoaceticus, A. lwoffii, A. junii, A. soli, A. ursingii, A. bereziniae, A. nosocomialis, A. portensis, A. guerrae, A. baylyi, A. calcoaceticus, A. disperses, A. johnsonii, A. junii, A. lwoffii, A. nosocomialis, A. oleivorans, A. oryzae, A. pittii, A. radioresistens, and A. venetianus. The most common genes were those coding for different β-lactamases, including the carbapenemase genes blaNDM-1 and blaOXA-58. A. pittii was the species with the most β-lactamase resistance genes reported. Other genes that were commonly found include those encoding some aminoglycoside modifying enzymes, the most common being aph(6)-Id, ant(3″)-IIa, and aph(3″)-Ib, and efflux pumps. All or part of the genes coding for the AdeABC, AdeFGH, and AdeIJK efflux pumps were the most commonly found. This article incorporates all the current information about A. non-baumannii resistance genes. The comparison of the different resistomes shows that there are similarities in the genes present, but there are also significant differences that could impact the efficiency of treatments depending on the etiologic agent. This article is a comprehensive resource about A. non-baumannii resistomes.

show abstract

Section: Methodsmentioning

confidence: 99%

An Acinetobacter non-baumannii Population Study: Antimicrobial Resistance Genes (ARGs)

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Pathogenic genes, antibiotic resistance genes, and virulence factors were identified to assess the safety of P. acidilactici HN9 use. The genomic sequences were searched against several databases, including the Comprehensive Antibiotic Resistance Database (CARD) [ 65 ], ResFinder [ 66 ] and Virulence Factors Database (VFDB) [ 67 ]. Resistance Gene Identifier (RGI) was used against the CARD database to predict resistomes from proteins based on homology and SNP models [ 65 ].…”

Section: Methodsmentioning

confidence: 99%

Genomic Insight into Pediococcus acidilactici HN9, a Potential Probiotic Strain Isolated from the Traditional Thai-Style Fermented Beef Nhang

et al. 2020

View full text Add to dashboard Cite

Pediococcus acidilactici HN9 is a beneficial lactic acid bacterium isolated from Nhang, a traditional Thai-style fermented beef. In this study, the molecular properties of P. acidilactici HN9 were characterized to provide insights into its potential probiotic activity. Specifically, this work sought to report the complete genome of P. acidilactici HN9 and perform a comparative genome analysis with other bacterial strains belonging to the genus Pediococcus. Genomic features of HN9 were compared with those of all other bacterial Pediococcus strains to examine the adaptation, evolutionary relationships, and diversity within this genus. Additionally, several bioinformatic approaches were used to investigate phylogenetic relationships, genome stability, virulence factors, bacteriocin production, and antimicrobial resistance genes of the HN9 strain, as well as to ensure its safety as a potential starter culture in food applications. A 2,034,522 bp circular chromosome and two circular plasmids, designated pHN9-1 (42,239-bp) and pHN9-2 (30,711-bp), were detected, and used for pan-genome analysis, as well as for identification of bacteriocin-encoding genes in 129 strains belonging to all Pediococcus species. Two CRISPR regions were identified in P. acidilactici HN9, including type II-A CRISPR/CRISPR-associated (Cas). This study provides an in-depth analysis on P. acidilactici HN9, facilitating a better understanding of its adaptability to different environments and its mechanism to maintain genome stability over time.

show abstract

“…To identify ARGs hosted by plasmids, the assembled putative plasmids for each isolate were submitted to Resfinder 4.0 [ 26 ] and resistance gene identifier tool from Comprehensive Antibiotic Resistance Database—CARD [ 27 ]. In both Resfinder and CARD, only hits showing ≥95% identity and ≥98% length coverage were considered as ARGs.…”

Section: Methodsmentioning

confidence: 99%

Plasmid Identification and Plasmid-Mediated Antimicrobial Gene Detection in Norwegian Isolates

2020

View full text Add to dashboard Cite

Norway is known for being one of the countries with the lowest levels of antimicrobial resistance (AMR). AMR, through acquired genes located on transposons or conjugative plasmids, is the horizontal transmission of genes required for a given bacteria to withstand antibiotics. In this work, bioinformatic analysis of whole-genome sequences and hybrid assembled data from Escherichia coli, and Klebsiella pneumoniae isolates from Norwegian patients was performed. For detection of putative plasmids in isolates, the plasmid assembly mode in SPAdes was used, followed by annotation of resulting contigs using PlasmidFinder and two curated plasmid databases (Brooks and PLSDB). Furthermore, ResFinder and Comprehensive Antibiotic Resistance Database (CARD) were used for the identification of antibiotic resistance genes (ARGs). The IncFIB plasmid was detected as the most prevalent plasmid in both E. coli, and K. pneumoniae isolates. Furthermore, ARGs such as aph(3″)-Ib, aph(6)-Id, sul1, sul2, tet(D), and qnrS1 were identified as the most abundant plasmid-mediated ARGs in Norwegian E. coli and K. pneumoniae isolates, respectively. Using hybrid assembly, we were able to locate plasmids and predict ARGs more confidently. In conclusion, plasmid identification and ARG detection using whole-genome sequencing data are heavily dependent on the database of choice; therefore, it is best to use several tools and/or hybrid assembly for obtaining reliable identification results.

show abstract

ResFinder 4.0 for predictions of phenotypes from genotypes

Cited by 1,980 publications

References 42 publications

An Acinetobacter non-baumannii Population Study: Antimicrobial Resistance Genes (ARGs)

An Acinetobacter non-baumannii Population Study: Antimicrobial Resistance Genes (ARGs)

Genomic Insight into Pediococcus acidilactici HN9, a Potential Probiotic Strain Isolated from the Traditional Thai-Style Fermented Beef Nhang

Plasmid Identification and Plasmid-Mediated Antimicrobial Gene Detection in Norwegian Isolates

Contact Info

Product

Resources

About