ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes

Florensa, Alfred Ferrer; Kaas, Rolf Sommer; Clausen, Philip Thomas Lanken Conradsen; Aytan-Aktug, Derya; Aarestrup, Frank Møller

doi:10.1099/mgen.0.000748

Cited by 229 publications

(188 citation statements)

References 40 publications

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“…The presence of virulence genes was searched by comparing all the coding DNA sequences (CDS) to the Virulence Factor DataBase [ 52 ] by BlastX (thresholds: 90% identity, 60% coverage). The presence of antibiotic resistance genes were searched using ResFinder [ 53 ] using the same thresholds.…”

Section: Methodsmentioning

confidence: 99%

Virulent Phages Isolated from a Smear-Ripened Cheese Are Also Detected in Reservoirs of the Cheese Factory

Paillet

Lossouarn

Figueroa

et al. 2022

Viruses

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Smear-ripened cheeses host complex microbial communities that play a crucial role in the ripening process. Although bacteriophages have been frequently isolated from dairy products, their diversity and ecological role in such this type of cheese remain underexplored. In order to fill this gap, the main objective of this study was to isolate and characterize bacteriophages from the rind of a smear-ripened cheese. Thus, viral particles extracted from the cheese rind were tested through a spot assay against a collection of bacteria isolated from the same cheese and identified by sequencing the full-length small subunit ribosomal RNA gene. In total, five virulent bacteriophages infecting Brevibacterium aurantiacum, Glutamicibacter arilaitensis, Leuconostoc falkenbergense and Psychrobacter aquimaris species were obtained. All exhibit a narrow host range, being only able to infect a few cheese-rind isolates within the same species. The complete genome of each phage was sequenced using both Nanopore and Illumina technologies, assembled and annotated. A sequence comparison with known phages revealed that four of them may represent at least new genera. The distribution of the five virulent phages into the dairy-plant environment was also investigated by PCR, and three potential reservoirs were identified. This work provides new knowledge on the cheese rind viral community and an overview of the distribution of phages within a cheese factory.

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Section: Methodsmentioning

confidence: 99%

Virulent Phages Isolated from a Smear-Ripened Cheese Are Also Detected in Reservoirs of the Cheese Factory

Paillet

Lossouarn

Figueroa

et al. 2022

Viruses

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“…A comprehensive analysis of all of the genes that may contribute to the isolate resistance was performed using CARD, by utilizing the Resistance Gene Identifier (RGI) function ( Table S1, Supplementary Materials ). In addition, Table S2 (Supplementary Materials) includes comprehensive information about the mobile genetic elements (MGEs), detected by the MobileElementFinder web tool [ 28 ] at the Center for Genomic Epidemiology [ 29 ].…”

Section: Resultsmentioning

confidence: 99%

“…The read quality was assessed using FastQC v0.11.8 and MultiQC v1.7, and the taxonomic sequence classification of the Enterobacterales isolates was determined using KRAKEN2 ( Table S1, Supplementary Materials ). The multilocus sequence type (MLST) profile was determined using the MLST 2.0 server at the Center for Genomic Epidemiology, DTU, Research group for Genomic Epidemiology-National Food Institute-Technical University of Denmark [ 29 ] and PubMLST ( Table 1 ) [ 49 ]. The antibiotic resistance genes were identified using the NCBI National Database of Antibiotic Resistant Organisms (NDARO) and the PATRIC v3.5.36 platform.…”

Section: Methodsmentioning

confidence: 99%

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Prevalence and Molecular Characterization of Extended-Spectrum β-Lactamase Producing Enterobacterales in Healthy Community Dogs in Israel

et al. 2022

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Background: antimicrobial resistance is a global problem in human and veterinary medicine. We aimed to investigate the extended spectrum β-lactamase-producing Enterobacterales (ESBL-PE) gut colonization in healthy community dogs in Israel. Methods: Rectal swabs were sampled from 145 healthy dogs, enriched, plated on selective plates, sub-cultured to obtain pure cultures, and ESBL production was confirmed. Bacterial species and antibiotic susceptibility profiles were identified. WGS was performed on all of the ESBL-PE isolates and their resistomes were identified in silico. Owners’ questionnaires were collected for risk factor analysis. Results: ESBL-PE gut colonization rate was 6.2% (n = 9/145, 95% CI 2.9–11.5). Overall, ten isolates were detected (one dog had two isolates); the main species was Escherichia coli (eight isolates), belonging to diverse phylogenetic groups—B1, A and C. Two isolates were identified as Citrobacter braakii, and C. portucalensis. A phylogenetic analysis indicated that all of the isolates were genetically unrelated and sporadic. The isolates possessed diverse ESBL genes and antibiotic-resistance gene content, suggesting independent ESBL spread. In a multivariable risk factor analysis, coprophagia was identified as a risk factor for ESBL-PE gut colonization (p = 0.048, aOR = 4.408, 95% CI 1.014–19.169). Conclusions: healthy community dogs may be colonized with ESBL-PE MDR strains, some of which were previously reported in humans, that carry wide and diverse resistomes and may serve as a possible source for AMR.

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“…Movile Cave's galleries (Chiciudean et al 2022). Detected MAGs were then analyzed for the presence of BGCs by antiSMASH (v. 6.1.1) (Blin et al 2021) whereas antibiotic resistance genes were predicted by ResFinder (v. 4.1) (Florensa et al 2022). The statistical analysis of BGCs data was performed by Past (v. 4.03).…”

mentioning

confidence: 99%

A glimpse into the biosynthetic potential and resistome of microbial communities inhabiting sulfidic, chemoautotrophic Movile Cave ecosystem

Chiciudean¹,

Bogdan²,

Moldovan³

et al. 2022

ACA

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Background: Microbial secondary metabolites (SM), especially those produced by soil microorganisms, have been a valuable source of antibiotics, antitumor agents, pigments, growth-promoting substances, etc., with tremendous market potential. These molecules are encoded by biosynthetic gene clusters (BGCs) within the bacterial genome. Their synthesis confers survival advantages by facilitating chemical defense, interspecies communication, and adaptation to well-defined ecological niches. Caves, particularly Movile Cave (Romania) - a sulfidic autotrophic-based ecosystem - can be considered extreme environments suited to investigate and discover novel bioactive microbial molecules. Here, low nutrient availability can lead to resource competition and, consequently, antimicrobial production to deter nearby microbial competitors. Aim: Our study focused on highlighting the biosynthetic gene clusters (BGCs) and biosynthetic potential of the sediment-associated microbiome in Movile Cave. Methods: Over 100 high-quality metagenome-assembled genomes (MAGs) were retrieved by whole-community shotgun-sequencing of 7 sediment samples collected in different Movile Cave’s galleries (Chiciudean et al. 2022). Detected MAGs were then analyzed for the presence of BGCs by antiSMASH (v. 6.1.1) (Blin et al. 2021) whereas antibiotic resistance genes were predicted by ResFinder (v. 4.1) (Florensa et al. 2022). The statistical analysis of BGCs data was performed by Past (v. 4.03). Results: We detected 637 BGCs across 106 high-quality MAGs that were affiliated to 22 phyla. The diversity of predicted BGCs varies across sediment samples with no apparent correlation to the number of analyzed MAGs per sample. The MAGs recovered from the sulfidic water-sediment interface (sample code PMV4) had the lowest alpha BGCs diversity among all sampled locations and it was clearly distinct in BGCs composition and abundance (β-diversity) from dry gallery samples (PMV7 and PMV8). The most abundant BGCs predicted in Movile Cave metagenomic dataset encode for terpenes, non-ribosomal peptides (NRPs) and ribosomally synthesised and post-translationally modified peptides (RIPPs). Acidobacteriota and Chloroflexota- affiliated MAGs were most enriched in BCG containing 20 and 23 BGCs per MAG, respectively, in contrast with the candidate phylum Ca. Patescibacteria-related MAGs that showed no SM biosynthetic capabilities. Two antimicrobial resistance (AR) genes (ole(C), oqxB) encoding resistance to antibiotics (i.e. oleandomycin, chloramphenicol, ciprofloxacin, trimethoprim) and disinfectants were identified in MAGs affiliated with the class Actinomycetia and Gammaproteobacteria. Based on the analyzed data, the biosynthetic potential of Movile Cave is significant compared with other microbiomes (Donia et al. 2014) and has a pronounced degree of novelty whereas the resistome (that is the genetic potential for antibiotic resistance) is reduced. Considering the uncommon futures of Movile Cave environment, future in-depth analysis of the identified BGCs might lead to the discovery of novel bioactive compounds. Additionally, the seclusion of this environment may provide an exciting opportunity for surveying the occurrence and environmental drivers of natural AR traits.

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ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes

Cited by 229 publications

References 40 publications

Virulent Phages Isolated from a Smear-Ripened Cheese Are Also Detected in Reservoirs of the Cheese Factory

Virulent Phages Isolated from a Smear-Ripened Cheese Are Also Detected in Reservoirs of the Cheese Factory

Prevalence and Molecular Characterization of Extended-Spectrum β-Lactamase Producing Enterobacterales in Healthy Community Dogs in Israel

A glimpse into the biosynthetic potential and resistome of microbial communities inhabiting sulfidic, chemoautotrophic Movile Cave ecosystem

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