Resistance Determinants of Pseudomonas Species from Aquaculture in Australia

Ndi, Olasumbo

doi:10.4172/2155-9546.1000119

Cited by 13 publications

(15 citation statements)

References 48 publications

(54 reference statements)

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“…Integrons though have been found in different genera but very few have been reported in Pseudomonas spp. [ 22 ] and rarer is the dhfrA1 gene association with class I integron.…”

Section: Resultsmentioning

confidence: 99%

“…Integrons though have been attributed to the acquisition of antibiotic resistant genes since 1980’s but till date their occurrence in Pseudomonas spp. has been rare and precisely limited to P. aeruginosa , P. putida , and P. stutzeri [ 22 ]. Environmental sequence data from the HCH contaminated pond sediment (45 mg HCH g −1 ) together with previous metagenomic survey of HCH contaminated dumpsite (450 mg HCH g −1 ) and adjoining agricultural soils (0.07 mg HCH g −1 ) [ 8 ] were also used to reveal the metagenomic recruitment of this integron unit.…”

Section: Introductionmentioning

confidence: 99%

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Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite

et al. 2015

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BackgroundPhylogenetic heterogeneity across Pseudomonas genus is complemented by its diverse genome architecture enriched by accessory genetic elements (plasmids, transposons, and integrons) conferring resistance across this genus. Here, we sequenced a stress tolerant genotype i.e. Pseudomonas sp. strain RL isolated from a hexachlorocyclohexane (HCH) contaminated pond (45 mg of total HCH g−1 sediment) and further compared its gene repertoire with 17 reference ecotypes belonging to P. stutzeri, P. mendocina, P. aeruginosa, P. psychrotolerans and P. denitrificans, representing metabolically diverse ecosystems (i.e. marine, clinical, and soil/sludge). Metagenomic data from HCH contaminated pond sediment and similar HCH contaminated sites were further used to analyze the pan-genome dynamics of Pseudomonas genotypes enriched across increasing HCH gradient.ResultsAlthough strain RL demonstrated clear species demarcation (ANI ≤ 80.03%) from the rest of its phylogenetic relatives, it was found to be closest to P. stutzeri clade which was further complemented functionally. Comparative functional analysis elucidated strain specific enrichment of metabolic pathways like α-linoleic acid degradation and carbazole degradation in Pseudomonas sp. strain RL and P. stutzeri XLDN-R, respectively. Composition based methods (%codon bias and %G + C difference) further highlighted the significance of horizontal gene transfer (HGT) in evolution of nitrogen metabolism, two-component system (TCS) and methionine metabolism across the Pseudomonas genomes used in this study. An intact mobile class-I integron (3,552 bp) with a captured gene cassette encoding for dihydrofolate reductase (dhfra1) was detected in strain RL, distinctly demarcated from other integron harboring species (i.e. P. aeruginosa, P. stutzeri, and P. putida). Mobility of this integron was confirmed by its association with Tnp21-like transposon (95% identity) suggesting stress specific mobilization across HCH contaminated sites. Metagenomics data from pond sediment and recently surveyed HCH adulterated soils revealed the in situ enrichment of integron associated transposase gene (TnpA6100) across increasing HCH contamination (0.7 to 450 mg HCH g−1 of soil).ConclusionsUnlocking the potential of comparative genomics supplemented with metagenomics, we have attempted to resolve the environment and strain specific demarcations across 18 Pseudomonas gene complements. Pan-genome analyses of these strains indicate at astoundingly diverse metabolic strategies and provide genetic basis for the cosmopolitan existence of this taxon.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1488-2) contains supplementary material, which is available to authorized users.

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“…Integrons though have been found in different genera but very few have been reported in Pseudomonas spp. [ 22 ] and rarer is the dhfrA1 gene association with class I integron.…”

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite

et al. 2015

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“…Nevertheless, class 2 and class 3 integrons were not detected [30]. The same result was obtained with isolates from Pseudomonas spp., where 23% was positive for class 1 integrons, while class 2 and class 3 integrons were not detected either [31]. The same was found in catfish farming, where 33% of the isolates from Pseudomonas and 28% of the isolates from Aeromonas showed class 1 integrases, but all of them were negative for class 2 and class 3 intregrases [32].…”

Section: Discussionmentioning

confidence: 88%

High prevalence of class 1 integrase and characterization of class 1 integron gene cassettes in multiresistant bacteria isolated from the gut microbiota of extended antibiotic treated Salmo salar fish farms

Vásquez-Ponce

Higuera-Llantén

Cortés

et al. 2019

Preprint

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The use of antimicrobials in aquaculture is a common practice. Chile is second larger producer of salmon worldwide, but unfortunately is the first consumer of antibiotics. Tonnes of florfenicol and oxytetracycline yearly are used in the Chilean salmoniculture to control the pathogens that threaten the sustainability of the industry. This excessive use of antibiotics have selected populations of resistant bacteria from the sediments and the water column that sorround the fish farms. In a recent work, our lab described the high prevalence of multiresistant bacteria and Antibiotic Resistance Genes (ARGs) in the gut microbiota of Antlactic salmon (Salmo salar) treated with high doses of antibiotics. In this work, we revisited the analysis of the previously described gut multiresistant bacteria grouped in banks of florfenicol resistant isolates (FB) and oxytetracycline resistant isolates (OB) looking for the presence of integron-integrase elements. These elements have been described as an important players in the Antimicrobial Resistance (AMR) phenomenon and they are considered a good markers of the anthopogenic activities pollution. The results showed that the 100% of the multiresistant isolates present the class 1 intagrase. Despite this result, no isolate from FB showed the typical structure of class 1 integrons: the presence in 3’-CS of qacEΔ1/sul1 genes. While in OB, only 23% of the isolates showed this characteristic structure. Additionally, only four isolates of OB and none of FB showed recognisable gene cassettes and no genes of resistance to florfenicol and oxytetacycline appeared in them. Of these four isolates, three of them showed a single gene cassette containing the dfrA-14 gene, which confers resistance to trimethoprim. Whilst the other isolate showed the aac(6’)31-qacH-blaoxa2 genes, which confers resistance to aminoglycosides, quaternary ammonium compounds and beta-lactams, respectively. Finally, it was possible to demonstrate that the described integrons probably come from anthropogenic activities like clinical settings and/or industrial animal husbandry, since they show integrases proteins identical to those carried by human pathogens.

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“…putida strains isolated from rainbow trout in another study were found to be susceptible to streptomycin and resistant to erythromycin, even though it was reported to be susceptible to chloramphenicol (Capkin et al 2017). Interestingly, 78% of 129 different Pseudomonas strains isolated from sediment and fish in different trout farms did not have the streptomycin-resistant gene (Ndi and Barton 2012).…”

Section: Discussionmentioning

confidence: 97%

“…). Interestingly, 78% of 129 different Pseudomonas strains isolated from sediment and fish in different trout farms did not have the streptomycin‐resistant gene (Ndi and Barton ).…”

Section: Discussionmentioning

confidence: 99%

Antimicrobial activity oftrans-cinnamic acid and commonly used antibiotics against important fish pathogens and nonpathogenic isolates

2018

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Resistance Determinants of Pseudomonas Species from Aquaculture in Australia

Cited by 13 publications

References 48 publications

Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite

Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite

High prevalence of class 1 integrase and characterization of class 1 integron gene cassettes in multiresistant bacteria isolated from the gut microbiota of extended antibiotic treated Salmo salar fish farms

Antimicrobial activity oftrans-cinnamic acid and commonly used antibiotics against important fish pathogens and nonpathogenic isolates

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