Antibiotic and metal resistance in a ST395 Pseudomonas aeruginosa environmental isolate: A genomics approach

Teixeira, Pedro; Tacão, Marta; Alves, Artur; Henriques, Isabel

doi:10.1016/j.marpolbul.2016.06.086

Cited by 37 publications

(25 citation statements)

References 62 publications

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“…T21 contained an elevated number of RND-family efflux pump operons compared to previous reports (Lloyd et al, in preparation). This result is consistent with a recent report on the dominance of efflux pump-based cross-resistance in the whole genome sequence of an environmental Pseudomonas strain from a metal-contaminated estuary (Teixeira et al, 2016) and the increased extrusion of antibiotics via RND efflux pumps in marine biofilms exposed to heavy metals (Flach et al, 2017). These results highlight the need to examine cross-resistance as well as co-regulation as mechanisms of co-selection, ideas currently under investigation in our lab.…”

Section: Discussionsupporting

confidence: 92%

Whole genome sequences to assess the link between antibiotic and metal resistance in three coastal marine bacteria isolated from the mummichog gastrointestinal tract

Lloyd

Nazaret

Barkay

2018

Marine Pollution Bulletin

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Antibiotic resistance is a global public health issue and metal exposure can co-select for antibiotic resistance. We examined genome sequences of three multi-drug and metal resistant bacteria: one Shewanella sp., and two Vibrio spp., isolated from the gut of the mummichog fish (Fundulus heteroclitus). Our primary goal was to understand the mechanisms of co-selection. Phenotypically, the strains showed elevated resistance to arsenate, mercury, and various types of β-lactams. The genomes contained genes of public health concern including one carbapenemase (bla OXA-48). Our analyses indicate that the co-selection phenotype is mediated by chromosomal resistance genes and cross-resistance. No evidence of co-resistance was found; most resistance genes were chromosomally located. Moreover, the identification of many efflux pump gene homologs indicates that cross-resistance and/or co-regulation may further contribute to resistance. We suggest that the mummichog gut microbiota may be a source of clinically relevant antibiotic resistance genes.

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Section: Discussionsupporting

confidence: 92%

Whole genome sequences to assess the link between antibiotic and metal resistance in three coastal marine bacteria isolated from the mummichog gastrointestinal tract

Lloyd

Nazaret

Barkay

2018

Marine Pollution Bulletin

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“…The introduction of ST395 during the construction of a hospital was already suspected in the United Kingdom (3). This is consistent with the frequent isolation of the ST395 clone in water (19,20) and the probable role of drinking water as a source of P. aeruginosa infection (21,22). Overall, the ST395 clone has presumably contaminated the water network of the hospital before its opening but the pathogen further spread among patients by other routes of transmission (e.g.…”

Section: Bessupporting

confidence: 74%

The rise and the fall of aPseudomonas aeruginosaepidemic lineage in a hospital

Petitjean

Juarez

Meunier³

et al. 2020

Preprint

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The biological features that allow a pathogen to survive in the hospital environment are mostly unknown. The extinction of bacterial epidemics in hospitals is mostly attributed to changes in medical practice, including infection control, but the role of bacterial adaptation has never been documented. We analyzed a collection of Pseudomonas aeruginosa isolates belonging to the Besançon Epidemic Strain (BES), responsible for a 12-year nosocomial outbreak, using a genotype-to-phenotype approach. Bayesian analysis estimated the emergence of the clone in the hospital five years before its opening, during the creation of its water distribution network made of copper. BES survived better than the reference strains PAO1 and PA14 in a copper solution due to a genomic island containing 13 metal-resistance genes and was specifically able to proliferate in the ubiquitous amoeba Vermamoeba vermiformis. Mutations affecting amino-acid metabolism, antibiotic resistance, lipopolysaccharide biosynthesis, and regulation were enriched during the spread of BES. Seven distinct regulatory mutations attenuated the overexpression of the genes encoding the efflux pump MexAB-OprM over time. The fitness of BES decreased over time in correlation with its genome size. Overall, the resistance to inhibitors and predators presumably aided the proliferation and propagation of BES in the plumbing system of the hospital. The pathogen further spread among patients via multiple routes of contamination. The decreased prevalence of patients infected by BES mirrored the parallel and convergent genomic evolution and reduction that affected bacterial fitness. Along with infection control measures, this may have participated in the extinction of BES in the hospital setting.ImportanceBacterial pathogens are responsible for nosocomial outbreaks, but the sources of contamination of the hospitals are mostly unclear and the role of bacterial evolution in the extinction of outbreaks has never been considered. Here, we found that an epidemic strain of the pathogen Pseudomonas aeruginosa contaminated the drinking water network of a hospital due to its tolerance to copper and predatory amoeba, both present in the water pipes. The extinction of the outbreak occurred concomitantly with parallel and convergent genome evolution and a reduction in the size of the bacterial genome that correlated with the fitness of the pathogen. Our data suggest that pathogen evolution participated in the extinction of an outbreak in a hospital setting.

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“…This association, if confirmed by further studies, is in agreement with a previously formulated hypothesis that considers the exposure of environmental landscapes to pollutants (antibiotics, metals, and disinfectants) a risk for the selection and appearance of multidrug resistant strains (Berendonk et al, 2015). Moreover, a link between heavy metals and the maintenance/acquisition of antibiotic resistances has been documented (Knapp et al, 2011; Chen et al, 2015; Teixeira et al, 2016). This correlation is caused by cross- and co-resistance phenomena.…”

Section: Discussionmentioning

confidence: 99%

Viromes As Genetic Reservoir for the Microbial Communities in Aquatic Environments: A Focus on Antimicrobial-Resistance Genes

et al. 2017

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Despite studies of viromes isolated from aquatic environments are becoming increasingly frequent, most of them are limited to the characterization of viral taxonomy. Bacterial reads in viromes are abundant but the extent to which this genetic material is playing a role in the ecology of aquatic microbiology remains unclear. To this aim, we developed of a useful approach for the characterization of viral and microbial communities of aquatic environments with a particular focus on the identification of microbial genes harbored in the viromes. Virus-like particles were isolated from water samples collected across the Lambro River, from the spring to the high urbanized Milan area. The derived viromes were analyzed by shotgun metagenomic sequencing looking for the presence, relative abundance of bacterial genes with particular focus on those genes involved in antimicrobial resistance mechanisms. Antibiotic and heavy metal resistance genes have been identified in all virome samples together with a high abundance of reads assigned to cellular processes and signaling. Virome data compared to those identified in the microbiome isolated from the same sample revealed differences in terms of functional categories and their relative abundance. To verify the role of aquatic viral population in bacterial gene transfer, water-based mesocosms were perturbed or not perturbed with a low dose of tetracycline. The results obtained by qPCR assays revealed variation in abundance of tet genes in the virome and microbiome highlighting a relevant role of viral populations in microbial gene mobilization.

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Antibiotic and metal resistance in a ST395 Pseudomonas aeruginosa environmental isolate: A genomics approach

Cited by 37 publications

References 62 publications

Whole genome sequences to assess the link between antibiotic and metal resistance in three coastal marine bacteria isolated from the mummichog gastrointestinal tract

Whole genome sequences to assess the link between antibiotic and metal resistance in three coastal marine bacteria isolated from the mummichog gastrointestinal tract

The rise and the fall of aPseudomonas aeruginosaepidemic lineage in a hospital

Viromes As Genetic Reservoir for the Microbial Communities in Aquatic Environments: A Focus on Antimicrobial-Resistance Genes

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