Biology subjects

Snaith, A. E.

Publications and source records attributed to Snaith, A. E..

4 recordsLinked to original sources

bioRxiv2023

Multidrug resistance plasmids commonly reprogramme expression of metabolic genes in Escherichia coli

Multidrug resistant Escherichia coli is a leading cause of global mortality. Transfer of plasmids carrying genes encoding beta-lactamases, carbapenamases, and colistin resistance genes between lineages is driving the rising rates of hard to treat nosocomial and community infections. Multidrug resistance (MDR) plasmid acquisition commonly causes transcriptional disruption, and whilst a number of studies have shown strain-specific fitness and transcriptional effects of an MDR plasmid across diverse bacterial lineages, fewer studies have compared impacts of different MDR plasmids in a common bacterial host. As such, our ability to predict which MDR plasmids are the most likely to be maintained and spread in bacterial populations is limited. Here, we introduced eight diverse MDR plasmids encoding resistances against a range of clinically important antibiotics into E. coli K-12 MG1655 and measured their fitness costs and transcriptional impacts. The scale of the transcriptional responses varied substantially between plasmids, ranging from >650 to <20 chromosomal genes being differentially expressed. However, neither the scale of regulatory disruption nor the plasmid size correlated with the magnitude of the plasmid fitness cost, which also varied between plasmids. The identities of differentially expressed genes varied among plasmids, although expression of certain metabolic genes and functions were convergently affected by multiple plasmids, including the downregulation of genes involved in L-methionine transport and metabolism. Our data show the complexity of interaction between host genetic background and plasmid genetic background in determining the impact of MDR plasmid acquisition on E. coli. ImportanceThe increase of infections that are resistant to multiple classes of antibiotics, including those isolates that carry carbapenamases, beta-lactamases, and colistin resistance genes, is of global concern. Many of these resistances are spread by conjugative plasmids. Understanding more about how an isolate responds to an incoming plasmid that encodes antibiotic resistance will provide information that could be used to predict the emergence of MDR lineages. Here, the identification of metabolic networks as being particularly sensitive to incoming plasmids suggests possible targets for reducing plasmid transfer.

microbiology↗

bioRxiv2023

Non-antibiotic pharmaceuticals exhibit toxicity against Escherichia coli at environmentallyrelevant concentrations with no evolution of cross-resistance to antibiotics

Antimicrobial resistance can arise in the natural environment via prolonged exposure to the effluent surrounding manufacturing facilities. These facilities also produce non-antibiotic pharmaceuticals, and the effect of these on the surrounding microbial communities is less clear; whether they have inherent toxicity, or whether long-term exposure might select for cross-resistance to antibiotics. To this end, we screened four non-antibiotic pharmaceuticals (acetaminophen, ibuprofen, propranolol, met formin) and titanium dioxide for toxicity against Escherichia coli K-12 MG1655 and conducted a 30 day selection experiment to assess the effect of long-term exposure. All compounds reduced the maximum optical density reached by E. coli at a range of concentrations including one of environmental relevance, with transcriptome analysis identifying upregulated genes related to stress response and multidrug efflux in response ibuprofen treatment. The non-antibiotic pharmaceuticals did not select for significant genetic changes following a 30 day exposure, and no evidence of selection for cross-resistance to antibiotics was observed for population evolved in the presence of ibuprofen in spite of the differential gene expression after exposure to this compound. This work suggests that these non-antibiotic pharmaceuticals, at environmental concentrations, do not select for cross-resistance to antibiotics in E. coli.

microbiology↗

bioRxiv2023

A novel resistance reversion mechanism in a vancomycin-variable Enterococcus faecium strain

ObjectivesTo investigate an outbreak of Enterococcus faecium in a hospital haematology ward and uncover the mechanism of a vancomycin resistance phenotype-genotype disparity in an isolate from this outbreak. MethodsWhole genome shotgun sequencing was used for the phylogenetic analysis of E. faecium isolates (n = 39) and to identify the carriage of antibiotic resistance genes. A long-read sequencing approach was adopted to identify structural variations in the vancomycin resistance region of a vancomycin-variable E. faecium (VVE) and to uncover the resistance reversion mechanism in this isolate. RT-qPCR and RT-PCR were used to determine differences in the expression of vanRS and vanHAX among strains. ResultsThe E. faecium strains isolated in the hospital haematology ward were extensively drug resistant and highly diverse. The notable expansion of ST262 among patients was the likely driver of a VRE outbreak. A VVE isolate was identified that could rapidly revert to a vancomycin-resistant state in the presence of vancomycin. Disruption of the vanR gene in this isolate by an IS6-family element impaired its response to vancomycin. However, when the isolate was evolved to vancomycin resistance, it could constitutively express the vanHAX genes at levels up to 36,000-fold greater than the parent isolate via co-transcription with a ribosomal RNA operon. ConclusionIn this study, we report a VVE isolate that was isolated during a VRE outbreak. This strain was capable of rapidly reverting to a resistant phenotype through a novel mechanism involving integration of vanHAX downstream of a ribosomal RNA operon. During VRE outbreaks, attention should be paid to contemporaneous vancomycin-susceptible strains as these may carry silent vancomycin resistance genes that can be activated through genomic rearrangements upon exposure to vancomycin.

microbiology↗

bioRxiv2022

The highly diverse and complex plasmid population found in Escherichia coli colonising travellers to Laos and their role in antimicrobial resistance gene carriage

Increased colonisation by antimicrobial resistant organisms is closely associated with international travel. This study investigated the diversity of mobile genetic elements involved with antimicrobial resistance (AMR) gene carriage in extended-spectrum beta-lactamase (ESBL) -producing Escherichia coli that colonised travellers to Laos. Long-read sequencing was used to reconstruct complete plasmid sequences from 49 isolates obtained from the daily stool samples of 23 travellers over a three-week period. This method revealed a collection of 105 distinct plasmids, 38.1% of which carried AMR genes. The plasmids in this population were diverse, mostly unreported and included 38 replicon types, with F-type plasmids (n=22) the most prevalent amongst those carrying AMR genes. Fine-scale analysis of all plasmids identified numerous AMR gene contexts and emphasised the importance of IS elements, specifically members of the IS6/IS26 family, in the creation of complex multi-drug resistance regions. We found a concerning convergence of ESBL and colistin resistance determinants, with three plasmids from two different F-type lineages carrying blaCTX-M and mcr genes. The extensive diversity seen here highlights the worrying probability that stable new vehicles for AMR will evolve in E. coli populations that can disseminate internationally through travel networks. Impact StatementThe global spread of AMR is closely associated with international travel. AMR is a severe global concern and has compromised treatment options for many bacterial pathogens, among them pathogens carrying ESBL and colistin resistance genes. Colonising MDR organisms have the potential to cause serious consequences. Infections caused by MDR bacteria are associated with longer hospitalisation, poorer patient outcomes, greater mortality, and higher costs compared to infections with susceptible bacteria. This study elucidates the numerous different types of plasmids carrying AMR genes in colonising ESBL-producing E. coli isolates found in faecal samples from in travellers to Vientiane, Laos. Here we add to known databases of AMR plasmids by adding these MDR plasmids found in Southeast Asia, an area of high AMR prevalence. We characterised novel AMR plasmids including complex ESBL (blaCTX-M) and colistin (mcr) resistance co-carriage plasmids, emphasising the potential exposure of travellers to Laos to a wide variety of mobile genetic elements that may facilitate global AMR spread. This in-depth study has revealed further detail of the numerous factors that may influence AMR transfer, therefore potential routes of AMR spread internationally, and is a step towards finding methods to combat AMR spread. Data SummaryLong-read sequencing data is available through National Center for Biotechnology Information under the BioProject PRJNA853172. Complete plasmid sequences have been uploaded to GenBank with accession numbers in supplementary S1. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

microbiology↗