Biology subjects

Sheppard, A. E.

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

12 recordsLinked to original sources

bioRxiv2025

Lineage-Specific Evolution, Structural Diversity, and Activity of R2 Retrotransposons in Animals

Retrotransposons play outsized roles in the evolution of gene regulation, genome function, and disease pathogenesis and more recently, have sparked interest as workhorses for new gene therapy approaches. R2 retrotransposons insert site-specifically to the multicopy genes encoding 28S ribosomal RNA at a target sequence conserved broadly across eukaryotic evolution. R2 retrotransposons have been detected in many animals, but previous surveys have been limited in scope and methodology. Here, we substantially expand the known distribution of R2 retrotransposons from previously unrepresented or underrepresented taxonomic groups ranging from ctenophores to amphibians and reptiles. We discover diverse R2 domain architectures and motifs and identify many new avian R2 candidates for genome engineering development. Overall, phylogenetic analyses reveal two highly successful R2 lineages. We observe properties of each lineage in several features of the domains that mediate DNA recognition and in co-evolving signatures within the reverse transcriptase domain. Within each of the two lineages, R2 protein sequences do not necessarily preserve the unifying configuration of N-terminal DNA-binding domains implied in the current clade classification scheme. We show that recombinant R2 proteins with distinctive domain architectures and distribution across major animal classes support target-primed reverse transcription with conserved site specificity. Our analysis of the surprisingly varied domain architectures that support target-site specificity informs new R2 classification criteria and provides a greatly expanded foundation for additional structure/function insights about DNA binding selectivity. This expanded perspective on R2 evolution informs approaches for engineering therapeutic gene insertion technologies and offers an opportunity to investigate the conservation and diversification of retrotransposons.

evolutionary biology↗

bioRxiv2025

Understanding the population structure of Moraxella catarrhalis using core genome multilocus sequence typing (cgMLST) and a life identification number (LIN) code classification system

Moraxella catarrhalis is an important cause of infectious exacerbations of chronic obstructive pulmonary disease and otitis media. Previously, seroresistant (SR) and serosensitive (SS) lineages that differed in virulence potential were described, which raised questions about their evolutionary relationship and species classification. To investigate the population structure of M. catarrhalis, we developed a core-genome multilocus sequence typing (cgMLST) scheme using 1,319 core genes, and a life identification number (LIN) barcode classification system. Whole-genome analyses of nearly 2,000 genomes confirmed two divergent SR and SS M. catarrhalis lineages with distinct evolutionary trajectories. SR genomes were more conserved, while SS genomes exhibited greater genetic variability. Virulence gene analyses revealed lineage-specific variations in ubiquitous surface proteins (UspA1 and UspA2) and lipooligosaccharide (LOS) types, and SR genomes had more diverse LOS variants. The bro {beta}-lactamase gene, and the mcb bacteriocin cluster, were more common in SR, which suggested different selective pressures and ecological adaptation. This cgMLST scheme and LIN code system provides a robust method for characterising M. catarrhalis, distinguishes between SR and SS lineages, and offers a unified framework for population structure analyses. Implemented within PubMLST, this open-access resource facilitates high-resolution genomic studies and supports the scientific community in understanding the evolutionary complexity of M. catarrhalis.

genomics↗

bioRxiv2023

Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies

Improvements in the accuracy and availability of long-read sequencing mean that complete bacterial genomes are now routinely reconstructed using hybrid (i.e. short- and long-reads) assembly approaches. Complete genomes allow a deeper understanding of bacterial evolution and genomic variation beyond single nucleotide variants (SNVs). They are also crucial for identifying plasmids, which often carry medically significant antimicrobial resistance (AMR) genes. However, small plasmids are often missed or misassembled by long-read assembly algorithms. Here, we present Hybracter which allows for the fast, automatic, and scalable recovery of near-perfect complete bacterial genomes using a long-read first assembly approach. Hybracter can be run either as a hybrid assembler or as a long-read only assembler. We compared Hybracter to existing automated hybrid and long-read only assembly tools using a diverse panel of samples of varying levels of long-read accuracy with manually curated ground truth reference genomes. We demonstrate that Hybracter as a hybrid assembler is more accurate and faster than the existing gold standard automated hybrid assembler Unicycler. We also show that Hybracter with long-reads only is the most accurate long-read only assembler and is comparable to hybrid methods in accurately recovering small plasmids. Data SummaryO_LIHybracter is developed using Python and Snakemake as a command-line software tool for Linux and MacOS systems. C_LIO_LIHybracter is freely available under an MIT License on GitHub (https://github.com/gbouras13/hybracter) and the documentation is available at Read the Docs (https://hybracter.readthedocs.io/en/latest/). C_LIO_LIHybracter is available to install via PyPI (https://pypi.org/project/hybracter/) and Bioconda (https://anaconda.org/bioconda/hybracter). A Docker/Singularity container is also available at https://quay.io/repository/gbouras13/hybracter. C_LIO_LIAll code used to benchmark Hybracter, including the reference genomes, is publicly available on GitHub (https://github.com/gbouras13/hybracter_benchmarking) with released DOI (https://zenodo.org/doi/10.5281/zenodo.10910108) available at Zenodo. C_LIO_LIThe subsampled FASTQ files used for benchmarking are publicly available at Zenodo with DOI (https://doi.org/10.5281/zenodo.10906937). C_LIO_LIAll super accuracy simplex ATCC FASTQ reads sequenced as a part of this study can be found under BioProject PRJNA1042815. C_LIO_LIAll Hall et al. fast accuracy simplex and super accuracy duplex ATCC FASTQ read files (prior to subsampling) can be found in the SRA under BioProject PRJNA1087001. C_LIO_LIAll raw Lermaniaux et al. FASTQ read files and genomes (prior to subsampling) can be found in the SRA under BioProject PRJNA1020811. C_LIO_LIAll Staphylococcus aureus JKD6159 FASTQ read files and genomes can be found under BioProject PRJNA50759. C_LIO_LIAll Mycobacterium tuberculosis H37R2 FASTQ read files and genomes can be found under BioProject PRJNA836783. C_LIO_LIThe complete list of BioSample accession numbers for each benchmarked sample can be found in Supplementary Table 1. C_LIO_LIThe benchmarking assembly output files are publicly available on Zenodo with DOI (https://doi.org/10.5281/zenodo.10906937). C_LIO_LIAll Pypolca benchmarking outputs and code are publicly available on Zenodo with DOI (https://zenodo.org/doi/10.5281/zenodo.10072192). C_LI Impact StatementComplete bacterial genome assembly using hybrid sequencing is a routine and vital part of bacterial genomics, especially for identification of mobile genetic elements and plasmids. As sequencing becomes cheaper, easier to access and more accurate, automated assembly methods are crucial. With Hybracter, we present a new long-read first automated assembly tool that is faster and more accurate than the widely-used Unicycler. Hybracter can be used both as a hybrid assembler and with long-reads only. Additionally, it solves the problems of long-read assemblers struggling with small plasmids, with plasmid recovery from long-reads only performing on par with hybrid methods. Hybracter can natively exploit the parallelisation of high-performance computing (HPC) clusters and cloud-based environments, enabling users to assemble hundreds or thousands of genomes with one line of code. Hybracter is available freely as source code on GitHub, via Bioconda or PyPi.

bioinformatics↗

bioRxiv2021

Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli

2.Several bioinformatics genotyping algorithms are now commonly used to characterise antimicrobial resistance (AMR) gene profiles in whole genome sequencing (WGS) data, with a view to understanding AMR epidemiology and developing resistance prediction workflows using WGS in clinical settings. Accurately evaluating AMR in Enterobacterales, particularly Escherichia coli, is of major importance, because this is a common pathogen. However, robust comparisons of different genotyping approaches on relevant simulated and large real-life WGS datasets are lacking. Here, we used both simulated datasets and a large set of real E. coli WGS data (n=1818 isolates) to systematically investigate genotyping methods in greater detail. Simulated constructs and real sequences were processed using four different bioinformatic programs (ABRicate, ARIBA, KmerResistance, and SRST2, run with the ResFinder database) and their outputs compared. For simulations tests where 3,079 AMR gene variants were inserted into random sequence constructs, KmerResistance was correct for 3,076 (99.9%) simulations, ABRicate for 3,054 (99.2%), ARIBA for 2,783 (90.4%) and SRST2 for 2,108 (68.5%). For simulations tests where two closely related gene variants were inserted into random sequence constructs, KmerResistance the correct alleles in 35,338/46,318 (76.3%) ABRicate identified in 11,842/46,318 (25.6%) of simulations, ARIBA in 1679/46,318 (3.6%), and SRST2 in 2000/46,318 (4.3%). In real data, across all methods, 1392/1818 (76%) isolates had discrepant allele calls for at least one gene. Our evaluations revealed poor performance in scenarios that would be expected to be challenging (e.g. identification of AMR genes at <10x coverage, discriminating between closely related AMR gene sequences), but also identified systematic sequence classification (i.e. naming) errors even in straightforward circumstances, which contributed to 1081/3092 (35%) errors in our most simple simulations and at least 2530/4321 (59%) discrepancies in real data. Further, many of the remaining discrepancies were likely "artefactual" with reporting cut-off differences accounting for at least 1430/4321 (33%) discrepants. Comparing outputs generated by running multiple algorithms on the same dataset can help identify and resolve these artefacts, but ideally new and more robust genotyping algorithms are needed. 3. Impact statementWhole-genome sequencing is widely used for studying the epidemiology of antimicrobial resistance (AMR) genes in bacteria; however, there is some concern that outputs are highly dependent on the bioinformatics methods used. This work evaluates these concerns in detail by comparing four different, commonly used AMR gene typing methods using large simulated and real datasets. The results highlight performance issues for most methods in at least one of several simulated and real-life scenarios. However most discrepancies between methods were due to differential labelling of the same sequences related to the assumptions made regarding the underlying structure of the reference resistance gene database used (i.e. that resistance genes can be easily classified in well-defined groups). This study represents a major advance in quantifying and evaluating the nature of discrepancies between outputs of different AMR typing algorithms, with relevance for historic and future work using these algorithms. Some of the discrepancies can be resolved by choosing methods with fewer assumptions about the reference AMR gene database and manually resolving outputs generated using multiple programs. However, ideally new and better methods are needed.

microbiology↗

bioRxiv2019

Genomic analysis of carbapenemase-encoding plasmids from Klebsiella pneumoniae across Europe highlights three major patterns of dissemination

The incidence of Klebsiella pneumoniae infections that are resistant to carbapenems, a last-line class of antibiotics, has been rapidly increasing. The primary mechanism of carbapenem resistance is production of carbapenemase enzymes, which are most frequently encoded on plasmids by blaOXA-48-like, blaVIM, blaNDM and blaKPC genes. Using short-read sequence data, we previously analysed genomes of 1717 isolates from the K. pneumoniae species complex submitted during the European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE). Here, we investigated the diversity, prevalence and transmission dynamics of carbapenemase-encoding plasmids using long-read sequencing of representative isolates (n=79) from this collection in combination with short-read data from all isolates. We highlight three major patterns by which carbapenemase genes have disseminated via plasmids. First, blaOXA-48-like genes have spread across diverse lineages primarily via a highly conserved, epidemic pOXA-48-like plasmid. Second, blaVIM and blaNDM genes have spread via transient associations of diverse plasmids with numerous lineages. Third, blaKPC genes have transmitted predominantly by stable association with one clonal lineage (ST258/512) despite frequent mobilisation between pre-existing yet diverse plasmids within the lineage. Despite contrasts in these three modes of carbapenemase gene spread, which can be summarised as using one plasmid/multiple lineages, multiple plasmids/multiple lineages, and multiple plasmids/one lineage, all are underpinned by significant propagation along high-risk clonal lineages.

microbiology↗

bioRxiv2019

The Role of fosA in Challenges with Fosfomycin Susceptibility Testing of Multispecies Klebsiella pneumoniae Carbapenemase-Producing Clinical Isolates

With multidrug resistant (MDR) Enterobacteriales on the rise, a non-toxic agent with a unique mechanism of action such as fosfomycin seems attractive. However, establishing accurate fosfomycin susceptibility testing for non-E. coli in a clinical microbiology laboratory remains problematic. We evaluated fosfomycin susceptibility by multiple methods with multiple strains and species of KPC-producing clinical isolates collected at a single center between 2008 and 2016. In addition, we assessed the presence of fosfomycin resistance genes from whole genome sequencing (WGS) data using NCBIs AMRFinder and custom HMM search. Susceptibility testing was performed using glucose-6-phosphate supplemented fosfomycin E-Test and Kirby-Bauer disk diffusion (DD) assays, and compared to agar dilution. Clinical Laboratory and Standards Institute (CLSI) breakpoints for E. coli were applied for interpretation. Overall, 63% (60/96) of isolates were susceptible by E-Test, 70% (67/96) by DD, and 88% (84/96) by agar dilution. FosA was detected in 80% (70/88) of previously sequenced isolates, with species-specific associations and alleles, and fosA-positive isolates were associated with higher MIC distributions. Disk potentiation testing was performed using sodium phosphonoformate to inhibit fosA and showed significant increases in the zone diameter of DD testing for isolates that were fosA-positive compared to fosA-negative. The addition of sodium phosphonoformate (PPF) corrected 10/14 (71%) major errors in categorical agreement with agar dilution. Our results indicate that fosA influences the inaccuracy of susceptibility testing by methods readily available in a clinical laboratory when compared to agar dilution. Further research is needed to determine the impact of fosA on clinical outcomes.

microbiology↗

bioRxiv2019

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes

Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome assembly. Long read sequencing greatly assists with resolving complex bacterial genomes, particularly when combined with short-read Illumina data (hybrid assembly). However, it is not clear how different long-read sequencing methods impact on assembly accuracy. Relative automation of the assembly process is also crucial to facilitating high-throughput complete bacterial genome reconstruction, avoiding multiple bespoke filtering and data manipulation steps. In this study, we compared hybrid assemblies for 20 bacterial isolates, including two reference strains, using Illumina sequencing and long reads from either Oxford Nanopore Technologies (ONT) or from SMRT Pacific Biosciences (PacBio) sequencing platforms. We chose isolates from the Enterobacteriaceae family, as these frequently have highly plastic, repetitive genetic structures and complete genome reconstruction for these species is relevant for a precise understanding of the epidemiology of antimicrobial resistance. We de novo assembled genomes using the hybrid assembler Unicycler and compared different read processing strategies. Both strategies facilitate high-quality genome reconstruction. Combining ONT and Illumina reads fully resolved most genomes without additional manual steps, and at a lower consumables cost per isolate in our setting. Automated hybrid assembly is a powerful tool for complete and accurate bacterial genome assembly. IMPACT STATEMENTIllumina short-read sequencing is frequently used for tasks in bacterial genomics, such as assessing which species are present within samples, checking if specific genes of interest are present within individual isolates, and reconstructing the evolutionary relationships between strains. However, while short-read sequencing can reveal significant detail about the genomic content of bacterial isolates, it is often insufficient for assessing genomic structure: how different genes are arranged within genomes, and particularly which genes are on plasmids - potentially highly mobile components of the genome frequently carrying antimicrobial resistance elements. This is because Illumina short reads are typically too short to span repetitive structures in the genome, making it impossible to accurately reconstruct these repetitive regions. One solution is to complement Illumina short reads with long reads generated with SMRT Pacific Biosciences (PacBio) or Oxford Nanopore Technologies (ONT) sequencing platforms. Using this approach, called hybrid assembly, we show that we can automatically fully reconstruct complex bacterial genomes of Enterobacteriaceae isolates in the majority of cases (best-performing method: 17/20 isolates). In particular, by comparing different methods we find that using the assembler Unicycler with Illumina and ONT reads represents a low-cost, high-quality approach for reconstructing bacterial genomes using publicly available software. DATA SUMMARYRaw sequencing data and assemblies have been deposited in NCBI under BioProject Accession PRJNA422511 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA422511). We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

bioinformatics↗

bioRxiv2019

Reconciling the potentially irreconcilable? Genotypic and phenotypic amoxicillin-clavulanate resistance in Escherichia coli

Resistance to amoxicillin-clavulanate, a widely used beta-lactam/beta-lactamase inhibitor combination antibiotic, is rising globally, yet susceptibility testing remains challenging. To test whether whole-genome sequencing (WGS) could provide a more reliable assessment of susceptibility than traditional methods, we predicted resistance from WGS for 976 E. coli bloodstream infection isolates from Oxfordshire, UK, comparing against phenotypes from the BD Phoenix (calibrated against EUCAST guidelines). 339/976 (35%) isolates were amoxicillin-clavulanate resistant. Predictions based solely on beta-lactamase presence/absence performed poorly (sensitivity 23% (78/339)) but improved when genetic features associated with penicillinase hyper-production (e.g. promoter mutations, copy number estimates) were considered (sensitivity 82% (277/339); p<0.0001). Most discrepancies occurred in isolates with peri-breakpoint MICs. We investigated two potential causes; the phenotypic reference and the binary resistant/susceptible classification. We performed reference standard, replicated phenotyping in a random stratified subsample of 261/976 (27%) isolates using agar dilution, following both EUCAST and CLSI guidelines, which use different clavulanate concentrations. As well as disagreeing with each other, neither agar dilution phenotype aligned perfectly with genetic features. A random-effects model investigating associations between genetic features and MICs showed that some genetic features had small, variable and additive effects, resulting in variable resistance classification. Using model fixed-effects to predict MICs for the non-agar dilution isolates, predicted MICs were in essential agreement ({+/-}1 doubling dilution) with observed (BD Phoenix) MICs for 691/715 (97%) isolates. This suggests amoxicillin-clavulanate resistance in E. coli is quantitative, rather than qualitative, explaining the poorly reproducible binary (resistant/susceptible) phenotypes and suboptimal concordance between different phenotypic methods and with WGS-based predictions.

microbiology↗

bioRxiv2018

Klebsiella quasipneumonaiae provides a window into carbapenemase gene transfer, plasmid rearrangements and nosocomial acquisition from the hospital environment

Several emerging pathogens have arisen as a result of selection pressures exerted by modern healthcare. Klebsiella quasipneumoniae was recently defined as a new species, yet its prevalence, niche, and propensity to acquire antimicrobial resistance genes are not fully described. We have been tracking inter- and intra-species transmission of the Klebsiella pneumoniae carbapenemase (KPC) gene, blaKPC, between bacteria isolated from a single institution. We applied a combination of Illumina and PacBio whole-genome sequencing to identify and compare K. quasipneumoniae from patients and the hospital environment over 10 and five-year periods respectively. There were 32 blaKPC-positive K. quasipneumoniae isolates, all of which were identified as K. pneumoniae in the clinical microbiology laboratory, from eight patients and 11 sink drains, with evidence for seven separate blaKPC plasmid acquisitions. Analysis of a single subclade of K. quasipneumoniae subspecies quasipneumoniae (n=23 isolates) from three patients and six rooms demonstrated seeding of a sink by a patient, subsequent persistence of the strain in the hospital environment, and then probable transmission to another patient. Longitudinal analysis of this strain demonstrated the acquisition of two unique blaKPC plasmids and then subsequent within-strain genetic rearrangement through transposition and homologous recombination. Our analysis highlights the apparent molecular propensity of K. quasipneumoniae to persist in the environment as well as acquire carbapenemase plasmids from other species and enabled an assessment of the genetic rearrangements which may facilitate horizontal transmission of carbapenemases.

microbiology↗

bioRxiv2018

TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data

Much of the worldwide dissemination of antibiotic resistance has been driven by resistance gene associations with mobile genetic elements (MGEs), such as plasmids and transposons. Although increasing, our understanding of resistance spread remains relatively limited, as methods for tracking mobile resistance genes through multiple species, strains and plasmids are lacking. We have developed a bioinformatic pipeline for tracking variation within, and mobility of, specific transposable elements (TEs), such as transposons carrying antibiotic resistance genes. TETyper takes short-read whole-genome sequencing data as input and identifies single-nucleotide mutations and deletions within the TE of interest, to enable tracking of specific sequence variants, as well as the surrounding genetic context(s), to enable identification of transposition events. To investigate global dissemination of Klebsiella pneumoniae carbapenemase (KPC) and its associated transposon Tn4401, we applied TETyper to a collection of >3000 publicly available Illumina datasets containing blaKPC. This revealed surprising diversity, with >200 distinct flanking genetic contexts for Tn4401, indicating high levels of transposition. Integration of sample metadata revealed insights into associations between geographic locations, host species, Tn4401 sequence variants and flanking genetic contexts. To demonstrate the ability of TETyper to cope with high copy number TEs and to track specific short-term evolutionary changes, we also applied it to the insertion sequence IS26 within a defined K. pneumoniae outbreak. TETyper is implemented in python and is freely available at https://github.com/aesheppard/TETyper.

bioinformatics↗

bioRxiv2017

Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing E. coli

The dissemination of carbapenem resistance in Escherichia coli has major implications for the management of common human infections. blaKPC, encoding a transmissible carbapenemase (KPC), has historically largely been associated with Klebsiella pneumoniae, a predominant plasmid (pKpQIL), and a specific transposable element (Tn4401, ~10kb). Here we characterize the genetic features of the emergence of blaKPC in global E. coli, 2008-2013, using both long-and short-read whole genome sequencing.\n\nAmongst 43/45 successfully sequenced blaKPC-E. coli strains, we identified high strain (n=21 sequence types, 18% of annotated genes in the core genome); plasmid ([≥]9 replicon types); and blaKPC-associated, mobile genetic element (MGE) diversity (50% not within complete Tn4401 elements). We also found evidence of interspecies, regional and international plasmid spread. In several cases blaKPC was found on high copy number, small Col-like plasmids, previously associated with horizontal transmission of resistance genes in the absence of antimicrobial selection pressures.\n\nE. coli is a common human pathogen, but also a commensal in a multiple environmental and animal reservoirs, and easily transmissible. The association of blaKPC with a range of MGEs previously linked to the successful spread of widely endemic resistance mechanisms (e.g. blaTEM, blaCTX-M) suggests that it is likely to become similarly prevalent.

microbiology↗

bioRxiv2017

High rates of human faecal carriage of mcr-1-positive multi-drug resistant isolates emerge in China in association with successful plasmid families

SynopsisO_ST_ABSBackgroundC_ST_ABSmcr-1-mediated transmissible colistin resistance in Enterobacteriaceae is concerning, given colistin is frequently used as a treatment of last resort in multidrug-resistant Enterobacteriaceae infections. Reported rates of human mcr-1 gastrointestinal carriage have historically been low.\n\nObjectivesTo identify trends in human gastrointestinal carriage of mcr-1 positive and mcr-1-positive/cefotaxime-resistant Enterobacteriaceae in Guangzhou, China, 2011-2016, and investigate the genetic contexts of mcr-1 in a subset of mcr-1-positive/cefotaxime-resistant strains using whole genome sequencing (WGS).\n\nMethodsOf 8,022 faecal samples collected, 497 (6.2%) were mcr-1- positive, and 182 (2.3%) mcr-1-positive/cefotaxime-resistant. Trends in carriage were assessed using iterative sequential regression. A subset of mcr-1-positive isolates was sequenced (Illumina), and genetic contexts of mcr-1 were characterised.\n\nResultsWe observed marked increases in mcr-1 (now ~30% prevalence) and more recent (since January 2014) increases in mcr-1-positive/third-generation cephalosporin-resistant Enterobacteriaceae human colonisation (p<0.001). Sub-cultured mcr-1-positive/third-generation cephalosporin-resistant isolates were commonly multi-drug resistant.\n\nWGS of 50 mcr-1/third-generation cephalosporin-resistant isolates (49 Escherichia coli; 1 Klebsiella pneumoniae) demonstrated bacterial strain diversity (39 E. coli sequence types); mcr-1 in association with common plasmid backbones (IncI, IncHI2/HI2A, IncX4) and sometimes in multiple plasmids; frequent mcr-1 chromosomal integration; and loss of the mcr-1-associated insertion sequence ISApl1 in some plasmids. Significant sequence similarity with published mcr-1 plasmid sequences was consistent with spread amongst pig, chicken and human reservoirs.\n\nConclusionsThe high positivity rate (~10%) of mcr-1 in multidrug-resistant E. coli colonising humans is a clinical threat; the diverse genetic mechanisms (strains/plasmids/insertion sequences) associated with mcr-1 have likely contributed to its dissemination, and will facilitate its persistence.

microbiology↗