Biology subjects

Shaw, L. P.

Publications and source records attributed to Shaw, L. P..

At least 19 recordsLinked to original sources

bioRxiv2026

Global genomic epidemiology of multi-carbapenemase Enterobacterales

Enterobacterales pathogens that encode multiple carbapenemase genes are an emerging public health threat. The genomic and plasmid context of the multi-carbapenemase producers has not yet been explored at scale. We analysed 1501 publicly-available global genomes that encoded two or more genes from the five prevalent carbapenemase families (IMP, KPC, NDM, OXA-48-like, and VIM). We observed 241 distinct allelic combinations, with NDM/OXA-48-like (25.6%), multiple KPC (25.3%), KPC/NDM (18.8%), and multiple NDM (10.9%) being the most common groups. We found that many genomes were part of high-risk lineages (48.0%). Most genomes carried carbapenemase genes on two plasmids (59.2%) or one plasmid (23.5%), and most genomes encoded different carbapenemase families (56.2%) rather than copies of the same allele (36.2%). We observed multiple mechanisms of multi-carbapenemase evolution including plasmid co-integration, convergence with virulence, and generation of novel allele diversity through duplication. Multi-carbapenemase plasmids had more AMR genes that conferred resistance to more AMR classes compared to plasmids encoding a single carbapenemase. The proportion of cross-class combinations (KPC/NDM and NDM/OXA-48-like) increased significantly over time, with NDM-5/OXA-181 (3.3-fold) and NDM-4/OXA-181 (8.9-fold) combinations enriched. These findings provide valuable insights into the genomic features of multi-carbapenemase Enterobacterales to support the development of effective surveillance programmes.

microbiology↗

bioRxiv2026

Plasmid copy numbers reflect distinct evolutionary strategies

Different plasmids exist at different copy numbers per cell, and there is an inverse relationship between a plasmids copy number and its size. Two recent studies quantified this relationship into a scaling law, but both the form and the interpretation of this law are contested. Here, I explore the issues with fitting a single law across plasmid diversity and suggest a consistent synthesis. First, I explore some potential problems with using sequencing-based estimates of copy number. Then, I discuss plasmid copy number through a series of case studies. I argue in favour of interpreting plasmid copy numbers not through a single law, but through the lens of two dominant evolutionary strategies. I suggest that small plasmids which lack active segregation mechanisms have a resulting tradeoff between plasmid inheritance and fitness cost to the host, which is responsible for an inverse relationship between copy number and size. In contrast, larger plasmids with active segregation mechanisms show a much weaker relationship, in line with evidence that their metabolic costs are dominated by the expression of specific genes rather than their size. Where plasmids in the 20-100kb range have higher copy numbers, I argue these probably arise more from selection at the level of the host cell for plasmid-associated phenotypes (e.g. antibiotic resistance) rather than from plasmid-level selection for inheritance.

microbiology↗

bioRxiv2026

Benchmarking strain-level profiling of Escherichia coli in short-read gut metagenomes

2.Metagenomes offer the potential to characterise Escherichia coli strain-level diversity within the human gut microbiome, informing our understanding of colonisation diversity and the genetic features distinguishing infection from carriage. Among numerous reference-based tools for short-read metagenomic strain-level profiling, the best approach remains unclear. Here, we benchmarked six published tools--PanTax, PathoScope, StrainGE, Strainify, StrainR2 and StrainScan--for their ability to detect co-existing strains of E. coli and estimate their relative abundance across real and simulated metagenomes of increasing complexity with varying reference database composition. In the ZymoBIOMICS(R) D6331 dataset, only PanTax achieved zero error when predicting the equal abundance of five E. coli strains. In a differentially abundant four-strain mock community dataset (SRR13355226), StrainScan had the lowest mean absolute proportional error (0.89), driven by reduced sensitivity (0.5), followed by PathoScope (4.08). Across simulated metagenomes reflecting the healthy adult gut microbiome, all tools demonstrated high sensitivity ([≥]0.833), but specificity, precision and F1 score were selectively improved in some tools through detection thresholds to remove low abundance false positives. Outright, StrainGE achieved the highest F1 score (0.978). Predicted relative abundances of the E. coli K12-MG1655 (phylogroup A) and O157:H7 Sakai (phylogroup E) strains spiked into simulated metagenomes across varying abundance ratios were generally accurate, with PanTax and StrainR2 showing the lowest mean absolute proportional error (0.06). When truly present strains were removed from the reference database, out-of-phylogroup assignments were observed for some tools. Collectively, our results demonstrate that published metagenomic strain-level profiling tools vary in their ability to profile E. coli strains, indicating that method selection should be guided by intended application. These findings will facilitate characterisation of E. coli strain-level diversity within short-read gut metagenomes with greater accuracy than previously possible. 3. Impact statementStrain-level diversity within the human gut microbiome can be important for human health, with species such as Escherichia coli existing as both commensal and pathogenic strains. Most existing gut microbiome datasets are from short-read i.e., Illumina, sequencing, and numerous bioinformatic tools have been developed to profile strain-level variation from these data. However, the existing literature is often difficult to navigate given that the available tools have been benchmarked in various ways and are subject to author bias. This is, to our knowledge, the first independent benchmarking of six published tools for profiling E. coli at strain-level resolution from short-read metagenomes. Using both real and simulated datasets of increasing complexity, we demonstrate substantial variation in tool performance in terms of strain detection and relative abundance estimation, highlighting that tool choice should be guided by the specific research question, as no single method performs optimally across all scenarios. This work provides an unbiased framework for tool selection and will support more accurate and reproducible E. coli strain-level analyses in gut microbiome research from short-metagenomic data. 4. Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. Supplementary methods, six supplementary tables and four supplementary figures are available in the online Supplementary Material. Code for simulating metagenomes using InSilicoSeq, SLURM job scripts for the simulated metagenomes dataset and R visualization and statistical analysis scripts are available within a dedicated public GitHub repository (https://github.com/mattgal11/benchmarking_short_read_strain_profilers). The following supplementary data are available on FigShare (https://doi.org/10.6084/m9.figshare.32125474): O_LINormalised per-contig relative abundances for 98 species assemblies used to construct the baseline gut microbiome profile for InSilicoSeq metagenome simulation (Normalised_relative_abundance_for_InSilicoSeq_simulated_metagenomes_ gut_microbiome_profile.csv) C_LIO_LIZymoBIOMICS(R) D6331 gut microbiome standard dataset predicted relative abundance data (Zymobiomics_D6331_raw_predicted_abundance.csv) C_LIO_LISRR13355226 mock community (99% human reads; 1% E. coli reads) paired-end reads with human reads depleted (SRR13355226_depleted_R1.fastq.gz & SRR13355226_depleted_R2.fastq.gz) C_LIO_LISRR13355226 mock community dataset raw predicted abundance data, with and without human read removal (SRR13355226_raw_predicted_abundance_with_and_without_human_read_r emoval.csv) C_LIO_LISimulated metagenomes dataset raw call types and detection metric values with increasing detection thresholds (Simulated_metagenomes_raw_call_type_assingments_and_detection_thres holds.csv) C_LIO_LISimulated metagenomes dataset (all references) predicted relative abundance data (Simulated_metagenomes_all_references_raw_predicted_abundances.csv) C_LIO_LISimulated metagenomes dataset (all references) mapped reads for PathoScope and Strainify (all_refs_pathoscope_reads_mapped.csv & all_refs_strainify_reads_mapped.csv) C_LIO_LISimulated metagenomes dataset (reduced reference database) predicted relative abundance data (Simulated_metagenomes_K12_and_Sakai_removed_from_reference_datab ase_raw_predicted_abundance.csv) C_LI

bioinformatics↗

bioRxiv2025

The leading region of many conjugative plasmids is depleted in restriction-modification targets

To successfully transfer into a recipient, conjugative plasmids must overcome the new cells defense mechanisms. The leading region of many plasmids - the first part to enter the recipient - is highly enriched in anti-defense genes. Here, we investigate whether selective pressure from defense systems has also affected its sequence composition. We consider two possibilities: greater target depletion (to avoid triggering target-based defense systems) or greater codon adaptation (to more quickly express anti-defense genes). We analyse the leading region of 1,751 conjugative plasmids belonging to 13 plasmid taxonomic units (PTUs) present in the bacterial order Enterobacterales. First, we investigate GC content and possible depletion of short palindromic motifs (4-8bp) which could be a signature of selective pressure from Type II restriction-modification systems, and find evidence of depletion in certain PTUs. Then we use the codon adaptation index (CAI) to assess codon usage and find that different conjugative PTUs shown different patterns. We show that the leading region of plasmids with MOB-F and MOB-P relaxases is more adapted to optimal host codon usage, consistent with a selective pressure for translational efficiency in anti-defense genes that are transcribed while still single-stranded DNA. In particular, anti-restriction genes in the leading region have high CAI, and we use this fact to identify a single-stranded promoter in the F plasmid. Our findings uncover a new facet of plasmid evolution and emphasise the intensity of the selective pressure that plasmids face from defense systems.

microbiology↗

bioRxiv2024

Evolutionary dynamics of genome structure and content among closely related bacteria

Bacterial genomes primarily diversify via gain, loss, and rearrangement of genetic material in their flexible accessory genome. Yet the dynamics of accessory genome evolution are very poorly understood, in contrast to the core genome where diversification is readily described by mutations and homologous recombination. Here, we tackle this problem for the case of very closely related genomes. We comprehensively describe genome evolution within n=222 genomes of E. coli ST131, which likely shared a common ancestor around one hundred years ago. After removing putative recombinant diversity, the total length of the phylogeny is 6000 core genome mutations. Within this diversity, we find 22 modifications to core genome synteny and estimate around 2000 structural changes within the accessory genome, i.e. one structural change for every 3 core genome mutations. 63% of loci with structural diversity could be resolved into individual gain and loss events with ten-fold more gains than losses, demonstrating a dominance of gains due to insertion sequences and prophage integration. Our results suggest the majority of synteny changes and insertions in bacterial genomes are likely deleterious and only persist for a short time before being removed by purifying selection.

evolutionary biology↗

bioRxiv2024

Adaptation of Pseudomonas aeruginosa to repeated invasion into a commensal competitor

The host-associated microbiome is an important barrier to bacterial pathogen colonization and can mediate protection through a variety of mechanisms. We wanted to investigate the potential consequences of selection imposed by commensal bacterial competitors on an invading bacterial pathogen. To do this, we tested the ability of the opportunistic pathogen Pseudomonas aeruginosa to invade pre-established communities of an abundant commensal bacterium in the human microbiome, Staphylococcus epidermidis. We passaged ten independent lines of P. aeruginosa through daily invasion into a pre-established S. epidermidis population (coculture evolved lines), alongside daily passage through monoculture conditions (monoculture evolved lines). The monoculture evolved lines showed strong parallel evolution in the Wsp (Wrinkly spreader phenotype) signal transducing system involved in biofilm formation, and significantly elevated biofilm formation. On the other hand, adaptation to S. epidermidis occurred via mutations in a diverse set of genes, and the coculture evolved lines showed much weaker evidence for parallel evolution, suggesting that the selective pressure imposed by competition with S. epidermidis is more complex than the pressure imposed by culture conditions. Interestingly, the elevated biofilm formation phenotype seen in the monoculture evolved lines was not observed in the lines evolved in the presence of S. epidermidis, raising the question of whether enhanced biofilm formation did not evolve with S. epidermidis present because it was not beneficial, or because S. epidermidis may be able to restrict this evolutionary path by inhibiting biofilm formation.

microbiology↗

bioRxiv2024

Global genomic epidemiology of blaGES-5 carbapenemase-associated integrons

Antimicrobial resistance (AMR) gene cassettes comprise an AMR gene flanked by short recombination sites (attI x attC or attC x attC). Integrons are genetic elements able to capture, excise, and shuffle these cassettes, providing adaptation on demand, and can be found on both chromosomes and plasmids. Understanding the patterns of integron diversity may help to understand the epidemiology of AMR genes. As a case study, we examined the clinical resistance gene blaGES-5, an integron-associated class A carbapenemase first reported in Greece in 2004 and since observed worldwide, which to our knowledge has not been the subject of a previous global analysis. Using a dataset comprising all NCBI contigs containing blaGES-5 (n = 431), we developed a pangenome graph-based workflow to characterise and cluster the diversity of blaGES-5 -associated integrons. We demonstrate that blaGES-5-associated integrons on plasmids are different to those on chromosomes. Chromosomal integrons were almost all identified in P. aeruginosa ST235, with a consistent gene cassette content and order. We observed instances where insertion sequence IS110 disrupted attC sites, which might immobilise the gene cassettes and explain the conserved integron structure despite the presence of intI1 integrase promoters, which would typically facilitate capture or excision and rearrangement. The plasmid-associated integrons were more diverse in their gene cassette content and order, which could be an indication of greater integrase activity and shuffling of integrons on plasmids.

genomics↗

bioRxiv2023

Visualizing and quantifying structural diversity around mobile AMR genes

Understanding the evolution of mobile genes is important for understanding the spread of antimicrobial resistance (AMR). Many clinically important AMR genes have been mobilized by mobile genetic elements (MGEs) on the kilobase scale, such as integrons and transposons, which can integrate into both chromosomes and plasmids and lead to rapid spread of the gene through bacterial populations. Looking at the flanking regions of these mobile genes in diverse genomes can highlight common structures and reveal patterns of MGE spread. However, historically this has been a largely descriptive process, relying on gene annotation and expert knowledge. Here we describe a general method to visualize and quantify the structural diversity around genes using pangraph to find blocks of homologous sequence. We apply this method to a set of twelve clinically important beta-lactamase genes and provide interactive visualizations of their flanking regions at https://liampshaw.github.io/flanking-regions. We show that nucleotide-level variation in the mobile gene itself generally correlates with increased structural diversity in its flanking regions, demonstrating a relationship between rates of mutational evolution and rates of structural evolution, and find a bias for greater structural diversity upstream. Our framework is a starting point to investigate general rules that apply to the horizontal spread of new genes through bacterial populations. Impact statementUnderstanding the evolution and spread of mobile resistance genes is challenging because of the high variability in their genomic contexts. Here we outline a fast computational approach that identifies stretches of homologous sequence in the flanking regions of a gene, simultaneously producing interactive visualizations of these regions and quantifying the diversity within them. As an example, we apply the method to twelve clinically important beta-lactamase genes. We find that structural diversity around the resistance gene is correlated with mutations within it and that there is greater structural diversity upstream of many genes. There may be other general patterns about the evolution of mobile resistance genes that can be recovered with this kind of analysis.

bioinformatics↗

bioRxiv2022

Restriction-modification systems have shaped the evolution and distribution of plasmids across bacteria

Many novel traits such as antibiotic resistance are spread by plasmids between species. Yet plasmids have different host ranges. Restriction-modification systems (R-M systems) are by far the most abundant bacterial defense system and therefore represent one of the key barriers to plasmid spread. However, their effect on plasmid evolution and host range has been neglected. Here we analyse the avoidance of targets of the most abundant R-M systems (Type II) for complete genomes and plasmids across bacterial diversity. For the most common target length (6 bp) we show that target avoidance is strongly correlated with the taxonomic distribution of R-M systems and is greater in plasmid genes than core genes. We find stronger avoidance of R-M targets in plasmids which are smaller and have a broader host range. Our results suggest two different evolutionary strategies for plasmids: small plasmids primarily adapt to R-M systems by tuning their sequence composition, and large plasmids primarily adapt through the carriage of additional genes protecting from restriction. Our work provides systematic evidence that R-M systems are important barriers to plasmid transfer and have left their mark on plasmids over long evolutionary time.

microbiology↗

bioRxiv2022

Plasmid overlap and evolution between Enterobacterales isolates from bloodstream infections and non-human compartments

Plasmids enable the dissemination of antimicrobial resistance (AMR) in common Enterobacterales pathogens, representing a major public health challenge. However, the extent of plasmid sharing and evolution between Enterobacterales causing human infections and other niches remains unclear, including the emergence of resistance plasmids. Dense, unselected sampling is highly relevant to developing our understanding of plasmid epidemiology and designing appropriate interventions to limit the emergence and dissemination of plasmid-associated AMR. We established a geographically and temporally restricted collection of human bloodstream infection (BSI)-associated, livestock-associated (cattle, pig, poultry, and sheep faeces, farm soils) and wastewater treatment work (WwTW)-associated (influent, effluent, waterways upstream/downstream of effluent outlets) Enterobacterales. Isolates were collected between 2008-2020 from sites <60km apart in Oxfordshire, UK. Pangenome analysis of plasmid clusters revealed shared "backbones", with phylogenies suggesting an intertwined ecology where well-conserved plasmid backbones carry diverse accessory functions, including AMR genes. Many plasmid "backbones" were seen across species and niches, raising the possibility that plasmid movement between these followed by rapid accessory gene change could be relatively common. Overall, the signature of identical plasmid sharing is likely to be a highly transient one, implying that plasmid movement might be occurring at greater rates than previously estimated, raising a challenge for future genomic One Health studies. FundingThis study was funded by the Antimicrobial Resistance Cross-council Initiative supported by the seven research councils and the NIHR, UK.

genomics↗

bioRxiv2022

Pre-existing chromosomal polymorphisms in pathogenic E. coli potentiate the evolution of antibiotic resistance by MCR-1 plasmid acquisition

Bacterial pathogens show high levels of standing genetic diversity, but the influence of this diversity on the evolution of antibiotic resistance remains unclear. Here we address this problem in the context of colistin, a last line of defense antibiotic. Using experimental evolution, we show that a plasmid carrying the MCR-1 colistin resistance gene dramatically increases the ability of E. coli populations to evolve high-level colistin resistance by acquiring mutations in lpxC, an essential chromosomal gene involved in lipopolysaccharide biosynthesis. Crucially, lpxC mutations increase colistin resistance in the presence of the MCR-1 gene, but decrease the resistance of wild-type cells, revealing positive sign epistasis for antibiotic resistance. Analysis of public genomic datasets shows that lpxC polymorphisms are common in pathogenic E. coli carrying MCR-1, highlighting the clinical relevance of this interaction. Importantly, lpxC diversity is high in pathogenic E. coli from regions with no history of MCR-1 acquisition, suggesting that pre-existing lpxC polymorphisms have potentiated the evolution of high-level colistin resistance by MCR-1 acquisition. More broadly, these findings highlight the importance of standing genetic variation and plasmid/chromosomal interactions in the evolutionary dynamics of antibiotic resistance.

evolutionary biology↗

bioRxiv2021

A phylogeny-based metric for estimating changes in transmissibility from recurrent mutations in SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2019 and spread globally to cause the COVID-19 pandemic. Despite the constant accumulation of genetic variation in the SARS-CoV-2 population, there was little evidence for the emergence of significantly more transmissible lineages in the first half of 2020. Starting around November 2020, several more contagious and possibly more virulent Variants of Concern (VoCs) were reported in various regions of the world. These VoCs share some mutations and deletions that haven arisen recurrently in distinct genetic backgrounds. Here, we build on our previous work modelling the association of mutations to SARS-CoV-2 transmissibility and characterise the contribution of individual recurrent mutations and deletions to estimated viral transmissibility. We then assess how patterns of estimated transmissibility in all SARS-CoV-2 clades have varied over the course of the COVID-19 pandemic by summing transmissibility estimates for all individual mutations carried by any sequenced genome analysed. Such an approach recovers the Delta variant (21A) as the most transmissible clade currently in circulation, followed by the Alpha variant (20I). By assessing transmissibility over the time of sampling, we observe a tendency for estimated transmissibility within clades to slightly decrease over time in most clades. Although subtle, this pattern is consistent with the expectation of a decay in transmissibility in mainly non-recombining lineages caused by the accumulation of weakly deleterious mutations. SARS-CoV-2 remains a highly transmissible pathogen, though such a trend could conceivably play a role in the turnover of different global viral clades observed over the pandemic so far. CaveatsO_LIThis work is not about the severity of disease. We do not analyse the severity of disease. We do not present any evidence that SARS-CoV-2 has decreased in severity. C_LIO_LILineage replacement dynamics are affected by many factors. The trend we recover for a decrease in inferred transmissibility of a clade over time is a small effect. We caution against over-interpretation. This result would not affect the management of the SARS-CoV-2 pandemic: for example, we make no claims about any impact on the efficacy of particular non-pharmaceutical interventions (NPIs). C_LIO_LIOur phylogeny-based method to infer changes in estimated transmissibility due to recurrent mutations and deletions makes a number of simplifying assumptions. These may not all be valid. The consistent trend for the slight decrease we report might be due to an as-yet-unidentified systematic bias. C_LI

genomics↗

bioRxiv2021

Flanker: a tool for comparative genomics of gene flanking regions

Analysing the flanking sequences surrounding genes of interest is often highly relevant to understanding the role of mobile genetic elements (MGEs) in horizontal gene transfer, particular for antimicrobial resistance genes. Here, we present Flanker, a Python package which performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of MGEs without prior knowledge of their structure. These clusters, known as flank patterns, are based on Mash distances, allowing for easy comparison of similarity across sequences. Additionally, Flanker can be flexibly parameterised to finetune outputs by characterising upstream and downstream regions separately and investigating variable lengths of flanking sequence. We apply Flanker to two recent datasets describing plasmid-associated carriage of important carbapenemase genes (blaOXA-48 and blaKPC-2/3) and show that it successfully identifies distinct clusters of flank patterns, including both known and previously uncharacterised structural variants. For example, Flanker identified four Tn4401 profiles that could not be sufficiently characterised using TETyper or MobileElementFinder, demonstrating the utility of Flanker for flanking gene characterisation. Similarly, using a large (n=226) European isolate dataset, we confirm findings from a previous smaller study demonstrating association between Tn1999.2 and blaOXA-48 upregulation and demonstrate 17 flank patterns (compared to the 5 previously identified). More generally the demonstration in this study that flank patterns are associated with to geographical regions and antibiotic susceptibility phenotypes suggests that they may be useful as epidemiological markers. Flanker is freely available under an MIT license at https://github.com/wtmatlock/flanker. Data SummaryNCBI accession numbers for all sequencing data used in this study is provided in Supplementary Table 1. The analysis performed in this manuscript can be reproduced in a binder environment provided on the Flanker Github page (https://github.com/wtmatlock/flanker).

bioinformatics↗

bioRxiv2021

Role of the mobilome in the global dissemination of the carbapenem resistance gene blaNDM

The mobile resistance gene blaNDM encodes the NDM enzyme which hydrolyses carbapenems, a class of antibiotics used to treat some of the most severe bacterial infections. blaNDM is globally distributed across a variety of Gram-negative bacteria on multiple plasmids, typically located within a highly recombining and transposon-rich genomic region. This complexity means the dynamics underlying the dissemination of blaNDM remain poorly resolved. In this work, we compile a dataset of over 6000 bacterial genomes harbouring the blaNDM gene including 104 newly generated PacBio hybrid assemblies from clinical and livestock associated isolates across China. We develop a novel computational approach to track structural variants surrounding blaNDM in bacterial genomes. This allows us to identify the prevalent genomic contexts of blaNDM and reconstruct the key mobile genetic elements and events in its global spread. We estimate that blaNDM emerged on a Tn125 transposon before 1985 but only reached a global prevalence around a decade after its first recorded observation in 2005. We find that the Tn125 transposon played an important role in early plasmid-mediated jumps of blaNDM but was overtaken by other elements in recent years including IS26-flanked pseudo-composite transposons and Tn3000. Lastly, we observe a notable correlation between plasmid backbones bearing blaNDM and the sampling location of isolates. This observation suggests that the dissemination of resistance genes is mainly driven by successive between-plasmid transposon jumps, with plasmid exchange much more restricted due to the adaptation of plasmids to specific bacterial hosts.

microbiology↗

bioRxiv2020

Genomic network analysis of an environmental and livestock IncF plasmid population

IncF plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum {beta}-lactamases, particularly in Enterobacteriaceae. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of IncF plasmids from environmental (influent, effluent, and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable IncF plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The recent association of IncF plasmids with AMR likely reflects their suitability for rapid niche adaptation.

bioinformatics↗

bioRxiv2020

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae

Escherichia coli and other Enterobacteriaceae are highly diverse species with open pangenomes1,2, where genes move intra- and inter-species via horizontal gene transfer3. These species can cause clinical infections4,5 as well as persist environmentally6,7. Environmental populations have been suggested as important reservoirs of antimicrobial resistance (AMR) genes. However, as most analyses focus on clinical isolates8,9, the pangenome dynamics of natural populations remain understudied, particularly the role of plasmids. Here, we reconstructed near-complete genomes for 828 Enterobacteriaceae, including 553 Escherichia spp. and 275 non-Escherichia species with 2,293 circularised plasmids in total, collected from nineteen locations (livestock farms and wastewater treatment works in the United Kingdom) within a 30km radius at three timepoints over the course of a year. We find different dynamics for the chromosomal and plasmid-borne components of the pangenome, showing that plasmids have a higher burden of both AMR genes and insertion sequences, and AMR plasmids show evidence of being under stronger selective pressure. Focusing on E. coli, we observe that plasmid dynamics are more strongly dominated by niche and local geography, rather than phylogeny or season. Our results highlight the diversity of the AMR reservoir in these species and niches, and the importance of local strategies for controlling the emergence and spread of AMR.

microbiology↗

bioRxiv2020

Hospital outbreak of carbapenem-resistant Enterobacteriales associated with an OXA-48 plasmid carried mostly by Escherichia coli ST399

A hospital outbreak of carbapenem-resistant Enterobacteriales was detected by routine surveillance. Whole genome sequencing and subsequent analysis revealed a conserved promiscuous OXA-48 carrying plasmid as the defining factor within this outbreak. Four different species of Enterobacteriales were involved in the outbreak. Escherichia coli ST399 accounted for 20/55 of all the isolates. Comparative genomics with publicly available E. coli ST399 sequence data showed that the outbreak isolates formed a unique clade. The OXA-48 plasmid identified in the outbreak differed from other known plasmids by an estimated five homologous recombination events. We estimated a lower bound to the plasmid conjugation rate to be 0.23 conjugation events per lineage per year. Our analysis suggests co-evolution between the plasmid and its main bacterial host to be a key driver of the outbreak. This is the first study to report carbapenem-resistant E. coli ST399 carrying OXA48 as the main cause of a plasmid-borne outbreak within a hospital setting. This study supports complementary roles for both plasmid conjugation and clonal expansion in the emergence of this outbreak.

evolutionary biology↗

bioRxiv2020

No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2

The COVID-19 pandemic is caused by the coronavirus SARS-CoV-2, which jumped into the human population in late 2019 from a currently uncharacterised animal reservoir. Due to this extremely recent association with humans, SARS-CoV-2 may not yet be fully adapted to its human host. This has led to speculations that some lineages of SARS-CoV-2 may be evolving towards higher transmissibility. The most plausible candidate mutations under putative natural selection are those which have emerged repeatedly and independently (homoplasies). Here, we formally test whether any of the recurrent mutations that have been observed in SARS-CoV-2 are significantly associated with increased viral transmission. To do so, we develop a phylogenetic index to quantify the relative number of descendants in sister clades with and without a specific allele. We apply this index to a carefully curated set of recurrent mutations identified within a dataset of 46,723 SARS-CoV-2 genomes isolated from patients worldwide. We do not identify a single recurrent mutation in this set convincingly associated with increased viral transmission. Instead, recurrent SARS-CoV-2 mutations currently in circulation appear to be evolutionary neutral. Recurrent mutations also seem primarily induced by the human immune system via host RNA editing, rather than being signatures of adaptation to the novel human host. In conclusion, we find no evidence at this stage for the emergence of significantly more transmissible lineages of SARS-CoV-2 due to recurrent mutations.

genomics↗