Biology subjects

Thomson, N.

Publications and source records attributed to Thomson, N..

At least 19 recordsLinked to original sources

bioRxiv2026

Enteroaggregative Escherichia clade I from Nigeria

Escherichia coli, the Escherichia type species, is present in mammalian and avian intestinal microbiota, and includes both commensals and pathogens. Other Escherichia species are understudied because they are less commonly associated with human disease and because of paucity of tools that can correctly delineate them from E. coli. However, other species of this genus including Escherichia albertii and Escherichia fergusonii are repeatedly reported as diarrhoeagenic. We hypothesized that some bacteria fitting the definition of enteroaggregative E. coli (EAEC) belong to species other than E. coli. We used phylogeny to determine the species of 2,818 Escherichia genomes from diarrhoea epidemiology studies in Nigeria. Phylogeny speciation was confirmed using GTDB-tk and ClermonTyping. Virulence genes were detected using ARIBA/Virulencefinder database and multilocus sequence typing performed using the Achtman scheme. Fourteen non-coli Escherichia genomes were identified-- Escherichia clade I ST485 (11), Escherichia ruysiae ST5792 (2) and Escherichia fergusonii ST5636 (1). All the Escherichia clade I ST485 carry EAEC virulence genes aap, aar, astA and air, as well as hlyF, eatA, tsh, traT, and chuA virulence genes. Interestingly, 62% of enteroaggregative Escherichia clade I ST485 genomes listed on Enterobase are from Africa isolates, despite only 3% of genomes overall coming from the continent. Our results suggest that non-coli Escherichia species are infrequently isolated from human stool, but, when they are, they are misidentified as E. coli so that their significance is largely overlooked. Escherichia clade I ST485 is a globally disseminated enteroaggregative Escherichia clade I lineage that is common in Africa. Author SummaryEscherichia clade I are rarely associated with disease and because of the difficulty in differentiating them from Escherichia coli in routine laboratory, they are often misidentified as Escherichia coli leading to the underestimation of their impact on the burden of disease. Additionally, some clones of Escherichia clade I also carry genetic markers that have been used to define Enteroaggregative Escherichia coli (EAEC), a cause of persistent diarrhoea in developing countries and travellers diarrhoea in developed economies. EAEC has also been associated with malnutrition and poor growth among children in developing economies. We here describe clones of Escherichia clade I (ST485) that carries enteroaggregative genes and in some cases, recovered from diarrhoeal cases. We show from genomes deposited on Enterobase and our study, that this clone is globally disseminated, often associated with human infections and often misidentified as Escherichia coli. We also describe other non-coli Escherichia other than Escherichia clade I isolated from humans. We suggest that the Escherichia clade I clone carrying enteroaggregative genes may be described as Enteroaggregative Escherichia clade I.

microbiology↗

bioRxiv2026

A 28-year evolution experiment on Burkholderia pseudomallei survival in nutrient-depleted sterile water

Environmental persistence allows opportunistic pathogens to survive a range of harsh conditions, increasing the likelihood of eventual infection. Burkholderia pseudomallei, the causative agent of melioidosis, can endure long-term nutrient-depletion in the environment, but its adaptive mechanisms remain poorly understood. Here, we investigated the evolutionary trajectory of a clinical B. pseudomallei strain maintained in sterile water since 1994. The strain was inoculated into nine individual tubes at nine initial concentrations (102-1010 CFU/mL) and has remained viable to date. Liquid chromatography-mass spectrometry analysis of the water identified potential carbon sources, including phthalic acid -- a plastic degradation product likely leached from inoculation tubes -- which the strain can metabolise via an intact catabolic operon. Genomic variations accumulated between 1994 and 2022 were characterised using both single-colony and plate-sweep sequencing which provided complementary insights. Across all tubes, we identified 249 single-nucleotide polymorphisms (SNPs), 73 indels, and a large-scale deletion. Cultures from each tube displayed a consistently low mutation rate (3.18 x 10- SNPs per site per year), suggesting that cells entered a dormant or slow-growth state. Of 393 genes with mutations, 193 were independently mutated in more than one tube, particularly those involved in signal transduction, cell wall and membrane biogenesis, and secondary metabolite synthesis. These patterns indicate parallel adaptation to long-term nutrient deprivation through modulation of cell-density-related functions and loss of metabolically costly pathways. Remarkably, B. pseudomallei from this experiment remain viable after nearly three decades, providing a rare natural model for understanding how environmental bacteria endure and adapt in extremely nutrient-depleted conditions.

evolutionary biology↗

bioRxiv2025

Trade-offs between phage resistance and conjugative ability shape the ecological and evolutionary response of a multidrug resistance plasmid to plasmid-dependent phage

Phage therapy is a promising alternative to antibiotics to treat multidrug resistant infections. Plasmid dependent phages (PDPs) are particularly attractive as therapeutics because they can both kill targeted pathogen cells, whilst also potentially preventing the further spread of antibiotic resistance genes encoded by plasmids. However, we lack experimental studies of the ecological and evolutionary response of multidrug resistance plasmids against plasmid dependent phage treatment under ecologically relevant scenarios allowing plasmid conjugation. We experimentally evolved populations of E. coli carrying the multidrug resistance RP4 plasmid with the PRD1 PDP under conditions where conjugation was associated with either strong or weak benefits. When opportunities for conjugation were rare, PRD1 only transiently suppressed the conjugative plasmid population due to the rapid evolution of PRD1 resistant plasmids that lacked conjugative ability. Increasing the ecological opportunity for conjugation enhanced plasmid suppression and delayed the evolution of PRD1 resistant plasmids. PRD1 resistance was associated with reduced conjugative ability, but this trade-off was complex due to the heterogeneous impacts of resistance mutations on pilus production and conjugative ability. Mutations and IS element insertions in conjugation genes caused a wide range of PRD1 resistance phenotypes, ranging from complete resistance (virB4) to partial resistance (trbB, trbL). Bioinformatic analysis of publicly available IncP plasmid sequences showed that truncated variants of VirB4 protein are common in natural populations, suggesting that plasmid-dependent phages are an important selective pressure in microbial communities. Our results demonstrate an evolutionary trade-off between conjugative ability and phage resistance that cannot be easily circumvented by plasmids. Targeting multidrug resistance plasmids with PDPs is likely to drive loss of conjugation limiting the transfer of antibiotic resistance genes in bacterial communities.

evolutionary biology↗

bioRxiv2025

Evaluating a Standard Benchmark for Gene Prioritization: The InheriNext(R) Algorithm's Integration of Genomic and Phenotypic Information

This study presents a comprehensive benchmark analysis of InheriNext(R), a domain-specific, AI-powered tool designed for phenotype-driven pathogenic variant prioritization. For this study, 7,244 whole exome test cases were generated using phenotype and genotype data from Phenopackets, along with pools of variants from healthy individuals to serve as genomic backgrounds. Performance was evaluated across diverse testing scenarios and compared against four established tools. The results show InheriNext(R) achieving a 98.6% sensitivity in identifying pathogenic variants and consistent performance across diverse tests for variant types, phenotype counts, and disease groups--supporting the robustness and adaptability of its methodology. Sharing these benchmarking results and samples is intended to drive progress by assisting clinicians and researchers in evaluating interpretation tools and identifying areas for improvement.

genomics↗

bioRxiv2025

Genomic epidemiology of enteropathogenic Escherichia coli (EPEC) in southwestern Nigeria

BackgroundEnteropathogenic Escherichia coli (EPEC) are etiological agents of diarrhea. We studied the genetic diversity and virulence factors of EPEC in southwestern Nigeria, where this pathotype is rarely characterized. Methodology/ Principal findingsEPEC isolates (n=96) recovered from recent southwestern Nigeria diarrhea case-control studies were whole genome-sequenced using Illumina technology. Genomes were assembled using SPAdes and quality was evaluated using QUAST. Virulencefinder, SeroTypefinder, and Resfinder were used to identify virulence genes, serotypes, and resistance genes, while multilocus sequence typing was done by STtyping. Single nucleotide polymorphisms (SNPs) were called out of whole genome alignment using SNP-sites and a phylogenetic tree was constructed using IQtree. Thirty-nine of the 96 (40.6%) EPEC isolates were from cases of diarrhea. Nine isolates from diarrhea patients and four from healthy controls were typical EPEC, harboring bundle-forming pilus (bfp) genes whilst the rest were atypical EPEC. Fifteen isolates were EPEC-EAEC hybrids. Atypical serotypes O71:H19 (16, 16.6%), O108:H21 (6, 6.3%), O157:H39 (5, 5.2%), and O165:H9 (4, 4.2%) were most prevalent; only 8(8.3%) isolates belonged to classical EPEC serovars. The largest clade comprised ST517 isolates, of O71:H19 and O165:H9 serovars harboring multiple siderophore and serine protease autotransporter genes. An O71:H19 subclade comprised isolates <10 SNPs apart, representing a likely outbreak involving 15 children, four presenting with diarrhea. Conclusion/ SignificanceLikely outbreaks, of typical O119:H6(ST28) and atypical O127:H29(ST7798) were additionally identified. EPEC circulating in southwestern Nigeria are diverse and differ substantially from well-characterized lineages seen previously elsewhere. EPEC carriage and outbreaks could be commonplace but are largely undetected, hence, unreported, and require genomic surveillance for identification.

microbiology↗

bioRxiv2024

Genetic basis for antimicrobial resistance in Escherichia coli isolated from household water in municipal Ibadan, Nigeria

Escherichia coli serves as an indicator of recent faecal contamination in water, signaling the potential presence of enteric pathogens. The public health impact of E. coli in water becomes more significant when strains harbor virulence genes, and may themselves be pathogenic, or antimicrobial resistance genes that can be transferred to pathogens. In this study, we used whole genome sequencing (WGS) to characterize E. coli isolated from household water in municipal Ibadan, Nigeria across two seasons. Antimicrobial susceptibility testing was performed on 97 E. coli isolates, and their genomes were assembled using SPAdes. Multi-Locus Sequence Types (MLST), virulence genes and plasmid replicons were determined using ABRicate. Antimicrobial resistance genes (ARGs) were detected using AMRFinderplus. Phylogroups and serotypes were determined using ClermonTyper and ECTyper, respectively. A phylogenetic tree was built using RAxML. Of the 97 isolates, 39(40.2%) were multidrug resistant and 13(15.9%) possessed diarrheagenic E. coli (DEC) virulence genes. Resistance to individual antibiotics was higher and DEC characteristics more frequent among isolates recovered in the dry season compared to the wet season. Thirty-seven resistance genes belonging to nine antibiotic classes were detected. Majority of the isolates belonged to phylogroup A or B1, 35unique Sequence Types (STs) were detected and there were seven expanded clones of four or more isolates. This study determined that multidrug-resistant E. coli, including DEC, were recovered from household water sources in Ibadan. Some isolates were likely derived from point-sources, highlighting the importance of improved water quality management and sanitation in preventing waterborne disease and antimicrobial resistance transmission. IMPORTANCEContamination of household drinking water sources by disease-causing microorganisms is a serious public health concern common in African settings. Escherichia coli, an indicator of faecal contamination, can also be a reservoir for resistance genes. We have previously reported high frequencies of E. coli contamination of household water in municipal Ibadan. In this study we characterized antimicrobial resistance and virulence genes harboured by contaminating isolates. We found potential diarrhoea-causing E. coli in water which often carried antimicrobial resistance genes, irrespective of whether or not they were disease causing. Resistance gene carriage was more common among isolates recovered in the dry, as compared to the wet season. This was attributable to resistant lineages of E. coli bacteria spreading in the dry season. The work shows the importance of monitoring drinking water in urban African cities like Ibadan and that treating ground water sources may be necessary, particularly in the dry season.

microbiology↗

bioRxiv2024

One Health in Eastern Africa: No barriers for ESBL producing E. coli transmission or independent antimicrobial resistance gene flow across ecological compartments

The One Health paradigm considers the interdependence of human, animal and environmental health. In high-income countries, limited evidence has been found from recent studies to support the importance of a One Health approach to addressing spread of antimicrobial resistance (AMR). Given AMR is a global threat, and we are all interconnected it would be important to know if closer interaction of humans with animals and the environment in low-income present a contrasting picture. We used whole genome sequencing to investigate the genomic diversity and to infer transmission of extended spectrum beta-lactamase producing Escherichia coli (ESBL-Ec) between different ecological niches (humans, animals and the environment). We found high diversity of ESBL-Ec with 172 genomic clusters and 167 sequence types identified from 2,344 genomes. Common ESBL genes, blaCTX-M-15 (67.6%) and blaCTX-M-27 (14.2%) were carried on a complex network of different plasmids, presenting multiple pathways for dissemination and revealing the high force of selection. Using fine-scale genomic clustering across multiple thresholds ranging from 0 to 20 single nucleotide polymorphisms, we found that genomes isolated from humans, animals and the environment formed overlapping clusters, indicating recent ESBL-Ec transmission and co-circulation both within and between ecological compartments. These findings demonstrate that the One Health approach is highly relevant to tackling AMR in low-income settings, and therefore critical to consider if we are to address the rise of AMR globally.

genomics↗

bioRxiv2024

Pre and Post antibiotic epoch: insights into the historical spread of antimicrobial resistance

Plasmids are now the primary vectors of antimicrobial resistance, but our understanding of how human industrialisation of antibiotics influenced this is limited by a paucity of data predating the antibiotic era (PAE). By investigating plasmids from clinically relevant bacteria isolated between 1917 and 1954 and comparing them to modern plasmids, we captured over 100 years of evolution. We show that while all PAE plasmids were devoid of resistance genes and most never acquired them, a small minority evolved to drive the global spread of resistance to first-line and last-resort antibiotics in Gram-negative bacteria. They have evolved through complex microevolution and fusion events into a distinct group of highly recombinogenic, multi-replicon, self-transmissible plasmids that now pose the highest risk to resistance dissemination, and therefore human health. One Sentence SummaryPre-antibiotic era bacteria reveal the origin and evolution of drug-resistance vectors.

genomics↗

bioRxiv2024

Bright New Resources for Syphilis Research: Genetically Encoded Fluorescent Tags for Treponema pallidum and Sf1Ep Cells

The recently discovered methodologies to cultivate and genetically manipulate Treponema pallidum subsp. pallidum (T. pallidum) have significantly helped syphilis research, allowing the in vitro evaluation of antibiotic efficacy, performance of controlled studies to assess differential treponemal gene expression, and generation of loss-of-function mutants to evaluate the contribution of specific genetic loci to T. pallidum virulence. Building on this progress, we engineered the T. pallidum SS14 strain to express a red-shifted Green Fluorescent Protein (GFP) and Sf1Ep cells to express mCherry and blue fluorescent protein (BFP) for enhanced visualization. These new resources improve microscopy- and cell sorting-based applications for T. pallidum, better capturing the physical interaction between the host and pathogen, among other possibilities. Continued efforts to develop and share new tools and resources are required to help our overall knowledge of T. pallidum biology and syphilis pathogenesis reach that of other bacterial pathogens, including spirochetes. Graphical abstractBy employing genetic engineering, T. pallidum was modified to express GFP, and Sf1Ep cells to express mCherry on the cytoplasmic membrane and BFP in the nucleus. These new resources for syphilis research will facilitate experimental designs to better define the complex interplay between T. pallidum and the host during infection. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/596454v1_ufig1.gif" ALT="Figure 1"> View larger version (114K): org.highwire.dtl.DTLVardef@1cc5bcborg.highwire.dtl.DTLVardef@19e8a12org.highwire.dtl.DTLVardef@17aafdborg.highwire.dtl.DTLVardef@1af6823_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Behavioural Investigations of Psilocybin in Animals 1962-2021: A Scoping Review

Background and AimsPsilocybin is a psychedelic drug that may hold promise for a wide range of human health conditions, yet the identification of therapeutic processes and mechanisms of action remains exploratory. We conducted a scoping review on pre-clinical behavioural investigations of psilocybin in non-human animals to help determine the behavioural effects of psilocybin in non-human animals, to identify studies completed, behavioural tests employed, and what dosing modalities had been studied. MethodsA librarian-conducted literature search was performed using predefined key terms and search criteria and additional searching was conducted by reviewers, using electronic databases, grey literature sources, and reference lists of relevant articles or reviews. The final search updated occurred in October, 2021. Studies were reviewed, screened and selected against an a priori protocol using Covidence software by multiple reviewers with results plotted across the Research Domains Criteria construct. ResultsFrom 4124 records identified by database searching, 260 publications were subjected to full-text review with 77 studies included in this scoping review, published between 1962-2021. The preponderance of studies (n=64) investigated behavioural outcomes in rodents. Only 43 studies (55.8%) reported on housing conditions, and seventeen studies (22.1%) failed to report sample size. All studies reported behavioural outcomes following drug administration, with fifty-one studies (66.2%) using psilocybin, thirty studies (42.9%) psilocin, four studies (5.2%) administering whole mushroom extracts (WME), and a further eight studies investigating both psilocybin and psilocin and one study reporting the effects of both psilocin and WME. One hundred and thirty distinct behavioural investigations using fifty different behavioral paradigms were identified. Few adverse events were reported, and even exceedingly high doses were apparently well tolerated. ConclusionWith seventy-seven publications spanning close to sixty years, there is huge variation in study design and quality. Overall psilocybin presents a unique and strong safety profile with no evidence of biological toxicity, is characterized by unique time and dose-dependent effects, and its pattern of drug action is significantly context and training-sensitive. Data suggest putative effects of psilocybin include acute arousal, dose-dependent sedation, reductions in fear conditioning at low doses, reduced aggression, improved valence, acute disruption of working memory, the rescuing of deficits from chronic stress, and improved learning when combined with repeated environmental exposure after resolution of drug effect.

animal behavior and cognition↗

bioRxiv2023

Household geckos as a potential vector for Salmonella transmission in Malawi

Salmonella was isolated from 23/79 (29.1%) gecko stool samples from households in southern Malawi. Whole genome sequencing of 47 isolates revealed 27 Salmonella serovars spanning two subspecies. Our results demonstrate that geckos play an important role in the carriage and potentially, transmission of Salmonella within households.

ecology↗

bioRxiv2022

High-throughput transposon mutagenesis in the family Enterobacteriaceae reveals core essential genes and rapid turnover of essentiality

The Enterobacteriaceae are a scientifically and medically important clade of bacteria, containing the gut commensal and model organism Escherichia coli, as well as several major human pathogens including multiple serovars of Salmonella enterica and Klebsiella pneumoniae. Essential gene sets have been determined for several members of the Enterobacteriaceae, with the E. coli Keio single-gene deletion library often regarded as a gold standard for gene essentiality studies. However, it remains unclear how gene essentiality varies between related strains and species. To investigate this, we have assembled a collection of thirteen sequenced high-density transposon mutant libraries from five genera within the Enterobacteriaceae. We first benchmark a number of gene essentiality prediction approaches, investigate the effects of transposon density on essentiality prediction, and identify biases in transposon insertion sequencing data. Based on these investigations we develop a new classifier for gene essentiality. Using this new classifier, we define a core essential genome in the Enterobacteriaceae of 201 universally essential genes, and reconstruct an ancestral essential gene set of 296 genes. Despite the presence of a large cohort of variably essential genes, surprisingly we find an absence of evidence for genus-specific essential genes. A clear example of this sporadic essentiality is given by the set of genes regulating the {sigma}E extracytoplasmic stress response, which appears to have independently become essential multiple times in the Enterobacteriaceae. Finally, we compare our essential gene sets to the natural experiment of gene loss in obligate insect endosymbionts that have emerged from within the Enterobacteriaceae. This isolates a remarkably small set of genes absolutely required for survival, and uncovers several instances of essential stress responses masked by redundancy in free-living bacteria.

microbiology↗

bioRxiv2022

The phylogenomic landscape of the genus Serratia

The genus Serratia has been studied for over a century and includes clinically-important and diverse environmental members. Despite this, there is a paucity of genomic information across the genus and a robust whole genome-based phylogenetic framework is lacking. Here, we have assembled and analysed a representative set of 664 genomes from across the genus, including 215 historic isolates originally used in defining the genus. Phylogenomic analysis of the genus reveals a clearly-defined population structure which displays deep divisions and aligns with ecological niche, as well as striking congruence between historical biochemical phenotyping data and contemporary genomics data. We show that Serratia is a diverse genus which displays striking plasticity and ability to adapt to its environment, including a highly-varied portfolio of plasmids, and provide evidence of different patterns of gene flow across the genus. This work provides an essential platform for understanding the emergence of clinical and other lineages of Serratia.

microbiology↗

bioRxiv2021

Genomic characteristics of recently recognized Vibrio cholerae El Tor lineages associated with cholera in Bangladesh, 1991-2017

Comparative genomic analysis of Vibrio cholerae El Tor associated with endemic cholera in Asia revealed two distinct lineages, one dominant in Bangladesh and the other in India. An in depth whole genome study of V. cholerae El Tor clinical strains isolated during endemic cholera in Bangladesh (1991 - 2017) included reference genome sequence data obtained online. Core genome phylogeny established using single nucleotide polymorphisms (SNPs) showed V. cholerae El Tor strains comprised two lineages, BD-1 and BD-2, which, according to Bayesian phylodynamic analysis, originated from paraphyletic group BD-0 around 1981. BD-1 and BD-2 lineages overlapped temporally but were negatively associated as causative agents of cholera 2004-2017. Genome wide association study (GWAS) revealed 140 SNPs and 31 indels, resulting in gene alleles unique to BD-1 and BD-2. Regression analysis of root to tip distance and year of isolation indicated early BD-0 strains at the base, whereas BD-1 and BD-2 subsequently emerged and progressed by accumulating SNPs. Pangenome analysis provided evidence of gene acquisition by both BD-1 and BD-2, of which six crucial proteins of known function were predominant in BD-2. BD-1 and BD-2 diverged and have distinctively different genomic traits, namely heterogeneity in VSP-2, VPI-1, mobile elements, toxin encoding elements, and total gene abundance. In addition, the observed phage-inducible chromosomal island-like element (PLE1), and SXT ICE elements (ICETET) in BD-2 presumably provided a fitness advantage for the lineage to outcompete BD-1 as the etiological agent of the endemic cholera in Bangladesh, with implications for global cholera epidemiology. ImportanceCholera is a global disease with specific reference to the Bay of Bengal Ganges Delta where Vibrio cholerae O1 El Tor, causative agent of the disease showed two circulating lineages, one dominant in Bangladesh and the other in India. Results of in-depth genomic study of V. cholerae associated with endemic cholera during the past 27 years (1991 - 2017) indicate emergence and succession of the two lineages, BD-1 and BD-2, arising from a common ancestral paraphylatic group, BD-0, comprising the early strains and short-term evolution of the bacterium in Bangladesh. Among the two V. cholerae lineages, BD-2 supersedes BD-1 and is predominant in the most recent endemic cholera in Bangladesh. The BD-2 lineage contained significantly more SNPs and indels, and showed richness in gene abundance, including antimicrobial resistance genes, gene cassettes, and PLE to fight against bacteriophage infection, acquired over time. These findings have important epidemic implications at a global scale.

genomics↗

bioRxiv2021

The consequences of reciprocally exchanging the genomic sites of Integration Host Factor (IHF) subunit production for subunit stoichiometry and bacterial physiology in Salmonella enterica serovar Typhimurium

Integration host factor (IHF) is a heterodimeric nucleoid-associated protein that plays roles in bacterial nucleoid architecture and genome-wide gene regulation. The ihfA and ihfB genes encode the subunits and are located 350 kilobase pairs apart, in the Right replichore of the Salmonella chromosome. IHF is composed of one IhfA and one IhfB subunit. Despite this 1:1 stoichiometry, mass spectrometry revealed that IhfB is produced in 2-fold excess over IhfA. We re-engineered Salmonella to exchange reciprocally the protein-coding regions of ihfA and ihfB, such that each relocated protein-encoding region was driven by the expression signals of the others gene. Mass spectrometry showed that in this rewired strain, IhfA is produced in excess over IhfB, correlating with enhanced stability of the hybrid ihfB-ihfA mRNA that was expressed from the ihfB promoter. Nevertheless, the rewired strain grew at a similar rate to the wild type, had identical cell morphology, and was similar in competitive fitness. However, compared to the wild type, it was less motile, had growth-phase-specific reductions in SPI-1 and SPI-2 gene expression and was engulfed at a higher rate by RAW macrophage. Our data show that while exchanging the physical locations of its ihf genes and the rewiring of their regulatory circuitry are well tolerated in Salmonella, genes involved in the production of type 3 secretion systems exhibit dysregulation accompanied by altered phenotypes. IMPACT STATEMENTIntegration Host Factor (IHF) is an abundant nucleoid-associated protein that organises DNA architecturally, influencing gene expression globally in Salmonella and other bacteria. IHF is composed of two related, non-identical, subunits, produced by genes that are 350 kilobase pairs apart. Each ihf gene has unique expression controls and is embedded in a complex genetic network that supports mRNA translation. Given that the subunits are thought to be required in a 1:1 ratio to form functional IHF, we were surprised by this physical and regulatory separation. We rewired the Salmonella genome so that each subunit was produced using the others regulatory signals and gene location. This revealed a high degree of tolerance to the effects of this rewiring. However, we discovered that bacterial motility was disrupted, as was the expression of virulence genes that have been acquired by horizontal gene transfer. Proteomic analysis using mass spectroscopy (MS) showed the extent of the alterations to cell composition. Our MS data also demonstrated that the subunits of IHF are not produced in a 1:1 ratio in either the wild type or the rewired strain. We discuss this finding in terms of the ability of each subunit to stabilise its partner. DATA SUMMARYO_LIWhole genome sequence data for strain OrfSwapihfA-ihfB are available from the European Nucleotide Archive with accession number ERS4653309. C_LIO_LIData from mass spectrometry analyses are available via ProteomeXchange with identifier PXD027465 (login: reviewer_pxd027465@ebi.ac.uk and password: GVeNIUB2). C_LIO_LIAll supporting data have been provided in the article or through supplementary data files. C_LI RepositoriesWhole genome sequence data for strain OrfSwapihfA-ihfB are available from the European Nucleotide Archive with accession number ERS4653309. Data from mass spectrometry analyses are available via ProteomeXchange with identifier PXD027465 (login: reviewer_pxd027465@ebi.ac.uk and password: GVeNIUB2).

microbiology↗

bioRxiv2021

Inhibitory concentrations of ciprofloxacin induce an adaptive response promoting the intracellular survival of Salmonella Typhimurium

Antimicrobial resistance (AMR) is a pressing global health crisis, which has been fuelled by the sustained use of certain classes of antimicrobials, including fluoroquinolones. While the genetic mutations responsible for decreased fluoroquinolone (ciprofloxacin) susceptibility are known, the implications of ciprofloxacin exposure on bacterial growth, survival, and interactions with host cells are not well described. Aiming to understand the influence of inhibitory concentrations of ciprofloxacin in vitro, we subjected three clinical isolates of S. Typhimurium to differing concentrations of ciprofloxacin, dependent on their minimum inhibitory concentrations (MIC), and assessed the impact on bacterial growth, morphology, and transcription. We further investigated the differential morphology and transcription that occurred following ciprofloxacin exposure and measured the ability of ciprofloxacin-treated bacteria to invade and replicate in host cells. We found that ciprofloxacin-exposed S. Typhimurium are able to recover from inhibitory concentrations of ciprofloxacin, and that the drug induces specific morphological and transcriptional signatures associated with the bacterial SOS response, DNA repair, and intracellular survival. In addition, ciprofloxacin-treated S. Typhimurium have increased capacity for intracellular replication in comparison to untreated organisms. These data suggest that S. Typhimurium undergoes an adaptive response under ciprofloxacin perturbation that promotes cellular survival, a consequence that may justify more measured use of ciprofloxacin for Salmonella infections. The combination of multiple experimental approaches provides new insights into the collateral effects that ciprofloxacin and other antimicrobials have on invasive bacterial pathogens. ImportanceAntimicrobial resistance is a critical concern in global health. In particular, there is rising resistance to fluoroquinolones, such as ciprofloxacin, a first-line antimicrobial for many Gram-negative pathogens. We investigated the adaptive response of clinical isolates of Salmonella Typhimurium to ciprofloxacin, finding that the bacteria adapt in short timespans to high concentrations of ciprofloxacin in a way that promotes intracellular survival during early infection. Importantly, by studying three clinically relevant isolates, we were able to show that individual isolates respond differently to ciprofloxacin, and for each isolate, there was a heterogeneous response under ciprofloxacin treatment. The heterogeneity that arises from ciprofloxacin exposure may drive survival and proliferation of Salmonella during treatment and lead to drug resistance.

microbiology↗

bioRxiv2020

A comprehensive and high-quality collection of E. coli genomes and their genes

Escherichia coli is a highly diverse organism which includes a range of commensal and pathogenic variants found across a range of niches and worldwide. In addition to causing severe intestinal and extraintestinal disease, E. coli is considered a priority pathogen due to high levels of observed drug resistance. The diversity in the E. coli population is driven by high genome plasticity and a very large gene pool. All these have made E. coli one of the most well-studied organisms, as well as a commonly used laboratory strain. Today, there are thousands of sequenced E. coli genomes stored in public databases. While data is widely available, accessing the information in order to perform analyses can still be a challenge. Collecting relevant available data requires accessing different sources, where data may be stored in a range of formats, and often requires further manipulation, and processing to apply various analyses and extract useful information. In this study, we collated and intensely curated a collection of over 10,000 E. coli and Shigella genomes to provide a single, uniform, high-quality dataset. Shigella were included as they are considered specialised pathovars of E. coli. We provide these data in a number of easily accessible formats which can be used as the foundation for future studies addressing the biological differences between E. coli lineages and the distribution and flow of genes in the E. coli population at a high resolution. The analysis we present emphasises our lack of understanding of the true diversity of the E. coli species, and the biased nature of our current understanding of the genetic diversity of such a key pathogen. Author NotesAll supporting data have been provided within the article or through supplementary data files. All supporting code is provided in the git repository https://github.com/ghoresh11/ecoli_genome_collection. Significance as a BioResource to the communityAs of today, there are more than 140,000 E. coli genomes available on public databases. While data is widely available, collating the data and extracting meaningful information from it often requires multiple steps, computational resources and expert knowledge. Here, we collate a high quality and comprehensive set of over 10,000 E. coli genomes, isolated from human hosts, into a set of manageable files that offer an accessible and usable snapshot of the currently available genome data, linked to a minimal data quality standard. The data provided includes a detailed synopsis of the main lineages present, including their antimicrobial and virulence profiles, their complete gene content, and all the associated metadata for each genome. This includes a database which enables the user to compare newly sequenced isolates against the assembled genomes. Additionally, we provide a searchable index which allows the user to query any DNA sequence against the assemblies of the collection. This collection paves the path for many future studies, including those investigating the differences between E. coli lineages, following the evolution of different genes in the E. coli pan-genome and exploring the dynamics of horizontal gene transfer in this important organism. Data SummaryO_LIThe complete aggregated metadata of 10,146 high quality genomes isolated from human hosts (doi.org/10.6084/m9.figshare.12514883, File F1). C_LIO_LIA PopPUNK database which can be used to query any genome and examine its context relative to this collection (Deposited to doi.org/10.6084/m9.figshare.12650834). C_LIO_LIA BIGSI index of all the genomes which can be used to easily and quickly query the genomes for any DNA sequence of 61 bp or longer (Deposited to doi.org/10.6084/m9.figshare.12666497). C_LIO_LIDescription and complete profiling the 50 largest lineages which represent the majority of publicly available human-isolated E. coli genomes (doi.org/10.6084/m9.figshare.12514883, File F2). Phylogenetic trees of representative genomes of these lineages, presented in this manuscript, are also provided (doi.org/10.6084/m9.figshare.12514883, Files tree_500.nwk and tree_50.nwk). C_LIO_LIThe complete pan-genome of the 50 largest lineages which includes: O_LIA FASTA file containing a single representative sequence of each gene of the gene pool (doi.org/10.6084/m9.figshare.12514883, File F3). C_LIO_LIComplete gene presence-absence across all isolates (doi.org/10.6084/m9.figshare.12514883, File F4). C_LIO_LIThe frequency of each gene within each of the lineages (doi.org/10.6084/m9.figshare.12514883, File F5). C_LIO_LIThe representative sequences from each lineage for all the genes (doi.org/10.6084/m9.figshare.12514883, File F6). C_LI C_LI

genomics↗

bioRxiv2020

Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia

Increasing contact between humans and non-human primates provides an opportunity for the transfer of potential pathogens or antimicrobial resistance between host species. We have investigated genomic diversity, and antimicrobial resistance in Escherichia coli isolates from four species of non-human primate in the Gambia: Papio papio (n=22), Chlorocebus sabaeus (n=14), Piliocolobus badius (n=6) and Erythrocebus patas (n=1). We performed Illumina whole-genome sequencing on 101 isolates from 43 stools, followed by nanopore long-read sequencing on eleven isolates. We identified 43 sequence types (STs) by the Achtman scheme (ten of which are novel), spanning five of the eight known phylogroups of E. coli. The majority of simian isolates belong to phylogroup B2--characterised by strains that cause human extraintestinal infections--and encode factors associated with extraintestinal disease. A subset of the B2 strains (ST73, ST681 and ST127) carry the pks genomic island, which encodes colibactin, a genotoxin associated with colorectal cancer. We found little antimicrobial resistance and only one example of multi-drug resistance among the simian isolates. Hierarchical clustering showed that simian isolates from ST442 and ST349 are closely related to isolates recovered from human clinical cases (differences in 50 and seven alleles respectively), suggesting recent exchange between the two host species. Conversely, simian isolates from ST73, ST681 and ST127 were distinct from human isolates, while five simian isolates belong to unique core-genome ST complexes--indicating novel diversity specific to the primate niche. Our results are of public health importance, considering the increasing contact between humans and wild non-human primates. Impact statementLittle is known about the population structure, virulence potential and the burden of antimicrobial resistance among Escherichia coli from wild non-human primates, despite increased exposure to humans through the fragmentation of natural habitats. Previous studies, primarily involving captive animals, have highlighted the potential for bacterial exchange between non-human primates and humans living nearby, including strains associated with intestinal pathology. Using multiple-colony sampling and whole-genome sequencing, we investigated the strain distribution and population structure of E. coli from wild non-human primates from the Gambia. Our results indicate that these monkeys harbour strains that can cause extraintestinal infections in humans. We document the transmission of virulent E. coli strains between monkeys of the same species sharing a common habitat and evidence of recent interaction between strains from humans and wild non-human primates. Also, we present complete genome assemblies for five novel sequence types of E. coli. Author notesAll supporting data, code and protocols have been provided within the article or through supplementary data files. Nine supplementary figures and six supplementary files are available with the online version of this article. AbbreviationsExPEC, Extraintestinal pathogenic Escherichia coli; ST, Sequence type; AMR, Antimicrobial resistance; MLST, Multi-locus sequence typing; VFDB, Virulence factors database; SNP, single nucleotide polymorphism; SPRI, Solid phase reversible immobilisation. Data summaryThe raw sequences and polished assemblies from this study are available in the National Center for Biotechnology Information (NCBI) Short Read Archive, under the BioProject accession number PRJNA604701. The full list and characteristics of these strains and other reference strains used in the analyses are presented in Table 1 and Supplementary Files 1-4 (available with the online version of this article).

genomics↗