Publications
99 results found
Horsfield ST, Croucher NJ, Lees JA, 2023, Accurate and fast graph-based pangenome annotation and clustering with ggCaller
<jats:title>Abstract</jats:title><jats:p>Bacterial genomes differ in both gene content and sequence mutations, which can cause important clinical phenotypic differences such as vaccine escape or antimicrobial resistance. To identify and quantify important variants, all genes within a population must be predicted, functionally annotated and clustered, representing the ‘pangenome’. Despite the volume of genome data available, gene prediction and annotation are currently conducted in isolation on individual genomes, which is computationally inefficient and frequently inconsistent across genomes. Here, we introduce the open-source software graph-gene-caller (ggCaller;<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/samhorsfield96/ggCaller">https://github.com/samhorsfield96/ggCaller</jats:ext-link>). ggCaller combines gene prediction, functional annotation and clustering into a single step using population-wide de Bruijn Graphs, removing redundancy in gene annotation, and resulting in more accurate gene predictions and orthologue clustering. We applied ggCaller to simulated and real-world bacterial genome datasets, comparing it to current state-of-the-art tools. ggCaller is ~50x faster with equivalent or greater accuracy, particularly in datasets with complex sources of error, such as assembly contamination or fragmentation. ggCaller is also an important extension to bacterial genome-wide association studies, enabling querying of annotated graphs for functional analyses. We highlight this application by functionally annotating DNA sequences with significant associations to tetracycline and macrolide resistance in<jats:italic>Streptococcus pneumoniae</jats:italic>, identifying key resistance determinants that were missed when using only a single reference genome. ggCaller is a novel bacterial genome analysis tool with applications
Croucher N, Kwun MJ, Alexandru I, et al., 2022, Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA, Genome Medicine: medicine in the post-genomic era, Vol: 14, ISSN: 1756-994X
Background:The respiratory pathogen Streptococcus pneumoniae (the pneumococcus) is a genetically diverse bacterium associated with over 101 immunologically distinct polysaccharide capsules (serotypes). Polysaccharide conjugate vaccines (PCVs) have successfully eliminated multiple targeted serotypes, yet the mucoid serotype 3 has persisted despite its inclusion in PCV13. This capsule type is predominantly associated with a single globally disseminated strain, GPSC12 (clonal complex 180).Methods:A genomic epidemiology study combined previous surveillance datasets of serotype 3 pneumococci to analyse the population structure, dynamics, and differences in rates of diversification within GPSC12 during the period of PCV introductions. Transcriptomic analyses, whole genome sequencing, mutagenesis, and electron microscopy were used to characterise the phenotypic impact of loci hypothesised to affect this strain’s evolution.Results:GPSC12 was split into clades by a genomic analysis. Clade I, the most common, rarely underwent transformation, but was typically infected with the prophage ϕOXC141. Prior to the introduction of PCV13, this clade’s composition shifted towards a ϕOXC141-negative subpopulation in a systematically sampled UK collection. In the post-PCV13 era, more rapidly recombining non-Clade I isolates, also ϕOXC141-negative, have risen in prevalence. The low in vitro transformation efficiency of a Clade I isolate could not be fully explained by the ~100-fold reduction attributable to the serotype 3 capsule. Accordingly, prophage ϕOXC141 was found to modify csRNA3, a non-coding RNA that inhibits the induction of transformation. This alteration was identified in ~30% of all pneumococci and was particularly common in the unusually clonal serotype 1 GPSC2 strain. RNA-seq and quantitative reverse transcriptase PCR experiments using a genetically tractable pneumococcus demonstrated the altered csRNA3 was more effective at inhibiting production of the competen
Tonkin-Hill G, Ling C, Chaguza C, et al., 2022, Pneumococcal within-host diversity during colonization, transmission and treatment, NATURE MICROBIOLOGY, Vol: 7, Pages: 1791-+, ISSN: 2058-5276
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- Citations: 2
Mallawaarachchi S, Tonkin-Hill G, Croucher NJ, et al., 2022, Genome-wide association, prediction and heritability in bacteria with application to Streptococcus pneumoniae, NAR Genomics and Bioinformatics, Vol: 4, Pages: 1-11, ISSN: 2631-9268
Whole-genome sequencing has facilitated genome-wide analyses of association, prediction and heritability in many organisms. However, such analyses in bacteria are still in their infancy, being limited by difficulties including genome plasticity and strong population structure. Here we propose a suite of methods including linear mixed models, elastic net and LD-score regression, adapted to bacterial traits using innovations such as frequency-based allele coding, both insertion/deletion and nucleotide testing and heritability partitioning. We compare and validate our methods against the current state-of-art using simulations, and analyse three phenotypes of the major human pathogen Streptococcus pneumoniae, including the first analyses of minimum inhibitory concentrations (MIC) for penicillin and ceftriaxone. We show that the MIC traits are highly heritable with high prediction accuracy, explained by many genetic associations under good population structure control. In ceftriaxone MIC, this is surprising because none of the isolates are resistant as per the inhibition zone criteria. We estimate that half of the heritability of penicillin MIC is explained by a known drug-resistance region, which also contributes a quarter of the ceftriaxone MIC heritability. For the within-host carriage duration phenotype, no associations were observed, but the moderate heritability and prediction accuracy indicate a moderately polygenic trait.
Chaguza C, Tonkin-Hill G, Lo SW, et al., 2022, RCandy: an R package for visualizing homologous recombinations in bacterial genomes, BIOINFORMATICS, Vol: 38, Pages: 1450-1451, ISSN: 1367-4803
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- Citations: 1
Lochen A, Truscott JE, Croucher NJ, 2022, Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates, PLOS COMPUTATIONAL BIOLOGY, Vol: 18, ISSN: 1553-734X
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- Citations: 3
Wan Y, Mills E, Leung RCY, et al., 2021, Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in escherichia coli from the UK, Microbial Genomics, Vol: 7, Pages: 1-19, ISSN: 2057-5858
Antimicrobial resistance in enteric or urinary Escherichia coli is a risk factor for invasive E. coli infections. Due to widespread trimethoprim resistance amongst urinary E. coli and increased bacteraemia incidence, a national recommendation to prescribe nitrofurantoin for uncomplicated urinary tract infection was made in 2014. Nitrofurantoin resistance is reported in <6% urinary E. coli isolates in the UK, however, mechanisms underpinning nitrofurantoin resistance in these isolates remain unknown. This study aimed to identify the genetic basis of nitrofurantoin resistance in urinary E. coli isolates collected from north west London and then elucidate resistance-associated genetic alterations in available UK E. coli genomes. As a result, an algorithm was developed to predict nitrofurantoin susceptibility.Deleterious mutations and gene-inactivating insertion sequences in chromosomal nitroreductase genes nfsA and/or nfsB were identified in genomes of nine nitrofurantoin-resistant urinary E. coli isolates, as well as all further 11 E. coli isolates that were experimentally validated to be nitrofurantoin resistant. Eight categories of allelic changes in nfsA, nfsB, and the associated gene ribE were detected in 12,412 E. coli genomes from the UK. Evolutionary analysis of these three genes revealed homoplasic mutations and explained the previously reported order of stepwise mutations. The mobile gene complex oqxAB, which is associated with reduced nitrofurantoin susceptibility, was identified in only one of the 12,412 genomes.In conclusion, mutations and insertion sequences in nfsA and nfsB were leading causes of nitrofurantoin resistance in UK E. coli. As nitrofurantoin exposure increases in human populations, the prevalence of nitrofurantoin resistance in carriage E. coli isolates and those from urinary and bloodstream infections should be monitored.
Løchen A, Truscott JE, Croucher NJ, 2021, Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates
<jats:title>Abstract</jats:title><jats:p>The disease burden attributable to opportunistic pathogens depends on their prevalence in asymptomatic colonisation and the rate at which they progress to cause symptomatic disease. Increases in infections caused by commensals can result from the emergence of “hyperinvasive” strains. Such pathogens can be identified through quantifying progression rates using matched samples of typed microbes from disease cases and healthy carriers. This study describes Bayesian models for analysing such datasets, implemented in an RStan package (<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/nickjcroucher/progressionEstimation">https://github.com/nickjcroucher/progressionEstimation</jats:ext-link>). The models converged on stable fits that accurately reproduced observations from meta-analyses of <jats:italic>Streptococcus pneumoniae</jats:italic> datasets. The estimates of invasiveness, the progression rate from carriage to invasive disease, in cases per carrier per year correlated strongly with the dimensionless values from meta-analysis of odds ratios when sample sizes were large. At smaller sample sizes, the Bayesian models produced more informative estimates. This identified historically rare but high-risk <jats:italic>S. pneumoniae</jats:italic> serotypes that could be problematic following vaccine-associated disruption of the bacterial population. The package allows for hypothesis testing through model comparisons with Bayes factors. Application to datasets in which strain and serotype information were available for <jats:italic>S. pneumoniae</jats:italic> found significant evidence for within-strain and within-serotype variation in invasiveness. The heterogeneous geographical distribution of these genotypes is therefore likely to contribute to differences in the impac
D'Aeth JC, van der Linden MPG, McGee L, et al., 2021, The role of interspecies recombinations in the evolution of antibiotic-resistant pneumococci, eLife, Vol: 10, ISSN: 2050-084X
The evolutionary histories of the antibiotic-resistant Streptococcus pneumoniae lineages PMEN3 and PMEN9 were reconstructed using global collections of genomes. In PMEN3, one resistant clade spread worldwide, and underwent 25 serotype switches, enabling evasion of vaccine-induced immunity. In PMEN9, only 9 switches were detected, and multiple resistant lineages emerged independently and circulated locally. In Germany, PMEN9’s expansion correlated significantly with the macrolide:penicillin consumption ratio. These isolates were penicillin sensitive but macrolide resistant, through a homologous recombination that integrated Tn1207.1 into a competence gene, preventing further diversification via transformation. Analysis of a species-wide dataset found 183 acquisitions of macrolide resistance, and multiple gains of the tetracycline-resistant transposon Tn916, through homologous recombination, often originating in other streptococcal species. Consequently, antibiotic selection preserves atypical recom- bination events that cause sequence divergence and structural variation throughout the S. pneumoniae chromosome. These events reveal the genetic exchanges between species normally counter-selected until perturbed by clinical interventions.
Gladstone RA, McNally A, Pontinen AK, et al., 2021, Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002-17: a nationwide, longitudinal, microbial population genomic study, The Lancet Microbe, Vol: 2, Pages: E331-E341, ISSN: 2666-5247
BackgroundThe clonal diversity underpinning trends in multidrug resistant Escherichia coli causing bloodstream infections remains uncertain. We aimed to determine the contribution of individual clones to resistance over time, using large-scale genomics-based molecular epidemiology.MethodsThis was a longitudinal, E coli population, genomic, cohort study that sampled isolates from 22 512 E coli bloodstream infections included in the Norwegian surveillance programme on resistant microbes (NORM) from 2002 to 2017. 15 of 22 laboratories were able to share their isolates, and the first 22·5% of isolates from each year were requested. We used whole genome sequencing to infer the population structure (PopPUNK), and we investigated the clade composition of the dominant multidrug resistant clonal complex (CC)131 using genetic markers previously reported for sequence type (ST)131, effective population size (BEAST), and presence of determinants of antimicrobial resistance (ARIBA, PointFinder, and ResFinder databases) over time. We compared these features between the 2002–10 and 2011–17 time periods. We also compared our results with those of a longitudinal study from the UK done between 2001 and 2011.FindingsOf the 3500 isolates requested from the participating laboratories, 3397 (97·1%) were received, of which 3254 (95·8%) were successfully sequenced and included in the analysis. A significant increase in the number of multidrug resistant CC131 isolates from 71 (5·6%) of 1277 in 2002–10 to 207 (10·5%) of 1977 in 2011–17 (p<0·0001), was the largest clonal expansion. CC131 was the most common clone in extended-spectrum β-lactamase (ESBL)-positive isolates (75 [58·6%] of 128) and fluoroquinolone non-susceptible isolates (148 [39·2%] of 378). Within CC131, clade A increased in prevalence from 2002, whereas the global multidrug resistant clade C2 was not observed until 2007. Multiple de-n
Croucher N, Harrow G, Lees J, et al., 2021, Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures, The ISME Journal: multidisciplinary journal of microbial ecology, Vol: 15, Pages: 1523-1538, ISSN: 1751-7362
Streptococcus pneumoniae can be divided into many strains, each a distinct set of isolates sharing similar core and accessorygenomes, which co-circulate within the same hosts. Previous analyses suggested the short-term vaccine-associated dynamicsof S. pneumoniae strains may be mediated through multi-locus negative frequency-dependent selection (NFDS), whichmaintains accessory loci at equilibrium frequencies. Long-term simulations demonstrated NFDS stabilised clonally-evolvingmulti-strain populations through preventing the loss of variation through drift, based on polymorphism frequencies,pairwise genetic distances and phylogenies. However, allowing symmetrical recombination between isolates evolving undermulti-locus NFDS generated unstructured populations of diverse genotypes. Replication of the observed data improvedwhen multi-locus NFDS was combined with recombination that was instead asymmetrical, favouring deletion of accessoryloci over insertion. This combination separated populations into strains through outbreeding depression, resulting fromrecombinants with reduced accessory genomes having lower fitness than their parental genotypes. Although simplisticmodelling of recombination likely limited these simulations’ ability to maintain some properties of genomic data asaccurately as those lacking recombination, the combination of asymmetrical recombination and multi-locus NFDS couldrestore multi-strain population structures from randomised initial populations. As many bacteria inhibit insertions into theirchromosomes, this combination may commonly underlie the co-existence of strains within a niche.
Lochen A, Croucher N, Anderson R, 2020, Divergent serotype replacement trends and increasing diversity in pneumococcal disease in high income settings reduce the benefit of expanding vaccine valency, Scientific Reports, Vol: 10, ISSN: 2045-2322
Streptococcus pneumoniae is a significant cause of otitis media, pneumonia, and meningitis. Only seven of the approximately 100 serotypes were initially included in the pneumococcal conjugate vaccine (PCV) in 2000 before it was expanded in subsequent years. Although the invasive pneumococcal disease (IPD) incidence due to vaccine serotypes (VT) has declined, partial replacement by non-vaccine serotypes (NVT) was observed following widespread vaccine uptake. We conducted a trend analysis assembling all the available evidence for PCV impact on European, North American and Australian national IPD. Significant effectiveness against VT IPD in infants was observed, although the impact on national IPD incidence varied internationally due to serotype replacement. Currently, NVT serotypes 8, 9N, 15A and 23B are increasing in the countries assessed, although a variety of other NVTs are affecting each country and age group. Despite these common emerging serotypes, there has not been a dominant IPD serotype post-vaccination as there was pre-vaccination (serotype 14) or post-PCV7 (serotype 19A), suggesting that future vaccines with additional serotypes will be less effective at targeting and reducing IPD in global populations than previous PCVs. The rise of diverse NVTs in all settings’ top-ranked IPD-causing serotypes emphasizes the urgent need for surveillance data on serotype distribution and serotype-specific invasiveness post-vaccination to facilitate decision making concerning both expanding current vaccination programmes and increasing vaccine valency.
Azarian T, Martinez PP, Arnold BJ, et al., 2020, Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae, PLOS BIOLOGY, Vol: 18, ISSN: 1544-9173
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- Citations: 8
Zamudio R, Haigh RD, Ralph JD, et al., 2020, Lineage-specific evolution and gene flow inListeria monocytogenesare independent of bacteriophages, ENVIRONMENTAL MICROBIOLOGY, Vol: 22, Pages: 5058-5072, ISSN: 1462-2912
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- Citations: 10
Harrow GL, Lees JA, Hanage WP, et al., 2020, Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures
<jats:title>Abstract</jats:title><jats:p><jats:italic>Streptococcus pneumoniae</jats:italic>can be split into multiple strains, each with a characteristic combination of core and accessory genome variation, able to co-circulate and compete within the same hosts. Previous analyses of epidemiological datasets suggested the short-term vaccine-associated dynamics of<jats:italic>S. pneumoniae</jats:italic>strains may be mediated through multi-locus negative frequency-dependent selection (NFDS), acting to maintain accessory loci at equilibrium frequencies. To test whether this model could explain how such multi-strain populations were generated, it was modified to incorporate recombination. The outputs of simulations featuring symmetrical recombination were compared with genomic data on locus frequencies and distributions between genotypes, pairwise genetic distances and tree shape. These demonstrated NFDS prevented the loss of variation through neutral drift, but generated unstructured populations of diverse isolates. Making recombination asymmetrical, favouring deletion of accessory loci over insertion, alongside multi-locus NFDS significantly improved the fit to genomic data. In a population at equilibrium, structuring into multiple strains was stable due to outbreeding depression, resulting from recombinants with reduced accessory genomes having lower fitness than their parental genotypes. As many bacteria inhibit the integration of insertions into their chromosomes, this combination of asymmetrical recombination and multi-locus NFDS may underlie the co-existence of strains within a single ecological niche.</jats:p>
Lehtinen S, Chewapreecha C, Lees J, et al., 2020, Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae, SCIENCE ADVANCES, Vol: 6, ISSN: 2375-2548
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- Citations: 9
Gladstone RA, Lo SW, Goater R, et al., 2020, Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates, MICROBIAL GENOMICS, Vol: 6, ISSN: 2057-5858
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- Citations: 21
Colijn C, Corander J, Croucher NJ, 2020, Designing ecologically optimized pneumococcal vaccines using population genomics, Nature Microbiology, Vol: 5, Pages: 473-485, ISSN: 2058-5276
Streptococcus pneumoniae (the pneumococcus) is a common nasopharyngeal commensal that can cause invasive pneumococcal disease (IPD). Each component of current protein–polysaccharide conjugate vaccines (PCVs) generally induces immunity specific to one of the approximately 100 pneumococcal serotypes, and typically eliminates it from carriage and IPD through herd immunity. Overall carriage rates remain stable owing to replacement by non-PCV serotypes. Consequently, the net change in IPD incidence is determined by the relative invasiveness of the pre- and post-PCV-carried pneumococcal populations. In the present study, we identified PCVs expected to minimize the post-vaccine IPD burden by applying Bayesian optimization to an ecological model of serotype replacement that integrated epidemiological and genomic data. We compared optimal formulations for reducing infant-only or population-wide IPD, and identified potential benefits to including non-conserved pneumococcal carrier proteins. Vaccines were also devised to minimize IPD resistant to antibiotic treatment, despite the ecological model assuming that resistance levels in the carried population would be preserved. We found that expanding infant-administered PCV valency is likely to result in diminishing returns, and that complementary pairs of infant- and adult-administered vaccines could be a superior strategy. PCV performance was highly dependent on the circulating pneumococcal population, further highlighting the advantages of a diversity of anti-pneumococcal vaccination strategies.
Pensar J, Puranen S, Arnold B, et al., 2019, Genome-wide epistasis and co-selection study using mutual information, NUCLEIC ACIDS RESEARCH, Vol: 47, ISSN: 0305-1048
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- Citations: 17
Dewe TCM, D'Aetht JC, Croucher NJ, 2019, Genomic epidemiology of penicillin-non-susceptible Streptococcus pneumoniae, Microbial Genomics, Vol: 5, Pages: 1-8, ISSN: 2057-5858
Penicillin-non-susceptible Streptococcus pneumoniae (PNSP) were first detected in the 1960s, and are now common worldwide, predominantly through the international spread of a limited number of strains. Extant PNSP are characterized by mosaic pbp2x, pbp2b and pbp1a genes generated by interspecies recombinations, with the extent of these alterations determining the range and concentrations of β-lactams to which the genotype is non-susceptible. The complexity of the genetics underlying these phenotypes has been the subject of both molecular microbiology and genome-wide association and epistasis analyses. Such studies can aid our understanding of PNSP evolution and help improve the already highly-performing bioinformatic methods capable of identifying PNSP from genomic surveillance data.
Furi L, Crawford LA, Rangel-Pineros G, et al., 2019, Methylation Warfare: Interaction of Pneumococcal Bacteriophages with Their Host, JOURNAL OF BACTERIOLOGY, Vol: 201, ISSN: 0021-9193
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- Citations: 15
Kwun M, Oggioni MR, Bentley SD, et al., 2019, Synergistic activity of mobile genetic element defences in Streptococcus pneumoniae, Genes, Vol: 10, ISSN: 2073-4425
A diverse set of mobile genetic elements (MGEs) transmit between Streptococcus pneumoniae cells, but many isolates remain uninfected. The best-characterised defences against horizontal transmission of MGEs are restriction-modification systems (RMSs), of which there are two phase-variable examples in S. pneumoniae. Additionally, the transformation machinery has been proposed to limit vertical transmission of chromosomally integrated MGEs. This work describes how these mechanisms can act in concert. Experimental data demonstrate RMS phase variation occurs at a sub-maximal rate. Simulations suggest this may be optimal if MGEs are sometimes vertically inherited, as it reduces the probability that an infected cell will switch between RMS variants while the MGE is invading the population, and thereby undermine the restriction barrier. Such vertically inherited MGEs can be deleted by transformation. The lack of between-strain transformation hotspots at known prophage att sites suggests transformation cannot remove an MGE from a strain in which it is fixed. However, simulations confirmed that transformation was nevertheless effective at preventing the spread of MGEs into a previously uninfected cell population, if a recombination barrier existed between co-colonising strains. Further simulations combining these effects of phase variable RMSs and transformation found they synergistically inhibited MGEs spreading, through limiting both vertical and horizontal transmission.
Nasher F, Kwun MJ, Croucher NJ, et al., 2019, Peptide Occurring in Enterobacteriaceae Triggers Streptococcus pneumoniae Cell Death, FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY, Vol: 9, ISSN: 2235-2988
De Ste Croix M, Chen Y, Vacca I, et al., 2019, Recombination of the phase variable spnIII locus is independent of all known pneumococcal site-specific recombinases, Journal of Bacteriology, Vol: 201, ISSN: 0021-9193
Streptococcus pneumoniae is one of the world's leading bacterial pathogens, causing pneumonia, septicaemia and meningitis. In recent years it has been shown that genetic rearrangements in a type I restriction-modification system (SpnIII) can impact colony morphology and gene expression. By generating a large panel of mutant strains, we have confirmed a previously reported result that the CreX (also known as IvrR and PsrA) recombinase found within the locus is not essential for hsdS inversions. In addition, mutants of homologous recombination pathways also undergo hsdS inversions. In this work we have shown that these genetic rearrangements, which result in different patterns of genome methylation, occur across a wide variety of serotypes and sequence types including two strains (a 19F and a 6B strain) naturally lacking CreX. Our gene expression analysis, by RNAseq, confirm that the level of creX expression is impacted by these genomic rearrangements. In addition, we have shown that the frequency of hsdS recombination is temperature dependent. Most importantly we have demonstrated that the other known pneumococcal site-specific recombinases XerD, XerS and SPD_0921 are not involved in spnIII recombination, suggesting a currently unknown mechanism is responsible for the recombination of these phase variable type I systems.ImportanceStreptococcus pneumoniae is a leading cause of pneumonia, septicaemia and meningitis. The discovery that genetic rearrangements in a type I restriction modification locus can impact gene regulation and colony morphology have led to a new understanding of how this pathogen switches from harmless coloniser to invasive pathogen. These rearrangements, which alter the DNA specificity of the type I restriction modification enzyme, occur across many different pneumococcal serotypes and sequence types, and in the absence of all known pneumococcal site-specific recombinases. This finding suggests that this is a truly global mechanism of pneumococcal
Lehtinen S, Chewapreecha C, Lees J, et al., 2019, Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in <i>Streptococcus pneumoniae</i>
<jats:p>The extent to which evolution is constrained by the rate at which horizontal gene transfer (HGT) allows DNA to move between genetic lineages is an open question, which we address in the context of antibiotic resistance in <jats:italic>Streptococcus pneumoniae</jats:italic>. We analyze microbiological, genomic and epidemiological data from the largest-to-date sequenced pneumococcal carriage study in 955 infants from a refugee camp on the Thailand-Myanmar border. Using a unified framework, we simultaneously test prior hypotheses on rates of HGT and a key evolutionary covariate (duration of carriage) as determinants of resistance frequencies. We conclude that in this setting, there is only weak evidence for the rate of HGT playing a role in the evolutionary dynamics of resistance. Instead, observed resistance frequencies are best explained as the outcome of selection acting on a pool of variants, irrespective of the rate at which resistance determinants move between genetic lineages.</jats:p>
Lees JA, Ferwerda B, Kremer PHC, et al., 2019, Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis, NATURE COMMUNICATIONS, Vol: 10, ISSN: 2041-1723
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- Citations: 41
Lehtinen S, Blanquart F, Lipsitch M, et al., 2019, On the evolutionary ecology of multidrug resistance in bacteria, PLoS Pathogens, Vol: 15, ISSN: 1553-7366
Resistance against different antibiotics appears on the same bacterial strains more oftenthan expected by chance, leading to high frequencies of multidrug resistance. There are multiple explanations for this observation, but these tend to be specific to subsets of antibioticsand/or bacterial species, whereas the trend is pervasive. Here, we consider the questionin terms of strain ecology: explaining why resistance to different antibiotics is often seen onthe same strain requires an understanding of the competition between strains with differentresistance profiles. This work builds on models originally proposed to explain another aspectof strain competition: the stable coexistence of antibiotic sensitivity and resistance observedin a number of bacterial species. We first identify a partial structural similarity in these models: either strain or host population structure stratifies the pathogen population into evolutionarily independent sub-populations and introduces variation in the fitness effect of resistancebetween these sub-populations, thus creating niches for sensitivity and resistance. We thengeneralise this unified underlying model to multidrug resistance and show that models withthis structure predict high levels of association between resistance to different drugs andhigh multidrug resistance frequencies. We test predictions from this model in six bacterialdatasets and find them to be qualitatively consistent with observed trends. The higher thanexpected frequencies of multidrug resistance are often interpreted as evidence that thesestrains are out-competing strains with lower resistance multiplicity. Our work provides analternative explanation that is compatible with long-term stability in resistance frequencies.
Gladstone RA, Lo SW, Lees JA, et al., 2019, International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact, EBioMedicine, Vol: 43, Pages: 338-346, ISSN: 2352-3964
BackgroundPneumococcal conjugate vaccines have reduced the incidence of invasive pneumococcal disease, caused by vaccine serotypes, but non-vaccine-serotypes remain a concern. We used whole genome sequencing to study pneumococcal serotype, antibiotic resistance and invasiveness, in the context of genetic background.MethodsOur dataset of 13,454 genomes, combined with four published genomic datasets, represented Africa (40%), Asia (25%), Europe (19%), North America (12%), and South America (5%). These 20,027 pneumococcal genomes were clustered into lineages using PopPUNK, and named Global Pneumococcal Sequence Clusters (GPSCs). From our dataset, we additionally derived serotype and sequence type, and predicted antibiotic sensitivity. We then measured invasiveness using odds ratios that relating prevalence in invasive pneumococcal disease to carriage.FindingsThe combined collections (n = 20,027) were clustered into 621 GPSCs. Thirty-five GPSCs observed in our dataset were represented by >100 isolates, and subsequently classed as dominant-GPSCs. In 22/35 (63%) of dominant-GPSCs both non-vaccine serotypes and vaccine serotypes were observed in the years up until, and including, the first year of pneumococcal conjugate vaccine introduction.Penicillin and multidrug resistance were higher (p < .05) in a subset dominant-GPSCs (14/35, 9/35 respectively), and resistance to an increasing number of antibiotic classes was associated with increased recombination (R2 = 0.27 p < .0001). In 28/35 dominant-GPSCs, the country of isolation was a significant predictor (p < .05) of its antibiogram (mean misclassification error 0.28, SD ± 0.13).We detected increased invasiveness of six genetic backgrounds, when compared to other genetic backgrounds expressing the same serotype. Up to 1.6-fold changes in invasiveness odds ratio were observed.InterpretationWe define GPSCs that can be assigned to any pneumococcal genomic dataset, to aid international comparisons. Existing n
McNally A, Kallonen T, Connor C, et al., 2019, Diversification of colonization factors in a multidrug-resistant escherichia coli lineage evolving under negative frequency-dependent selection, mBio, Vol: 10, ISSN: 2150-7511
Escherichia coli is a major cause of bloodstream and urinary tract infections globally. The wide dissemination of multidrug-resistant (MDR) strains of extraintestinal pathogenic E. coli (ExPEC) poses a rapidly increasing public health burden due to narrowed treatment options and increased risk of failure to clear an infection. Here, we present a detailed population genomic analysis of the ExPEC ST131 clone, in which we seek explanations for its success as an emerging pathogenic strain beyond the acquisition of antimicrobial resistance (AMR) genes. We show evidence for evolution toward separate ecological niches for the main clades of ST131 and differential evolution of anaerobic metabolism, key colonization, and virulence factors. We further demonstrate that negative frequency-dependent selection acting across accessory loci is a major mechanism that has shaped the population evolution of this pathogen.IMPORTANCE Infections with multidrug-resistant (MDR) strains of Escherichia coli are a significant global public health concern. To combat these pathogens, we need a deeper understanding of how they evolved from their background populations. By understanding the processes that underpin their emergence, we can design new strategies to limit evolution of new clones and combat existing clones. By combining population genomics with modelling approaches, we show that dominant MDR clones of E. coli are under the influence of negative frequency-dependent selection, preventing them from rising to fixation in a population. Furthermore, we show that this selection acts on genes involved in anaerobic metabolism, suggesting that this key trait, and the ability to colonize human intestinal tracts, is a key step in the evolution of MDR clones of E. coli.
Mitchell PK, Azarian T, Croucher NJ, et al., 2019, Population genomics of pneumococcal carriage in Massachusetts children following introduction of PCV-13, Microbial Genomics, Vol: 5, ISSN: 2057-5858
The 13-valent pneumococcal conjugate vaccine (PCV-13) was introduced in the United States in 2010. Using a large paediatric carriage sample collected from shortly after the introduction of PCV-7 to several years after the introduction of PCV-13, we investigate alterations in the composition of the pneumococcal population following the introduction of PCV-13, evaluating the extent to which the post-vaccination non-vaccine type (NVT) population mirrors that from prior to vaccine introduction and the effect of PCV-13 on vaccine type lineages. Draft genome assemblies from 736 newly sequenced and 616 previously published pneumococcal carriage isolates from children in Massachusetts between 2001 and 2014 were analysed. Isolates were classified into one of 22 sequence clusters (SCs) on the basis of their core genome sequence. We calculated the SC diversity for each sampling period as the probability that any two randomly drawn isolates from that period belong to different SCs. The sampling period immediately after the introduction of PCV-13 (2011) was found to have higher diversity than preceding (2007) or subsequent (2014) sampling periods {Simpson’s D 2007: 0.915 [95 % confidence interval (CI) 0.901, 0.929]; 2011: 0.935 [0.927, 0.942]; 2014 : 0.912 [0.901, 0.923]}. Amongst NVT isolates, we found the distribution of SCs in 2011 to be significantly different from that in 2007 or 2014 (Fisher’s exact test P=0.018, 0.0078), but did not find a difference comparing 2007 to 2014 (Fisher’s exact test P=0.24), indicating greater similarity between samples separated by a longer time period than between samples from closer time periods. We also found changes in the accessory gene content of the NVT population between 2007 and 2011 to have been reduced by 2014. Amongst the new serotypes targeted by PCV-13, four were present in our sample. The proportion of our sample composed of PCV-13-only vaccine serotypes 19A, 6C and 7F decreased between 2007 and 2014, but no
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