Biology subjects

Calland, J. K.

Publications and source records attributed to Calland, J. K..

9 recordsLinked to original sources

bioRxiv2025

Co-evolution between colibactin production and resistance is linked to clonal expansions in Escherichia coli

Specific strains of Escherichia coli employ the polyketide synthase island to produce a metabolite called colibactin that is implicated in colorectal tumorigenesis via its genotoxic effect on human DNA. However, the damage to host DNA is essentially collateral from ecological competition during bacterial colonisation, where colibactin is used to displace other gut bacteria. Despite intensive recent research on colibactin and its involvement in tumorigenesis, the evolutionary dynamics related to its production remain poorly characterised. We map evolution of colibactin production in E. coli using a large collection of high-resolution genomes and show that its introduction via a mobile element has induced multiple plasmid-mediated acquisitions of previously unrecognised colibactin immunity genes in non-producing multi-drug resistant lineages. Our study suggests that in E. coli, multi-drug resistance is incompatible with colibactin production due to the unbearable combined fitness costs, supported by colibactin-producing phenotypes remaining susceptible to most classes of antibiotics and thriving in regions with low antimicrobial usage. Consequently, resistant lineages circulating in these regions are under selective pressure to acquire colibactin immunity to compete with the endemic colibactin-producing bacteria during colonisation. Conversely, high antimicrobial usage selects for a colibactin susceptible antimicrobial resistant phenotype as it drives the colibactin-producing E. coli towards extinction. Such a duality of evolutionary strategies to become endemic in a host population structured by varying ecological pressures may hold more generally across bacterial species colonizing the human gut.

microbiology↗

bioRxiv2023

Genomic tailoring of autogenous poultry vaccines to reduce Campylobacter from farm to fork

Campylobacter is a leading cause of food-borne gastroenteritis worldwide, linked to the consumption of contaminated poultry meat. Targeting this pathogen at source, vaccines for poultry can provide short term caecal reductions in Campylobacter numbers in the chicken intestine. However, this approach is unlikely to reduce Campylobacter in the food chain or human incidence. This is likely as vaccines typically target only a subset of the high strain diversity circulating among chicken flocks and rapid evolution diminishes vaccine efficacy over time. To address this, we used a genomic approach to develop a whole-cell autogenous vaccine targeting isolates harbouring genes linked to survival outside of the host. We hyper-immunised a whole major UK breeder farm to passively target offspring colonisation using maternally-derived antibody. Monitoring progeny, broiler flocks revealed a near-complete shift in the post-vaccination Campylobacter population with a [~]50% reduction in isolates harbouring extra-intestinal survival genes and a significant reduction of Campylobacter cells surviving on the surface of meat. Based on these findings, we developed a logistic regression model that predicted that vaccine efficacy could be extended to target 46% of a population of clinically relevant strains. Immuno-manipulation of poultry microbiomes towards less harmful commensal isolates by competitive exclusion, has major potential for reducing pathogens in the food production chain.

microbiology↗

bioRxiv2023

Detecting co-selection through excess linkage disequilibrium in bacterial genomes

Population genomics has revolutionised our ability to study bacterial evolution by enabling data-driven discovery of the genetic architecture of trait variation. Genome-wide association studies (GWAS) have more recently become accompanied by genome-wide epistasis and co-selection (GWES) analysis, which offers a phenotype-free approach to generating hypotheses about selective processes that simultaneously impact multiple loci across the genome. However, existing GWES methods only consider associations between distant pairs of loci within the genome due to the strong impact of linkage-disequilibrium (LD) over short distances. Based on the general functional organisation of genomes it is nevertheless expected that the majority of co-selection and epistasis will act within relatively short genomic proximity, on co-variation occurring within genes and their promoter regions, and within operons. Here we introduce LDWeaver, which enables an exhaustive GWES across both short- and long-range LD, to disentangle likely neutral co-variation from selection. We demonstrate the ability of LDWeaver to efficiently generate hypotheses about co-selection using large genomic surveys of multiple major human bacterial pathogen species and validate several findings using functional annotation and phenotypic measurements. Our approach will facilitate the study of bacterial evolution in the light of rapidly expanding population genomic data.

bioinformatics↗

bioRxiv2021

Local accessory gene sharing drives lineage-specific acquisition of antimicrobial resistance in Egyptian Campylobacter spp.

Campylobacter is the most common cause of bacterial gastroenteritis worldwide and diarrheal disease is a major cause of child morbidity, growth faltering and mortality in low- and middle-income countries (LMICs). Despite evidence of high incidence and differences in disease epidemiology, there is limited genomic data from studies in developing countries. In this study, we characterised the genetic diversity and accessory genome content of a collection of Campylobacter isolates from Cairo, Egypt. In total, 112 Campylobacter isolates were collected from broiler carcasses (n=31), milk and dairy products (n=24) and patients (n=57) suffering from gastroenteritis. Among the most common sequence types (STs) we identified were the globally disseminated, host generalist ST-21 clonal complex (CC21) and the poultry specialist CC206, CC464 and CC48. Notably, CC45 and the cattle-specialist CC42 were under-represented with a total absence of CC61. Comparative genomics were used to quantify core and accessory genome sharing among isolates from the same country compared to sharing between countries. Lineage-specific accessory genome sharing was significantly higher among isolates from the same country, particularly CC21 which demonstrated greater local geographical clustering. In contrast, no geographic clustering was noted in either the core or accessory genomes of the CC828, suggesting a highly admixed population. A greater proportion of C. coli isolates were multidrug resistant (MDR) compared to C. jejuni. This is a significant public health concern as MDR food chain pathogens are difficult to treat and often pose increased mortality risk demanding enhanced prevention strategies in the Egyptian market to combat such a threat. Impact statementCampylobacter is the leading bacterial cause of gastroenteritis worldwide and despite high incidence in low- and middle-income countries, where infection can be fatal, culture-based isolation is rare and the genotypes responsible for disease are seldom identified. Here, we sequenced the genomes of a collection of isolates from clinical cases and potential infection reservoirs from Cairo in Egypt and characterised their genetic diversity. Among the most common genotypes we identified were globally disseminated lineages implicated in human disease worldwide, including the host generalist ST-21 clonal complex (CC21) and the poultry specialist genotypes CC206, CC464 and CC48. Notably however, some other globally common genotypes were under-represented or entirely absent from our collection, including those from cattle-specialist lineages, CC42 and CC61. By focussing on specific lineages, we demonstrate that there is increased accessory genome sharing in specific clonal complexes. This increased local sharing of genes may have contributed to a greater proportion of C. coli isolates possessing antimicrobial resistance determinants that suggest they could be multidrug resistant (MDR). This is a significant public health concern as MDR food chain pathogens are difficult to treat and often pose increased mortality risk demanding enhanced prevention strategies. Data summaryShort read data are available on the NCBI Sequence Read Archive, associated with BioProject PRJNA576513 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA576513). Assembled genomes, supplementary material and additional analysis files are available from FigShare: https://doi.org/10.6084/m9.figshare.9956597. Phylogenetic trees can be visualised and manipulated on Microreact for C. jejuni (https://next.microreact.org/project/Cjejuni_Egypt) and C. coli (https://next.microreact.org/project/Ccoli_Egypt) separately, or combined Cairo and Oxford data with additional PopPunk network clustering (https://microreact.org/project/Campy-Egypt).

microbiology↗

bioRxiv2021

Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter

Horizontal gene transfer (HGT) can allow traits that have evolved in one bacterial species to transfer to another. This has potential to rapidly promote new adaptive trajectories such as zoonotic transfer or antimicrobial resistance. However, for this to occur requires gaps to align in barriers to recombination within a given time frame. Chief among these barriers is the physical separation of species with distinct ecologies in separate niches. Within the genus Campylobacter there are species with divergent ecologies, from rarely isolated single host specialists to multi-host generalist species that are among the most common global causes of human bacterial gastroenteritis. Here, by characterising these contrasting ecologies, we can quantify HGT among sympatric and allopatric species in natural populations. Analysing recipient and donor population ancestry among genomes from 30 Campylobacter species we show that cohabitation in the same host can lead to a 6-fold increase in HGT between species. This accounts for up to 30% of all SNPs within a given species and identifies highly recombinogenic genes with functions including host adaptation and antimicrobial resistance. As described in some animal and plant species, ecological factors are a major evolutionary force for speciation in bacteria and changes to the host landscape can promote partial convergence of distinct species through HGT.

microbiology↗

bioRxiv2021

Non-serotype 2 isolates from healthy pigs are a potential zoonotic reservoir of Streptococcus suis genetic diversity and antimicrobial resistance

Streptococcus suis is a leading cause of bacterial meningitis in SE Asia, with frequent zoonotic transfer to humans associated with close contact with pigs. A small number of invasive lineages are responsible for endemic infection in the swine industry causing considerable global economic losses. A lack of surveillance and a rising trend in clinical treatment failure has raised concerns of growing antimicrobial resistance (AMR) among invasive S. suis. The source-sink dynamics between healthy and disease isolates is poorly understood and, in this study, we sample and sequence a collection of isolates predominantly from healthy pigs in Chiang Mai province, Northern Thailand. Pangenome comparisons with a selection of invasive serotype 2 isolates identified increased genetic diversity and more frequent AMR carriage in isolates from healthy pigs. Multiple antimicrobial resistance genes were identified conferring resistance to aminoglycosides, lincosamides, tetracycline and macrolides. All isolates were non-susceptinle to three or more different antimicrobial classes, and 75% of non-serotype 2 isolates were non-susceptible to 6 or more classes (compared to 37.5% of serotype 2 isolates). Antimicrobial resistance genes were found on integrative and conjugative elements (ICE) previously observed in other species, suggesting mobile gene pool which can be accessed by invasive disease isolates. Significance statementThe zoonotic pathogen Streptococcus suis causes respiratory disease in pigs and is among the most common causative agents of human clinical bacterial meningitis in SE Asia. We collected isolates from farmed healthy pigs in Northern Thailand, representing a source population from which invasive isolates have recently emerged - linked to the pork production industry. Pangenome characterisation of the isolates revealed a reservoir of genetic diversity and antimicrobial resistance suggesting that One Health approaches may be beneficial in tackling the increase in antimicrobial resistance.

microbiology↗

bioRxiv2021

Cross-species evolutionary rewiring in the enteric bacterium Campylobacter

Significance StatementGenetic exchange among bacteria shapes the microbial world. From the acquisition of antimicrobial resistance genes to fundamental questions about the nature of bacterial species, this powerful evolutionary force has preoccupied scientists for decades. However, the mixing of genes between species rests on a paradox. On one hand, promoting adaptation by conferring novel functionality, on the other potentially introducing disharmonious gene combinations (negative epistasis) that will be selected against. Taking an interdisciplinary approach to analyse natural populations of the enteric bacteria Campylobacter, an ideal example of long-range admixture, we demonstrate that genes can independently transfer across species boundaries and rejoin in epistasis in a recipient genome. This challenges conventional ideas and highlights the possibility of single step evolution by saltation. AbstractRecombination of short DNA fragments via horizontal gene transfer (HGT) can both introduce beneficial alleles and create genomic disharmony through negative epistasis. For non-core (accessory) genes, the negative epistatic cost is likely to be minimal because the incoming genes have not co-evolved with the recipient genome. By contrast, for the core genome, interspecific recombination is expected to be rare because disruptive allelic replacement is likely to introduce negative epistasis. Why then is homologous recombination common in the core of bacterial genomes? To understand this enigma we take advantage of an exceptional model system, the common enteric pathogens Campylobacter jejuni and Campylobacter coli, that are known for very high magnitude interspecies gene flow in the core genome. As expected, HGT does indeed disrupt co-adapted allele pairings (negative epistasis). However, multiple HGT events enable recovery of the genomes co-adaption between introgressing alleles, even in core metabolism genes (e.g., formate dehydrogenase). These findings demonstrate that, even for complex traits, genetic coalitions can be decoupled, transferred and independently reinstated in a new genetic background - facilitating transition between fitness peaks. In this example, the two-step recombinational process is associated with C. coli that are adapted to the agricultural niche.

microbiology↗

bioRxiv2020

Quantifying bacterial evolution in the wild: a birthday problem for Campylobacter lineages

Measuring molecular evolution in bacteria typically requires estimation of the rate at which nucleotide changes accumulate in strains sampled at different times that share a common ancestor. This approach has been useful for dating ecological and evolutionary events that coincide with the emergence of important lineages, such as outbreak strains and obligate human pathogens. However, in multi-host (niche) transmission scenarios, where the pathogen is essentially an opportunistic environmental organism, sampling is often sporadic and rarely reflects the overall population, particularly when concentrated on clinical isolates. This means that approaches that assume recent common ancestry are not applicable. Here we present a new approach to estimate the molecular clock rate in Campylobacter that draws on the popular probability conundrum known as the birthday problem. Using large genomic datasets and comparative genomic approaches, we use isolate pairs that share recent common ancestry to estimate the rate of nucleotide change for the population. Identifying synonymous and non-synonymous nucleotide changes, both within and outside of recombined regions of the genome, we quantify clock-like diversification to estimate synonymous rates of nucleotide change for the common pathogenic bacteria Campylobacter coli (2.4 x 10-6 s/s/y) and Campylobacter jejuni (3.4 x 10-6 s/s/y). Finally, using estimated total rates of nucleotide change, we infer the number of effective lineages within the sample time-frame - analogous to a shared birthdays - and assess the rate of turnover of lineages in our sample set over short evolutionary timescales. This provides a generalizable approach to calibrating rates in populations of environmental bacteria and shows that multiple lineages are maintained, implying that large-scale clonal sweeps may take hundreds of years or more in these species. Author SummaryGrowth and reproduction in living organisms require DNA replication but this process is error prone. Along with variation introduced by horizontal gene transfer, it can lead to alterations in the nucleotide sequence. These nucleotide changes accumulate over time in successive generations at an approximately constant rate termed the molecular clock. Therefore, if this rate is known, one can estimate the date when two or more lineages diverged. In bacteria, this can be informative for understanding the time-scale of emergence and spread of pathogenic strains. Such analyses are robust when the ancestral population is known, such as for obligate pathogens that only infect humans. However, when the bacterium inhabits multiple hosts or niches it is difficult to infer direct ancestry from one strain to another, reducing the accuracy of molecular clock estimates. Here we focus on one such multi-host organism, Campylobacter, a leading cause of food-borne gastroenteritis. Reconstructing the population history by estimating empirical nucleotide change rates from carefully selected isolate pairs, and evaluating the maintenance of multiple lineages over time, we provide information about strain diversification. Our method is a new addition to the bacterial genomics toolkit that will help in understanding the spread of opportunistic pathogens.

genomics↗

bioRxiv2019

Domestication of Campylobacter jejuni NCTC 11168

Reference and type strains of well-known bacteria have been a cornerstone of microbiology research for decades. The sharing of well-characterised isolates among laboratories has parallelised research efforts and enhanced the reproducibility of experiments, leading to a wealth of knowledge about trait variation in different species and the underlying genetics. Campylobacter jejuni strain NCTC 11168, deposited at the National Collection of Type Cultures in 1977, has been adopted widely as a reference strain by researchers worldwide and was the first Campylobacter for which the complete genome was published (in 2000). In this study, we collected 23 C. jejuni NCTC 11168 reference isolates from laboratories across the UK and compared variation in simple laboratory phenotypes with genetic variation in sequenced genomes. Putatively identical isolates identified previously to have aberrant phenotypes varied by up to 281 SNPs (in 15 genes) compared to the most recent reference strain. Isolates also display considerable phenotype variation in motility, morphology, growth at 37{degrees}C, invasion of chicken and human cell lines and susceptibility to ampicillin. This study provides evidence of ongoing evolutionary change among C. jejuni isolates as they are cultured in different laboratories and highlights the need for careful consideration of genetic variation within laboratory reference strains.\n\nImpact statementIn this paper, we comment on the changing role of laboratory reference strains. While the model organism allows basic comparison within and among laboratories, it is important to remember the effect even small differences in isolate genomes can have on the validity and reproducibility of experimental work. We quantify differences in 23 reference Campylobacter genomes and compare them with observable differences in common laboratory phenotypes.\n\nData summaryShort read data are archived on the NCBI SRA associated with BioProject accession PRJNA517467 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517467).\n\nAll assembled genomes are also available on FigShare (doi: 10.6084/m9.figshare.7849268). Phylogeny visualised on microreact: https://microreact.org/project/NCTC11168.\n\nRepositoriesShort read data are archived on the NCBI SRA repository, associated with BioProject accession PRJNA517467 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517467; Table S1).\n\nThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

microbiology↗