Ben Pascoe

University of Oxford | OX · Big Data Institute

Campylobacter is the leading bacterial cause of gastroenteritis worldwide and its incidence is especially high in low-and middle-income countries (LMIC). Disease epidemiology in LMICs is different compared to high income countries like the USA or in Europe. Children in LMICs commonly have repeated and chronic infections even in the absence of sympt...

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 clinica...

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 amon...

Campylobacter enterocolitis may lead to post-infection irritable bowel syndrome (PI-IBS) and while some C. jejuni strains are more likely than others to cause human disease, genomic and virulence characteristics promoting PI-IBS development remain uncharacterized. We combined pangenome-wide association studies and phenotypic assays to compare C. je...

Campylobacter is the most common cause of bacterial gastroenteritis worldwide, and diarrhoeal disease is a major cause of child morbidity, growth faltering and mortality in low-and middle-income countries. Despite evidence of high incidence and differences in disease epidemiology, there is limited genomic data from studies in developing countries....

Campylobacter remains the most common cause of bacterial diarrhoeal disease worldwide, with particularly high incidence in low- and middle-income countries (LMICs). Population genomics studies have identified common lineages (sequence types) responsible for human disease and Infection source reservoirs have been identified and analysed in developed...

Helicobacter pylori lives in the human stomach and has a population structure resembling that of its host. However, H. pylori from Europe and the Middle East trace substantially more ancestry from modern African populations than the humans that carry them. Here, we use a collection of Afro-Eurasian H. pylori genomes to show that this African ancest...

Streptococcus suis is a leading cause of bacterial meningitis in SouthEast 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...

Staphylococci are the most common cause of orthopedic device-related infections (ODRIs), with Staphylococcus aureus responsible for a third or more of cases. This prospective clinical and laboratory study investigated the association of genomic and phenotypic variation with treatment outcomes in ODRI isolates. Eighty-six invasive S. aureus isolates...

The results from this study are of importance as they fill a gap in the data available on environmental AMR in South Africa to date. This study was done in parallel with co-investigators focusing on the prevalence of various antimicrobials at the same sites selected in our study, verifying that the sites that are influenced by informal settlements...

Salmonella is a prevalent zoonotic foodborne pathogen. Swine and pork are implicated as important sources of salmonellosis in humans. In Chiang Mai and Lamphun Provinces in northern Thailand, there has been a high prevalence of Salmonella persistence for over a decade. Infection is usually with dominant S. enterica serotypes, including serotypes Ri...

Salmonella is a frequent zoonotic foodborne pathogen, with swine and pork meats the most common source of human infection. In Chiang Mai and Lamphun Province in northern Thailand, there has been a high prevalence of salmonellosis for over a decade. Infection is usually with several dominant S. enterica serotypes, including serotypes Rissen and Mono...

Recombination of short DNA fragments via horizontal gene transfer (HGT) can both introduce beneficial alleles and create disharmony in coadapted genomes (negative epistasis). Owing to a lack of protracted intragenomic co-evolution, negative epistatic costs of HGT into non-core (accessory) bacterial genomes are likely to be minimal. By contrast, for...

Bacterial clades are often ecologically distinct, despite extensive horizontal gene transfer (HGT). How selection works on different parts of bacterial pan‐genomes to drive and maintain the emergence of clades is unclear. Focussing on the three largest clades in the diverse and well‐studied Bacillus cereus sensu lato group, we identified clade‐spec...

Wastewater treatment plants have been highlighted as a potential hotspot for the development and spread of antibiotic resistance. Although antibiotic resistant bacteria in wastewater present a public health threat, it is also possible that these bacteria play an important role in the bioremediation through the metabolism of antibiotics before they...

Streptococcus suis (S. suis) belongs to the critical streptococcal swine pathogens affecting financial losses in pig production globally and being concerned as a zoonotic bacterial that causes a severe invasive disease emerging in pigs and humans. Serotype 2 is considered the major serotype and is the most pathogenic S. suis obtained from human cas...

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 amon...

Background and aim: Respiratory tract infections (RTIs) are common in the community. There is some evidence that microbial biomarkers can be used to identify individuals most susceptible to RTI acquisition. We investigated the feasibility of recruiting healthy adults to collect at-home self-reported socio-demographic data and biological samples, sa...

Determining the composition of bacterial communities beyond the level of a genus or species is challenging because of the considerable overlap between genomes representing close relatives. Here, we present the mSWEEP pipeline for identifying and estimating the relative sequence abundances of bacterial lineages from plate sweeps of enrichment cultur...

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 an...

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 coun...

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 coun...

Pseudomonas aeruginosa (PA) is an opportunistic pathogen that causes diverse human infections including chronic airway infection in patients with cystic fibrosis (CF). Comparing the genomes of CF and non-CF PA isolates has great potential to identify the genetic basis of pathogenicity. To gain a deeper understanding of PA adaptation in CF airways,...

Salmonella spp. is an important foodborne pathogen associated with consumption of contaminated food, especially food of livestock origin. Antimicrobial resistance (AMR) in Salmonella has been reported globally and increasing AMR in food production is a major public health issue worldwide. The objective of this study was to describe the genetic rela...

All genomes mutate but the consequences of the resulting deleterious mutational load are poorly understood. Helicobacter pylori lives in the human stomach, has a higher mutation rate than most bacteria and has accompanied anatomically modern humans in migrations including the out-of-Africa expansion more than 50,000 years ago. H. pylori from East A...

Background The surrounding areas of the middle Mekong basin, particularly along the border between Thailand and Lao People’s Democratic Republic (Lao PDR), are high-risk areas for many livestock-associated foodborne illnesses, especially salmonellosis. This study aimed to determine the prevalence and characteristics of Salmonella spp. contamination...

Although molecular genetic approaches have greatly increased our understanding of the evolution and spread of antibiotic resistance genes, there are fewer studies on the dynamics of antibiotic-bacterial (A-B) interactions, especially with respect to stereochemistry. Addressing this knowledge gap requires an interdisciplinary synthesis, and the deve...

A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-22238-5

The lateral transfer of genes among bacterial strains and species has opposing effects, conferring potentially beneficial adaptations whilst introducing disharmony in coadapted genomes. The prevailing outcome will depend upon the fitness cost of disrupting established epistatic interactions between genes. It is challenging to understand this in nat...

Salmonella is one of the major foodborne pathogens, often as the result of pork consumption. Currently, with the situation of antimicrobial resistance, organic farming has been suggested as an alternative for healthier options. However, there is little evidence to support this. In this study, we investigated the occurrence of Salmonella circulating...

Chickens are the most common birds on Earth and colibacillosis is among the most common diseases affecting them. This major threat to animal welfare and safe sustainable food production is difficult to combat because the etiological agent, avian pathogenic Escherichia coli (APEC), emerges from ubiquitous commensal gut bacteria, with no single virul...

We investigated the prevalence of Salmonella circulating in local organic pig farms in northern Thailand and typed isolated clones to better understand the population structure of the underlying Salmonella contamination. In total, 112 samples from 11 organic pig farms were processed from October to December 2018. Salmonella were detected in 9 farms...

Salmonella spp. is an important foodborne pathogen associated with consumption of contaminated food, especially livestock products. Antimicrobial resistance (AMR) in Salmonella has been reported globally and increasing AMR in food production is a major public health issue worldwide. The objective of this study was to describe the genetic relatednes...

One of the emerging conundrums of Campylobacter food-borne illness is the bacterial ability to survive stressful environmental conditions. We evaluated the heterogeneity among 90 C. jejuni and 21 C. coli isolates from different sources in Egypt with respect to biofilm formation capabilities (under microaerobic and aerobic atmosphere) and resistance...

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 an...

Campylobacter is among the most common causes of gastroenteritis worldwide. Campylobacter jejuni and Campylobacter coli are the most common species causing human-disease. DNA-sequence-based methods for strain characterization have focussed largely on C. jejuni , responsible for 80-90% of infections, meaning that C. coli epidemiology has lagged behi...

Helicobacter pylori is a common component of the human stomach microbiota, possibly dating back to the speciation of Homo sapiens. A history of pathogen evolution in allopatry has led to the development of genetically distinct H. pylori subpopulations, associated with different human populations, and more recent admixture among H. pylori subpopulat...

Background: Monophasic Salmonella Typhimurium or S. enterica 1,4,[5],12:i:- is among the top five serotypes reported in Thailand. In this study, nineteen monophasic S. Typhimurium from the pig production chain in Chiang Mai and Lamphun provinces during 2011–2014 were sequenced and compared to a globally disseminated clone. Isolates were probed in s...

Campylobacter is the leading bacterial cause of gastroenteritis worldwide and its incidence is especially high in low- and middle-income countries (LMIC). Disease epidemiology in LMICs is different compared to high income countries like the USA or in Europe. Children in LMICs commonly have repeated and chronic infections even in the absence of symp...

Modern agriculture has dramatically changed the distribution of animal species on Earth. Changes to host ecology have a major impact on the microbiota, potentially increasing the risk of zoonotic pathogens being transmitted to humans, but the impact of intensive livestock production on host-associated bacteria has rarely been studied. Here, we use...

Campylobacter is the leading bacterial cause of gastroenteritis worldwide and its incidence is especially high in low- and middle-income countries (LMIC). Disease epidemiology in LMICs is different compared to high income countries like the USA or in Europe. Children in LMICs commonly have repeated and chronic infections even in the absence of symp...

Objectives Linezolid is one of the last resort antibiotics effectively used in the treatment of infections caused by multidrug-resistant Gram-positive bacteria. Recent outbreaks of Linezolid resistance have been the great concern world wide, while many countries have not experienced it. In this work, we aimed to evaluate the existence of linezolid...

Determining the composition of bacterial communities beyond the level of a genus or species is challenging because of the considerable overlap between genomes representing close relatives. Here, we present the mSWEEP pipeline for identifying and estimating the relative sequence abundances of bacterial lineages from plate sweeps of enrichment cultur...

The only known elements encoding enterotoxins in coagulase-negative staphylococci (CoNS) are composite Staphylococcus epidermidis pathogenicity islands (SePIs), including SePI and SeCI regions. We investigated 1545 Staphylococcus spp. genomes using whole genome MLST, and queried them for genes of staphylococcal enterotoxin family and for 29 ORFs id...

The use of antimicrobials in human and veterinary medicine has coincided with a rise in antimicrobial resistance (AMR) in the food‐borne pathogens Campylobacter jejuni and Campylobacter coli. Faecal contamination from the main reservoir hosts (livestock, especially poultry) is the principal route of human infection but little is known about the spr...

Reference and type strains of well-known bacteria have been a cornerstone of microbiology research for decades. The sharing of well-characterized isolates among laboratories has run in parallel with research efforts and enhanced the reproducibility of experiments, leading to a wealth of knowledge about trait variation in different species and the u...

Background: Diarrhoeal disease remains a major cause of child morbidity, growth faltering and mortality in low and middle income countries (LMICs), with Campylobacter among the most common causes. Previous work has identified source reservoirs in developed countries (e.g. contaminated poultry or unpasteurised milk), however little is known about th...

Motivation Protein structure predictions, that combine theoretical chemistry and bioinformatics, are an increasingly important technique in biotechnology and biomedical research, for example in the design of novel enzymes and drugs. Here, we present a new ensemble bi-layered machine learning architecture, that directly builds on ten existing pipeli...

Salmonella enterica subsp. enterica serotype Rissen is the predominant serotype found in Thai pork production and can be transmitted to humans through contamination of the food chain. This study was conducted to investigate the genetic relationships between serovar Rissen isolates from all levels of the pork production chain and evaluate the abilit...

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 underlyin...

Protocol for DNA extraction from Campylobacter isolates using the QIAGEN QIAamp DNA Mini Kit (QIAGEN, Crawley, UK).

Extended-spectrum β-lactamase (ESBL)-producing bacteria causing clinical infections are often also multidrug-resistant (MDR; resistance to ≥3 antimicrobial drug classes), therefore treatment options may be limited. High carriage rates of these potentially zoonotic bacteria have been found in livestock and companion animals. Therefore, people workin...

Some of the most common infectious diseases are caused by bacteria that naturally colonise humans asymptomatically. Combating these opportunistic pathogens requires an understanding of the traits that differentiate infecting strains from harmless relatives. Staphylococcus epidermidis is carried asymptomatically on the skin and mucous membranes of v...

Campylobacter is the leading cause of bacterial enteritis in the developed world, and infections with the organism are largely sporadic in nature. Links between sporadic cases have not been established, with the majority of infections thought to be caused by genetically distinct isolates. Using a read-mapping approach, 158 clinical isolates collect...

Background: Helicobacter pylori are stomach-dwelling bacteria that are present in about 50% of the global population. Infection is asymptomatic in most cases, but it has been associated with gastritis, gastric ulcers and gastric cancer. Epidemiological evidence shows that progression to cancer depends upon the host and pathogen factors, but questi...