A5056553844- Escherichia coli research studies
- Viral gastroenteritis research and epidemiology
- Salmonella and Campylobacter epidemiology
- Antibiotic Resistance in Bacteria
- Bacteriophages and microbial interactions
- Vibrio bacteria research studies
- Enterobacteriaceae and Cronobacter Research
- Clostridium difficile and Clostridium perfringens research
- Yersinia bacterium, plague, ectoparasites research
- Aquaculture disease management and microbiota
- Zoonotic diseases and public health
- Mycobacterium research and diagnosis
- Listeria monocytogenes in Food Safety
- Parasitic Infections and Diagnostics
- Genomics and Phylogenetic Studies
- Pharmacological Effects of Natural Compounds
- Herpesvirus Infections and Treatments
- Infections and bacterial resistance
- Identification and Quantification in Food
- Plant-based Medicinal Research
- Reproductive tract infections research
- Food Safety and Hygiene
- Cassava research and cyanide
- Vector-borne infectious diseases
- Pharmaceutical and Antibiotic Environmental Impacts
Health Protection Research Unit in Emerging and Zoonotic Infections at University of Liverpool
2022-2025
University of Liverpool
2022-2025
UK Health Security Agency
2022-2024
Roslin Institute
2019-2024
University of Edinburgh
2019-2024
Public Health England
2017-2022
National Institute for Health Research
2021
Shigellosis, also known as bacillary dysentery, is caused by Shigella spp that spread through fecal-oral contact and was traditionally associated with international travel in England. However, sexual transmission of flexneri sonnei among gay, bisexual, other men who have sex (MSM) now common. In September, 2021, emergence extensively drug-resistant (XDR) S harbouring plasmid-encoded blaCTX-M-27 raised concerns over further this extended-spectrum β-lactamase-producing gene. Using national...
Shigella sonnei causes shigellosis, a severe gastrointestinal illness that is sexually transmissible among men who have sex with (MSM). Multidrug resistance in S. common including against World Health Organisation recommended treatment options, azithromycin, and ciprofloxacin. Recently, an MSM-associated outbreak of extended-spectrum β-lactamase producing, extensively drug resistant was reported the United Kingdom. Here, we aimed to identify genetic basis, evolutionary history, international...
Rapid and accurate differentiation of Salmonella spp. causing enteric fever from nontyphoidal is essential for clinical management cases, laboratory risk management, implementation public health measures. Current methods used confirmation identification, including biochemistry serotyping as well whole-genome sequencing analyses, take several days. Here we report the development evaluation a real-time PCR assay that can be performed directly on crude DNA extracts bacterial colonies rapid...
Abstract Background We aimed to compare Illumina and Oxford Nanopore Technology sequencing data from the 2 isolates of Shiga toxin–producing Escherichia coli (STEC) O157:H7 determine whether concordant single-nucleotide variants were identified inference relatedness was consistent with technologies. Results For workflow, time DNA extraction availability results ~40 hours, whereas ONT workflow serotyping toxin subtyping variant identification available within 7 hours. After optimization...
Introduction. Shiga toxin-producing Escherichia coli (STEC) can cause severe disease and large outbreaks. In England, the incidence clinical significance of STEC serogroups other than O157 (non-O157) is unknown due to a testing bias for detection O157. Since 2013, implementation PCR detect all by an increasing number diagnostic laboratories has led increase in non-O157 STEC. Hypothesis/Gap statement. Due methodologies select serogroup frontline most countries, very little surveillance data...
Salmonella enterica serovar Infantis is the fifth most common isolated in England and Wales. Epidemiological, genotyping antimicrobial-resistance data for S . isolates were used to analyse English Welsh demographics over a 5 year period. Travel cases associated with mainly from Asia, followed by Europe North America. Since 2000, increasing numbers of had multidrug resistance determinants harboured on large plasmid termed ‘plasmid emerging Infantis’ (pESI). Between 2013 2018, 42 humans food...
The aim of this study was to use single-molecule, nanopore sequencing explore the genomic environment resistance determinants in a multidrug-resistant (MDR) strain enteroaggregative Escherichia coli serotype O51 : H30, sequence type (ST) 38. Sequencing performed on MinION Flow cell MIN-106 R9.4. Nanopore raw FAST5 reads were base-called using Albacore v1.2.1, converted FASTA and FASTQ formats Poretools v0.6.0, assembled Unicycler v0.4.2, combining long-read data with short-read produced by...
To establish the prevalence of mobile colistin resistance (mcr) genes amongst Salmonella enterica isolates obtained through public health surveillance in England (April 2014 to September 2017), 33 205 S. genome sequences from human, food, animal and environmental were screened for presence mcr variants 1 8. The mcr-positive genomes assembled, annotated characterized according plasmid type. Nanopore sequencing was performed on six selected with putative novel plasmids, phylogenetic analysis...
Over the last 35 years in UK, burden of Shiga toxin-producing Escherichia coli (STEC) O157:H7 infection has, during different periods time, been associated with five sub-lineages (1983-1995, Ia, I/IIa and I/IIb; 1996-2014, Ic; 2015-2018, IIb). The acquisition a stx2a-encoding bacteriophage by these appears to have coincided their respective emergences. Oxford Nanopore Technologies (ONT) system was used sequence, characterize compare stx-encoding prophages harboured each sub-lineage...
Abstract Escherichia albertii is a recently identified gastrointestinal bacterial pathogen of humans and animals which typically misidentified as pathotypes diarrhoeagenic coli or Shigella species generally only detected during genomic surveillance other Enterobacteriaceae. The incidence E. likely underestimated, its epidemiology clinical relevance are poorly characterised. Here, we whole genome sequenced isolates from ( n = 83) birds 79) isolated in Great Britain between 2000 2021 analysed...
In June 2023, UKHSA surveillance systems detected an outbreak of severe gastrointestinal symptoms caused by a rare serotype Shiga toxin-producing Escherichia coli , STEC O183:H18. There were 26 cases aged 6 months to 74 years (42 % 0–9 years), distributed across the UK with onset dates range between 22 May 2023 and 4 July 2023. The epidemiological food chain investigations inconclusive, although meat products made from beef mince implicated as potential vehicle. strain belonged sequence type...
Epidemiological and microbiological data on Vibrio cholerae strains isolated between April 2004 March 2018 (n = 836) held at the Public Health England culture archive were reviewed. The traditional biochemical species identification serological typing results compared with genome-derived serotype for a subset of isolates 152). Of 836 isolates, 750 (89.7%) from fecal specimen, 206 (24.6%) belonged to serogroup O1, 7 (0.8%) O139; 792 (94.7%) patients reporting recent travel abroad, most...
Sequence similarity of pathogen genomes can infer the relatedness between isolates as fewer genetic differences identified pairs isolates, less time since divergence from a common ancestor. Clustering based on hierarchical single linkage clustering pairwise SNP distances has been employed to detect and investigate outbreaks. Here, we evaluated evidence-base for interpretation phylogenetic clusters Shiga toxin-producing Escherichia coli (STEC) O157:H7. Whole genome sequences 1193 STEC O157:H7...
Abstract In November 2019, an outbreak of Shiga toxin-producing Escherichia coli O157:H7 was detected in South Yorkshire, England. Initial investigations established consumption milk from a local dairy as common exposure. A sample pasteurised tested the next day failed phosphatase test, indicating contamination by unpasteurised (raw) milk. The owner agreed to immediately cease production and initiate recall. Inspection pasteuriser revealed damaged seal on flow divert valve. Ultimately, there...
Evidence is accumulating in the literature that horizontal spread of antimicrobial resistance (AMR) genes mediated by bacteriophages and bacteriophage-like plasmid (phage-plasmid) elements much more common than previously envisioned. For instance, we recently identified characterized a circular P1-like phage-plasmid harbouring bla CTX-M-15 gene conferring extended-spectrum beta-lactamase (ESBL) Salmonella enterica serovar Typhi. As prevalence epidemiological relevance such mechanisms has...
National surveillance of Shigella flexneri ensures the rapid detection outbreaks to facilitate public health investigation and intervention strategies. In this study, we used whole-genome sequencing (WGS) type S. in order detect linked cases support epidemiological investigations. We prospectively analyzed 330 isolates received at Gastrointestinal Bacteria Reference Unit Public Health England between August 2015 January 2016. Traditional phenotypic WGS sub-typing methods were compared. PCR...
PurposeandMethodology. Epidemiological and microbiological data on Yersinia enterocolitica (n=699) pseudotuberculosis (n=35) isolated from human clinical specimens in England between April 2004 March 2018 were reviewed. Traditional biochemical species identification serological typing results compared with identifications serotypes derived whole-genome sequencing (WGS) for a sub-set of these isolates (n=179).Results. Most Y. faecal (74.4%) adults (80.7%) 50.7 % male patients. blood cultures...
Yersinia enterocolitica is an underreported cause of foodborne gastroenteritis. Little known the diversity Y. isolated from food and which commodities contribute to human disease. In this study, was 37/50 raw chicken, 8/10 pork, salmon 1/10 leafy green samples collected at retail in UK. Up 10 presumptive isolates per positive sample underwent whole genome sequencing (WGS) were compared with publicly available genomes. total, 207 analyzed belonged 38 sequence types (STs). five STs individual...
BackgroundThe number of cholera cases reported to the World Health Organization (WHO) in 2022 was more than double that 2021. Nine countries WHO European Region 51 vs five 2021.AimWe aimed confirm
Introduction. Diarrhoeagenic Escherichia coli (DEC) pathotypes are defined by genes located on mobile genetic elements, and more than one definitive pathogenicity gene may be present in the same strain. In August 2022, UK Health Security Agency (UKHSA) surveillance systems detected an outbreak of hybrid Shiga toxin-producing E. /enterotoxigenic (STEC–ETEC) serotype O101:H33 harbouring both toxin ( stx ) heat-stable st ). Gap statement. These strains DEC a public health concern, as they often...
Shigellosis in men who have sex with (MSM) is caused by multidrug resistant Shigellae, exhibiting resistance to antimicrobials including azithromycin, ciprofloxacin and more recently the third-generation cephalosporins. We sequenced four blaCTX-M-27-positive MSM Shigella isolates (2018-20) using Oxford Nanopore Technologies; three S. sonnei (identified as two clade 2, one 5) flexneri 3a, explore AMR context. All harboured Tn7/Int2 chromosomal integrons, whereas 3a contained Resistance Locus....
Introduction. Shiga toxin-producing Escherichia coli (STEC) belong to a diverse group of gastrointestinal pathogens defined by the presence toxin genes (stx) which there are at least ten subtypes (Stx1a-Stx1d and Stx2a-Stx2g).Gap Statement. Initially thought be associated with mild symptoms, more recently STEC encoding stx2f have been isolated from cases haemolytic uraemic syndrome (HUS) clinical significance public health burden require further investigation.Aim. We analysed outcomes...
Compared to short-read sequencing data, long-read facilitates single contiguous de novo assemblies and characterization of the prophage region genome. Here, we describe our methodological approach using Oxford Nanopore Technology (ONT) data quantify genetic relatedness look for microevolutionary events in core accessory genomes assess within-outbreak variation four genetically epidemiologically linked isolates. Analysis both Illumina ONT detected one SNP between sequences outbreak The...