Characterization of a plasmid with antibiotic and stress resistance genes.

Listeriosis is a predominantly foodborne infection causing severe, invasive disease in the immunocompromised, with the causative agent being . While possesses innate resistance to several classes of antibiotics, acquired antibiotic resistance is low compared with other foodborne pathogens. Conversely, plasmids possessing stress tolerance mechanisms are common and contribute to their ability to persist in food production environments.

Epidemiologic and Genomic Investigation of Sexually Transmitted Shigella sonnei, England.

Shigellosis is a bacterial infection that causes enteric illness and can be sexually transmitted, particularly among gay, bisexual, and other men who have sex with men. Multiple extensively drug-resistant Shigella strains have been detected through genomic surveillance and are associated with plasmids carrying the gene variant bla in the United Kingdom. We report an increase in possible sexually transmitted cases of Shigella bacteria carrying the bla gene variant, which was previously associated with travel.

Enhanced laboratory surveillance study of species in England.

Campylobacteriosis is the leading cause of gastroenteritis worldwide, and species are the most frequently reported zoonotic, bacterial foodborne pathogens in England. Currently, less than 2.0% of isolates in England undergo strain identification and typing, resulting in limited insight into their molecular epidemiology.

Hybrid strains of enterotoxigenic/Shiga toxin-producing , United Kingdom, 2014-2023.

Diarrhoeagenic (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 /enterotoxigenic (STEC-ETEC) serotype O101:H33 harbouring both Shiga toxin () and heat-stable toxin (). These hybrid strains of DEC are a public health concern, as they are often associated with enhanced pathogenicity.

Genomic analysis of an outbreak of Shiga toxin-producing O183:H18 in the United Kingdom, 2023.

In June 2023, UKHSA surveillance systems detected an outbreak of severe gastrointestinal symptoms caused by a rare serotype of Shiga toxin-producing , STEC O183:H18. There were 26 cases aged 6 months to 74 years (42 % cases were aged 0-9 years), distributed across the UK with onset dates range between 22 May 2023 and 4 July 2023. The epidemiological and food chain investigations were inconclusive, although meat products made from beef mince were implicated as a potential vehicle.

Surveillance of antimicrobial resistant Shiga toxin-producing E. coli O157:H7 in England, 2016-2020.

Objectives: Shiga toxin-producing Escherichia coli (STEC) O157:H7 are zoonotic pathogens and transmission to humans occurs via contaminated food or contact with infected animals. The aim of this study was to describe the frequency, and distribution across the phylogeny, of antimicrobial resistance (AMR) determinants in STEC O157:H7 isolated from human cases in England.

Methods: Short-read whole-genome sequencing data from 1473 isolates of STEC O157:H7 from all seven sub-lineages (Ia-Ic, IIa-IIc and I/II) were mapped to genes known to confer phenotypic resistance to 10 different classes of antibiotic.

encoding Shiga toxin subtype Stx2f causing human infections in England, 2015-2022.

Shiga toxin-producing (STEC) belong to a diverse group of gastrointestinal pathogens defined by the presence of Shiga toxin genes () of which there are at least ten subtypes (Stx1a-Stx1d and Stx2a-Stx2g). Initially thought to be associated with mild symptoms, more recently STEC encoding have been isolated from cases of haemolytic uraemic syndrome (HUS) and the clinical significance and public health burden require further investigation. We analysed clinical outcomes and genome-sequencing data linked to patients infected with STEC encoding- in England to assess the risk to public health.

Comparison of phenotypic and WGS-derived antimicrobial resistance profiles of Campylobacter jejuni and Campylobacter coli isolated from cases of diarrhoeal disease in England and Wales, 2015-16.

Objectives: To compare and evaluate phenotypic and genotypic methods for the detection of antimicrobial resistance (AMR) in Campylobacter jejuni and Campylobacter coli in England and Wales.

Methods: WGS data from 528 isolates of Campylobacter spp. (452 C.

Phylogenomic analysis of gastroenteritis-associated in England and Wales over a 7-year period indicates distribution of clonal toxigenic strains in multiple outbreaks and extensive involvement of enterotoxin-encoding (CPE) plasmids.

is a major enteric pathogen known to cause gastroenteritis in human adults. Although major outbreak cases are frequently reported, only limited whole-genome sequencing (WGS) based studies have been performed to understand the genomic epidemiology and virulence gene content of outbreak-associated strains. We performed phylogenomic analysis on 109 .

Utility of Whole Genome Sequencing To Describe the Persistence and Evolution of Listeria monocytogenes Strains within Crabmeat Processing Environments Linked to Two Outbreaks of Listeriosis.

This article describes the identification and investigation of two extended outbreaks of listeriosis in which crabmeat was identified as the vehicle of infection. Comparing contemporary and retrospective typing data of Listeria monocytogenes isolates from clinical cases and from food and food processing environments allowed the detection of cases going back several years. This information, combined with the analysis of routinely collected enhanced surveillance data, helped to direct the investigation and identify the vehicle of infection.

Tracking of Listeria monocytogenes in meat establishment using Whole Genome Sequencing as a food safety management tool: A proof of concept.

Repeated Listeria outbreaks particularly associated with Ready-To-Eat (RTE) delicatessen meat products have been reported annually at global level. The most frequent scenario that led to foodborne outbreaks was the post-thermal treatment cross-contamination of deli meat products during slicing and modified atmosphere packaging (MAP). The precondition for such cross contamination is the previous introduction of Listeria into meat processing facilities and subsequent colonization of the production environment, associated with formation of biofilms resilient to common sanitation procedures regularly applied in meat establishments.

Exploiting Bacterial Whole-Genome Sequencing Data for Evaluation of Diagnostic Assays: Campylobacter Species Identification as a Case Study.

The application of whole-genome sequencing (WGS) to problems in clinical microbiology has had a major impact on the field. Clinical laboratories are now using WGS for pathogen identification, antimicrobial susceptibility testing, and epidemiological typing. WGS data also represent a valuable resource for the development and evaluation of molecular diagnostic assays, which continue to play an important role in clinical microbiology.

MOST: a modified MLST typing tool based on short read sequencing.

Multilocus sequence typing (MLST) is an effective method to describe bacterial populations. Conventionally, MLST involves Polymerase Chain Reaction (PCR) amplification of housekeeping genes followed by Sanger DNA sequencing. Public Health England (PHE) is in the process of replacing the conventional MLST methodology with a method based on short read sequence data derived from Whole Genome Sequencing (WGS).

Utility of real-time amplification of selected 16S rRNA gene sequences as a tool for detection and identification of microbial signatures directly from clinical samples.

The potential of incorporating a real-time PCR for amplification and detection of 16S rRNA gene signatures directly from clinical samples was assessed as a tool for diagnostics. Universal PCR primers spanning short variable regions (~500 bp) were optimized for real-time PCR and tested in comparison with a longer fragment (~1400 bp) generated from block-based amplification. Real-time PCR had improved sensitivity of detection (8% increase), decreased amplification time and simplified downstream processing.

Human papillomavirus genotype detection and viral load in paired genital and urine samples from both females and males.

The ability to detect type-specific high risk HPV (HR-HPV) infections in samples from females and males is important for monitoring the epidemiology of HPV and the impact of vaccination. Type-specific detection concordance between paired urine and genital samples from females (n = 264) undergoing routine colposcopy and males (n = 88) attending a genito-urinary medicine clinic was evaluated using an in-house genotyping assay. The overall inter-rater agreement (κ) was 0.

Amoxicillin therapy of poultry flocks: effect upon the selection of amoxicillin-resistant commensal Campylobacter spp.

Background: The aim of this study was to investigate the effect of amoxicillin therapy of poultry flocks upon the persistence of commensal Campylobacter spp. and the incidence of antibiotic resistance.

Methods: Four poultry flocks naturally colonized with Campylobacter were treated with amoxicillin and monitored before, during and up to 4 weeks post-treatment.

Phase-variable surface structures are required for infection of Campylobacter jejuni by bacteriophages.

This study characterizes the interaction between Campylobacter jejuni and the 16 phages used in the United Kingdom typing scheme by screening spontaneous mutants of the phage-type strains and transposon mutants of the sequenced strain NCTC 11168. We show that the 16 typing phages fall into four groups based on their patterns of activity against spontaneous mutants. Screens of transposon and defined mutants indicate that the phage-bacterium interaction for one of these groups appears to involve the capsular polysaccharide (CPS), while two of the other three groups consist of flagellatropic phages.

Applicability of a rapid duplex real-time PCR assay for speciation of Campylobacter jejuni and Campylobacter coli directly from culture plates.

A rapid duplex real-time polymerase chain reaction (PCR) assay for speciation of Campylobacter jejuni and Campylobacter coli using the ABI Prism 7700 sequence detection system (Applied Biosystems) was developed based on two of the genes used in a conventional multiplex PCR. A rapid turnaround time of 3 h was achieved with the use of boiled cell lysates. Applicability of the assay was tested with 6015 random campylobacter strains referred to the Campylobacter Reference Unit, with 97.