Development and validation of a random forest algorithm for source attribution of animal and human Typhimurium and monophasic variants of Typhimurium isolates in England and Wales utilising whole genome sequencing data.

Source attribution has traditionally involved combining epidemiological data with different pathogen characterisation methods, including 7-gene multi locus sequence typing (MLST) or serotyping, however, these approaches have limited resolution. In contrast, whole genome sequencing data provide an overview of the whole genome that can be used by attribution algorithms. Here, we applied a random forest (RF) algorithm to predict the primary sources of human clinical Typhimurium ( Typhimurium) and monophasic variants (monophasic Typhimurium) isolates.

A One Health Perspective on Salmonella enterica Serovar Infantis, an Emerging Human Multidrug-Resistant Pathogen.

Salmonella enterica serovar Infantis presents an ever-increasing threat to public health because of its spread throughout many countries and association with high levels of antimicrobial resistance (AMR). We analyzed whole-genome sequences of 5,284 Salmonella Infantis strains from 74 countries, isolated during 1989-2020 from a wide variety of human, animal, and food sources, to compare genetic phylogeny, AMR determinants, and plasmid presence. The global Salmonella Infantis population structure diverged into 3 clusters: a North American cluster, a European cluster, and a global cluster.

Re-analysis of an outbreak of Shiga toxin-producing Escherichia coli O157:H7 associated with raw drinking milk using Nanopore sequencing.

The aim of this study was to compare Illumina and Oxford Nanopore Technology (ONT) sequencing data to quantify genetic variation to assess within-outbreak strain relatedness and characterise microevolutionary events in the accessory genomes of a cluster of 23 genetically and epidemiologically linked isolates related to an outbreak of Shiga toxin-producing Escherichia coli O157:H7 caused by the consumption of raw drinking milk. There were seven discrepant variants called between the two technologies, five were false-negative or false-positive variants in the Illumina data and two were false-negative calls in ONT data. After masking horizontally acquired sequences such as prophages, analysis of both short and long-read sequences revealed the 20 isolates linked to the outbreak in 2017 had a maximum SNP distance of one SNP between each other, and a maximum of five SNPs when including three additional strains identified in 2019.

Inspection of chicken wings and legs for animal welfare monitoring using X-ray computed tomography, visual examination, and histopathology.

In broiler chickens, fractures of wings and legs are recorded at poultry slaughterhouses based on the time of occurrence. Prekilling (PRE) fractures occur before the death of animal, so the chicken was still able to experience pain and distress associated with the injury (an animal welfare issue). Postkilling (POST) fractures occur when the chickens are deceased and fully bled-out and consequently unable to feel pain (not an animal welfare issue).

Prevalence and Persistence of Antibiotic Resistance Determinants in the Gut of Travelers Returning to the United Kingdom is Associated with Colonization by Pathogenic Escherichia coli.

The gut microbiota constitutes an ideal environment for the selection, exchange, and carriage of antibiotic resistance determinants (ARDs), and international travel has been identified as a risk factor for acquisition of resistant organisms. Here, we present a longitudinal metagenomic analysis of the gut resistome in travellers to "high-risk" countries (Gutback). Fifty volunteers, recruited at a travel clinic in London, United Kingdom, provided stool samples before (pre-travel), immediately after (post-travel), and 6 months after their return (follow-up) from a high-risk destination.

Rapid geographical source attribution of serovar Enteritidis genomes using hierarchical machine learning.

serovar Enteritidis is one of the most frequent causes of Salmonellosis globally and is commonly transmitted from animals to humans by the consumption of contaminated foodstuffs. In the UK and many other countries in the Global North, a significant proportion of cases are caused by the consumption of imported food products or contracted during foreign travel, therefore, making the rapid identification of the geographical source of new infections a requirement for robust public health outbreak investigations. Herein, we detail the development and application of a hierarchical machine learning model to rapidly identify and trace the geographical source of Enteritidis infections from whole genome sequencing data.

Increased phage resistance through lysogenic conversion accompanying emergence of monophasic Typhimurium ST34 pandemic strain.

serovar Typhimurium (. Typhimurium) comprises a group of closely related human and animal pathogens that account for a large proportion of all infections globally. The epidemiological record of .

A case report of serovar Corvallis from environmental isolates from Cambodia and clinical isolates in the UK.

subspecies serovar Corvallis (. Corvallis) has been identified as a human pathogen and as a food contaminant. Diarrhoeal disease is a common diagnosis in tourists visiting Southeast Asia, often with unknown aetiology.

Linkage of Whole Genome Sequencing, Epidemiological, and Clinical Data to Understand the Genetic Diversity and Clinical Outcomes of Shigella flexneri among Men Who Have Sex with Men in England.

The public health value of whole genome sequencing (WGS) for spp. in England has been limited by a lack of information on sexual identity and behavior. We combined WGS data with other data sources to better understand Shigella flexneri transmission in men who have sex with men (MSM).

Emergence and global spread of main clinical clonal complex.

The bacterial foodborne pathogen clonal complex 1 (-CC1) is the most prevalent clonal group associated with human listeriosis and is strongly associated with cattle and dairy products. Here, we analyze 2021 isolates collected from 40 countries, covering -CC1 first isolation to present days, to define its evolutionary history and population dynamics. We show that -CC1 spread worldwide from North America following the Industrial Revolution through two waves of expansion, coinciding with the transatlantic livestock trade in the second half of the 19th century and the rapid growth of cattle farming and food industrialization in the 20th century.

Genome structural variation in O157:H7.

The human zoonotic pathogen O157:H7 is defined by its extensive prophage repertoire including those that encode Shiga toxin, the factor responsible for inducing life-threatening pathology in humans. As well as introducing genes that can contribute to the virulence of a strain, prophage can enable the generation of large-chromosomal rearrangements (LCRs) by homologous recombination. This work examines the types and frequencies of LCRs across the major lineages of the O157:H7 serotype.

Emergence of novel strains of associated with sexual transmission in adult men in England, 2019-2020.

National surveillance of shigellosis in England revealed an increase in sexually transmitted in adult males in 2019 that persisted throughout 2020. We observed a resurgence of azithromycin-resistant serotype 3a, and the emergence of two novel multidrug-resistant clades of 2a and 1b.

Characterization of a pESI-like plasmid and analysis of multidrug-resistant Infantis isolates in England and Wales.

serovar Infantis is the fifth most common serovar isolated in England and Wales. Epidemiological, genotyping and antimicrobial-resistance data for . Infantis isolates were used to analyse English and Welsh demographics over a 5 year period.

Salmonella Paratyphi B; Public Health and Parental Choice: When to Treat Asymptomatic Carriers of Infection?

Background: Salmonella Paratyphi B (Paratyphoid B) is a rare infection and a notifiable disease in England. Disease is typically mild, and chronic carriage in children has been described in endemic countries. Almost all cases in England are imported, with very few cases of community transmission reported.

Development and evaluation of an outbreak surveillance system integrating whole genome sequencing data for non-typhoidal in London and South East of England, 2016-17.

An outbreak surveillance system for Salmonella integrating whole genome sequencing (WGS) and epidemiological data was developed in South East and London in 2016-17 to assess local WGS clusters for triage and investigation. Cases genetically linked within a 5 single-nucleotide polymorphism (SNP) single linkage cluster were assessed using a set of locally agreed thresholds based on time, person and place, for reporting to local health protection teams (HPTs). Between September 2016 and September 2017, 230 unique 5-SNP clusters (442 weekly reports) of non-typhoidal Salmonella 5-SNP WGS clusters were identified, of which 208 unique 5-SNP clusters (316 weekly reports) were not reported to the HPTs.

Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei.

Shigella sonnei is the most common agent of shigellosis in high-income countries, and causes a significant disease burden in low- and middle-income countries. Antimicrobial resistance is increasingly common in all settings. Whole genome sequencing (WGS) is increasingly utilised for S.

Accessory Genome Dynamics and Structural Variation of from Persistent Infections.

Shigellosis is a diarrheal disease caused mainly by and Infection is thought to be largely self-limiting, with short- to medium-term and serotype-specific immunity provided following clearance. However, cases of men who have sex with men (MSM)-associated shigellosis have been reported where of the same serotype were serially sampled from individuals between 1 and 1,862 days apart, possibly due to persistent carriage or reinfection with the same serotype. Here, we investigate the accessory genome dynamics of MSM-associated and isolates serially sampled from individual patients at various days apart to shed light on the adaptation of these important pathogens during infection.

Outbreak of Shiga toxin-producing Escherichia coli O157 linked with consumption of a fast-food product containing imported cucumbers, United Kingdom, August 2020.

Background: In August 2020, an outbreak of Shiga toxin-producing Escherichia coli (STEC) O157:H7 occurred in the United Kingdom. Whole genome sequencing revealed that these cases formed a genetically distinct cluster.

Methods: Hypotheses generated from case interviews were tested in analytical studies, and results informed environmental sampling and food chain analysis.

Ecological niche adaptation of Salmonella Typhimurium U288 is associated with altered pathogenicity and reduced zoonotic potential.

The emergence of new bacterial pathogens is a continuing challenge for agriculture and food safety. Salmonella Typhimurium is a major cause of foodborne illness worldwide, with pigs a major zoonotic reservoir. Two phylogenetically distinct variants, U288 and ST34, emerged in UK pigs around the same time but present different risk to food safety.

Phylogenetic context of Shiga toxin-producing serotype O26:H11 in England.

The increasing use of PCR for the detection of gastrointestinal pathogens in hospital laboratories in England has improved the detection of Shiga toxin-producing (STEC), and the diagnosis of haemolytic uraemic syndrome (HUS). We aimed to analyse the microbiological characteristics and phylogenetic relationships of STEC O26:H11, clonal complex (CC) 29, in England to inform surveillance, and to assess the threat to public health. There were 502 STEC belonging to CC29 isolated between 2014 and 2019, of which 416 were from individual cases.

Phylogenetic structure of Shiga toxin-producing O157:H7 from sub-lineage to SNPs.

Sequence similarity of pathogen genomes can infer the relatedness between isolates as the fewer genetic differences identified between pairs of isolates, the less time since divergence from a common ancestor. Clustering based on hierarchical single linkage clustering of pairwise SNP distances has been employed to detect and investigate outbreaks. Here, we evaluated the evidence-base for the interpretation of phylogenetic clusters of Shiga toxin-producing (STEC) O157:H7.