Diversity of the Genomes and Neurotoxins of Strains of Group I and Associated with Foodborne, Infant and Wound Botulism.

Group I and are closely related bacteria responsible for foodborne, infant and wound botulism. A comparative genomic study with 556 highly diverse strains of Group I and (including 417 newly sequenced strains) has been carried out to characterise the genetic diversity and spread of these bacteria and their neurotoxin genes. Core genome single-nucleotide polymorphism (SNP) analysis revealed two major lineages; Group I (most strains possessed botulinum neurotoxin gene(s) of types A, B and/or F) and (some strains possessed a type B botulinum neurotoxin gene).

Impact of whole genome sequencing on the investigation of food-borne outbreaks of Shiga toxin-producing serogroup O157:H7, England, 2013 to 2017.

We aim to provide insight and guidance on the utility of whole genome sequencing (WGS) data for investigating food-borne outbreaks of Shiga toxin-producing (STEC) O157:H7 in England between 2013 and 2017. Analysis of WGS data delivered an unprecedented level of strain discrimination when compared with multilocus variable number tandem repeat analysis. The robustness of the WGS method ensured confidence in the microbiological identification of linked cases, even when epidemiological links were obscured.

Whole genome sequencing reveals an outbreak of Salmonella Enteritidis associated with reptile feeder mice in the United Kingdom, 2012-2015.

Analysis of whole genome sequencing data uncovered a previously undetected outbreak of Salmonella Enteritidis that had been on-going for four years. Cases were resident in all countries of the United Kingdom and 40% of the cases were aged less than 11 years old. Initial investigations revealed that 30% of cases reported exposure to pet snakes.

Identification of Salmonella for public health surveillance using whole genome sequencing.

In April 2015, Public Health England implemented whole genome sequencing (WGS) as a routine typing tool for public health surveillance of Salmonella, adopting a multilocus sequence typing (MLST) approach as a replacement for traditional serotyping. The WGS derived sequence type (ST) was compared to the phenotypic serotype for 6,887 isolates of S. enterica subspecies I, and of these, 6,616 (96%) were concordant.

Applying phylogenomics to understand the emergence of Shiga-toxin-producing O157:H7 strains causing severe human disease in the UK.

Shiga-toxin-producing (STEC) O157:H7 is a recently emerged zoonotic pathogen with considerable morbidity. Since the emergence of this serotype in the 1980s, research has focussed on unravelling the evolutionary events from the O55:H7 ancestor to the contemporaneous globally dispersed strains observed today. In this study, the genomes of over 1000 isolates from both human clinical cases and cattle, spanning the history of STEC O157:H7 in the UK, were sequenced.

Public Health Investigation of Two Outbreaks of Shiga Toxin-Producing Escherichia coli O157 Associated with Consumption of Watercress.

An increase in the number of cases of Shiga toxin-producing Escherichia coli (STEC) O157 phage type 2 (PT2) in England in September 2013 was epidemiologically linked to watercress consumption. Whole-genome sequencing (WGS) identified a phylogenetically related cluster of 22 cases (outbreak 1). The isolates comprising this cluster were not closely related to any other United Kingdom strain in the Public Health England WGS database, suggesting a possible imported source.

Insight into Shiga toxin genes encoded by Escherichia coli O157 from whole genome sequencing.

The ability of Shiga toxin-producing Escherichia coli (STEC) to cause severe illness in humans is determined by multiple host factors and bacterial characteristics, including Shiga toxin (Stx) subtype. Given the link between Stx2a subtype and disease severity, we sought to identify the stx subtypes present in whole genome sequences (WGS) of 444 isolates of STEC O157. Difficulties in assembling the stx genes in some strains were overcome by using two complementary bioinformatics methods: mapping and de novo assembly.

Salmonella enterica serovar Enteritidis, England and Wales, 1945-2011.

In England and Wales, the emergence of Salmonella enterica serovar Enteritidis resulted in the largest and most persistent epidemic of foodborne infection attributable to a single subtype of any pathogen since systematic national microbiological surveillance was established. We reviewed 67 years of surveillance data to examine the features, underlying causes, and overall effects of S. enterica ser.

Epidemiology and microbiology of Shiga toxin-producing Escherichia coli other than serogroup O157 in England, 2009-2013.

The implementation of direct testing of clinical faecal specimens for gastrointestinal (GI) pathogens by PCR offers a sensitive and comprehensive approach for the detection of Shiga toxin-producing Escherichia coli (STEC). The introduction of a commercial PCR assay, known as GI PCR, for the detection of GI pathogens at three frontline hospital laboratories in England between December 2012 and December 2013 led to a significant increase in detection of STEC other than serogroup O157 (non-O157 STEC). In 2013, 47 isolates were detected in England, compared with 57 in the preceding 4 years (2009-2012).

An investigation of the diversity of strains of enteroaggregative Escherichia coli isolated from cases associated with a large multi-pathogen foodborne outbreak in the UK.

Following a large outbreak of foodborne gastrointestinal (GI) disease, a multiplex PCR approach was used retrospectively to investigate faecal specimens from 88 of the 413 reported cases. Gene targets from a range of bacterial GI pathogens were detected, including Salmonella species, Shigella species and Shiga toxin-producing Escherichia coli, with the majority (75%) of faecal specimens being PCR positive for aggR associated with the Enteroaggregative E. coli (EAEC) group.

Evaluating the use of multilocus variable number tandem repeat analysis of Shiga toxin-producing Escherichia coli O157 as a routine public health tool in England.

Multilocus variable number tandem repeat analysis (MLVA) provides microbiological support for investigations of clusters of cases of infection with Shiga toxin-producing E. coli (STEC) O157. All confirmed STEC O157 isolated in England and submitted to the Gastrointestinal Bacteria Reference Unit (GBRU) during a six month period were typed using MLVA, with the aim of assessing the impact of this approach on epidemiological investigations.

Infant botulism: advice on avoiding feeding honey to babies and other possible risk factors.

Botulism is a rare, but extremely serious, disease and Public Health England is responsible for its diagnosis and surveillance in the UK. Over the past five years (2008-2013), the most common form of the disease recognised in the UK has been infant botulism. The aim of this article is to raise awareness of infant botulism and highlight advice for parents and carers of infants that honey should not be fed to infants under 12 months old.

Whole genome sequencing of an unusual serotype of Shiga toxin-producing Escherichia coli.

Shiga toxin-producing Escherichia coli serotype O117:K1:H7 is a cause of persistent diarrhea in travelers to tropical locations. Whole genome sequencing identified genetic mechanisms involved in the pathoadaptive phenotype. Sequencing also identified toxin and putative adherence genes flanked by sequences indicating horizontal gene transfer from Shigella dysenteriae and Salmonella spp.

Infections with spore-forming bacteria in persons who inject drugs, 2000-2009.

Since 2000 in the United Kingdom, infections caused by spore-forming bacteria have been associated with increasing illness and death among persons who inject drugs (PWID). To assess temporal and geographic trends in these illnesses (botulism, tetanus, Clostridium novyi infection, and anthrax), we compared rates across England and Scotland for 2000-2009. Overall, 295 infections were reported: 1.

Real-time PCRs assay for serogrouping Listeria monocytogenes and differentiation from other Listeria spp.

A 5'-exonuclease real-time triplex-PCR assay was developed for serogrouping Listeria monocytogenes, and differentiation from other Listeria spp. The assay was evaluated on 109 Listeria cultures, and results were compared with a previously validated gel-based multiplex-PCR procedure. All L.

Characterization of a verocytotoxin-producing enteroaggregative Escherichia coli serogroup O111:H21 strain associated with a household outbreak in Northern Ireland.

A strain of Escherichia coli O111:H21 recently isolated in the United Kingdom harbored the phage-encoded vtx2c gene and the aggregative adherence plasmid. Although exhibiting the same pathogenic profile as the E. coli O104:H4 strain linked to the outbreak in Germany, there were important differences in strain characteristics and in the epidemiological setting.

Complete genome sequence of the proteolytic Clostridium botulinum type A5 (B3') strain H04402 065.

H04402 065 is one of a very small group of strains of proteolytic Clostridium botulinum that form type A5 neurotoxin. Here, we report the complete 3.9-Mb genome sequence and annotation of strain H04402 065, which was isolated from a botulism patient in the United Kingdom in 2004.

Report of two unlinked cases of infant botulism in the UK in October 2007.

Infant botulism is a rare disease in the UK, with the first case being recognized in 1978 and only five subsequent cases being reported before 2007. This study reports two unlinked cases of infant botulism, caused by two distinct strains of Clostridium botulinum (toxin types A and B, respectively), that occurred within a single month in the south-east of England in October 2007. The use of real-time PCR to detect C.

Association between a case study of asymptomatic ovine listerial mastitis and the contamination of soft cheese and cheese processing environment with Listeria monocytogenes in Portugal.

For 5 months, the udders of milking ewes, raw ewe's milk, cheese, and the plant and environment of a cheese manufacturer in Portugal were investigated using standard methods for the presence of Listeria spp. An association between subclinical mastitis and Listeria monocytogenes in a single lactating sheep was investigated by visual inspection of udders for signs of inflammation, application of somatic cell counts, the California mastitis test, pH measurement to milk, and culture of L. monocytogenes and Staphylococcus spp.

The identification and characterization of Clostridium perfringens by real-time PCR, location of enterotoxin gene, and heat resistance.

Clostridium perfringens carrying the enterotoxin gene is an important cause of both foodborne and non-foodborne diarrheal disease. Rapid identification of isolates carrying the enterotoxin gene is invaluable for outbreak investigation whilst information on the genomic location of the enterotoxin (cpe) gene can improve our understanding of disease transmission. This paper describes the validation of a real-time polymerase chain reaction (PCR) assay for the identification of C.

Changing pattern of human listeriosis, England and Wales, 2001-2004.

Microbiologic and epidemiologic data on 1,933 cases of human listeriosis reported in England and Wales from 1990 to 2004 were reviewed. A substantial increase in incidence occurred from 2001 to 2004. Ten clusters (60 cases), likely to represent common-source outbreaks, were detected.