Use of whole-genome sequencing to identify clusters of Shigella flexneri associated with sexual transmission in men who have sex with men in England: a validation study using linked behavioural data

Since the 1970s, shigellosis has been reported as a sexually transmissible infection, and in recent years, genomic data have revealed the breadth of Shigella spp. transmission among global networks of men who have sex with men (MSM). In 2015, Public Health England (PHE) introduced routine whole-genome sequencing (WGS) of Shigella spp. to identify transmission clusters. However, limited behavioural information for the cases hampers interpretation. We investigated whether WGS can distinguish between clusters representing sexual transmission in MSM and clusters representing community (non-sexual) transmission to inform infection control. WGS data for Shigella flexneri from August 2015 to July 2017 were aggregated into single linkage clusters based on SNP typing using a range of SNP distances (the standard for Shigella surveillance at PHE is 10 SNPs). Clusters were classified as 'adult male', 'household', 'travel-associated' or 'community' using routine demographic data submitted alongside laboratory cultures. From August 2015 to March 2017, PHE contacted those with shigellosis as part of routine public-health follow-up and collected exposure data on a structured questionnaire, which for the first time included questions about sexual identity and behaviour. The questionnaire data were used to determine whether clusters classified as 'adult male' represented likely sexual transmission between men, thereby validating the use of the SNP clustering tool for informing appropriate public-health responses. Overall, 1006 S. flexneri cases were reported, of which 563 clustered with at least one other case (10-SNP threshold). Linked questionnaire data were available for 106 clustered cases, of which 84.0 % belonged to an 'adult male' cluster. At the 10-SNP threshold, 95.1 % [95 % confidence interval (CI) 88.0-98.1%] of MSM belonged to an 'adult male' cluster, while 73.2 % (95 % CI 49.1-87.5%) of non-MSM belonged to a 'community' or 'travel-associated' cluster. At the 25-SNP threshold, all MSM (95 % CI 96.0-100%) belonged to an 'adult male' cluster and 77.8 % (95 % CI 59.2-89.4%) of non-MSM belonged to a 'community' or 'travel-associated' cluster. Within one phylogenetic clade of S. flexneri, 9 clusters were identified (7 'adult male'; 2 'community') using a 10-SNP threshold, while a single 'adult male' cluster was identified using a 25-SNP threshold. Genotypic markers of azithromycin resistance were detected in 84.5 % (294/348) of 'adult male' cases and 20.9 % (9/43) of cases in other clusters (10-SNP threshold), the latter of which contained gay-identifying men who reported recent same-sex sexual contact. Our study suggests that SNP clustering can be used to identify Shigella clusters representing likely sexual transmission in MSM to inform infection control. Defining clusters requires a flexible approach in terms of genetic relatedness to ensure a clear understanding of underlying transmission networks

Genome-Wide Mapping of Collier In Vivo Binding Sites Highlights Its Hierarchical Position in Different Transcription Regulatory Networks

Collier, the single Drosophila COE (Collier/EBF/Olf-1) transcription factor, is required in several developmental processes, including head patterning and specification of muscle and neuron identity during embryogenesis. To identify direct Collier (Col) targets in different cell types, we used ChIP-seq to map Col binding sites throughout the genome, at mid-embryogenesis. In vivo Col binding peaks were associated to 415 potential direct target genes. Gene Ontology analysis revealed a strong enrichment in proteins with DNA binding and/or transcription-regulatory properties. Characterization of a selection of candidates, using transgenic CRM-reporter assays, identified direct Col targets in dorso-lateral somatic muscles and specific neuron types in the central nervous system. These data brought new evidence that Col direct control of the expression of the transcription regulators apterous and eyes-absent (eya) is critical to specifying neuronal identities. They also showed that cross-regulation between col and eya in muscle progenitor cells is required for specification of muscle identity, revealing a new parallel between the myogenic regulatory networks operating in Drosophila and vertebrates. Col regulation of eya, both in specific muscle and neuronal lineages, may illustrate one mechanism behind the evolutionary diversification of Col biological roles

Listeriosis associated with pre-prepared sandwich consumption in hospital in England, 2017

A case of listeriosis occurred in a hospitalised patient in England in July 2017. Analysis by whole genome sequencing of the Listeria monocytogenes from the patient's blood culture was identified as clonal complex (CC) 121. This culture was indistinguishable to isolates from sandwiches, salads and the maufacturing environment of Company X which supplied these products widely to the National Health Service. Whilst an inpatient, the case was served sandwiches produced by this company on 12 occasions. No other cases infected by this type were detected in the UK between 2016 and 2020. Between 2016 and 2020, more than 3000 samples of food, food ingredients and environmental swabs from this company were tested. Listeria monocytogenes contamination rates declined after July 2017 from 31% to 0.3% for salads and 3% to 0% for sandwiches. A monophyletic group of 127 L. monocytogenes CC121 isolates was recovered during 2016-2019 and was used to estimate the time of the most recent common ancestor as 2014 (95% CI of between 2012 and 2016). These results represent persistent contamination of equipment, food contact surfaces and foods at a food manufacturer by a single L. monocytogenes strain. Colonisation and persistent contamination of food and production environments are risks for public health

Listeriosis associated with pre-prepared sandwich consumption in hospital in England, 2017

A case of listeriosis occurred in a hospitalised patient in England in July 2017. Analysis by whole genome sequencing of the Listeria monocytogenes from the patient's blood culture was identified as clonal complex (CC) 121. This culture was indistinguishable to isolates from sandwiches, salads and the maufacturing environment of Company X which supplied these products widely to the National Health Service. Whilst an inpatient, the case was served sandwiches produced by this company on 12 occasions. No other cases infected by this type were detected in the UK between 2016 and 2020. Between 2016 and 2020, more than 3000 samples of food, food ingredients and environmental swabs from this company were tested. Listeria monocytogenes contamination rates declined after July 2017 from 31% to 0.3% for salads and 3% to 0% for sandwiches. A monophyletic group of 127 L. monocytogenes CC121 isolates was recovered during 2016-2019 and was used to estimate the time of the most recent common ancestor as 2014 (95% CI of between 2012 and 2016). These results represent persistent contamination of equipment, food contact surfaces and foods at a food manufacturer by a single L. monocytogenes strain. Colonisation and persistent contamination of food and production environments are risks for public health

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. Of the 4% (n = 271) of isolates of subspecies I exhibiting a mismatch, 119 were due to a process error in the laboratory, 26 were likely caused by the serotype designation in the MLST database being incorrect and 126 occurred when two different serovars belonged to the same ST. The population structure of S. enterica subspecies II–IV differs markedly from that of subspecies I and, based on current data, defining the serovar from the clonal complex may be less appropriate for the classification of this group. Novel sequence types that were not present in the MLST database were identified in 8.6% of the total number of samples tested (including S. enterica subspecies I–IV and S. bongori) and these 654 isolates belonged to 326 novel STs. For S. enterica subspecies I, WGS MLST derived serotyping is a high throughput, accurate, robust, reliable typing method, well suited to routine public health surveillance. The combined output of ST and serovar supports the maintenance of traditional serovar nomenclature while providing additional insight on the true phylogenetic relationship between isolates. </p

Two Outbreaks of Foodborne Gastrointestinal Infection Linked to Consumption of Imported Melons, United Kingdom, March to August 2021

The aim of this study was to describe two foodborne outbreaks caused by contaminated imported melon and make recommendations for future practice. Between March and July 2021, there was an outbreak of 113 cases of Salmonella Braenderup in the UK (62% female, median age 61 years, 33% hospitalized). Analytical epidemiological studies identified Galia melons as the vehicle of infection (OR 671.9, 95% CI 39.0–58,074.0, p < 0.001). Subsequently, the outbreak strain was isolated from two samples of Galia melon imported from Latin America. In July and August 2021, there was an outbreak of 17 cases of Shiga toxin-producing Escherichia coli (STEC) O157:H7 in the UK (53% female, median age 21 years, 35% were hospitalized). Review of the STEC surveillance questionnaire data, followed by the analysis of responses from a modified hypothesis-generating questionnaire, implicated eating precut watermelon from retailer B sourced from Europe as the vehicle of infection. Outbreaks of gastrointestinal pathogens caused by contaminated food of nonanimal origin are a global public health concern. Given the difficulty in removing pathogens from the flesh of ready-to-eat fruit and vegetables, public health interventions should target all steps of the food chain prior to consumption, from cultivation on the farm to processing/packing and distribution

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. Of the 4% (n = 271) of isolates of subspecies I exhibiting a mismatch, 119 were due to a process error in the laboratory, 26 were likely caused by the serotype designation in the MLST database being incorrect and 126 occurred when two different serovars belonged to the same ST. The population structure of S. enterica subspecies II–IV differs markedly from that of subspecies I and, based on current data, defining the serovar from the clonal complex may be less appropriate for the classification of this group. Novel sequence types that were not present in the MLST database were identified in 8.6% of the total number of samples tested (including S. enterica subspecies I–IV and S. bongori) and these 654 isolates belonged to 326 novel STs. For S. enterica subspecies I, WGS MLST derived serotyping is a high throughput, accurate, robust, reliable typing method, well suited to routine public health surveillance. The combined output of ST and serovar supports the maintenance of traditional serovar nomenclature while providing additional insight on the true phylogenetic relationship between isolates. </p

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. Of the 4% (n = 271) of isolates of subspecies I exhibiting a mismatch, 119 were due to a process error in the laboratory, 26 were likely caused by the serotype designation in the MLST database being incorrect and 126 occurred when two different serovars belonged to the same ST. The population structure of S. enterica subspecies II–IV differs markedly from that of subspecies I and, based on current data, defining the serovar from the clonal complex may be less appropriate for the classification of this group. Novel sequence types that were not present in the MLST database were identified in 8.6% of the total number of samples tested (including S. enterica subspecies I–IV and S. bongori) and these 654 isolates belonged to 326 novel STs. For S. enterica subspecies I, WGS MLST derived serotyping is a high throughput, accurate, robust, reliable typing method, well suited to routine public health surveillance. The combined output of ST and serovar supports the maintenance of traditional serovar nomenclature while providing additional insight on the true phylogenetic relationship between isolates