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BackgroundLow- and middle-income countries (LMICs) have high morbidity and mortality from drug-resistant infections, especially from enteric bacteria such as Escherichia coli. LMICs have varying infrastructure and services in the community to separate people from human and animal waste, creating risks for ESBL-Enterobacterales (ESBL-E) transmission. Limited data exist from Southern Africa on the prevalence of ESBL-E the community.Methods and findingsIn this longitudinal cohort study we took a one-health approach to investigating prevalence and distribution of ESBL-E in urban, peri-urban and rural Malawian households between May 2018 and October 2020. We described human health, antibiotic usage (ABU), health seeking behaviour, structural and behavioural environmental health practices, and animal husbandry at these households. In parallel, human and animal stool and diverse environmental samples were collected and cultured to identify presence of ESBL E. coli and ESBL K. pneumoniae. Univariable and multivariable analysis was performed to determine associations with human ESBL-E colonisation.We recruited 300 households, totalling 841 visits, and a paucity of environmental health infrastructure and materials for safe sanitation was noted across all sites. In total, 11,975 samples were cultured and ESBL-E were isolated from 41.8% (n=1190) of human stool and 29.8% (n=290) of animal stool samples. Animal species with particularly high rates of ESBL-E colonisation included pigs (56.8%, n=21) poultry (32.5%, n=148) and dogs (58.8% n= 30). ESBL-E were isolated from 66.2% (n=339) of river water samples and 46.0% (n=138) of drain samples. Urban areas had greater ESBL-E contamination of food, household surfaces, floors and the external environment, alongside the highest rates of ESBL-E colonisation in humans (47.1%, n=384) and animals (55.1%, n=65). Multivariable models illustrated that human ESBL E. coli colonisation was associated with the wet season (aOR = 1.66, 95%CrI: 1.38-2.00), living in urban areas (aOR = 2.01, 95%CrI: 1.26-3.24), advanced age (aOR = 1.14, 95%CrI: 1.05-1.24) and in households where animals were observed interacting with food (aOR = 1.62, 95%CrI: 1.17-2.28) or kept inside (aOR = 1.58, 95%CrI: 1.00-2.43). Human ESBL K. pneumoniae colonisation was also associated with the wet season (aOR = 2.23, 95%CrI: 1.63-2.76.ConclusionWe identified extremely high levels of ESBL-E colonisation in humans and animals and contamination of the environment in Southern Malawi. Urbanisation and season are key risks for ESBL-E colonisation, perhaps reflecting environmental contamination as toilets overflow in high population density areas in heavy rains in the wet season. Without adequate efforts to improve environmental health, ESBL transmission is likely to persist in this setting.

In England and Wales, Public Health England applies whole genome sequencing to cultures of Listeria monocytogenes recovered from human cases of listeriosis, foods, and food production environments. Following the routine inspection of a small retailer in February and March 2016, two unopened packs of cooked chicken produced by the same manufacturer were found to be contaminated with L. monocytogenes at levels of 340 and 20 CFU/g. A public recall of this product was issued in March 2016. Early in 2017, a less than five single-nucleotide polymorphism single-linkage cluster was detected between the L. monocytogenes isolates from the two cooked chicken products and cultures from five cases of human listeriosis in England and Scotland with onsets of illness between March 2016 and February 2017. Epidemiological data provided further supportive evidence that this cluster was an outbreak linked to a manufacturer of cooked chicken whose products were supplied to the small retailer that initiated the outbreak investigation. Unrelated to this outbreak, 34 L. monocytogenes isolates recovered from routine food monitoring of 2,007 samples of cooked chicken during 2013 to 2017 were analyzed by whole genome sequencing. Previously undetected fewer than five single-nucleotide polymorphism single-linkage clusters were identified between cultures from cooked chicken and with those from two clusters and two sporadic cases of human listeriosis that were consistent with foodborne transmission. This analysis identified linkage of L. monocytogenes clusters within specific food chains more readily than traditional manual tracing. Linking of data associated with L. monocytogenes cultures from cases of listeriosis with those from unrelated food testing is a unique source of information for communicable disease risk assessment, epidemiological studies, and disease prevention and control. This report provides further evidence that should act as a reminder of the association between cooked chicken consumption and human listeriosis. HIGHLIGHTS

Results from monitoring of the microbiological quality of 2,721 samples of ready-to-eat cooked chicken collected between 2013 to 2017 in England were reviewed: 70% of samples were from retail, catering or manufacture and 30% were imported and collected at English ports. Samples were tested for a range of bacterial pathogens and indicator organisms. Six samples (

In sub-Saharan Africa (sSA), there is high morbidity and mortality from severe bacterial infection and this is compounded by antimicrobial resistance, in particular, resistance to 3rd-generation cephalosporins. This resistance is typically mediated by extended-spectrum beta lactamases (ESBLs). To interrupt ESBL transmission it will be important to investigate how human behaviour, water, sanitation, and hygiene (WASH) practices, environmental contamination, and antibiotic usage in both urban and rural settings interact to contribute to transmission of ESBL E. coli and ESBL K. pneumoniae between humans, animals, and the environment. Here we present the protocol for the Drivers of Resistance in Uganda and Malawi (DRUM) Consortium, in which we will collect demographic, geospatial, clinical, animal husbandry and WASH data from a total of 400 households in Uganda and Malawi. Longitudinal human, animal and environmental sampling at each household will be used to isolate ESBL E. coli and ESBL K. pneumoniae. This will be complimented by a Risks, Attitudes, Norms, Abilities and Self-Regulation (RANAS) survey and structured observations to understand the contextual and psychosocial drivers of regional WASH practices. Bacterial isolates and plate sweeps will be further characterised using a mixture of short-,long-read and metagenomic whole-genome sequencing. These datasets will be integrated into agent-based models to describe the transmission of EBSL resistance in Uganda and Malawi and allow us to inform the design of interventions for interrupting transmission of ESBL-bacteria.

Background: The World Health Organisation recommends prioritised use of recently prequalified typhoid conjugate vaccines in countries with the highest incidence of typhoid fever. However, representative typhoid surveillance data are lacking in many low-income countries because of the costs and challenges of diagnostic clinical microbiology. Environmental surveillance (ES) of Salmonella Typhi in sewage and wastewater using molecular methods may offer a low-cost alternative, but its performance in comparison with clinical surveillance has not been assessed. Methods: We developed a harmonised protocol for typhoid ES and its implementation in communities in India and Malawi where it will be compared with findings from hospital-based surveillance for typhoid fever. The protocol includes methods for ES site selection based on geospatial analysis, grab and trap sample collection at sewage and wastewater sites, and laboratory methods for sample processing, concentration and quantitative polymerase chain reaction (PCR) to detect Salmonella Typhi. The optimal locations for ES sites based on digital elevation models and mapping of sewage and river networks are described for each community and their suitability confirmed through field investigation. We will compare the prevalence and abundance of Salmonella Typhi in ES samples collected each month over a 12-month period to the incidence of blood culture confirmed typhoid cases recorded at referral hospitals serving the study areas. Conclusions: If environmental detection of Salmonella Typhi correlates with the incidence of typhoid fever estimated through clinical surveillance, typhoid ES may be a powerful and low-cost tool to estimate the local burden of typhoid fever and support the introduction of typhoid conjugate vaccines. Typhoid ES could also allow the impact of vaccination to be assessed and rapidly identify circulation of drug resistant strains.

Fresh betel leaves (Piper betle L.), imported into the UK are a traditional ready-to-eat food consumed by Asian populations. We report here the consolidation of routinely collected data to model the public health risks from consumption of this food. Amongst 2110 samples collected at Border Inspection, wholesale, catering or retail, Salmonella was detected in 488 (23%) of samples tested between 2011 and 2017 and was the most commonly Salmonella-contaminated ready-to-eat food examined by Public Health England during this period. Using data from multiple samples (usually 5) tested per consignment sampled at Border Inspection, contamination levels were calculated by most probable number: seasonal, temporal and country specific differences were detected. Quantitative contamination data was used to estimate the levels present at retail, and a β-Poisson dose response model the probability of illness was calculated. Using data for products imported from India, the probability of acquiring infection following a single exposure (comprising of a single leaf) was estimated to be between 0.00003 (January-March) and 0.0001 (July-September). Using British Asian population data for individuals over 30 years of age in England in 2011, two estimates of consumption were modelled as 2.1 and 12.8 million servings per annum. Results from the model estimated 160 cases (range 102 to 242) and 960 cases (range 612 to 1456) per year in England for the two consumption estimates and equated to 34 (range 22 to 51) and 204 (range 130 to 310) salmonellosis cases per year reported to national surveillance. Salmonella from 475 of the contaminated samples were further characterised which showed a heterogeneous population structure with 46 S. enterica subsp. Enterica serovars, together with S. enterica subs diarizonae and salamae identified. Isolates from individual consignments were diverse and close genetic relationships between independent isolates were very rare except from within an individual consignment. There were no outbreaks detected as associated with betel leaf consumption. However analysis by whole genome sequencing of the 2014-17 data identified two cases where the clinical isolate had5 single nucleotide polymorphism differences to isolates from betel leaves which is indicative of a likely epidemiological link and common source of contamination. Due to the diversity of the Salmonella contaminating this product, associations between salmonellosis cases and betel leaf consumption will appear sporadic and unlikely to be detected by current surveillance strategies based on outbreak detection.

Aims This study evaluated detection methods for Salmonella Typhi (S. Typhi) in the environment, to establish a novel pathway from field sampling to isolation of viable organisms and molecular confirmation from complex environmental samples, thus enabling environmental surveillance of typhoid. Methods and Results Multiple media were assessed using clinical isolates from the Public Health England’s (PHE) Culture collection. The culture pathway selected consisted of a primary 2% bile broth and secondary Selenite F broth, followed by modified Chromogenic Agar for Salmonella Esterase (mCASE). A qPCR assay was adapted from a validated S. Typhi PCR panel for confirmation of isolates, with comparison to biochemical and serological tests showing good specificity. Sampling locations in Blantyre, Malawi were used to compare sampling methods. Viable S. Typhi were isolated from a mixture of trap and grab river water samples on six occasions. Conclusions Culture of viable S. Typhi from environmental samples was possible using effective capture and culture techniques. Significance and impact of study Whilst several studies have attempted to detect S. Typhi from the environment, this is the first successful attempt to isolate the organism from river water since the 1980’s. Supplementing clinical data with environmental screening offers the potential for enhanced surveillance, which might inform interventions and assess vaccination programmes.

Foodborne outbreaks associated with transmission of norovirus are increasingly becoming a public health concern. Foods can be contaminated with faecal material at the point of production or during food preparation, in both the home and in commercial premises. Transmission of norovirus occurs through the faecal-oral route, either via person-to-person contact or through faecal-contamination of food, water, or environmental surfaces. Understanding the role and pathways of norovirus transmission - either via food handlers' hands, contaminated foods or the environment - remains a key public health priority to reduce the burden of norovirus-associated gastroenteritis. However the proportion of norovirus that is typically transferred remains unknown. Understanding this is necessary to estimate the risk of infection and the burden of gastroenteritis caused by norovirus. In this paper we present a novel method of capture, concentration and molecular detection of norovirus from a wider range of complex food matrices than those demonstrated in existing published methods. We demonstrate that this method can be used as a tool to detect and quantify norovirus from naturally contaminated food, and for monitoring norovirus transfer between food handlers' gloved hands, food or the environment. We measure the effect of introducing contamination at different food production process stages, to the final food product, to determine whether this could cause infection and disease. Between 5.9 and 6.3 Log10 cDNA copies/μl of norovirus GII were inoculated onto food handlers' gloved hands, food or the environment and 1.1-7.4% of norovirus contamination was recovered from all samples tested. When interpreted quantitatively, this percentage equates to levels predicted to be sufficient to cause infection and disease through consumption of the final food product, demonstrating a public health risk. Overall detection and quantification of norovirus from foods, food handlers' gloved hands and the environment, when suspected to be implicated in foodborne transmissions, is paramount for appropriate outbreak investigation.

Background The World Health Organisation recommends prioritised use of recently prequalified typhoid conjugate vaccines in countries with the highest incidence of typhoid fever. However, representative typhoid surveillance data are lacking in many low-income countries because of the costs and challenges of diagnostic clinical microbiology. Environmental surveillance (ES) of Salmonella Typhi in sewage and wastewater using molecular methods may offer a low-cost alternative, but its performance in comparison with clinical surveillance has not been assessed. Methodology/Principal Findings We developed a harmonised protocol for typhoid ES and its implementation in communities in India and Malawi where it will be compared with findings from hospital-based surveillance for typhoid fever. The protocol includes methods for ES site selection based on geospatial analysis, grab and trap sample collection at sewage and wastewater sites, and laboratory methods for sample processing, concentration and quantitative PCR to detect Salmonella Typhi. The optimal locations for ES sites based on digital elevation models and mapping of sewage and river networks are described for each community and their suitability confirmed through field investigation. We will compare the prevalence and abundance of Salmonella Typhi in ES samples collected each month over a 12-month period to the incidence of blood culture confirmed typhoid estimated from cases recorded at referral hospitals serving the study areas and community surveys of healthcare seeking for individuals with fever. Significance If environmental detection of Salmonella Typhi correlates with the incidence of typhoid fever estimated through clinical surveillance, typhoid ES may be a powerful and low-cost tool to estimate the local burden of typhoid fever and support the introduction of typhoid conjugate vaccines. Typhoid ES could also allow the impact of vaccination to be assessed and rapidly identify circulation of drug resistant strains. Author Summary Typhoid fever is a bacterial enteric infection that remains a significant health burden to the 6.4 billion people living in low- and middle-income countries. The WHO recently prequalified highly immunogenic typhoid conjugate vaccines (TCVs) and recommended that the introduction of public vaccination programmes should be based on an understanding of the local epidemiology of infection. However, representative data on the community level describing incidence of microbiologically confirmed typhoid cases are limited, reflecting the costs and challenges of implementing blood culture for Salmonella Typhi (S. Typhi). Therefore, cost-effective alternative means of community surveillance are required to assess overall burden of disease. We developed a protocol for typhoid environmental surveillance, including methods for the identification of suitable sampling sites, sample collection and laboratory processing. The detection of S. Typhi in wastewater and sewage samples will be examined against the outcomes of hospital-based surveillance for typhoid fever with healthcare utilisation surveys to evaluate and validate the use of ES as an effective means of assessing community level incidence of typhoid. The findings of this study will inform potential wider implementation of ES for typhoid to support the introduction of TCVs and monitor their impact.

Results from monitoring of the microbiological quality of 2,721 samples of ready-to-eat cooked chicken collected between 2013 to 2017 in England were reviewed: 70% of samples were from retail, catering or manufacture and 30% were imported and collected at English ports. Samples were tested for a range of bacterial pathogens and indicator organisms. Six samples (1%) had unsatisfactory levels of pathogens which were potentially injurious to health. Neither Salmonella nor Campylobacter were recovered from any sample. Two samples from catering settings contained either an unsatisfactory level of Bacillus cereus (5 x 10 6 CFU/g) or an unsatisfactory level of coagulase positive staphylococci (1.6 x 10 4 CFU/g). Listeria monocytogenes was recovered from 36 samples (one at manufacture, 26 at catering and nine at retail) and in four instances, unsatisfactory levels (≥10 2 CFU/g) were detected (three samples collected at catering and one at retail). For L. monocytogenes there were no significant differences between the rates of contamination with between the samples collected from ports, manufacture, retail supermarkets and other retailers (p = 0.288). There were no differences between the rates of contamination for other potential pathogens detected between samples from different settings. The prevalence of hygiene indicators ( Escherichia coli , Enterobacteriaceae and Aerobic Colony Counts) at import was significantly lower than in samples collected from manufacturers, retail or catering (p0.01). Samples collected from catering gave poorer results than all other settings. Regardless of the stage in the food chain, samples from Thailand and from other non-EU countries were of significantly better microbiological quality with respect to indicator organisms than those from the UK or from other EU countries (p =0.001).

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. Retrospective whole genome sequencing (WGS) analysis of isolates provided robust microbiological evidence of links between cases, foods, and the environments in which they were produced and demonstrated that for some cases and foods, identified by fluorescent amplified fragment length polymorphism, the molecular typing method in routine use at the time, were not part of the outbreak. WGS analysis also showed that the strains causing illness had persisted in two food production environments for many years and in one producer had evolved into two strains over a period of around 8 years. This article demonstrates the value of reviewing L. monocytogenes typing data from clinical cases together with that from foods as a means of identifying potential vehicles and sources of infection in outbreaks of listeriosis. It illustrates the importance of reviewing retrospective L. monocytogenes typing alongside enhanced surveillance data to characterize extended outbreaks and inform control measures. Also, this article highlights the advantages of WGS analysis for strain discrimination and clarification of evolutionary relationships that refine outbreak investigations and improve our understanding of L. monocytogenes in the food chain.

Aims To investigate the microbiological quality of imported fresh leaves on retail sale during 2017 with respect to Salmonella, Shiga-toxin-producing Escherichia coli (STEC) and levels of E. coli. Methods and results Two hundred and seventy-nine samples of imported edible leaves (69 banana, 77 betel, 118 curry and 15 other types) were tested. Salmonella spp. were confirmed by whole-genome sequencing and isolated from 44 samples, 26% from curry leaves, 14% from betel and 2·4% from all other leaf types: 80% of all samples contained ≥102 , 44% ≥103 and 22% ≥104 CFU of E. coli CFU per g. All samples where Salmonella were detected also yielded ≥20 CFU of E. coli/g. 54 samples were tested for STEC which was detected in six samples and isolated from three: one was identified as STEC O157:H7. Conclusions This report further highlights an ongoing problem of Salmonella contamination of imported fresh edible leaves. Significance and impact of the study Among all food tested by Public Health England (approximately 11 000 per annum), curry leaves were the herb most commonly contaminated with Salmonella, and betel leaves were the most commonly contaminated ready-to-eat food. The high proportion with unsatisfactory E. coli levels and the detection of STEC suggests risks of contamination by multiple enteric pathogens.

We determined the prevalence and types of extended-spectrum β-lactamase (ESBL)-producing and carbapenem-resistant Escherichia coli in raw retail beef, chicken, pork, fruit and vegetables in five UK regions in 2013-14. Raw meat (n=397), and fruit and vegetable samples (n=400) were purchased from retail stores in London, East Anglia, North West England, Scotland and Wales. Samples were tested for the presence of ESBL-producing E. coli by plating enriched samples on CHROMagar CTX and CHROMagar ESBL, for AmpC-type E. coli by plating on "CHROMagar FOX" (CHROMagar ECC+16mg/L cefoxitin), and for carbapenem-resistant E. coli by plating on CHROMagar KPC. Additionally, pre-enrichment counts were performed on the above agars, and on CHROMagar ECC. Isolates of interest were characterised by MALDI-ToF to confirm identification, by PCR for blaCIT,blaCTX-M,blaOXA, blaSHV and blaTEM genes; ESBL or blaCIT genes were sequenced. Only 1.9% and 2.5% of beef and pork samples, respectively were positive for ESBL-producing E. coli after enrichment compared with 65.4% of chicken samples. 85.6% positive samples from chicken meat carried blaCTX-M-1; blaCTX-M-15 was not detected. None of the fruits or vegetables yielded ESBL-producing E. coli and none of the meat, fruit or vegetable samples yielded carbapenem-resistant E. coli. Retail chicken was more frequently a source of ESBL-producing E. coli than were beef, pork, fruit or vegetables. None of the foodstuffs yielded E. coli with CTX-M-15 ESBL, which dominates in human clinical isolates in the UK, and none yielded carbapenem-resistant E. coli.

Since 2010, human salmonellosis outbreaks in the UK have been detected as associated with the consumption of duck eggs. Little data are available on the rate of occurrence of Salmonella in duck eggs. The aim of this study was to investigate the occurrence of Salmonella spp. in duck eggs on sale and from catering in England during 2011, particularly those from small-scale production. All samples were collected independently of human salmonellosis outbreak investigations. Composite samples of 6-10 eggs (shells and contents were examined separately) were examined for the presence of Salmonella spp. using the ISO 6579:2002 method. Salmonella spp. was recovered from two of 145 samples (1·4%). In one sample, Salmonella Typhimurium DT 8 was isolated from the shells while Salm. Typhimurium DT 8 and Salm. Typhimurium DT30 were isolated from the contents. Salmonella Typhimurium DT8 was isolated from the egg shells only in the second contaminated sample. This study provides baseline data for risk assessors, regulators and the food industry and may be helpful in communicating risks associated with the consumption of this product as well as evaluating risk management options to control food safety including vaccination of ducks. SIGNIFICANCE AND IMPACT OF THE STUDY Human salmonellosis outbreaks in England and Northern Ireland due to Salmonella enterica serovar Typhimurium definitive phage type (DT) 8 have been identified as associated with the consumption of duck eggs since 2010. This study has shown that Salmonella spp. was detected in 1·4% of ducks egg samples providing baseline data for risk assessors, regulators and the food industry. This may be helpful in communicating risks associated with the consumption of this product as well as evaluating risk management options to control food safety including vaccination of ducks.

Outbreaks of foodborne illness caused by Bacillus cereus and Listeria monocytogenes in England associated with meat pie consumption were detected in 2012. To obtain baseline data for pies unrelated to outbreaks, 862 samples of ready-to-eat meat pies were collected at retail or from catering facilities in England in 2013 and examined to enumerate food-poisoning bacteria and indicator organisms using Organization for Standardization (ISO) methods for Listeria spp. including L. monocytogenes (ISO 11290), Clostridium perfringens (ISO 21528), coagulase-positive staphylococci including Staphylococcus aureus (ISO 6888), Bacillus spp. including B. cereus (ISO 1737), Escherichia coli (ISO 16649), Enterobacteriaceae (ISO 21528), and aerobic colony counts (ACCs; ISO 4833). Microbiological quality was satisfactory in 94% of samples, borderline in 5%, and unsatisfactory in 1%. The proportion of pies from markets that were borderline or unsatisfactory significantly increased, and the proportion of borderline or unsatisfactory pies from supermarkets significantly decreased. Among the refrigerated (0 to 15°C) pies, microbiological quality significantly decreased in pies stored at >8°C and further significantly decreased at in pies stored at ambient temperature (>15 to 25°C). Samples collected at 25 to 40°C had the highest proportion of borderline or unsatisfactory results, but results improved in pies stored at >40°C. The most common cause for borderline or unsatisfactory results was elevated ACCs (5% of all samples). Within the individual microbiological parameters, borderline or unsatisfactory results resulted from elevated Enterobacteriaceae or Bacillus levels (10 samples for each), C. perfringens levels (2 samples), and S. aureus or E. coli levels (1 sample each). L. monocytogenes was recovered from one pie at

Fresh fruit has been associated with a number of foodborne outbreaks in recent years. In particular, a large outbreak of listeriosis in the United States in 2011 was associated with consumption of cantaloupe melon, and an outbreak of Salmonella Newport in the United Kingdom and Europe (also in 2011) was linked to watermelon consumption. A study of precut fruit products from catering and retail premises in the United Kingdom was, therefore, carried out to assess their microbiological safety. Between January and March 2012, samples (1,188) of ready-to-eat precut fruit were collected from retail and catering premises in the United Kingdom, and 99% were of satisfactory microbiological quality. However, four samples (0.3%) were of an unsatisfactory quality (one with 800 CFU/g Listeria monocytogenes and three with >100 CFU/g Escherichia coli), and five samples (0.4%) were of a borderline quality owing to the presence of E. coli (two samples with a level of 20 CFU/g), Staphylococcus aureus (two samples with levels of >50 CFU/g), or L. monocytogenes (one sample with a level of 80 CFU/g). L. monocytogenes or other Listeria species were detected in a further 54 samples (4.5%) at levels below the threshold considered to be borderline or unsatisfactory. A significantly larger proportion of samples from one national supermarket chain was contaminated with L. monocytogenes than other supermarkets, and two types were, in this study, unique to this supermarket. This study shows that overall, the microbiological quality of ready-to-eat precut fruit was good. However, the presence of Listeria species in 5% of samples highlights the need for good hygiene during preparation and satisfactory temperature and time control during storage of these food products.

Frozen vegetables have previously been associated with outbreaks of listeriosis in both the USA and Europe. An outbreak of Listeria monocytogenes serogroup 4 caused 53 cases in five European countries between 2015 and 2018. Whole genome sequencing (WGS) indicated that frozen sweet corn from a producer in Hungary was the source of illness. However, limited data is available on the prevalence of Listeria in frozen produce. A study of frozen fruit and vegetables from catering and retail premises in England was therefore carried out to assess their microbiological quality with respect to Listeria and Escherichia coli. Between December 2018 and April 2019, 1050 frozen fruit and vegetable samples were collected. Of these, 99% were of a satisfactory or borderline microbiological quality. Eleven samples (1%) contained ≥100 cfu/g of Escherichia coli (considered unsatisfactory in products labelled as ready-to-eat). Listeria monocytogenes or other Listeria species were detected in six samples (2%) of fruit compared to 167 samples (24%) of vegetables and six samples (26%) of fruit and vegetable mixes, but none at a level of ≥100 cfu/g. Characterisation by WGS of 74 L. monocytogenes isolates identified ten genetic clusters indicating a common source. For 8 of the 10 clusters, the isolates came from homogenous food types: four were sweet corn, and there was one cluster each for beans, peas, peppers and broccoli. There were five genetic associations between isolates from frozen vegetables and from clinical cases of listeriosis, including two cultures from frozen beans that were indistinguishable from the 2015–2018 sweet corn outbreak strain. This study indicates that L. monocytogenes was present in 10% of frozen vegetables and even though products are generally not ready-to-eat and are intended to be cooked prior to consumption, these have the potential to cause illness. Clear cooking and handling instructions are therefore required on these products to ensure that the health of consumers is not put at risk, and appropriate Good Manufacturing Practice measures should be followed by all fruit and vegetable freezing plants in order to reduce contamination with Listeria during processing.

BackgroundExtended-spectrum β-lactamase-producing Escherichia coli isolates (ESBL-E coli) cause more than 5000 cases of bacteraemias annually in the UK. The contribution of the food chain to these infections is debated. We aimed to identify the most important reservoirs of ESBL-E coli that colonise and infect humans to identify strategic intervention points.MethodsSampling for ESBL-E coli was done between Aug 1, 2013, and Dec 15, 2014. We used selective media to seek ESBL-E coli in routinely submitted samples from human faeces, and prospectively collected samples from sewage, farm slurry, and retail foodstuffs in London, East Anglia, northwest England, Scotland, and Wales. We sequenced recovered isolates and compared these isolates with 293 bloodstream and 83 veterinary surveillance ESBL-E coli isolates from the same regions.Findings2157 (11%) of 20 243 human faeces samples contained ESBL-E coli, including 678 (17%) of 3995 in London. ESBL-E coli also were frequent in sewage and retail chicken (104 [65%] of 159 meat samples), but were rare in other meats and absent from plant-based foods (0 of 400 fruit and vegetable samples). Sequence type (ST) 131 dominated among ESBL-E coli from human blood (188 [64%] of 293 isolates), faeces (128 [36%] of 360), and sewage (14 [22%] of 65) with STs 38 and 648 also widespread; CTX-M-15 was the predominant ESBL in these lineages (319 [77%] of 416). By contrast, STs 602, 23, and 117—mostly with CTX-M-1 ESBL—dominated among food and veterinary isolates (68 [31%] of 218), with only two ST131 organisms recovered. ST10 occurred in both animals and humans, being frequent in surveillance bovines (11 [22%] of 51 cattle) and representing 15 (4%) of 360 human faecal isolates (but only three [1%] of 293 from bacteraemias); however, both human and animal ST10 isolates were diverse in serotype.InterpretationMost human bacteraemias with ESBL-E coli in the UK involve internationally prevalent human-associated STs, particularly ST131; non-human reservoirs made little contribution to invasive human disease. Any interventions that seek to target food or livestock can affect the numbers of human infections caused by ESBL-E coli; prevention of the spread of resistant lineages among humans is more vital.

We report a national

We report a national Pseudomonas aeruginosa outbreak from a common source following piercings between July and September 2016 in England. The multi-agency outbreak investigation included active case finding, microbiological testing of environmental samples and case specimens including Variable Number Tandem Repeat (VNTR) typing and a retrospective cohort study. Overall, 162 outbreak cases (29 confirmed, 14 probable and 119 possible) and 14 non-outbreak cases were identified; all confirmed cases had ear piercings (93% cartilage). Outbreak cases were predominantly female (95%) and had a median age of 18 years (interquartile range: 13–56 years). Nineteen outbreak cases required surgery under general anaesthetic The same outbreak VNTR type (11,3,5,3,3,3,6,4,7) was isolated from bottles of an aftercare solution from a single manufacturer and in specimens from confirmed cases who attended eight different piercing studios supplied with this product. In the cohort study, use of aftercare solution was associated with becoming a case (aOR: 4.60, 95% confidence interval: 1.65–12.90). Environmental, microbiological and epidemiological investigations confirmed that contamination during production of aftercare solution was the source of this national outbreak; highlighting challenges in the regulation of a cosmetic products used in the piercing industry and that guidance on piercing aftercare may need to be reviewed.

UNLABELLED A total of 554 samples of bean sprouts or other sprouted seeds were collected at retail sale and submitted to nine Official Control Laboratories in England and Northern Ireland during January to March 2011. Samples (100 g) were tested for the presence of Salmonella using the EN ISO 6579:2002 method. Products labelled as ready-to-eat comprised 23% of the samples and 61% were labelled as raw or to-cook: the remaining 12% had no indication if the food was intended as ready-to-eat or ready-to-cook, and 4% were not recorded. Salmonella spp. were detected from four samples of mung-bean sprouts (0·7% of all the 554 samples) and all four isolates were confirmed as Salmonella enterica serovar Abaetetuba (11 : k : 1,5). Two of the samples where Salmonella was detected were sold as ready-to-eat (labelled 'rinse and serve' only): The remaining two were from samples labelled as ready-to-cook. SIGNIFICANCE AND IMPACT OF THE STUDY Consumption of sprouted seeds have been associated with infections from a range of foodborne pathogens, particularly Salmonella and shigatoxin producing Escherichia coli (STEC). However, there is limited data (including that from EU monitoring) on foodborne pathogens in samples of this food type which are not associated with outbreaks of infection. Out of 554 raw and ready-to-eat bean sprouts and sprouted seeds sampled at retail, Salmonella spp. was detected from four samples. This study illustrated the potential of this product to be contaminated with a human pathogen and the importance of considering the intended use and preparation of specific food in assessing microbiological risks.

AIMS Fresh herbs have been associated with a number of outbreaks in recent years, in the UK and elsewhere. A study of fresh herbs was carried out to assess their microbiological safety in relation to Salmonella contamination and levels of Escherichia coli. METHODS AND RESULTS Between January and March 2014, 774 samples of ready-to-eat, fresh, whole-leaf herbs were collected from retail premises in the UK. Overall, Salmonella was detected in 9 samples (1.2%). Of these, five were curry leaves. Other herbs contaminated with Salmonella were basil (2 samples), walleria (1) and coriander (1). Escherichia coli was detected in 13% of samples, with 11% containing unsatisfactory levels (≥ 10(2) /g). CONCLUSIONS Whilst 88% of samples in this study were of an acceptable microbiological quality, the presence of Salmonella and/or elevated E. coli levels in 12% is a cause for concern. Curry leaves, in particular, had significantly higher rates of contamination with both Salmonella and E. coli than other herbs. SIGNIFICANCE AND IMPACT This study highlights the potential public health risk associated with the consumption of certain ready-to-eat fresh herbs, and the need for good hygiene practices and effective decontamination procedures during the growth, harvesting and subsequent handling of these products. This article is protected by copyright. All rights reserved.

AIMS This study aimed to review the microbiological results for raw drinking milk (RDM) samples submitted to Public Health England laboratories between 2014 and 2016 in order to produce up-to-date data on the microbiological safety of RDM and inform future risk assessments on its sale. METHODS AND RESULTS A total of 902 samples of RDM were collected from retail sale in England for microbiological examination. Overall, 454 of 770 samples (59·0%) taken for routine monitoring were of a satisfactory quality, whilst eight (1·0%) were 'unsatisfactory and potentially injurious to health' due to the presence of Shiga toxin-producing Escherichia coli, Campylobacter or elevated levels of Listeria monocytogenes or coagulase-positive staphylococci. In contrast, 16 of 114 (14·0%) of samples taken in follow-up to a previous unsatisfactory result and 5 of 18 (27·8%) of samples related to illness were potentially injurious. A total of 229 of 902 samples (25·4%) gave unsatisfactory results due to elevated aerobic colony counts and/or coliforms, whilst 139 of 902 samples (15·4%) were of borderline quality due to coagulase-positive staphylococci. Listeria monocytogenes was detected at levels of

SUMMARYThis observational study aims to investigate the microbiological quality of commercially prepared lightly cooked foods with a major component of food of animal origin and collected as would be served to a consumer. A total of 356 samples were collected from catering (92%), retail (7%) or producers (1%) and all were independent of known incidents of foodborne illness. Using standard methods, all samples were tested for: the presence of Campylobacter spp. and Salmonella spp. and enumerated for levels of, Bacillus spp. including B. cereus, Clostridium perfringens, Listeria spp. including L. monocytogenes, Staphylococcus aureus, Escherichia coli, Enterobacteriacea and aerobic colony count (ACC). Results were interpreted as unsatisfactory, borderline or satisfactory according to the Health Protection Agency guidelines for assessing the microbiological safety of ready-to-eat foods placed on the market. Amongst all samples, 70% were classified as satisfactory, 18% were borderline and 12% were of unsatisfactory microbiological quality. Amongst the unsatisfactory samples, six (2%) were potentially injurious to health due to the presence of: Salmonella spp. (one duck breast); Campylobacter spp. (two duck breast and one chicken liver pâté); L. monocytogenes at 4·3 × 103 cfu (colony-forming units)/g (one duck confit with foie gras ballotin) and C. perfringens at 2·5 × 105 cfu/g (one chicken liver pâté). The remaining unsatisfactory samples were due to high levels of indicator E. coli, Enterobacteriaceae or ACC.

SUMMARYThe purpose of this study was to investigate the microbiological quality of liver pâté. During 2012–13, a total of 870 samples, unrelated to the investigation of food-poisoning outbreaks, were collected either at retail (46%), catering (53%) or the point of manufacture (1%) and were tested using standard methods to detect Salmonella spp. or Campylobacter spp., and to enumerate for Listeria spp., including Listeria monocytogenes, Clostridium perfringens, coagulase-positive staphylococci including Staphylococcus aureus, Bacillus spp., including Bacillus cereus, Escherichia coli, Enterobacteriaceae, and aerobic colony counts (ACCs). Seventy-three percent of samples were of satisfactory microbiological quality, 18% were borderline and 9% unsatisfactory. Salmonella spp. or Campylobacter spp. was not recovered from any sample. The most common causes of unsatisfactory results were elevated ACCs (6% of the samples) and high Enterobacteriaceae counts (4% of samples). The remaining unsatisfactory results were due to elevated counts of: E. coli (three samples); B. cereus (one sample at 2·6 × 105 cfu/g); or L. monocytogenes (one sample at 2·9 × 103 cfu/g). Pâté from retail was less likely to be contaminated with L. monocytogenes than samples collected from catering and samples from supermarkets were of significantly better microbiological quality than those from catering establishments.

This Local Authorities Co-ordinators of Regulatory Services/Health Protection Agency study was prompted by the increasing concern regarding the microbiological safety of ready-to-eat salad vegetable products, particularly fresh herbs. During May to October 2007, 3760 ready-to-eat fresh herbs, of different varieties, were sampled across the UK to assess their microbiological safety in relation to salmonella contamination and levels of Escherichia coli. Sixty (1.6%) herb samples were found to be of unsatisfactory quality according to Regulation (EC) No. 2073/2005 on the microbiological criteria of foodstuffs, i.e. contaminated with Salmonella spp. and/or containing E. coli at >10(3) cfu/g. When criteria in the PHLS Microbiological Guidelines for some ready-to-eat foods (2000) were used, 117 (3.9%) of herb samples were of unsatisfactory quality due to the presence of salmonella and/or E. coli at > or = 10(2) cfu/g. Eighteen (0.5%) samples of six different herb types were contaminated with Salmonella spp.: identified as serotypes Senftenberg (8), Agona (2), Anatum (1), Durban (1), Javiana (1), Mgulani (1), Montevideo (1), Unnamed (I 16:g, t: z42) (1), Virchow (1) and mixed Newport & Virchow (1). In each case the retailer and the UK Food Standards Agency were immediately informed and remedial action taken. Samples contaminated with S. Senftenberg were specifically associated with basil grown in Israel. Thirty-two human cases of S. Senftenberg infection were subsequently identified throughout England and Wales and a further 19 in Scotland, Denmark, The Netherlands and the USA. The strain of S. Senftenberg identified from the basil and that from cases had an indistinguishable molecular profile, suggesting a likely connection between consumption of basil and human infection. The presence of Salmonella spp. is unacceptable in ready-to-foods such as fresh herbs. This study highlights the necessity of applying good agricultural and hygiene practices pre-, during and post-harvest, at processing, retail and use. These practices help to prevent cross-contamination and/or bacterial growth occurring in these products. Best practice is to store and display such products at, or below, 8 degrees C as this inhibits bacterial growth.

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. A second outbreak of STEC O157 PT2 (outbreak 2) was identified epidemiologically following the detection of outbreak 1. Isolates associated with outbreak 2 were phylogenetically distinct from those in outbreak 1. Epidemiologically unrelated isolates on the same branch as the outbreak 2 cluster included those from human cases in England with domestically acquired infection and United Kingdom domestic cattle. Environmental sampling using PCR resulted in the isolation of STEC O157 PT2 from irrigation water at one implicated watercress farm, and WGS showed this isolate belonged to the same phylogenetic cluster as outbreak 2 isolates. Cattle were in close proximity to the watercress bed and were potentially the source of the second outbreak. Transfer of STEC from the field to the watercress bed may have occurred through wildlife entering the watercress farm or via runoff water. During this complex outbreak investigation, epidemiological studies, comprehensive testing of environmental samples, and the use of novel molecular methods proved invaluable in demonstrating that two simultaneous outbreaks of STEC O157 PT2 were both linked to the consumption of watercress but were associated with different sources of contamination.

Aims To investigate food hygiene practices at large events by assessing the microbiological quality of ready-to-eat food, drinking water, food preparation surfaces, cleaning cloths and wristbands worn by food handlers for event security purposes. Methods and Results Over a 7-month period, 1662 samples were collected at 153 events and examined for microbiological contamination. Eight per cent of food samples were of an unsatisfactory quality. A further one per cent contained potentially hazardous levels of human pathogenic bacteria. 27% of water samples, 32% of swabs and 56% of cloths were also unsatisfactory. These results represented an improvement in hygiene compared to a previous study carried out 12 months previously. A fifth of food handler wristbands were contaminated with Enterobacteriaceae, Escherichia coli and/or coagulase-positive staphylococci, with those bands made from fabric being more frequently contaminated than those made from plastic or other materials. Conclusions This study provides evidence that the food hygiene at large-scale events may have improved. However, there is still a need for continued efforts to maintain an ongoing improvement in cleaning regimes and food hygiene management. Significance and Impact of the Study This study was part of an ongoing focus on large events in the lead-up to the London 2012 Olympics. Lessons learnt here will be important in the planning of future large events.