Salmonella Hadar linked to two distinct transmission vehicles highlights challenges to enteric disease outbreak investigations.

In 2020, an outbreak of Salmonella Hadar illnesses was linked to contact with non-commercial, privately owned (backyard) poultry including live chickens, turkeys, and ducks, resulting in 848 illnesses. From late 2020 to 2021, this Salmonella Hadar strain caused an outbreak that was linked to ground turkey consumption. Core genome multilocus sequence typing (cgMLST) analysis determined that the Salmonella Hadar isolates detected during the outbreak linked to backyard poultry and the outbreak linked to ground turkey were closely related genetically (within 0-16 alleles). Epidemiological and traceback investigations were unable to determine how Salmonella Hadar detected in backyard poultry and ground turkey were linked, despite this genetic relatedness. Enhanced molecular characterization methods, such as analysis of the pangenome of Salmonella isolates, might be necessary to understand the relationship between these two outbreaks. Similarly, enhanced data collection during outbreak investigations and further research could potentially aid in determining whether these transmission vehicles are truly linked by a common source and what reservoirs exist across the poultry industries that allow Salmonella Hadar to persist. Further work combining epidemiological data collection, more detailed traceback information, and genomic analysis tools will be important for monitoring and investigating future enteric disease outbreaks.

The epidemiology of Shiga toxin-producing Escherichia coli serogroup O157 in England, 2009-2019.

Shiga toxin-producing Escherichia coli (STEC) serogroup O157 is a zoonotic, foodborne gastrointestinal pathogen of major public health concern. We describe the epidemiology of STEC O157 infection in England by exploring the microbiological and clinical characteristics, the demographic and geographical distribution of cases, and examining changes in environmental exposures over 11 years of enhanced surveillance. Enhanced surveillance data including microbiological subtyping, clinical presentations and exposures were extracted for all cases resident in England with evidence of STEC O157 infection, either due to faecal culture or serology detection. Incidence rates were calculated based on mid-year population estimates from the Office of National Statistics (ONS). Demographics, geography, severity and environmental exposures were compared across the time periods 2009-2014 and 2015-2019. The number of cases reported to national surveillance decreased, with the mean cases per year dropping from 887 for the period 2009-2014 to 595 for the period 2015-2019. The decline in STEC O157 infections appears to be mirrored by the decrease in cases infected with phage type 21/28. Although the percentage of cases that developed HUS decreased, the percentage of cases reporting bloody diarrhoea and hospitalisation remained stable. The number of outbreaks declined over time, although more refined typing methods linked more cases to each outbreak. Integration of epidemiological data with microbiological typing data is essential to understanding the changes in the burden of STEC infection, assessment of the risks to public health, and the prediction and mitigation of emerging threats.

Integrated surveillance of extended-spectrum beta-lactamase (ESBL)-producing Salmonella and Escherichia coli from humans and animal species raised for human consumption in Canada from 2012 to 2017.

Resistance to beta-lactam antimicrobials caused by extended-spectrum beta-lactamase (ESBL)-producing organisms is a global health concern. The objectives of this study were to (1) summarise the prevalence of potential ESBL-producing Escherichia coli (ESBL-EC) and Salmonella spp. (ESBL-SA) isolates from agrifood and human sources in Canada from 2012 to 2017, and (2) describe the distribution of ESBL genotypes among these isolates. All data were obtained from the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). CIPARS analysed samples for the presence of ESBLs through phenotypic classification and identified beta-lactamase genes (blaTEM, blaSHV, blaCTX, blaOXA, blaCMY-2) using polymerase chain reaction (PCR) and whole genome sequencing (WGS). The prevalence of PCR-confirmed ESBL-EC in agrifood samples ranged from 0.5% to 3% across the surveillance years, and was detected most frequently in samples from broiler chicken farms. The overall prevalence of PCR-confirmed ESBL-SA varied between 1% and 4% between 2012 and 2017, and was most frequently detected in clinical isolates from domestic cattle. The TEM-CMY2 gene combination was the most frequently detected genotype for both ESBL-EC and ESBL-SA. The data suggest that the prevalence of ESBL-EC and ESBL-SA in Canada was low (i.e. <5%), but ongoing surveillance is needed to detect emerging or changing trends.

Subtype-specific differences in the risk of hospitalisation among patients infected with hepatitis E virus genotype 3 in Belgium, 2010-2018.

Some European countries recently reported an increase in hepatitis E virus genotype 3 (HEV-3) of the subtype 3c. No link between HEV-3 subtypes and severity is established to date. Here, we report that patients infected with HEV-3c were at lower risk of hospitalisation, compared to those infected with HEV-3f, the other main subtype circulating in Belgium.

An outbreak of Shiga toxin-producing Escherichia coli O157:H7 associated with contaminated salad leaves: epidemiological, genomic and food trace back investigations.

In August 2015, Public Health England detected an outbreak of Shiga toxin-producing Escherichia coli (STEC) serotype O157:H7 caused by contaminated salad leaves in a mixed leaf prepacked salad product from a national retailer. The implicated leaves were cultivated at five different farms and the zoonotic source of the outbreak strain was not determined. In March 2016, additional isolates from new cases were identified that shared a recent common ancestor with the outbreak strain. A case-case study involving the cases identified in 2016 revealed that ovine exposures were associated with illness (n = 16; AOR 8·24; 95% CI 1·55-39·74). By mapping the recent movement of sheep and lambs across the United Kingdom, epidemiological links were established between the cases reporting ovine exposures. Given the close phylogenetic relationship between the outbreak strain and the isolates from cases with ovine exposures, it is plausible that ovine faeces may have contaminated the salad leaves via untreated irrigation water or run-off from fields nearby. Timely and targeted veterinary and environmental sampling should be considered during foodborne outbreaks of STEC, particularly where ready to eat vegetables and salads are implicated.

Pork products associated with human infection caused by an emerging phylotype of hepatitis E virus in England and Wales.

Since 2010, human hepatitis E infections have increased in England and Wales. Most cases are locally acquired and caused by hepatitis E virus genotype 3 (HEV G3). HEV G3 is linked to the consumption of pork products. The increase is associated with the emergence of a new phylotype, HEV G3-group 2 (G3-2, also known as G3abcdhij). Sixty individuals with confirmed hepatitis E infection and no history of travel outside the UK were recruited: 19 were infected with HEV G3-group 1 (G3-1 or G3efg) and 41 with G3-2. Epidemiological data relating to usual shopping habits and consumption of ham and sausages were analysed together with typing data to identify any associations with HEV phylotype. Study participants who purchased ham and/or sausage from a major supermarket were more likely to have HEV G3-2 infection (Relative risks 1·85, P = 0·06, CI 0·97-3·53). The HEV G3-2 phylotype has not been detected in indigenous UK pigs and it is suggested that human infections could be the result of consumption of products made from pork originating outside the UK. This does not infer blame on the supermarket but the epidemiology of HEV is dynamic and reflects complex animal husbandry practices which need to be explored further.

Molecular characterization and antimicrobial resistance of STEC strains isolated from healthy cattle in 2011 and 2013 in Spain.

Prevention of Shiga toxin-producing Escherichia coli (STEC) foodborne outbreaks is hampered by its complex epidemiology. We assessed the distribution of virulence genes (VGs), main serogroups/serotypes for public health [haemolytic uraemic syndrome (HUS)-related], antimicrobial resistance (AMR) profiles and pulsed-field gel electrophoresis (PFGE) patterns in a collection of STEC isolates obtained from cattle hide (n = 149) and faecal (n = 406) samples collected during a national survey conducted in Spain in 2011 and 2013. Isolates were cultured using McConkey and CT-SMAC agar after enrichment, and confirmed as STEC by PCR. STEC prevalence in hides (15·4%) was higher than in faeces (10·7%) and O157:H7 was more frequent in the former (2·7% vs. 0·99%). Non-O157 HUS-related serogroups were present albeit at low frequencies. The non-O157 isolates were more heterogeneous than O157:H7 in their VG patterns, with 25/64 presenting VGs from both STEC and enterotoxigenic pathotypes (hybrid isolates). Of the STEC isolates, 62·5% were resistant at least to one antimicrobial, and no differences in AMR between O157:H7 and non-O157 were detected. All isolates had different profiles by PFGE and did not form a cluster. Overall, our results demonstrated that STEC in the cattle reservoir is still a matter of concern for human health due to the presence of HUS-related serogroups, the occurrence of certain VGs, AMR and the additional risks that hybrid isolates may pose, and thus warrants further investigation.

Daily shedding dynamics of E. coli O157 in an Australian grass-fed beef herd.

This study aimed to describe the diurnal shedding dynamics of Escherichia coli O157 in cattle managed on pasture. The purpose was to identify the value of a single measurement for predicting the shedding status on subsequent days. Over a 14-day period, 24 beef cows with known E. coli O157 shedding status were sampled twice daily or daily (21 sampling points) and E. coli O157 was enumerated from faeces. No association between shedding status of individual animals within a 7-h period was identified (odds ratio 1·5, P = 0·08). Short-interval sampling demonstrated substantial diurnal volatility in shedding of E. coli O157 that is not evident in studies based on long-interval (>7 days) sampling. The findings contribute to and support previous findings on the question why it has been difficult to achieve progress in understanding the epidemiology of E. coli O157 infection in cattle.

A large outbreak of Campylobacter jejuni infection in a university college caused by chicken liver pâté, Australia, 2013.

In October 2013, public health authorities were notified of a suspected outbreak of gastroenteritis in students and guests following a catered function at a university residential college. A retrospective cohort study was undertaken to examine whether foods served at the function caused illness. A total of 56 cases of gastroenteritis, including seven laboratory-confirmed cases of Campylobacter jejuni infection, were identified in 235 eligible respondents. Univariate analysis showed a significant association with a chicken liver pâté entrée [relative risk (RR) 3·64, 95% confidence interval (CI) 2·03-6·52, P < 0·001], which retained significance after adjustment for confounding via multivariable analysis (adjusted RR 2·80, 95% CI 1·26-6·19, P = 0·01). C. jejuni and C. coli were also isolated in chicken liver pâté recovered from the college's kitchen. Subsequent whole genome multilocus sequence typing (wgMLST) of clinical and food-derived C. jejuni isolates showed three genetically distinct sequence types (STs) comprising ST528, ST535 (both clinically derived) and ST991 (food derived). The study demonstrates the value of utilizing complementary sources of evidence, including genomic data, to support public health investigations. The use of wgMLST highlights the potential for significant C. jejuni diversity in epidemiologically related human and food isolates recovered during outbreaks linked to poultry liver.

A prevalence study of Salmonella spp., Yersinia spp., Toxoplasma gondii and porcine reproductive and respiratory syndrome virus in UK pigs at slaughter.

An abattoir-based study was undertaken between January and May 2013 to estimate the prevalence of Salmonella spp. and Yersinia spp. carriage and seroprevalence of antibodies to Toxoplasma gondii and porcine reproductive and respiratory syndrome virus (PRRSv) in UK pigs at slaughter. In total, 626 pigs were sampled at 14 abattoirs that together process 80% of the annual UK pig slaughter throughput. Sampling was weighted by abattoir throughput and sampling dates and pig carcasses were randomly selected. Rectal swabs, blood samples, carcass swabs and the whole caecum, tonsils, heart and tongue were collected. Salmonella spp. was isolated from 30·5% [95% confidence interval (CI) 26·5-34·6] of caecal content samples but only 9·6% (95% CI 7·3-11·9) of carcass swabs, which was significantly lower than in a UK survey in 2006-2007. S. Typhimurium and S. 4,[5],12:i:- were the most commonly isolated serovars, followed by S. Derby and S. Bovismorbificans. The prevalence of Yersinia enterocolitica carriage in tonsils was 28·7% (95% CI 24·8-32·7) whereas carcass contamination was much lower at 1·8% (95% CI 0·7-2·8). The seroprevalence of antibodies to Toxoplasma gondii and PRRSv was 7·4% (95% CI 5·3-9·5) and 58·3% (95% CI 53·1-63·4), respectively. This study provides a comparison to previous abattoir-based prevalence surveys for Salmonella and Yersinia, and the first UK-wide seroprevalence estimates for antibodies to Toxoplasma and PRRSv in pigs at slaughter.

Environmental factors and public health policy associated with human and rodent infection by leptospirosis: a land cover-based study in Nan province, Thailand.

Leptospirosis incidence has increased markedly since 1995 in Thailand, with the eastern and northern parts being the most affected regions, particularly during flooding events. Here, we attempt to overview the evolution of human prevalence during the past decade and identify the environmental factors that correlate with the incidence of leptospirosis and the clinical incidence in humans. We used an extensive survey of Leptospira infection in rodents conducted in 2008 and 2009 and the human incidence of the disease from 2003 to 2012 in 168 villages of two districts of Nan province in Northern Thailand. Using an ad-hoc developed land-use cover implemented in a geographical information system we showed that humans and rodents were not infected in the same environment/habitat in the land-use cover. High village prevalence was observed in open habitat near rivers for the whole decade, or in 2008-2009 mostly in rice fields prone to flooding, whereas infected rodents (2008-2009) were observed in patchy habitat with high forest cover, mostly situated on sloping ground areas. We also investigated the potential effects of public health campaigns conducted after the dramatic flood event of 2006. We showed that, before 2006, human incidence in villages was explained by the population size of the village according to the environmental source of infection of this disease, while as a result of the campaigns, human incidence in villages after 2006 appeared independent of their population size. This study confirms the role of the environment and particularly land use, in the transmission of bacteria, emphasized by the effects of the provincial public health campaigns on the epidemiological pattern of incidence, and questions the role of rodents as reservoirs.

The epidemiology, microbiology and clinical impact of Shiga toxin-producing Escherichia coli in England, 2009-2012.

Between 1 January 2009 and 31 December 2012 in England, a total of 3717 cases were reported with evidence of Shiga toxin-producing E. coli (STEC) infection, and the crude incidence of STEC infection was 1·80/100 000 person-years. Incidence was highest in children aged 1-4 years (7·63/100 000 person-years). Females had a higher incidence of STEC than males [rate ratio (RR) 1·24, P < 0·001], and white ethnic groups had a higher incidence than non-white ethnic groups (RR 1·43, P < 0·001). Progression to haemolytic uraemic syndrome (HUS) was more frequent in females and children. Non-O157 STEC strains were associated with higher hospitalization and HUS rates than O157 STEC strains. In STEC O157 cases, phage type (PT) 21/28, predominantly indigenously acquired, was also associated with more severe disease than other PTs, as were strains encoding stx2 genes. Incidence of STEC was over four times higher in people residing in rural areas than urban areas (RR 4·39, P < 0·001). Exposure to livestock and/or their faeces was reported twice as often in cases living in rural areas than urban areas (P < 0·001). Environmental/animal contact remains an important risk factor for STEC transmission and is a significant driver in the burden of sporadic STEC infection. The most commonly detected STEC serogroup in England was O157. However, a bias in testing methods results in an unquantifiable under-ascertainment of non-O157 STEC infections. Implementation of PCR-based diagnostic methods designed to detect all STEC, to address this diagnostic deficit, is therefore important.

Risk factors for sporadic Shiga toxin-producing Escherichia coli O157 and non-O157 illness in The Netherlands, 2008-2012, using periodically surveyed controls.

Shiga toxin-producing Escherichia coli (STEC) infections have been associated with severe illness. Ruminants are seen as the main reservoir and the major transmission route is considered to be foodborne. In The Netherlands, a case-control study was conducted, using data collected during 2008-2012. Patients were interviewed and controls completed a self-administered questionnaire. Patients travelling abroad were excluded from the analyses. STEC O157 and non-O157 were examined separately and differentiated into two age groups (<10 years, ⩾10 years). We included 130 O157 cases, 78 non-O157 cases and 1563 controls. In both age groups of O157 patients, raw spreadable sausage was the main risk factor for infection. For STEC non-O157 cases aged <10 years, contact with farm animals was the main risk factor and in non-O157 cases aged ⩾10 years, consumption of beef was the main risk factor. During 2008-2012, risk factors for STEC infections in the Dutch population differed between age groups and serogroup categories, and were related to eating meat and contact with farm animals. Advising the public about the risks of consuming raw or undercooked meat (products) and hygiene habits in case of contact with farm animals, could help in the prevention of STEC infections.

Prevalence of hepatitis E virus in slaughter-age pigs in Scotland.

The prevalence of anti-HEV isotype-specific antibodies and viraemia were investigated in serum samples collected from slaughter-age pigs (aged 22-24 weeks) from 23 farms in Scotland. Of 176 serum samples tested, 29·0% (n = 51) were anti-HEV IgG positive, 36·9% (n = 65) anti-HEV IgA positive and 29·0% (n = 51) anti-HEV IgM positive. Overall seroprevalence (anti-HEV IgG+ and/or IgA+ and/or IgM+) was 61·4% (n = 108). HEV RNA was detected in 72/162 serum samples (44·4%). Partial sequence of ORF2 (98 nt) was obtained from eight HEV RNA-positive samples and phylogenetic analysis confirmed that they were all of genotype 3. This is the first report on the prevalence of HEV in pigs in Scotland. Given the increasing incidence of locally acquired HEV infection in the UK, evidence that HEV is a foodborne zoonosis emphasizes the need for surveillance in pigs.