Subdural Empyema from Streptococcus suis Infection, South Korea.

In Jeju Island, South Korea, a patient who consumed raw pig products had subdural empyema, which led to meningitis, sepsis, and status epilepticus. We identified Streptococcus suis from blood and the subdural empyema. This case illustrates the importance of considering dietary habits in similar clinical assessments to prevent misdiagnosis.

Outbreak-associated Salmonella Baildon found in wastewater demonstrates how sewage monitoring can supplement traditional disease surveillance.

Non-typhoidal Salmonella is a common cause of gastroenteritis worldwide, but current non-typhoidal Salmonella surveillance is suboptimal. Here, we evaluated the utility of wastewater monitoring to enhance traditional surveillance for this foodborne pathogen. In June 2022, we tested raw sewage collected twice a week from two treatment plants in central Pennsylvania for non-typhoidal Salmonella and characterized isolates using whole-genome sequencing. We recovered 43 Salmonella isolates from wastewater samples, differentiated by genomic analysis into seven serovars: 16 Panama (37.2%), 9 Senftenberg (20.9%), 8 Baildon (18.6%), and 3 or fewer of four other serovars. We assessed genetic relatedness and epidemiologic links between these wastewater isolates with those from patients with salmonellosis. All S. Baildon isolates from wastewater were genetically similar to those associated with a known contemporaneous salmonellosis outbreak. S. Baildon from wastewater and 42 outbreak-related isolates in the national outbreak detection database had the same core genome multilocus sequence typing, and outbreak code differed by zero or one single polynucleotide polymorphism. One of the 42 outbreak-related isolates was obtained from a patient residing in the wastewater sample collection catchment area, which serves approximately 17000 people. S. Baildon is a rare serovar (reported in <1% cases nationally, over five years). Our study underscores the value of monitoring sewage from a defined population to supplement traditional surveillance methods for the evidence of Salmonella infections and to determine the extent of outbreaks.IMPORTANCEDuring the COVID-19 pandemic, monitoring for SARS-CoV-2 in wastewater was highly effective in identifying the variants of concern earlier than clinical surveillance methods. Here, we show that monitoring domestic sewage can also augment traditional reporting of foodborne illnesses to public health authorities. Our study detected multiple Salmonella enterica serovars in samples from two wastewater treatment plants in central Pennsylvania. Using whole-genome sequencing, we demonstrated that the isolates of variant S. Baildon clustered with those from a foodborne salmonellosis outbreak that occurred in a similar time frame. Cases were primarily from Pennsylvania, and one individual lived within the wastewater treatment catchment area. This study highlights the effectiveness of domestic sewage testing as a proactive public health strategy to track and respond to infectious disease outbreaks.

Availability of Hand Sanitizers in Food Establishments of New York City: An Observational Study.

Hand hygiene is a crucial tool to limit the transmission of common respiratory and gastrointestinal infections. While hand sanitizers were ubiquitous early in the COVID-19 pandemic, the number of food establishments that have adequately maintained them remains unknown. Through systematic observations in 89 New York City food establishments, we found that hand sanitizer dispensers were present in only 40% of the stores, and only 23% had functional ones. This scarcity highlights the necessity of providing ongoing support to small business owners nationwide to promote and maintain primary prevention measures at all times, extending beyond periods of public health crises.

Understanding the impact of the COVID-19 pandemic response on GI infection surveillance trends in England, January 2020-April 2022.

Stepwise non-pharmaceutical interventions and health system changes implemented as part of the COVID-19 response have had implications on the incidence, diagnosis, and reporting of other communicable diseases. Here, we established the impact of the COVID-19 outbreak response on gastrointestinal (GI) infection trends using routinely collected surveillance data from six national English laboratory, outbreak, and syndromic surveillance systems using key dates of governmental policy to assign phases for comparison between pandemic and historic data. Following decreases across all indicators during the first lockdown (March-May 2020), bacterial and parasitic pathogens associated with foodborne or environmental transmission routes recovered rapidly between June and September 2020, while those associated with travel and/or person-to-person transmission remained lower than expected for 2021. High out-of-season norovirus activity was observed with the easing of lockdown measures between June and October 2021, with this trend reflected in laboratory and outbreak systems and syndromic surveillance indicators. Above expected increases in emergency department (ED) attendances may have reflected changes in health-seeking behaviour and provision. Differential reductions across specific GI pathogens are indicative of the underlying routes of transmission. These results provide further insight into the drivers for transmission, which can help inform control measures for GI infections.

Molecular Diagnosis of Pseudoterranova decipiens Sensu Stricto Infections, South Korea, 2002‒2020.

Human Pseudoterranova decipiens larval infections were diagnosed by molecular analysis of mitochondrial cox1 and nd1 genes in 12 health check-up patients in South Korea during 2002-2020. Based on high genetic identity (99.3%-100% for cox1 and 96.7%-98.0% for nd1), we identified all 12 larvae as P. decipiens sensu stricto.

Sporadic Occurrence of Enteroaggregative Shiga Toxin-Producing Escherichia coli O104:H4 Similar to 2011 Outbreak Strain.

We describe the recent detection of 3 Shiga toxin-producing enteroaggregative Escherichia coli O104:H4 isolates from patients and 1 from pork in the Netherlands that were genetically highly similar to isolates from the 2011 large-scale outbreak in Europe. Our findings stress the importance of safeguarding food supply production chains to prevent future outbreaks.

A scoping review of factors potentially linked with antimicrobial-resistant bacteria from turkeys (iAM.AMR Project).

Antimicrobial resistance (AMR) is a complex problem that is a threat to global public health. Consumption of turkey meat may be an important source of foodborne exposure to resistant bacteria; recent outbreaks of multi-drug-resistant Salmonella Reading in Canada and the USA have implicated raw turkey products. To better understand the epidemiology of AMR in farmed turkey production, a scoping review was conducted. The objectives were to identify (1) modifiable factors potentially associated with antimicrobial-resistant Campylobacter, Enterococcus, Escherichia coli and Salmonella enterica along the farm-to-fork pathway in turkeys, and (2) data gaps with respect to factors potentially associated with AMR and Canadian commercial turkey production. A comprehensive search of the peer-reviewed literature was conducted in 2019 and updated in 2021. Thirteen references were included, reporting 36 factors. Antimicrobial use factors and their potential associations with AMR were most frequently reported (n = 15 factors; 42%), followed by biosecurity (n = 11; 31%) and management practices (n = 10; 28%). This review revealed important data gaps; no factors pertaining to S. enterica or to stages other than the farm (e.g. abattoir, retail) were identified, and only one Canadian reference was identified. These findings will inform priorities for future research and surveillance regarding turkeys and AMR.

Overview of basic epidemiological characteristics and descriptive analysis of the incidence of human yersiniosis in the Czech Republic in 2018-2020.

OBJECTIVE: The aim was to provide an overview of the basic epidemiological characteristics of human yersiniosis and to analyze the reported epidemiological data on the incidence of this disease in the Czech Republic (CZ) in 2018-2020. METHODS: A descriptive analysis was performed of cases of yersiniosis captured in the Infectious Disease Information System (ISIN) in the CZ in 2018-2020. MS Excel 2010 was used for data processing and sorting. RESULTS: In the CZ, a total of 1,686 cases of yersiniosis were reported in 2018-2020 (average annual incidence of 5/100,000 population). The highest average age-specific incidence was recorded in the age group 1-4 years (31.3/100,000), followed by 0-year-olds (26.9/100,000). In the study period, 942 cases were male and 744 cases were female, with the respective incidences of 6.0 /100,000 and 4.6/100,000. By administrative region, the highest average annual incidences were recorded in the South Moravian (9.1/100,000) and Moravian-Silesian (7.5/100,000) Regions. Hospital admission was required for 14.3% (n = 241) of reported cases. No death or outbreak was reported during the study period. A total of 31 cases were imported from usual recreational destinations. No seasonality was detected in the CZ; however, more cases always occur in January and in the second half of the year. Over the last three years, a stagnant trend in the incidence of the disease has been observed in the CZ. CONCLUSIONS: In 2018 and 2019, yersiniosis (caused by Y. enterocolitica and rarely Y. pseudotuberculosis) was the fourth most commonly reported zoonosis in humans in the European Union (EU), with a stable trend in 2014-2019. The CZ reports an incidence up to three times higher but a 2.5 lower share of hospitalized patients compared to the EU average, which probably indicates that the CZ has an effective surveillance system in place. The trend in the incidence of the disease has stagnated in the CZ and the EU in recent years. The most common vehicle for transmission of yersiniosis to humans is contaminated food, especially undercooked pork, less often vegetables or water. Contamination of products from home slaughtered animals intended for private consumption is likely and would also explain the increased incidence of the disease, particularly in the winter months.

Foodborne infections and intoxications in Poland in the years 2018-2020.

AIM: The purpose of this study is to assess the epidemiological situation of foodborne infections and intoxications in Poland in the years 2018-2020. MATERIALS AND METHODS: The evaluation was based on the analysis of information sent to Department of Epidemiology NIPH NIH - NRI through ROE (pol. Rejestr Ognisk Epidemicznych) - an electronic system created for uploading, transfer and analysis of data acquired during the outbreak investigations. Additional sources for the analysis were NIPH NIH - NRI annual bulletins (Czarkowski MP et al. "Infectious diseases and poisonings in Poland", 2014-2020. Warsaw, NIPH NIH and GIS). RESULTS: In the years 2018-2020 a total number of 2,108 foodborne outbreaks were reported in which 52,175 persons were exposed and 17,023 got sick (in 2016 n=916, in 2019 n=918, in 2020 n=274). In 2020 over 3 fold decrease in the number of outbreaks comparing to 2019 and over 4 fold decrease in the number of cases in those outbreaks was observed. Among outbreaks which took place in 3 most frequent settings (private household, food facility and hospital) the steepest decrease was in 12th week of 2020 (ISO 2020-W12). The most frequent etiological agent of outbreaks in the years 2018-2020 was Salmonella sp. (38.3% of outbreaks in 2018, 32.7% in 2019 and 47.8% in 2020) and specifically serotype Enteritidis (38.3%, 27% and 39.4% accordingly). The most frequent setting of outbreaks was private household (59.7% outbreaks in 2018, 66% in 2019 and 62% in 2020), followed by hospital (17.4%, 18.3% i 19.7% accordingly). Up until 2019 an increasing trend in the number of small outbreaks (up to 4 cases) caused by Salmonella sp. was observed (in 2018 - 605 and in 2019 - 612 were reported). CONCLUSIONS: Decrease in the number of outbreaks in selected settings from 12th ISO week of 2020 might have been due to introduction of restrictions during COVID-19 pandemic and enhancement of personal hygiene practices. An increase in identified and registered small outbreaks caused by Salmonella sp. comparing to the median of the number of those outbreaks from 2014-2016 could partly be a result of routine surveillance enhancement after introducing System for Registry of Epidemiological Interviews (pol. SRWE).

[Prospective molecular methods for sequencing microorganisms in the system of assessment and control of food safety].

To solve one of the most important tasks of food hygiene - ensuring foodstuff biosafety, the leading place is given to the use of nucleic acid sequencing methods that allow to identify and describe the nucleotide sequences of genomes both in individual microorganisms and metagenomic characteristics of microbial communities in environmental objects, in humans and animals. The purpose of the review was to analyze the main areas of sequencing application in food microbiology, biotechnology and epidemiology. Material and methods. The collection and analysis of scientific and informational materials published in domestic and foreign publications from Scopus, Web of Science, PubMed, RSCI databases, official reports of the World Health Organization (WHO), the European Food Safety Agency (EFSA) and other published sources has been carried out. Results. The review presents generalized characteristics of the most well-known sequencing formats based on different principles of reading and processing genetic information: capillary sequencing by Sanger, pyrosequencing, sequencing by ligation, sequencing by DNA synthesis, semiconductor high-performance sequencing, sequencing of individual DNA molecules. It is shown that multilocus analysis (MLST, MLVA) increases the specificity of genotyping and intraspecific identification of food-borne pathogens. It is used to assess the pathogenic potential and study the mechanisms of evolutionary variability of bacterial pathogens, leading to polymorphism of clonal lines and the appearance of strain-specific differences, to monitor the different genotypes of pathogens in production and other objects of the food chain. Nanopore sequencing is promising for studying bacterial plasmids and localization of resistance genes of MDR bacteria. Genome-wide analysis (WGS) makes it possible to identify detailed characteristics of pathogens of infectious diseases, including uncultivated and previously unknown microorganisms, as well as to study the features of the organization of individual pro- and eukaryotic genomes, gene regulation systems, pathogenicity factors and protein expression. The role of WGS methods for determining the degree of genetic kinship of infectious agents isolated from various sources in the investigation of outbreaks and sporadic food poisoning and infections is shown. The possibilities of metagenomic sequencing in the study of species composition, genetic diversity and metabolic potential of microbial communities are demonstrated. The main advantage of metagenomics is the possibility of direct sequencing of the genomes of microorganisms living in the human body, animals, water, soil and other objects. Metagenomic analysis plays a leading role in the detection of unexplored taxa, uncultivated and difficult-to-cultivate forms of a wide range of microorganisms. The most important direction of metagenomics is the study of the human or animal microbiome, the analysis of the relationship between the intestinal microbiota and metabolism, as well as the formation of the nutritional status of a person. Theoretical and practical aspects of the implementation of high-performance sequencing methods in the system of food biosafety assessment and control are reviewed: safety assessment of genetically modified strains of food producers, development of fundamentally new algorithms for investigating outbreaks of infectious diseases, creation of network systems for early diagnosis and notification of food infections of bacterial and viral etiology. Conclusion. Sequencing should become a standard methodology in the field of food safety for the identification and characterization of food pathogens, including those with resistance to antibiotics and adverse technological effects. The introduction of WGS into the food safety assessment and control system will make it possible to assess real food contamination with new and newly returning pathogens, create electronic databases and scientifically substantiate the most adequate measures for the prevention of food infections and ensuring the health of the population.

Seventh Pandemic Vibrio cholerae O1 Sublineages, Central African Republic.

Four cholera outbreaks were reported in the Central African Republic during 1997-2016. We show that the outbreak isolates were Vibrio cholerae O1 serotype Inaba from 3 seventh pandemic El Tor sublineages originating from West Africa (sublineages T7 and T9) or the African Great Lakes Region (T10).

Delineating and Analyzing Locality-Level Determinants of Cholera, Haiti.

Centre Department, Haiti, was the origin of a major cholera epidemic during 2010-2019. Although no fine-scale spatial delineation is officially available, we aimed to analyze determinants of cholera at the local level and identify priority localities in need of interventions. After estimating the likely boundaries of 1,730 localities by using Voronoi polygons, we mapped 5,322 suspected cholera cases reported during January 2015-September 2016 by locality alongside environmental and socioeconomic variables. A hierarchical clustering on principal components highlighted 2 classes with high cholera risk: localities close to rivers and unimproved water sources (standardized incidence ratio 1.71, 95% CI 1.02-2.87; p = 0.04) and urban localities with markets (standardized incidence ratio 1.69, 95% CI 1.25-2.29; p = 0.0006). Our analyses helped identify and characterize areas where efforts should be focused to reduce vulnerability to cholera and other waterborne diseases; these methods could be used in other contexts.

Non-O1/non-O139 vibrios - occurrence not only in Europe in recent years.

Non-O1/non-O139 vibrios refer to all vibrios except toxin producing Vibrio cholerae serogroups O1 and O139. The prevalence of illness caused by non-O1/non-O139 vibrios steadily increases all over the world in the last 20 years, which is very probably related to global warming. These infections are reported year-round from tropical and subtropical climate zones, but they were also detected in the mild climate zone of the United States of America and Europe. In mild climate, they have markedly seasonal occurrence, typically peaking in May to October. A human can be infected after ingestion of contaminated food, especially seafood and fish, or water or while bathing. In Europe, non-O1/non-O139 vibrios were detected in the Baltic Sea, North Sea and Mediterranean Sea but also in ponds and rivers. Depending on the pathogen entry route, the clinical manifestation may appear as gastroenteritis, otitis, wound infection or severe up to fatal illness, predominantly in immunocompromised patients. There is no specific prevention. Non-specific prevention includes good personal and food handling hygiene practices and avoiding contact of unhealed wounds with sea or surface swimming water. Given the severity and increasing frequency of infections caused by non-O1/non-O139 vibrios, they should be considered in differential diagnosis of gastrointestinal and wound infections, especially in patients with a history of consumption of fish and seafood or with a history of contact of unhealed wounds with sea or other open swimming water.

Whole-Genome Sequencing to Detect Numerous Campylobacter jejuni Outbreaks and Match Patient Isolates to Sources, Denmark, 2015-2017.

In industrialized countries, the leading cause of bacterial gastroenteritis is Campylobacter jejuni. However, outbreaks are rarely reported, which may reflect limitations of surveillance, for which molecular typing is not routinely performed. To determine the frequency of genetic clusters among patients and to find links to concurrent isolates from poultry meat, broiler chickens, cattle, pigs, and dogs, we performed whole-genome sequencing on 1,509 C. jejuni isolates from 774 patients and 735 food or animal sources in Denmark during 2015-2017. We found numerous clusters; 366/774 (47.3%) clinical isolates formed 104 clusters of >2 isolates. A total of 41 patient clusters representing 199/366 (54%) patients matched a potential source, primarily domestic chickens/broilers. This study revealed serial outbreaks and numerous matches to concurrent food and animal isolates and highlighted the potential of whole-genome sequencing for improving routine surveillance of C. jejuni by enhancing outbreak detection, source tracing, and potentially prevention of human infections.

Hepatitis E Virus Genotype 7 RNA and Antibody Kinetics in Naturally Infected Dromedary Calves, United Arab Emirates.

Orthohepevirus A genotype 7 is a novel zoonotic variant of hepatitis E virus. To clarify infection in the animal reservoir, we virologically monitored 11 dromedary dam-calf pairs. All calves became infected during the first 6 months of life and cleared the virus after an average of 2 months. Dams did not become infected.

Comparing the performance of conventional PCR, RTQ-PCR, and droplet digital PCR assays in detection of Shigella.

The incidence of foodborne infections caused by Shigella spp. is still very high in every year, which poses a great potential threat to public health. Conventional quantification methods based on culture techniques, biochemical, and serological identification are time-consuming and labor-intensive. To develop a more rapid and efficient detection method of Shigella spp., we compared the sensitivity and specificity of three different polymerase chain reaction (PCR) methods, including conventional PCR, quantitative real-time PCR (RTQ-PCR), and droplet digital PCR (ddPCR). Our results indicated that ddPCR method exhibited higher sensitivity, and the limit of detection was 10-5 ng/µl for genomic DNA templates, 10-1 cfu/ml for Shigella bacteria culture. In addition, we found that ddPCR was a time-saving method, which required a shorter pre-culturing time. Collectively, ddPCR assay was a reliable method for rapid and effective detection of Shigella spp.

Population-based food consumption survey as an additional tool for foodborne outbreak investigations, Germany, 2017.

We conducted a food consumption survey in the general adult population of 18 years and older in Germany to obtain data on the frequency of consumption of food items that caused foodborne disease outbreaks in the past. A total of 1010 telephone interviews were completed that queried the consumption of 95 food items in the 7-day period before the interview. Survey results were weighted to be representative. Six exemplary 'high risk' food items were consumed by 6% to 16% of the general population. These were raw ground pork: 6.5%; 'Teewurst' (=spreadable sausage-containing raw pork): 15.7%; unpasteurised milk consumed without prior heating: 9.0%; food items prepared with raw eggs: 9.8%; unheated sprouts or seedlings: 8.8% and frozen berries consumed without prior heating: 6.2%. Data from our food consumption survey were comparable to data obtained from control persons in case-control studies conducted during past foodborne disease outbreak investigations. We consider our survey an additional helpful tool that will allow comparison with food consumption data from case-patients obtained in exploratory, hypothesis-generating interviews early on in outbreak investigations, and which may assist in forming hypotheses regarding associations of illnesses with suspected food vehicles. This may facilitate and accelerate investigations of future foodborne disease outbreaks.

Describing the Epidemiology of Foodborne Outbreaks in New South Wales from 2000 to 2017.

Foodborne disease causes an estimated 4.1 million cases of illness in Australia each year and is responsible for causing many significant common source outbreaks. We analyzed 18 years of foodborne outbreak data collected in New South Wales (NSW), and classified the likely pathogen type responsible for outbreaks of unknown etiology, to track broad trends over time. A total of 869 outbreaks were reported in NSW from 2000 to 2017. The majority (53%) of outbreaks did not have a pathogen identified and underwent pathogen type categorization based on the epidemiology of the outbreak. The proportion of outbreaks due to toxin producing bacteria decreased over time, whereas the proportion of outbreaks due to other bacterial pathogens increased. The proportion of outbreaks due to viral gastroenteritis pathogens had no overall changing trend over time. Bacterial outbreaks had significantly more identified cases and had more hospitalizations than other pathogen type causes. Other features associated with high case numbers, hospitalizations, and deaths in foodborne outbreaks included being due to food contaminated in primary production, involving consumption of raw products, and having evidence of poor sanitation in the food preparation areas. Eggs were the most commonly determined pathogen food source, occurring in 12% of outbreaks; however, most outbreak investigations (77%) did not have a pathogen food source identified. This analysis demonstrates a changing landscape of foodborne outbreaks over time. Increases in outbreaks due to bacterial and viral pathogens coincide with increases in sporadic notifications of the same pathogens, whereas decreases in toxin caused outbreaks followed the introduction of mandatory food safety training in retail food businesses. Recognizing issues in food production and implementing improvements that reduce the number of pathogens in food will be key to reducing the incidence of foodborne outbreaks.

Chronic Gastrointestinal and Joint-Related Sequelae Associated with Common Foodborne Illnesses: A Scoping Review.

To strengthen the burden estimates for chronic sequelae of foodborne illness, we conducted a scoping review of the current literature for common foodborne pathogens and their associated sequelae. We aim to describe the current literature and gaps in knowledge of chronic sequelae associated with common foodborne illnesses. A comprehensive search was conducted in PubMed, EMBASE, and Web of Science for peer-reviewed articles published January 1, 2000 to April 1, 2018. Articles available in English, of any epidemiological study design, for 10 common foodborne pathogens (Campylobacter, Salmonella, Escherichia coli, Listeria, Shigella, Cryptosporidium, Cyclospora, Giardia, Yersinia, and norovirus) and their associated gastrointestinal (GI)- and joint-related sequelae were included. Of the 6348 titles screened for inclusion, 380 articles underwent full-text review; of those 380, 129 were included for data extraction. Of the bacterial pathogens included in the search terms, the most commonly reported were Salmonella (n = 104) and Campylobacter (n = 99); E. coli (n = 55), Shigella (n = 49), Yersinia (n = 49), and Listeria (n = 15) all had fewer results. Norovirus was the only virus included in our search, with 28 article that reported mostly GI-related sequelae and reactive arthritis (ReA) reported once. For parasitic diseases, Giardia (n = 26) and Cryptosporidium (n = 18) had the most articles, and no results were found for Cyclospora. The most commonly reported GI outcomes were irritable bowel syndrome (IBS; n = 119) and inflammatory bowel disease (n = 29), and ReA (n = 122) or "joint pain" (n = 19) for joint-related sequelae. Salmonella and Campylobacter were most often associated with a variety of outcomes, with ReA (n = 34 and n = 27) and IBS (n = 17 and n = 20) reported most often. This scoping review shows there are still a relatively small number of studies being conducted to understand specific pathogen/outcome relationships. It also shows where important gaps in the impact of chronic sequelae from common foodborne illnesses still exist and where more focused research would best be implemented.

Multistate Outbreak of Listeriosis Associated with Packaged Leafy Green Salads, United States and Canada, 2015-2016.

We investigated an outbreak of listeriosis detected by whole-genome multilocus sequence typing and associated with packaged leafy green salads. Nineteen cases were identified in the United States during July 5, 2015-January 31, 2016; isolates from case-patients were closely related (median difference 3 alleles, range 0-16 alleles). Of 16 case-patients interviewed, all reported salad consumption. Of 9 case-patients who recalled brand information, all reported brands processed at a common US facility. The Public Health Agency of Canada simultaneously investigated 14 cases of listeriosis associated with this outbreak. Isolates from the processing facility, packaged leafy green salads, and 9 case-patients from Canada were closely related to US clinical isolates (median difference 3 alleles, range 0-16 alleles). This investigation led to a recall of packaged leafy green salads made at the processing facility. Additional research is needed to identify best practices and effective policies to reduce the likelihood of Listeria monocytogenes contamination of fresh produce.