Dissemination of IncC plasmids in Salmonella enterica serovar Thompson recovered from seafood and human diarrheic patients in China

Salmonella Thompson is a prevalent foodborne pathogen and a major threat to food safety and public health. This study aims to reveal the dissemination mechanism of S. Thompson with co-resistance to ceftriaxone and ciprofloxacin. In this study, 181 S. Thompson isolates were obtained from a retrospective screening on 2118 serotyped Salmonella isolates from foods and patients, which were disseminated in 12 of 16 districts in Shanghai, China. A total of 10 (5.5 %) S. Thompson isolates exhibited resistance to ceftriaxone (MIC ranging from 8 to 32 μg/mL) and ciprofloxacin (MIC ranging from 2 to 8 μg/mL). The AmpC β-lactamase gene blaCMY-2 and plasmid-mediated quinolone resistance (PMQR) genes of qnrS and qepA were identified in the 9 isolates. Conjugation results showed that the co-transfer of blaCMY-2, qnrS, and qepA occurred on the IncC plasmids with sizes of ∼150 (n = 8) or ∼138 (n = 1) kbp. Three typical modules of ISEcp1-blaCMY-2-blc-sugE, IS26-IS15DIV-qnrS-ISKpn19, and ISCR3-qepA-intl1 were identified in an ST3 IncC plasmid pSH11G0791. Phylogenetic analysis indicated that IncC plasmids evolved into Lineages 1, 2, and 3. IncC plasmids from China including pSH11G0791 in this study fell into Lineage 1 with those from the USA, suggesting their close genotype relationship. In conclusion, to our knowledge, it is the first report of the co-existence of blaCMY-2, qnrS, and qepA in IncC plasmids, and the conjugational transfer contributed to their dissemination in S. Thompson. These findings underline further challenges for the prevention and treatment of Enterobacteriaceae infections posed by IncC plasmids bearing blaCMY-2, qnrS, and qepA.

Persistence of microbiological hazards in food and feed production and processing environments

Listeria monocytogenes (in the meat, fish and seafood, dairy and fruit and vegetable sectors), Salmonella enterica (in the feed, meat, egg and low moisture food sectors) and Cronobacter sakazakii (in the low moisture food sector) were identified as the bacterial food safety hazards most relevant to public health that are associated with persistence in the food and feed processing environment (FFPE). There is a wide range of subtypes of these hazards involved in persistence in the FFPE. While some specific subtypes are more commonly reported as persistent, it is currently not possible to identify universal markers (i.e. genetic determinants) for this trait. Common risk factors for persistence in the FFPE are inadequate zoning and hygiene barriers; lack of hygienic design of equipment and machines; and inadequate cleaning and disinfection. A well-designed environmental sampling and testing programme is the most effective strategy to identify contamination sources and detect potentially persistent hazards. The establishment of hygienic barriers and measures within the food safety management system, during implementation of hazard analysis and critical control points, is key to prevent and/or control bacterial persistence in the FFPE. Once persistence is suspected in a plant, a 'seek-and-destroy' approach is frequently recommended, including intensified monitoring, the introduction of control measures and the continuation of the intensified monitoring. Successful actions triggered by persistence of L. monocytogenes are described, as well as interventions with direct bactericidal activity. These interventions could be efficient if properly validated, correctly applied and verified under industrial conditions. Perspectives are provided for performing a risk assessment for relevant combinations of hazard and food sector to assess the relative public health risk that can be associated with persistence, based on bottom-up and top-down approaches. Knowledge gaps related to bacterial food safety hazards associated with persistence in the FFPE and priorities for future research are provided.

Whole-Genome Sequencing Analysis of Non-Typhoidal Salmonella Isolated from Breeder Poultry Farm Sources in China, 2020-2021

Non-typhoidal salmonellosis is a dangerous foodborne disease that causes enormous economic loss and threatens public health worldwide. The consumption of food, especially poultry or poultry products, contaminated with non-typhoidal Salmonella (NTS) is the main cause of human salmonellosis. To date, no research has identified the molecular epidemiological characteristics of NTS strains isolated from breeder chicken farms in different provinces of China. In our study, we investigated the antimicrobial resistance, phylogenetic relationships, presence of antimicrobial resistance and virulence genes, and plasmids of NTS isolates recovered from breeder chicken farms in five provinces of China between 2020 and 2021 by using a whole-genome sequencing (WGS) approach and phenotypic methods. All sequenced isolates belonged to six serovars with seven sequence types. Nearly half of the isolates (44.87%) showed phenotypic resistance to at least three classes of antimicrobials. Salmonella enterica serotype Kentucky harbored more antimicrobial resistance genes than the others, which was highly consistent with phenotypic resistance. Furthermore, the carried rate of 104 out of 135 detected virulence genes was 100%. Overall, our WGS results highlight the need for the continuous monitoring of, and additional studies on, the antimicrobial resistance of NTS.

Antimicrobial Resistance, Virulence Properties and Genetic Diversity of Salmonella Typhimurium Recovered from Domestic and Imported Seafood

The quantity of seafood imported and produced by domestic aquaculture farming has increased. Recently, it has been reported that multidrug-resistant (MDR) Salmonella Typhimurium may be associated with seafood. However, information is limited to the antimicrobial resistance, virulence properties, and genetic diversity of S. Typhimurium recovered from imported and domestic seafood. This study investigated the antimicrobial resistance, virulence properties, and genetic diversity of S. Typhimurium isolated from domestic and imported catfish, shrimp, and tilapia. A total of 127 isolates were tested for the presence of multidrug-resistance (MDR), virulence genes (invA, pagC, spvC, spvR), and genetic diversity using the Sensititre micro-broth dilution method, PCR, and pulsed-field gel electrophoresis (PFGE), respectively. All isolates were uniformly susceptible to six (amoxicillin/clavulanic acid, ceftiofur, ceftriaxone, imipenem, nitrofurantoin, and trimethoprim/sulfamethoxazole) of the 17 tested antimicrobials and genetically diverse. Fifty-three percent of the Salmonella isolates were resistant to at least one antimicrobial and 49% were multidrug resistant. Ninety-five percent of the isolates possessed the invA gene, 67% pagC, and 43% for both spvC, and spvR. The results suggest that S. Typhimurium recovered from seafood is frequently MDR, virulent, and have the ability to cause salmonellosis.

Comparative Analysis of Salmonella enterica subsp. enterica Serovar Thompson Isolates associated with Outbreaks Using PFGE and wgMLST

The strains associated with foodborne Salmonella enterica Thompson outbreaks in Korea have not been identified. Therefore, we characterized S. Thompson strains isolated from chocolate cakes linked to foodborne outbreaks in Korea. A total of 56 strains were isolated from preserved cake products, products in the supply chain distribution, the manufacturer's apparatus, and egg white liquid products used for cream preparation. Subsequently, serological typing, pathogenic gene-targeted polymerase chain reaction (PCR), pulsed-field gel electrophoresis (PFGE), and whole-genome multi-locus sequence typing (wgMLST) were performed to characterize these isolates. The antigen formula of all isolates was 7:k:1,5, namely Salmonella enterica subsp. enterica Serovar Thompson. All 56 isolates harbored invA, his, hin, and stn, and were negative for sefA and spvC based on gene-targeted PCR analyses. Based on PFGE results, these isolates were classified into one group based on the same SP6X01.011 pattern with 100% similarity. We selected 19 strains based on the region and sample type, which were subjected to wgMLST. Although the examined strains showed 100% similarity, they were classified into seven clusters based on allelic differences. According to our findings, the cause of these outbreaks was chocolate cake manufactured with egg white liquid contaminated with the same Salmonella Thompson. Additionally, comparative analysis of wgMLST on domestic isolates of S. Thompson from the three outbreaks showed genetic similarities of over 99.6%. Based on the results, the PFGE and wgMLST combination can provide highly resolved phylogeny and reliable evidence during Salmonella outbreak investigations.

Accurate Detection of Salmonella Based on Microfluidic Chip to Avoid Aerosol Contamination

Salmonella is a type of common foodborne pathogen of global concern, seriously endangering human health. In molecular biological detection of Salmonella, the method of amplifying DNA often faces the problem of aerosol pollution. In this study, a microfluidic chip was developed to integrate loop-mediated isothermal amplification (LAMP) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a system to detect Salmonella. The LAMP reaction solution was initially injected into the chamber to amplify at 65 °C for 20 min; the CRISPR/Cas12a reaction solution was subsequently injected to mix with the amplicons for fluorescent signal production at 43 °C for 30 min. Then, the results can be confirmed by naked eyes under 495 nm light or by a fluorescence immunochromatographic reader. The detection limit of this method for Salmonella DNA was 118 pg/μL. The sensitivity and specificity of this method was 100%. Furthermore, this method was used to detect Salmonella after enrichment for 4 h in salmon and chicken samples spiked with 30 CFU/25 g, and was verified to have a stable detection capability in real samples. The microfluidic chip integrated with the LAMP and CRISPR/Cas12a system not only provides a possibility of highly sensitive endpoint fluorescent visual detection of a foodborne pathogen, but also greatly eliminates the risk of aerosol contamination.

Zoonotic diseases of fish and their prevention and control

Fish and aquatic-derived zoonotic diseases have caused considerable problems in the aquaculture industry and fishery worldwide. In particular, zoonotic diseases can pose widespread threats to humans. With the world’s growing population and potential global trade of aquaculture and fish, the risk of environmental contamination and development of fish and aquatic-derived zoonoses in humans are increasing. The important causes of zoonoses include bacteria, parasites, viruses, and fungi. The zoonotic bacterial agents are divided into two main groups: Gram-positive (Mycobacteriaceae, Streptococcaceae, Erysipelothricaceae families) and Gram-negative (Aeromonadaceae, Vibrionaceae, Pseudomondaceae, Enterobacteriaceae, and Hafniaceae families). The premier parasitic agents include cestodes (tapeworm; e.g. Diphyllobothrium spp.), trematodes (fluke; e.g. Opisthorchis spp.), and nematodes (round worm; e.g. Anisakis spp.). In addition, protozoan organisms such as Cryptosporidium spp. are also considered fish-derived zoonotic pathogens. Two groups of fish-associated fungi causing basidiobolomycosis and sporotrichosis also pose a zoonotic risk for humans. The majority of the fish-derived zoonotic diseases are transmitted to humans mainly via the consumption of improperly cooked or raw fish or fish products. Therefore, the incidence of zoonotic diseases can be reduced by properly processing fish and fish products, e.g. by thermal (heat/freezing) treatment. The prevalence of zoonotic agents in fishes varies seasonally and should be regularly monitored to evaluate the prevalence of pathogens in both wild and cultured fish populations. This review focuses on the fish zoonotic agents/diseases and their control and prevention.

Through the Looking Glass: Genome, Phenome, and Interactome of Salmonella enterica

This review revisits previous concepts on biological phenomenon contributing to the success of the Salmonella enterica subspecies I as a pathogen and expands upon them to include progress in epidemiology based on whole genome sequencing (WGS). Discussion goes beyond epidemiological uses of WGS to consider how phenotype, which is the biological character of an organism, can be correlated with its genotype to develop a knowledge of the interactome. Deciphering genome interactions with proteins, the impact of metabolic flux, epigenetic modifications, and other complex biochemical processes will lead to new therapeutics, control measures, environmental remediations, and improved design of vaccines.

Surveillance and characteristics of food-borne outbreaks in the Netherlands, 2006 to 2019

Background

A wide variety of pathogens can cause disease in humans via consumption of contaminated food. Although food-borne outbreaks only account for a small part of the food-borne disease burden, outbreak surveillance can provide insights about the pathogens, food products implied as vehicle, points of contamination, and the settings in which transmission occurs.

Aim

To describe the characteristics of food-borne outbreaks registered between 2006 and 2019 in the Netherlands.

Methods

All reported outbreaks in which the first case occurred during 2006–19 were analysed. We examined the number of outbreaks, cases and setting by year, aetiology, type of evidence and food commodities.

Results

In total, 5,657 food-borne outbreaks with 27,711 cases were identified. The contaminated food product could be confirmed in 152 outbreaks (2.7%); in 514 outbreaks (9.1%), a pathogen was detected in cases and/or environmental swabs. Norovirus caused most outbreaks (205/666) and most related cases (4,436/9,532), followed by Salmonella spp. (188 outbreaks; 3,323 cases) and Campylobacter spp. (150 outbreaks; 601 cases). Bacillus cereus was most often found in outbreaks with a confirmed food vehicle (38/152). Additionally, a connection was seen between some pathogens and food commodities. Public eating places were most often mentioned as a setting where the food implicated in the outbreak was prepared.

Conclusion

Long-term analysis of food-borne outbreaks confirms a persistent occurrence. Control and elimination of food-borne illness is complicated since multiple pathogens can cause illness via a vast array of food products and, in the majority of the outbreaks, the pathogen remains unknown.

Characterization of CRISPR array in Salmonella enterica from asymptomatic people and patients

Salmonella enterica is a major foodborne pathogen causing symptomatic diseases or asymptomatic infections in humans. To reveal the genetic difference of Salmonella strains from patients to that from asymptomatic people, we used CRISPR typing to analyze the phylogenetic relationship of 180 clinical strains during 2017-2018 in Jiangsu, China. The CRISPR typing divided these isolates into 76 CRISPR types with a discriminatory power of 97.6%. S. Typhimurium and its monophasic variants of 6 CRISPR types are the significant serotypes causing both human diseases and asymptomatic infection, while S. Enteritidis mainly resulted in diseases and shared one CRISPR type. The spacer HadB20 displayed as a new molecular marker to differentiate ST34-S. Typhimurium monophasic variant from ST19-S. Typhimurium. S. Derby, S. London, and S. Senftenberg frequently caused asymptomatic infection with diverse CRISPR types, while S. Mbandaka and S. Meleagridis, occasionally isolated from patients, had conserved CRISPR types. Additionally, 30 of 516 newly identified spacers showed homology to sequences in both plasmids and bacteriophages. Interestingly, some spacers from one serotype showed homology to the correspondent prophage or plasmid sequences in another serotype; and more than two spacers identified in one strain showed homology to the sequences located in the identical plasmids or phages, revealing the constant evolution of Salmonella CRISPR arrays during the interactions between bacteria and phages or plasmids.

Microbiome Population Dynamics of Cold-Smoked Sockeye Salmon during Refrigerated Storage and after Culture Enrichment

ABSTRACT

Cold-smoked salmon is a ready-to-eat seafood product of high commercial importance. The processing and storage steps facilitate the introduction, growth, and persistence of foodborne pathogens and spoilage bacteria. The growth of commensal bacteria during storage and once the product is opened also influence the quality and safety of cold-smoked salmon. Here we investigated the microbial community through targeted 16S rRNA gene and shotgun metagenomic sequencing as means to better understand the interactions among bacteria in cold-smoked salmon. Cold-smoked salmon samples were tested over 30 days of aerobic storage at 4°C and cultured at each time point in a buffered Listeria enrichment broth (BLEB) commonly used to detect Listeria in foods. The microbiomes were composed of Firmicutes and Proteobacteria, namely, Carnobacterium, Brochothrix, Pseudomonas, Serratia, and Psychrobacter. Pseudomonas species were the most diverse species, with 181 taxa identified. In addition, we identified potential homologs to 10 classes of bacteriocins in microbiomes of cold-smoked salmon stored at 4°C and corresponding BLEB culture enrichments. The findings presented here contribute to our understanding of microbiome population dynamics in cold-smoked salmon, including changes in bacterial taxa during aerobic cold storage and after culture enrichment. This may facilitate improvements to pathogen detection and quality preservation of this food.

HIGHLIGHTS

Nowcasting the Number of New Symptomatic Cases During Infectious Disease Outbreaks Using Constrained P-spline Smoothing

Supplemental Digital Content is available in the text.

During an infectious disease outbreak, timely information on the number of new symptomatic cases is crucial. However, the reporting of new cases is usually subject to delay due to the incubation period, time to seek care, and diagnosis. This results in a downward bias in the numbers of new cases by the times of symptoms onset towards the current day. The real-time assessment of the current situation while correcting for underreporting is called nowcasting. We present a nowcasting method based on bivariate P-spline smoothing of the number of reported cases by time of symptoms onset and delay. Our objective is to predict the number of symptomatic-but-not-yet-reported cases and combine these with the already reported symptomatic cases into a nowcast. We assume the underlying two-dimensional reporting intensity surface to be smooth. We include prior information on the reporting process as additional constraints: the smooth surface is unimodal in the reporting delay dimension, is (almost) zero at a predefined maximum delay and has a prescribed shape at the beginning of the outbreak. Parameter estimation is done efficiently by penalized iterative weighted least squares. We illustrate our method on a large measles outbreak in the Netherlands. We show that even with very limited information the method is able to accurately predict the number of symptomatic-but-not-yet-reported cases. This results in substantially improved monitoring of new symptomatic cases in real time.

Applications of Electrolyzed Water as a Sanitizer in the Food and Animal-By Products Industry

Food demand is increasing every year and, usually animal-derived products are generated far from consumer-places. New technologies are being developed to preserve quality characteristics during processing and transportation. One of them is electrolyzed water (EW) that helps to avoid or decrease the development of foodborne pathogens, or losses by related bacteria. Initially, EW was used in ready-to-eat foods such as spinach, lettuce, strawberries, among others; however, its application in other products is under study. Every product has unique characteristics that require an optimized application of EW. Different sanitizers have been developed; unfortunately, they could have undesirable effects like deterioration of quality or alterations in sensory properties. Therefore, EW is gaining popularity in the food industry due to its characteristics: easy application and storage, no corrosion of work surfaces, absence of mucosal membrane irritation in workers handling food, and it is considered environmentally friendly. This review highlights the advantages of using EW in animal products like chicken, pork, beef, eggs and fish to preserve their safety and quality.

Changing epidemiology of invasive non-typhoid Salmonella infection: a nationwide population-based registry study

OBJECTIVES

Non-typhoid Salmonella (NTS) may invade beyond the intestine, causing bacteraemia, sepsis, and infection of normally sterile sites. The epidemiology of invasive NTS (iNTS) infection is under-researched. We determined trends, risk factors, serotype distribution, antimicrobial resistance (AMR), and attributable sources of iNTS infection in a high-income setting.

METHODS

22,837 records of culture-confirmed human salmonellosis cases and 10,008 serotyped Salmonella isolates from five putative animal reservoirs (pigs, cattle, broilers, layers, reptiles) in the Netherlands during 2005-2018 were retrieved from national surveillance registries. Risk factors for iNTS infection were identified using logistic regression analysis. Source attribution modelling was based on serotyping, prevalence, and exposure data.

RESULTS

The average annual percentage of iNTS infections was 4.6% (range 3.5-5.7%). An increase in iNTS infections was observed since 2012 (odds ratio (OR) 1.09, 95% confidence interval (95% CI) 1.04-1.14). Increased iNTS infection risk was associated with wintertime (OR 1.37, 95% CI 1.12-1.66), male sex (OR 1.73, 95% CI 1.51-1.99), older age (ORs: 3.27 to 16.33, depending on age groups), and living in rural areas (OR 1.54, 95% CI 1.23-1.93). While 52% of iNTS infections (n = 950) were caused by serotypes Enteritidis and Typhimurium, those displaying the highest invasiveness relative to their occurrence were Dublin (32.9%, n = 163), Panama (21.6%, n = 106), and Poona (14.1%, n = 71). Cattle were a larger source of iNTS than non-iNTS infections (12.2% vs. 7.6%). Lower AMR and multi-resistance rates were observed among iNTS (37.9%) than non-iNTS isolates (48.6%).

DISCUSSION

The increase in iNTS infections, which is reported also in other countries, is of public health and clinical concern. The underlying reasons seem to be multi-factorial in nature. iNTS infection risk depends more on the infecting serotypes and patient demographics, and less on the attributable reservoirs and AMR profiles.

Critical Orientation in the Jungle of Currently Available Methods and Types of Data for Source Attribution of Foodborne Diseases

With increased interest in source attribution of foodborne pathogens, there is a need to sort and assess the applicability of currently available methods. Herewith we reviewed the most frequently applied methods for source attribution of foodborne diseases, discussing their main strengths and weaknesses to be considered when choosing the most appropriate methods based on the type, quality, and quantity of data available, the research questions to be addressed, and the (epidemiological and microbiological) characteristics of the pathogens in question. A variety of source attribution approaches have been applied in recent years. These methods can be defined as top–down, bottom–up, or combined. Top–down approaches assign the human cases back to their sources of infection based on epidemiological (e.g., outbreak data analysis, case-control/cohort studies, etc.), microbiological (i.e., microbial subtyping), or combined (e.g., the so-called ‘source-assigned case-control study’ design) methods. Methods based on microbial subtyping are further differentiable according to the modeling framework adopted as frequency-matching (e.g., the Dutch and Danish models) or population genetics (e.g., Asymmetric Island Models and STRUCTURE) models, relying on the modeling of either phenotyping or genotyping data of pathogen strains from human cases and putative sources. Conversely, bottom–up approaches like comparative exposure assessment start from the level of contamination (prevalence and concentration) of a given pathogen in each source, and then go upwards in the transmission chain incorporating factors related to human exposure to these sources and dose-response relationships. Other approaches are intervention studies, including ‘natural experiments,’ and expert elicitations. A number of methodological challenges concerning all these approaches are discussed. In absence of an universally agreed upon ‘gold’ standard, i.e., a single method that satisfies all situations and needs for all pathogens, combining different approaches or applying them in a comparative fashion seems to be a promising way forward.

Infection, colonization and shedding of Campylobacter and Salmonella in animals and their contribution to human disease: A review

Livestock meat and offal contribute significantly to human nutrition as sources of high-quality protein and micronutrients. Livestock products are increasingly in demand, particularly in low- and middle-income settings where economies are growing and meat is increasingly seen as an affordable and desirable food item. Demand is also driving intensification of livestock keeping and processing. An unintended consequence of intensification is increased exposure to zoonotic agents, and a contemporary emerging problem is infection with Campylobacter and Salmonella spp. from livestock (avian and mammalian), which can lead to disease, malabsorption and undernutrition through acute and chronic diarrhoea. This can occur at the farm, in households or through the food chain. Direct infection occurs when handling livestock and through bacteria shed into the environment, on food preparation surfaces or around the house and surroundings. This manuscript critically reviews Campylobacter and Salmonella infections in animals, examines the factors affecting colonization and faecal shedding of bacteria of these two genera as well as risk factors for human acquisition of the infection from infected animals or environment and analyses priority areas for preventive actions with a focus on resource-poor settings.

Identifying the source of food-borne disease outbreaks: An application of Bayesian variable selection

Early identification of contaminated food products is crucial in reducing health burdens of food-borne disease outbreaks. Analytic case-control studies are primarily used in this identification stage by comparing exposures in cases and controls using logistic regression. Standard epidemiological analysis practice is not formally defined and the combination of currently applied methods is subject to issues such as response misclassification, missing values, multiple testing problems and small sample estimation problems resulting in biased and possibly misleading results. In this paper, we develop a formal Bayesian variable selection method to account for misclassified responses and missing covariates, which are common complications in food-borne outbreak investigations. We illustrate the implementation and performance of our method on a Salmonella Thompson outbreak in the Netherlands in 2012. Our method is shown to perform better than the standard logistic regression approach with respect to earlier identification of contaminated food products. It also allows relatively easy implementation of otherwise complex methodological issues.

A large outbreak of Salmonella enterica serovar Thompson infections associated with chocolate cake in Busan, Korea

OBJECTIVES

This study aimed to reveal the epidemiologic characteristics of the outbreak of gastroenteritis caused by Salmonella enterica serovar Thompson in Busan Metropolitan City and to identify points for improvement to prevent of food-borne disease outbreak.

METHODS

This was a case-control study. The control group comprised asymptomatic students in the same classes of the cases. The presence or absence of symptoms, ingestion of each food provided by school meal service, and commonly ingested foods in addition to those foods in meal service were investigated. Moreover, specimens collected from rectal swab, preserved foods, and environmental surface were tested.

RESULTS

Of the 6,092 subjects, 1,111 (1,083 students, 22 school personnel, and 6 foodservice employees) were included in the case group; this corresponded to an 18.4% attack rate. Symptoms included diarrhea (n=1,051, 94.6%), abdominal pain (n=931, 83.8%), febrile sensation (n=502, 45.2%), and vomiting (n=275, 24.8%). The epidemic curves of each 10 schools were unimodal. Investigation of food intake showed a significantly high odds ratio for chocolate cake in 5 out of the 10 schools. Laboratory test detected Salmonella enterica serovar Thompson both in rectal swab specimens of 9 schools and in collected preserved chocolate cakes of 9 schools. Pulsed-field gel electrophoresis test result showed that Salmonella enterica seorvar Thompson isolated from human and foods were the same.

CONCLUSIONS

The source of infection for the Salmonella enterica serovar Thompson outbreak in the 10 schools of Busan Metropolitan City is chocolate cake. Traceback investigation for origin of contaminated food in food-borne disease outbreak and safety control during food production should be more enhanced.

Phenotypic Prediction: Linking in vitro Virulence to the Genomics of 59 Salmonella enterica Strains

The increased availability of whole-genome-sequencing techniques generates a wealth of DNA data on numerous organisms, including foodborne pathogens such as Salmonella. However, how these data can be used to improve microbial risk assessment and understanding of Salmonella epidemiology remains a challenge. The aim of this study was to assess variability in in vitro virulence and genetic characteristics between and within different serovars. The phenotypic behavior of 59 strains of 32 different Salmonella enterica serovars from animal, human and food origin was assessed in an in vitro gastro-intestinal tract (GIT) system and they were analyzed for the presence of 233 putative virulence genes as markers for phenotypic prediction. The probability of in vitro infection, P(inf), defined as the fraction of infectious cells passing from inoculation to host cell invasion at the last stage of the GIT system, was interpreted as the in vitro virulence. Results showed that the (average) P(inf) of Salmonella serovars ranged from 5.3E-05 (S. Kedougou) to 5.2E-01 (S. Typhimurium). In general, a higher P(inf) on serovar level corresponded to higher reported human incidence from epidemiological reporting data. Of the 233 virulence genes investigated, only 101 showed variability in presence/absence among the strains. In vitro P(inf) was found to be positively associated with the presence of specific plasmid related virulence genes (mig-5, pef, rck, and spv). However, not all serovars with a relatively high P(inf), > 1E-02, could be linked with these specific genes. Moreover, some outbreak related strains (S. Heidelberg and S. Thompson) did not reveal this association with P(inf). No clear association with in vitro virulence P(inf) was identified when grouping serovars with the same virulence gene profile (virulence plasmid, Typhoid toxin, peg operon and stk operon). This study shows that the in vitro P(inf) variation among individual strains from the same serovar is larger than that found between serovars. Therefore, ranking P(inf) of S. enterica on serovar level alone, or in combination with a serovar specific virulence gene profile, cannot be recommended. The attribution of single biological phenomena to individual strains or serovars is not sufficient to improve the hazard characterization for S. enterica. Future microbial risk assessments, including virulence gene profiles, require a systematic approach linked to epidemiological studies rather than revealing differences in characteristics on serovar level alone.

Selenite enrichment broth to improve the sensitivity in molecular diagnostics of Salmonella

Selenite enrichment broth (SEB) is used to optimize the recovery of Salmonella enterica subspecies enterica from stool samples. Compared to a direct culture approach, it enhances culture yield by reducing growth of faecal coliforms and faecal streptococci. Over the course of seven years from 2000 to 2017, 47,235 faecal samples were tested with a Salmonella PCR. We investigated the added value of using SEB in combination with faeces for DNA extraction, in order to improve the sensitivity of molecular diagnostics for detection of Salmonella. A Salmonella enterica subspecies enterica strain was tested for growth characteristics, with and without incubation in SEB, to determine the impact of Selenite enrichment in the Salmonella PCR. Retrospectively, a total of 102 Salmonella enterica subspecies enterica PCR positive faecal samples were re-analysed. DNA extraction was performed with the EasyMag® and MagNaPure96® system using three different input volumes of faeces and SEB. Prospectively, 114 Salmonella PCR positive faecal samples were retested within 2 days using five different input volumes for DNA extraction. Retrospectively, PCR that used SEB as part of input in the DNA extraction, 7/102 (7%) Salmonella PCR positive samples were additionally detected compared to no use of SEB. Of these, Salmonella enterica subspecies enterica serovariation Thompson, Enteritidis, 9,12:l.v and Senftenberg have been outbreak related in the past. Prospectively results were combined in collaboration with another microbiology laboratory, 15/114 (13.2%) additional specimens were detected with the Salmonella PCR, including processing Selenite enrichment broth. In conclusion, of the total 47,235 feacal samples, with SEB the prevalence of a positive PCR for Salmonella is 2.2%. Of these 2.2% positive Salmonella PCRs, 0.4% was not detected in culture. By using SEB an improved detection of Salmonella diagnostics could be realized and a substantial part of 13,2% additional Salmonella cases could be detected.

Microbiomes Associated With Foods From Plant and Animal Sources

Food microbiome composition impacts food safety and quality. The resident microbiota of many food products is influenced throughout the farm to fork continuum by farming practices, environmental factors, and food manufacturing and processing procedures. Currently, most food microbiology studies rely on culture-dependent methods to identify bacteria. However, advances in high-throughput DNA sequencing technologies have enabled the use of targeted 16S rRNA gene sequencing to profile complex microbial communities including non-culturable members. In this study we used 16S rRNA gene sequencing to assess the microbiome profiles of plant and animal derived foods collected at two points in the manufacturing process; post-harvest/pre-retail (cilantro) and retail (cilantro, masala spice mixes, cucumbers, mung bean sprouts, and smoked salmon). Our findings revealed microbiome profiles, unique to each food, that were influenced by the moisture content (dry spices, fresh produce), packaging methods, such as modified atmospheric packaging (mung bean sprouts and smoked salmon), and manufacturing stage (cilantro prior to retail and at retail). The masala spice mixes and cucumbers were comprised mainly of Proteobacteria, Firmicutes, and Actinobacteria. Cilantro microbiome profiles consisted mainly of Proteobacteria, followed by Bacteroidetes, and low levels of Firmicutes and Actinobacteria. The two brands of mung bean sprouts and the three smoked salmon samples differed from one another in their microbiome composition, each predominated by either by Firmicutes or Proteobacteria. These data demonstrate diverse and highly variable resident microbial communities across food products, which is informative in the context of food safety, and spoilage where indigenous bacteria could hamper pathogen detection, and limit shelf life.

Tracing Back the Source of an Outbreak of Salmonella Typhimurium; National Outbreak Linked to the Consumption of Raw and Undercooked Beef Products, the Netherlands, October to December 2015

INTRODUCTION

On 23 October 2015, six related cases with gastroenteritis called the Netherlands Food and Consumer Product Safety Authority. They suspected filet américain, a raw beef spread, to be the source of infection. Leftovers and stool samples tested positive for Salmonella Typhimurium. Multiple locus variable-number of tandem repeat analysis (MLVA) revealed a MLVA pattern (02-23-08-08-212), which had not been detected in the Netherlands before. Concomitantly, an increase of this MLVA type was observed in the national Salmonella surveillance, amounting to 46 cases between 26 October and 9 December.

METHODS

To investigate whether filet américain or an alternative (related) source could  be linked to surveillance-reported cases, cases (n=38) were invited to complete a questionnaire and upstream source tracing to map the food supply chain was initiated.

RESULTS

Rapid interdisciplinary action resulted in identification of a contaminated 46-ton batch of beef distributed via a Dutch deboning plant as the likely source of infection. In total, 24/29 respondents (83%) could be linked to the incriminated batch of beef products (predominantly filet américain and minced beef).

DISCUSSION

Repeated identification of raw meat products as a source of infection emphasizes the importance of awareness of the risk of infection when handling or consuming these products. Improved measures and procedures on product labelling, pre-treatment or product testing should be considered.

Outbreak of Salmonella Bovismorbificans associated with the consumption of uncooked ham products, the Netherlands, 2016 to 2017

In January 2017, an increase in reported Salmonellaenterica serotype Bovismorbificans cases in the Netherlands was observed since October 2016. We implemented a case-control study to identify the source, including all cases after December 2016. Adjusted odds ratios were calculated using logistic regression analysis. We traced back the distribution chain of suspected food items and sampled them for microbiological analysis. Human and food isolates were sequenced using whole genome sequencing (WGS). From October 2016 to March 2017, 54 S. Bovismorbificans cases were identified. Sequencing indicated that all were infected with identical strains. Twenty-four cases and 37 controls participated in the study. Cases were more likely to have consumed ham products than controls (aOR = 13; 95% CI: 2.0-77) and to have shopped at a supermarket chain (aOR = 7; 95% CI: 1.3-38). Trace-back investigations led to a Belgian meat processor: one retail ham sample originating from this processor tested positive for S. Bovismorbificans and matched the outbreak strain by WGS. All ham products related to the same batch were removed from the market to prevent further cases. This investigation illustrates the importance of laboratory surveillance for all Salmonella serotypes and the usefulness of WGS in an outbreak investigation.

The economic burden of a Salmonella Thompson outbreak caused by smoked salmon in the Netherlands, 2012-2013

Background

In 2012, the Netherlands experienced the most extensive food-related outbreak of Salmonella ever recorded. It was caused by smoked salmon contaminated with Salmonella Thompson during processing. In total, 1149 cases of salmonellosis were laboratory confirmed and reported to RIVM. Twenty percent of cases was hospitalised and four cases were reported to be fatal. The purpose of this study was to estimate total costs of the Salmonella Thompson outbreak.

Methods

Data from a case-control study were used to estimate the cost-of-illness of reported cases (i.e. healthcare costs, patient costs and production losses). Outbreak control costs were estimated based on interviews with staff from health authorities. Using the Dutch foodborne disease burden and cost-of-illness model, we estimated the number of underestimated cases and the associated cost-of-illness.

Results

The estimated number of cases, including reported and underestimated cases was 21 123. Adjusted for underestimation, the total cost-of-illness would be €6.8 million (95% CI €2.5-€16.7 million) with productivity losses being the main cost driver. Adding outbreak control costs, the total outbreak costs are estimated at €7.5 million.

Conclusion

In the Netherlands, measures are taken to reduce salmonella concentrations in food, but detection of contamination during food processing remains difficult. As shown, Salmonella outbreaks have the potential for a relatively high disease and economic burden for society. Early warning and close cooperation between the industry, health authorities and laboratories is essential for rapid detection, control of outbreaks, and to reduce disease and economic burden.

Population dynamics and antimicrobial resistance of the most prevalent poultry-associated Salmonella serotypes

Salmonella spp. is the most predominant bacterial cause of foodborne gastroenteritis in humans. Due to the risk of human infection associated with poultry products and the prevalence of antimicrobial resistance, Salmonella also poses a significant challenge to commercial poultry production. During the last decade (2002 to 2012), the 12 most prevalent poultry-associated Salmonella serotypes (MPPSTs) were frequently and consistently isolated from poultry products in the United States. These MPPSTs and their percent prevalence in poultry products include Kentucky (4%), Enteritidis (2%) Heidelberg (2%), Typhimurium (2%), S. I 4,[5],12:i:- (0.31%), Montevideo (0.20%), Infantis (0.16%) Schwarzengrund (0.15%), Hadar (0.15%), Mbandaka (0.13%), Thompson (0.12%), and Senftenberg (0.04%). All MPPSTs except Kentucky are among the top 30 clinically significant serotypes that cause human illnesses in the United States. However with the exception of a few widely studied serotypes such as S. Enteritidis and Typhimurium, the ecology and epidemiology of the majority of MPPSTs still remain poorly investigated. Published data from the United States suggests that MPPSTs such as Heidelberg, Typhimurium, Kentucky, and Sentfenberg are more likely to be multi-drug resistant (MDR, ≥3 antimicobial classes) whereas Enteritidis, Montevideo, Schwarzengrund, Hadar, Infantis, Thompson, and Mbandaka are generally pan-susceptible or display resistance to fewer antimicobials. In contrast, the majority of MPPSTs isolated globally have been reported to display MDR phenotype. There also appears to be an international spread of a few MDR serotypes including Kentucky, Schwarzengrund, Hadar, Thomson, Sentfenberg, and Enteritidis, which may pose significant challenges to the public health. The current knowledge gaps on the ecology, epidemiology, and antimicrobial resistance of MPPSTs are discussed.

Salmonella Thompson outbreak associated with consumption of chicken shawarma and the usefulness of genome sequencing in the investigation

Background

A sudden increase in Salmonella Thompson (S. Thompson) cases distributed throughout three border regions in the province of Quebec in November 2016 triggered a provincial investigation to identify a common source of contamination and to put the appropriate control measures into place.

Objective

To report on the outbreak and to describe the use of genomic sequencing to identify the salmonella serotype responsible.

Methods

A descriptive survey of all reported cases of Salmonella serogroup C1 that had occurred between October 1, 2016 and February 15, 2017 was conducted. A case definition was developed. Pulsed field gel electrophoresis supplemented by analyses of genome sequences using the single nucleotide variant phylogenomics method were used to demarcate and manage the outbreak.

Results

Eighteen cases of S. Thompson were identified through whole genome sequencing. The onset dates of symptoms for the 16 cases that presented enteric symptoms were November 21-December 2, 2016. Two cases that presented with atypical symptoms were not reported until February 2017. Among the 18 cases, 16 had eaten or probably eaten chicken shawarma at the same restaurant chain and nine of these cases ate it at the same restaurant. In total, five restaurants from this chain, spread throughout three border regions of Quebec, were identified.

Conclusion

Outbreaks associated with chicken shawarma have been identified in the past. Efforts must be made to ensure that the owners of this type of restaurant know the contamination risk associated with this type of cooking and take the necessary steps to reduce this risk. The use of the genome sequencing method was very useful in defining the outbreak.

Salmonella Thompson splenic abscess in a healthy female

A 26-year-old woman presented with a 5-day history of fever and 3-day history of left upper quadrant abdominal pain and cough associated with left shoulder tip pain. Initial blood cultures did not display growth. On CT imaging, there was a cyst measuring 7.2×8 cm originally interpreted to be haemorrhagic in nature. Repeat cultures during admission revealed Salmonella Thompson. Percutaneous drainage and antibiotic treatment, rather than splenectomy, was successfully pursued with the patient afebrile and in no pain at 6 weeks follow-up.

Salmonella Serogroup C: Current Status of Vaccines and Why They Are Needed

Nontyphoidal Salmonella (NTS; i.e., Salmonella enterica organisms that do not cause typhoid or paratyphoid) are responsible for 94 million infections and 155,000 deaths worldwide annually, 86% of which are estimated to be foodborne. Although more than 50 serogroups and 2,600 serovars have been described, not all Salmonella serovars cause disease in humans and animals. Efforts are being made to develop NTS vaccines, with most approaches eliciting protection against serovars Typhimurium and Enteritidis (serogroups B [O:4] and D [O:9], respectively), as they are widely considered the most prevalent. Here, we show that serogroup C (O:6,7, O:6,8, or O:8 epitopes) is the most common serogroup in the United States, and the prevalence of serovars from this serogroup has been increasing in Europe and the United States over the last decade. They are also the most commonly isolated serovars from healthy cattle and poultry, indicating the underlying importance of surveillance in animals. Four out of the 10 most lethal serovars in the United States are serogroup C, and reports from African countries suggest that strains within this serogroup are highly antibiotic resistant. Serogroup C consists of highly diverse organisms among which 37 serovars account for the majority of human cases, compared to 17 and 11 serovars for serogroups B and D, respectively. Despite these concerning data, no human vaccines targeting serogroup C NTS are available, and animal vaccines are in limited use. Here, we describe the underestimated burden represented by serogroup C NTS, as well as a discussion of vaccines that target these pathogens.

Microbiological Food Safety for Vulnerable People

Foodborne pathogens are more likely to cause infection and to result in serious consequences in vulnerable people than in healthy adults. People with some increase in susceptibility may form nearly 20% of the population in the UK and the USA. Conditions leading to increased susceptibility are listed. The main factors leading to foodborne disease caused by major pathogens are outlined and examples are given of outbreaks resulting from these factors. Measures to prevent foodborne disease include procedures based on Hazard Analysis Critical Control Point principles and prerequisite programmes and, especially for vulnerable people, the use of lower-risk foods in place of higher-risk products.