Food safety incidents in the red meat industry: A review of foodborne disease outbreaks linked to the consumption of red meat and its products, 1991 to 2021

Red meat is a significant source of human nutrition, and the red meat industry contributes to the economy of nations. Nonetheless, there is a widespread global concern about public health issues posed by severe food safety incidents within the red meat industry. Most of these incidents are associated with foodborne disease outbreaks that impact individual consumers, food businesses and society. This study adopts a systematic search and review approach to identify three decades of published investigation reports of global foodborne disease outbreaks linked with the consumption of red meat and products made from them. The review aims to evaluate the critical features of these outbreak incidents to get insight into their contributing factors and root causes. In particular, this review discusses the transmission setting (origin of pathogenic agents), the food vehicles mostly incriminated, the causative pathogens (bacteria, viruses, and parasites) causing the most illnesses, and the most commonly reported contributing factors to the outbreaks. This information can help researchers and food business operators (FBOs) inform future risk assessment studies and support risk management activities in developing risk-mitigating strategies for the industry. Findings from this study suggest that implementing food safety management strategies which include adequate control measures at all stages of the food chain, from farm to fork, is imperative in preventing outbreak incidents. Of equal importance is the need for enhanced and sustained public education about the risk of foodborne illnesses associated with meat and its products whilst discouraging the consumption of raw meat products, especially by high-risk groups.

Countrywide multi-serotype outbreak of Salmonella Bovismorbificans ST142 and monophasic Salmonella Typhimurium ST34 associated with dried pork sausages in France, September 2020* to January 2021

The French National Reference Centre for Escherichia coli, Shigella and Salmonella (FNRC-ESS) detected two human clusters of 33 cases (median age: 10 years; 17 females) infected by Salmonella enterica serotype Bovismorbificans, ST142, HC5_243255 (EnteroBase HierCC‑cgMLST scheme) in September-November 2020 and of 11 cases (median age: 11 years; seven males) infected by S. enterica serotype 4,12:i:-, ST34, HC5_198125 in October-December 2020. Epidemiological investigations conducted by Santé publique France linked these outbreaks to the consumption of dried pork sausages from the same manufacturer. S. Bovismorbificans and S. 4,12:i:- were isolated by the National Reference Laboratory from different food samples, but both strains were identified in a single food sample only by qPCR. Three recalls and withdrawals of dried pork products were issued by the French general directorate of food of the French ministry for agriculture and food in November 2020, affecting eight supermarket chains. A notification on the European Rapid Alert System for Food and Feed and a European urgent enquiry on the Epidemic Intelligence Information System for Food and Waterborne Diseases and Zoonoses (EPIS-FWD) were launched. No cases were reported outside France. Outbreaks caused by multiple serotypes of Salmonella may go undetected by protocols in standard procedures in microbiology laboratories.

Antibiotic Resistance of Salmonella Typhimurium Monophasic Variant 1,4,[5],12:i:- in China: A Systematic Review and Meta-Analysis

Antibiotic resistance in Salmonella is a global public health problem. Salmonella enterica serovar 1,4,[5],12:i:- (S. 1,4,[5],12:i:-), a monophasic variant of Salmonella Typhmurium, is one of the leading Salmonella serovars in several countries. This study aimed to assess the prevalence of antibiotic resistance to this serovar in China through a systematic review and meta-analysis. Nineteen eligible studies during 2011–2021 were included. A total of 4514 isolates from humans, animals, foods, and the environment were reported, which mainly concerned isolates found in Guangdong, Guangxi, Jiangsu, and Shanghai. A random-effects model was used to estimate the pooled resistance rate of S. 1,4,[5],12:i:-. Rates were found to be very high (values ≥ 75%) for tetracycline, ampicillin, sulfisoxazole, and streptomycin; high (50–75%) for nalidixic acid, amoxicillin–clavulanic acid, and chloramphenicol; and moderate (25–50%) for trimethoprim–sulfamethoxazole, kanamycin, trimethoprim, and gentamicin. The rates of resistance to ciprofloxacin, cefotaxime, ceftriaxone, cefepime, ceftazidime, and colistin were low (values ≤ 25%), but of great concern in terms of their current clinical importance. Furthermore, a high multidrug resistance rate (86%, 95% CI: 78–92%) was present in S. 1,4,[5],12:i:-, with the ASSuT pattern largely dominating. Subgroup analysis results showed that the high heterogeneity of resistance rates was not entirely dependent on isolated sources. Taken together, the severity of antibiotic resistance in S. 1,4,[5],12:i:- urgently requires the rational use of antibiotics in future infection control and antibiotic stewardship programs.

Mapping foodborne pathogen contamination throughout the conventional and alternative poultry supply chains

Recently, there has been a consumer push for natural and organic food products. This has caused alternative poultry production, such as organic, pasture, and free-range systems, to grow in popularity. Due to the stricter rearing practices of alternative poultry production systems, different types of levels of microbiological risks might be present for these systems when compared to conventional production systems. Both conventional and alternative production systems have complex supply chains that present many different opportunities for flocks of birds or poultry meat to be contaminated with foodborne pathogens. As such, it is important to understand the risks involved during each step of production. The purpose of this review is to detail the potential routes of foodborne pathogen transmission throughout the conventional and alternative supply chains, with a special emphasis on the differences in risk between the two management systems, and to identify gaps in knowledge that could assist, if addressed, in poultry risk-based decision making.

Identification of a Recently Dominant Sublineage in Salmonella 4,[5],12:i:- Sequence Type 34 Isolated From Food Animals in Japan

Salmonella enterica subsp. enterica serovar Typhimurium sequence type 34 (ST34) and its monophasic variant (Salmonella 4,[5],12:i:-) are among the most frequently isolated clones from both humans and animals worldwide. Our previous study demonstrated that Salmonella Typhimurium/4,[5],12:i:- strains isolated in Japan could be classified into nine clades and that clade 9 consisted of ST34 strains. In Japan, ST34/clade 9 was first found in the 1990s and has become predominant among food animals in recent years. In the present study, we analyzed the whole genome-based phylogenetic relationships and temporal information of 214 Salmonella Typhimurium/4,[5],12:i:- ST34/clade 9 strains isolated from 1998 to 2017 in Japan. The 214 strains were classified into two sublineages: the newly identified clade 9–2 diverged from clade 9 in the early 2000s and has predominated in recent years. Clonally expanding subclades in clades 9–1 or 9–2 lacked Gifsy-1 or HP1 prophages, respectively, and some strains in these subclades acquired plasmids encoding antimicrobial resistance genes. Additional genome reduction around the fljB gene encoding the phase 2-H antigen was generated by an IS26-mediated deletion adjacent to the transposon in clade 9–2. Although most of the clade 9 strains were isolated from cattle in Japan, the clonally expanding subclades in clade 9–2 (i.e., all and 24% strains of subclades 9–2a and 9–2b, respectively) were isolated from swine. The spread of clade 9 in recent years among food animals in Japan was responsible for the emergence of multiple host-adapted sublineages involving the clonally expanding subclades generated by mobile genetic element-mediated microevolution.

Salmonella enterica I 4,[5],12:i:- Associated with Lesions Typical of Swine Enteric Salmonellosis

Salmonella enterica serotype I 4,[5],12:i:- has been increasingly isolated from swine. However, its pathogenic potential is not well characterized. Analysis of swine cases confirmed a strong positive association between isolation of I 4,[5],12:i:- and lesions of enteric salmonellosis and suggested a similar pathogenic potential as that for Salmonella Typhimurium.

The Epidemiology of Monophasic Salmonella Typhimurium

Salmonella enterica remains an important foodborne pathogen in all regions of the world, with Typhimurium as one of the most frequent serotypes causing foodborne disease. However, the past two decades have seen a rapid worldwide emergence of a new Salmonella serotype, namely monophasic variant of S. Typhimurium, whose antigenic formula is 1,4,[5],12:i:-. It has become one of the 2-5 most common Salmonella serotypes responsible for animal and human infections in different regions. The global epidemic of monophasic S. 1,4,[5],12:i:- has mainly been characterized by an increase in multidrug-resistant S. 1,4,[5],12:i:- isolated in Europe since 1997. The unexpected link to swine has escalated monophasic S. Typhimurium infections to the status of a global public health emergency. The large-scale application of whole genome sequencing (WGS) in the last 10 years has revealed the phylogenetic associations of the bacterium and its antimicrobial resistance (AMR) genes. Local and global transmission reconstructed by WGS have shown that different clones have emerged following multiple independent events worldwide, and have elucidated the role of this zoonotic pathogen in the spread of AMR. This article discusses our current knowledge of the global ecology, epidemiology, transmission, bacterial adaptation, and evolution of this emerging Salmonella serotype.

Multidrug-Resistant Salmonella enterica Subspecies I Serovar 4,[5],12:i:- Isolates Recovered from Food Safety and Inspection Service-Regulated Products and Food Animal Ceca, 2007-2016

Salmonella enterica subspecies I serovar 4,[5],12:i:- (Salmonella I 4,[5],12:i:-) is among the five most common serovars associated with human salmonellosis in the United States. In 2010, human infections with Salmonella I 4,[5],12:i:- which exhibited resistance to ampicillin, streptomycin, sulfonamides, and tetracycline (ASSuT) emerged as a public health concern. Outbreak investigations identified live animal settings, meat and poultry, and pets as confirmed and suspect sources of infection. To shed further light on possible sources of ASSuT-resistant Salmonella I 4,[5],12:i:- infections, we described isolates recovered from meat and poultry products regulated by the Food Safety and Inspection Service (FSIS) and from food animal ceca collected at FSIS-regulated slaughter establishments during 2007-2016. During the time period of interest, ASSuT-resistant Salmonella I 4,[5],12:i:- was found at low levels in multiple FSIS product classes including swine, turkey, cattle and chicken, which suggests this pathogen has a relatively wide host range. Monitoring trends in the various FSIS production classes over time and developing commodity profiles may help focus preventative strategies.

Non-typhoidal Salmonella in the Pig Production Chain: A Comprehensive Analysis of Its Impact on Human Health

Salmonellosis remains one of the most frequent foodborne zoonosis, constituting a worldwide major public health concern. The most frequent sources of human infections are food products of animal origin, being pork meat one of the most relevant. Currently, particular pig food production well-adapted and persistent Salmonella enterica serotypes (e.g., Salmonella Typhimurium, Salmonella 1,4,[5],12:i:-, Salmonella Derby and Salmonella Rissen) are frequently reported associated with human infections in diverse industrialized countries. The dissemination of those clinically-relevant Salmonella serotypes/clones has been related to the intensification of pig production chain and to an increase in the international trade of pigs and pork meat. Those changes that occurred over the years along the food chain may act as food chain drivers leading to new problems and challenges, compromising the successful control of Salmonella. Among those, the emergence of antibiotic resistance in non-typhoidal Salmonella associated with antimicrobials use in the pig production chain is of special concern for public health. The transmission of pig-related multidrug-resistant Salmonella serotypes, clones and/or genetic elements carrying clinically-relevant antibiotic resistance genes, frequently associated with metal tolerance genes, from pigs and pork meat to humans, has been reported and highlights the contribution of different drivers to the antibiotic resistance burden. Gathered data strengthen the need for global mandatory interventions and strategies for effective Salmonella control and surveillance across the pig production chain. The purpose of this review was to provide an overview of the role of pig and pork meat in human salmonellosis at a global scale, highlighting the main factors contributing to the persistence and dissemination of clinically-relevant pig-related Salmonella serotypes and clones.

Prevalence, Serotypes, and Antimicrobial Resistance Profiles Among Salmonella Isolated from Food Catering Workers in Nantong, China

Salmonella is a worldwide foodborne pathogen causing human disease. Food handlers, who are potential carriers of Salmonella, may transmit the pathogen to consumers through food. To determine the prevalence of Salmonella enterica serovars among food handlers working in the catering industry in Nantong, China, a total of 214,542 food handlers' fecal samples were tested for Salmonella in the Nantong CDC (Centers for Disease Control) from 2012 to 2017. Among those tested, 193 (0.09%) were identified to be positive for Salmonella, and the highest detection rate was 0.16% during the period of July to September. Serotyping analysis showed that Salmonella enterica serovar Typhimurium was the predominant serotype (16.1%), followed by Salmonella Derby (13.5%), Salmonella Enteritidis (11.4%), and Salmonella London (11.4%). The high detection rate of Salmonella Derby was probably closely related to its high prevalence of the serotype in pork, which is the primary meat consumed by the Chinese. Antibiotic susceptibility analysis demonstrated that 73.4% of the isolates were multidrug-resistant (MDR) strains with predominant resistance to ampicillin (AMP, 64.6%), followed by resistance to sulfisoxazole (SUL, 58.1%), nalidixic acid (55.8%), and tetracycline (TET, 44.5%). Therefore, MDR Salmonella strain carriage among food handlers working in the catering industry might be a potential source of human salmonellosis, especially for the predominant MDR genotype isolates (32.3%) with resistance to AMP, SUL, and TET.

Analysis of consumer food purchase data used for outbreak investigations, a review

BackgroundInvestigations of food-borne outbreaks are frequently unsuccessful and new investigation methods should be welcomed. Aim: Describe the use of consumer purchase datasets in outbreak investigations and consider methodological and practical difficulties. Methods: We reviewed published papers describing the use of consumer purchase datasets, where electronic data on the foods that case-patients had purchased before onset of symptoms were obtained and analysed as part of outbreak investigations. Results: For the period 2006-17, scientific articles were found describing 20 outbreak investigations. Most outbreaks involved salmonella or Shiga toxin-producing Escherichia coli and were performed in eight different countries. The consumer purchase datasets were most frequently used to generate hypotheses about the outbreak vehicle where case-interviews had not been fruitful. Secondly, they were used to aid trace-back investigation, where a vehicle was already suspected. A number of methodological as well as (in some countries) legal and practical impediments exist. Conclusions: Several of the outbreaks were unlikely to have been solved without the use of consumer purchase datasets. The method is potentially powerful and with future improved access to big data purchase information, may become a widely applicable tool for outbreak investigations, enabling investigators to quickly find hypotheses and at the same time estimate odds ratios or relative risks hereof. We suggest using the term 'consumer purchase data' to refer to the approach in the future.

Phylogenetic Characterization of Salmonella enterica Serovar Typhimurium and Its Monophasic Variant Isolated from Food Animals in Japan Revealed Replacement of Major Epidemic Clones in the Last 4 Decades

Salmonella enterica serovar Typhimurium (Salmonella Typhimurium) and its monophasic variant (Salmonella 4,[5],12:i:-) are the major causes of gastroenteritis in both humans and animals. Pulsed-field gel electrophoresis and multilocus variable-number tandem-repeat analysis have been used widely as subtyping methods for these pathogens in molecular epidemiological analyses, but the results do not precisely reflect phylogenetic information. In this study, we performed a phylogenetic analysis of these serovars using whole-genome sequencing data and identified nine distinct genotypic clades. Then, we established an allele-specific PCR-based genotyping method detecting a clade-specific single nucleotide polymorphism to rapidly identify the clade of each isolate. Among a total of 815 isolates obtained from cattle in Japan between 1977 and 2017, clades 1, 7, and 9 contained 77% of isolates. Obvious replacement of the dominant clone was observed five times in this period, and clade 9, which mostly contains Salmonella 4,[5],12:i:-, is currently dominant. Among 140 isolates obtained from swine in Japan between 1976 and 2017, clades 3 and 9 contained 64% of isolates. Clade 9 is the latest clone as is the case in cattle isolates. Clade 9 is similar to an epidemic clone from Europe, which is characterized by sequence type 34 (ST34), chromosomal Salmonella genomic island 3, and a composite transposon containing antimicrobial resistance genes. The increased prevalence of clade 9 among food animals in Japan might be a part of the pandemic of the European Salmonella 4,[5],12:i:- clone.

Immunogenic potential of a Salmonella Typhimurium live vaccine for pigs against monophasic Salmonella Typhimurium DT 193

BACKGROUND

Monophasic Salmonella Typhimurium (mSTM) strains account for up to 8.6% of all human Salmonellosis cases. They have an increasing prevalence during recent years and several human cases with hospitalisation were reported. These strains are often isolated from pigs and pork - one primary source of human infection. A Salmonella Typhimurium (STM) live vaccine has been proven successful in controlling of STM infections in pigs for many years. The aim of this study was to test the immunogenicity of the vaccine in weaners during oral challenge with a virulent mSTM strain and to examine the kinetics of STM-specific IgA, IgM and IgG antibodies induced by vaccination and infection.

RESULTS

Despite clinical signs being present in both groups, the vaccination led to a significant reduction of diarrhoea, overall clinical symptoms and a milder elevation of the body temperature. Necropsy revealed fewer pathological lesions in the gastrointestinal tract of vaccinated compared to control animals. Moreover, in the ileal and caecal mucosa and in the ileocaecal lymph nodes the challenge strain burden was significantly reduced by vaccination. Significant differences in the antibody responses of both groups were present during the vaccination period and after infection. In vaccinated animals Salmonella-specific IgA and IgG antibody levels increased significantly after vaccination and were even more pronounced in response to challenge. In contrast, similarly low levels of IgM antibodies were detected during the vaccination period in both vaccinated and non-vaccinated animals. However, after challenge IgM antibody levels increased significantly in control pigs while neither IgA nor IgG antibodies were detectable.

CONCLUSION

The data demonstrate that mSTM can evoke clinical signs in weaners. Due to the vaccination their incidence and magnitude were significantly milder. Vaccination also led to a significantly reduced challenge strain burden in the intestine and the lymph nodes which is comparable to previous studies using the same vaccine in a challenge with biphasic STM. Therefore, it is concluded that this vaccine induces immunity against monophasic and biphasic STM strains. Furthermore, the results of antibody profiles in response to vaccination and infection provide additional evidence for humoral immune mechanisms triggered during Salmonella infection or vaccination.

Characterization of Nontyphoidal Salmonella Isolates from Asymptomatic Migrant Food Handlers in Peninsular Malaysia

Asymptomatic Salmonella carriers who work as food handlers pose food safety and public health risks, particularly during food preparation, and this has serious implications for the disease burden in society. Therefore, we conducted a study to determine the number of Salmonella carriers in a migrant cohort in several food establishments in three major cities in Peninsular Malaysia. Sociodemographic data and stool samples were collected and analyzed using standard methods of detection and isolation. Antimicrobial susceptibility tests of the positive samples were also performed. A total of 317 migrant food handlers, originating from South and Southeast Asian countries, were recruited voluntarily. Nine (2.8%) stool samples were confirmed to be Salmonella positive. PCR serotyping and pulsed-field gel electrophoresis identified four serotypes as Typhimurium (n = 3), Corvallis (n = 2), Hadar (n = 1), Agona (n = 1) and two unknown serovars. Antimicrobial susceptibility tests revealed that all nine isolates were susceptible to amoxicillin-clavulanic acid, cefotaxime, ceftazidime, ceftriaxone, and gentamycin. However, seven isolates were found to be multidrug resistant to ampicillin, chloramphenicol, trimethoprim-sulfamethoxazole, sulfonamides, streptomycin, and tetracycline. This study highlights that carriers of nontyphoidal Salmonella exist among migrant food handlers, which poses a health risk to consumers through food contamination. Our results indicate a need for authorities to enhance food safety awareness in the migrant workers and to reevaluate current health screening methods to include preventive measure such as mandatory stool screening as part of the preemployment and routine health examinations.

A liquid bead array for the identification and characterization of fljB-positive and fljB-negative monophasic variants of Salmonella Typhimurium

Salmonella1,4,[5],12:i:- accounts currently for one of the most common serotypes observed worldwide. These isolates do not express the FljB flagellin and mostly derive from Salmonella Typhimurium. They are therefore termed Salmonella Typhimurium monophasic variants (STMV) and are considered of comparable public health risk. Since serological identification of the somatic and flagellar antigens of STMV is not sufficient to demonstrate relatedness with Salmonella Typhimurium, additional assays detecting genetic markers unique to Salmonella Typhimurium are required. In addition, identification of the mutations affecting expression of the flagellar gene fljB can be useful to support the monophasic character observed phenotypically. Finally, genetic subtyping of the various mono- and biphasic Salmonella Typhimurium clonal groups can facilitate their epidemiological follow-up. Here, we present a home-made liquid bead array able to fulfill these requirements. This array confirmed the monophasic character of 240 STMV isolates collected in Belgium during 2014-2015 and identified 10 genetic subtypes. Microevolution in and around the fljB locus linked to IS26 insertions is probably one of the driven force accounting for STMV population diversity. Thanks to its open design, other genetic signatures could later be merged to the assay to subtype additional STMV clonal groups and to detect rare mutations.

Multinational outbreak of travel-related Salmonella Chester infections in Europe, summers 2014 and 2015

Between 2014 and 2015, the European Centre for Disease Prevention and Control was informed of an increase in numbers of Salmonella enterica serotype Chester cases with travel to Morocco occurring in six European countries. Epidemiological and microbiological investigations were conducted. In addition to gathering information on the characteristics of cases from the different countries in 2014, the epidemiological investigation comprised a matched case-case study involving French patients with salmonellosis who travelled to Morocco that year. A univariate conditional logistic regression was performed to quantify associations. The microbiological study included a whole genome sequencing (WGS) analysis of clinical and non-human isolates of S. Chester of varied place and year of isolation. A total of 162 cases, mostly from France, followed by Belgium, the Netherlands, Spain, Denmark and Sweden were reported, including 86 (53%) women. The median age per country ranged from 3 to 38 years. Cases of S. Chester were more likely to have eaten in a restaurant and visited the coast of Morocco. The results of WGS showed five multilocus sequence types (ST), with 96 of 153 isolates analysed clustering into a tight group that corresponded to a novel ST, ST1954. Of these 96 isolates, 46 (48%) were derived from food or patients returning from Morocco and carried two types of plasmids containing either qnrS1 or qnrB19 genes. This European-wide outbreak associated with travel to Morocco was likely a multi-source outbreak with several food vehicles contaminated by multidrug-resistant S. Chester strains.

Evaluation of an Alternative Experimental Infection Method, Which Closely Mimics the Natural Route of Transmission of Monophasic Salmonella Typhimurium in Pigs

Salmonella carriage in pigs is a significant food safety issue. This study describes a new protocol of Salmonella infection based on exposure to an artificially contaminated environment that closely mimics natural exposure to the organism. The aim of the study was to develop and evaluate the effectiveness of this protocol, which could then be used as a tool in the investigation of control measures. In addition, Salmonella shedding pattern and growth performance of the pigs were examined. Trial pigs (n = 10) were placed in a pen that had been previously contaminated by housing two pigs experimentally challenged with a monophasic Salmonella Typhimurium (mST). A further 10 pigs were placed in a Salmonella-free pen. Pigs were weighed on days 0 and 28. Feces was collected on days 0, 2, 3, 5, 7, 14, 21, and 28 and examined for the presence and quantity of Salmonella. The trial was replicated once. All pigs in the contaminated pens shed Salmonella within the first 2 days of exposure with values ranging from 10⁰ to 10⁴ CFU/g. The noninfected pigs had significantly higher final body weights on day 28 than those exposed to the Salmonella contaminated environment in both replicates. The pigs in the Salmonella-free pen had significantly higher average daily weight gain over the 28-day period compared to the infected animals (p < 0.001). Although not significant, numerical improvements in average daily feed intake and feed conversion efficiency were observed in the Salmonella-free pigs when compared to the contaminated pigs. The approach used was successful in infecting pigs with Salmonella without the need for direct inoculation or exposure to seeder pigs. This "natural" method of infection in which pigs are exposed to low levels of environmental contamination with Salmonella may be an effective tool that could be utilized when investigating control measures.

Outbreak of Salmonella Enteritidis linked to the consumption of frozen beefburgers received from a food bank and originating from Poland: northern France, December 2014 to April 2015

A prolonged outbreak of Salmonella enterica serotype Enteritidis occurred in northern France between December 2014 and April 2015. Epidemiological investigations following the initial notification on 30 December 2014 of five cases of salmonellosis (two confirmed S. Enteritidis) in young children residing in the Somme department revealed that all cases frequented the same food bank A. Further epidemiological, microbiological and food trace-back investigations indicated frozen beefburgers as the source of the outbreak and the suspected lot originating from Poland was recalled on 22 January 2015. On 2 March 2015 a second notification of S. Enteritidis cases in the Somme reinitiated investigations that confirmed a link with food bank A and with consumption of frozen beefburgers from the same Polish producer. In the face of a possible persistent source of contamination, all frozen beefburgers distributed by food bank A and from the same origin were blocked on 3 March 2015. Microbiological analyses confirmed contamination by S. Enteritidis of frozen beefburgers from a second lot remaining in cases' homes. A second recall was initiated on 6 March 2015 and all frozen beefburgers from the Polish producer remain blocked after analyses identified additional contaminated lots over several months of production.

Characterization of Salmonella enterica Serovar Typhimurium Isolates from Pigs and Pig Environment-Related Sources and Evidence of New Circulating Monophasic Strains in Spain

A total of 117 Salmonella enterica serovar Typhimurium and 59 monophasic Salmonella Typhimurium (S. enterica serovar 4,[5],12:i:-) strains isolated between 2008 and 2012 from pig, wild bird, rodent, and farm environment samples from the northeast of Spain were characterized by phage typing, antibiotic susceptibility testing, and multiple-locus variable-number tandem repeat analysis in order to evaluate their phenotypic and genetic relatedness. In Salmonella 4,[5],12:i:-, the most prevalent phage types were U311 (40.7%) and DT195 (22%), which did not correspond with the so-called Spanish clone and generally showed a different resistance pattern (ASSuT). Antibiotic resistance was found in 85.8% of the isolates, with 94.1% of them displaying multidrug resistance. Multiple-locus variable-number tandem repeat analysis identified 92 different profiles, six of them shared by both serovars. The minimum spanning tree showed one major cluster that included 95% of the Salmonella 4,[5],12:i:- isolates, which came from different animal sources, geographic locations, and time periods, suggesting high clonality among those Salmonella strains and the ability to spread among pig farms. Overall, isolates of Salmonella 4,[5],12:i:- were more similar to European strains than to the well-characterized Spanish clone. The spread of these new strains of Salmonella 4,[5],12:i:- would likely have been favored by the important pig trade between this Spanish region and other European countries. The overall high prevalence of multidrug resistance observed in these new strains should be noted.

Prevalence and Characterization of Monophasic Salmonella Serovar 1,4,[5],12:i:- of Food Origin in China

Salmonella enterica subsp. enterica serovar 1,4,[5],12:i:- is a monophasic variant of Salmonella Typhimurium, which has recently been recognized as an emerging cause of infection worldwide. This bacterium has also ranked among the four most frequent serovars causing human salmonellosis in China. However, there are no reports on its contamination in Chinese food. Serotyping, polymerase chain reaction, antibiotic resistance, virulotyping, and multilocus sequence typing (MLST) assays were used to investigate the prevalence of this serological variant in food products in China, and to determine phenotypic and genotypic difference of monophasic isolates and Salmonella Typhimurium isolated over the same period. Salmonella 1,4,[5],12:i:- was prevalent in various food sources, including beef, pork, chicken, and pigeon. The study also confirmed the high prevalence (53.8%) of resistance to ampicillin, streptomycin, sulfonamides, and tetracycline in Salmonella 1,4,[5],12:i:-, which was higher than that in Salmonella Typhimurium. Moreover, Salmonella 1,4,[5],12:i:- isolates in our study were different from Salmonella Typhimurium isolates by the absence of three plasmid-borne genes (spvC, pefA, and rck) and the presence of gipA in all isolates. All Salmonella 1,4,[5],12:i:- isolates demonstrated MLST pattern ST34. Genomic deletions within the fljBA operon and surrounding genes were only found in Salmonella 1,4,[5],12:i:- isolates, with all isolates containing a deletion of fljB. However, hin and iroB were identified in all Salmonella 1,4,[5],12:i:- isolates. Three different deletion profiles were observed and two of them were different from the reported Salmonella 1,4,[5],12:i:- clones from Spain, America, and Italy, which provided some new evidence on the independent evolution of the multiple successful monophasic clones from Salmonella Typhimurium ancestors. This study is the first report of Salmonella 1,4,[5],12:i:- in food products from China. The data are more comprehensive and representative, providing valuable information for epidemiological studies, risk management, and public health strategies.

Oral administration of the Salmonella Typhimurium vaccine strain Nal2/Rif9/Rtt to laying hens at day of hatch reduces shedding and caecal colonization of Salmonella 4,12:i:-, the monophasic variant of Salmonella Typhimurium

A new monophasic variant of Salmonella Typhimurium, Salmonella enterica serotype 4,12:i:-, is rapidly emerging. This serotype is now considered to be among the 10 most common serovars isolated from humans in many countries in Europe and in the United States. The public health risk posed by these emerging monophasic Salmonella Typhimurium strains is considered comparable to that of classical Salmonella Typhimurium strains. The serotype 4,12:i:- is frequently isolated from pigs but also poultry are carrying strains from this serotype. In the current study, we evaluated the efficacy of the Salmonella Typhimurium strain Nal2/Rif9/Rtt, a strain contained in the commercially available live vaccines AviPro Salmonella Duo and AviPro Salmonella VacT, against infection with the emerging monophasic variant in poultry. Three independent trials were conducted. In all trials, laying type chicks were orally vaccinated with the Salmonella Typhimurium strain Nal2/Rif9/Rtt at d hatch, while the birds were challenged the next d with a different infection dose in each trial (low, high, and intermediate). For the intermediate-dose study, a seeder bird model was used in which one out of 3 animals were infected while all individual birds were infected in the other trials. Data obtained from each independent trial show that oral administration of the Salmonella Typhimurium strain Nal2/Rif9/Rtt at d hatch reduced shedding, caecal, and internal organ colonization of Salmonella Typhimurium 4,12:i:-, administered at d 2 life. This indicates that Salmonella Typhimurium strain Nal2/Rif9/Rtt can help to control Salmonella 4,12:i:- infections in poultry.

Clonal distribution of monophasic Salmonella enterica subsp. enterica serotype 4,[5],12:i:- in the Czech Republic

Abstract Salmonella 4,[5],12:i:- has become the third most common serotype in Europe, including the Czech Republic. In this study, phenotypic and genotypic methods for a more detailed description of this serotype were used. Analysis of a limited number of isolates revealed that 76% of them belonged to phage type DT193. Also, rare phage types DT208 and U311 were identified. In total, 88.6% of the isolates were resistant to at least four antimicrobial agents. In this study, 24 multilocus variable-number tandem-repeat analysis profiles were detected, and some of them matched with the profiles recently described in Europe.

Molecular typing of monophasic Salmonella 4,[5]:i:- strains isolated in Belgium (2008-2011)

To assess the distribution of Salmonella 4,[5]:i:- subtypes in the Belgian food chain and compare it to the subtypes associated with human infections, a molecular assessment was initiated. Two hundred fifty-three Salmonella isolates serotyped as 4,[5]:i:- during the period 2008-2011 in Belgium and originating from animal productions, food or human clinical samples were analysed by a specific duplex PCR. One hundred ninety-four isolates (76.7%) fit the profile of a S. Typhimurium monophasic variant as defined by the European Food Safety Authority. The other isolates possessed but did not express the phase II flagellin gene (23.3%). Multiple Locus Variable Number of Tandem Repeats Analysis (MLVA) revealed many but closely related profiles in the fljB-negative S. Typhimurium monophasic variant isolates. Some MLVA types were associated with both human and animal isolates but no unique source of human contamination could be demonstrated.

Molecular characterization of Salmonella enterica serovar 4,[5],12:i:- DT193 ASSuT strains from two outbreaks in Italy

Salmonella enterica subsp. enterica serovar 4,[5],12:i:- DT193 is recognized as an emerging monophasic variant of Salmonella Typhimurium in many European countries. Resistance to ampicillin, streptomycin, sulphonamides, and tetracycline (R-type ASSuT) is described as one of the most common profiles of resistance within this clone. Recently, strains presenting such features were isolated from two unrelated outbreaks in Italy. Strains were characterized by pulsed-field gel electrophoresis (PFGE), performed with XbaI, BlnI, and SpeI, and multiple-locus variable-number tandem repeat analysis (MLVA). XbaI-PFGE showed strains related to the two outbreaks as indistinguishable. Conversely, both BlnI-PFGE and MLVA characterized the strains related the two outbreaks as different. XbaI-PFGE identified two profiles, differing by one band, within strains isolated from one of the two outbreaks. Also BlnI-PFGE and MLVA generated different profiles among the strains related to that outbreak. Combining the PFGE profiles obtained by XbaI and BlnI and comparing them with the MLVA profiles, the two methods grouped the same isolates based on identity. Moreover, genomic deletions of the genes included in the operon fljAB, the flanking iroB gene, and the closely located STM2757 gene were investigated. For all strains, the same profile of deletion characterized by the absence of fljA, fljB, and hin genes and the presence of STM2757 and iroB genes was identified. This profile of deletion represents a mixture between two profiles of Salmonella 4,[5],12:i:- described as the "Spanish" and the "U.S." clones. This study demonstrated that although strains of Salmonella 4,[5],12:i:- DT193 ASSuT are highly clonal, minor differences between strains may be seen during the same outbreak by using in parallel PFGE with different restriction enzymes, MLVA, and the analysis of molecular markers related to the operon fljAB. The combination of these different molecular approaches was essential to clarify the epidemiological relationship among the strains.

Characterization of Salmonella enterica subsp. enterica serovar 4,[5],12:i:- clones isolated from human and other sources in Switzerland between 2007 and 2011

Salmonella enterica subsp. enterica serovar 4,[5],12:i:- is a monophasic variant of Salmonella Typhimurium. In this study, a total of 651 human and 107 food and environmental isolates of serovar 4,[5],12:i:- recovered from 2007 through 2011 in Switzerland were characterized by antibiotic resistance profiles and pulsed-field gel electrophoresis (PFGE). In addition, a selection of isolates belonging to the most frequent PFGE patterns was further subjected to multilocus variable-number tandem-repeat analysis (MLVA) and phage typing. Over the years 2007-2011, the reports of salmonellosis caused by Salmonella enterica serovar 4,[5],12:i:- significantly increased. A high prevalence of multidrug-resistant isolates, mainly showing an ampicillin-streptomycin-sulfonamide-tetracycline resistance pattern (ASSuT), was observed. In addition, four extended spectrum beta lactamase (ESBL) (CTX-M-55)-producing isolates were found. XbaI PFGE analysis of all isolates revealed over 150 different pulsotypes, and generally showed a considerable diversity within the monophasic isolates. Nevertheless, among these we identified seven dominant profiles, which encompassed 66% of all isolates tested. The PFGE type STYMXB.0131 dominated among human as well as food isolates. Multilocus variable-number tandem-repeat analysis profile 3-12-10-0-0211, which, in many cases, coincided with PFGE type STYMXB.0131 and phage type DT193 were the most prevalent types found for the isolates further characterized by these typing methods. Our data provide strong evidence for a spread of two specific Salmonella serovar 4,[5],12:i:- clones (PFGE pattern STYMXB.0131, resistance type ASSuT) and (PFGE pattern STYMXB.0131, resistance type SSuT). In contrast to the human isolates, the pork/poultry isolates expressed predominantly the SSuT resistance type.

Genetic types, gene repertoire, and evolution of isolates of the Salmonella enterica serovar 4,5,12:i:- Spanish clone assigned to different phage types

Salmonella enterica subsp. enterica 4,[5],12:i:- is one of the most prevalent serovars associated with human infections worldwide. Two multidrug-resistant clones, designated Spanish and European clones, are recognized as having importance for public health and are subject to control measures in the European Union. In this study, 23 clinical isolates belonging to the Spanish clone were characterized by multilocus sequence typing, multiple-locus variable number tandem repeat analysis (MLVA), PCR amplification and sequencing, and a DNA microarray targeting 263 genes, in order to provide new insights into their origins and further evolution. The derived data were compared with information available from other studies for S. 4,[5],12:i:- isolates of both the Spanish and the European clones, to identify differential molecular markers which could be potentially used as surveillance tools in the control of dissemination of this serovar. The isolates analyzed were assigned to sequence type 19 and to 17 MLVA patterns, with 3-13-16-NA-311 being the most prevalent. Highly similar virulence, metabolic, and prophage-associated gene profiles were identified, but DNA mobility markers distinguished five genotypes. Two types of deletions, caused by insertion of IS26, presumably donated by pUO-STmR/RV1-like plasmids typically found in the Spanish clone, affected the fljAB operon and surrounding DNA. The Spanish and European clones differ in sequence type, MLVA patterns, gene repertoire, and fljAB deletion type. The observed variability supports an independent evolution of the two successful monophasic clones from different Salmonella enterica serovar Typhimurium ancestors and can be taken into consideration for epidemiological surveillance.

Molecular identification in monophasic and nonmotile variants of Salmonella enterica serovar Typhimurium

Variant strains of Salmonella enterica serovar Typhimurium, lacking one or both flagellar phases have been widely reported. The monophasic S.1,4,[5],12:i:- variant has emerged worldwide in the past few years and has become one of the most frequently encountered in many countries. In contrast, monophasic S.1,4,[5],12:-:1,2 and nonmotile S.1,4,[5],12:-:- strains are rarely described. This study investigated seven molecular markers to identify and delineate monophasic S.1,4,[5],12:i:- (n = 90), S.1,4,[5],12:-:1,2 (n = 25), nonmotile S.1,4,[5],12:-:- (n = 17) strains, and some serovar Typhimurium strains (n = 124) collected through the French Salmonella network between 2001 and 2010. Three markers were commonly detected in serovar Typhimurium and in all variant strains: STM2757, mdh and fliA-B. Monophasic S.1,4,[5],12:i:- were genotypically confirmed by the absence of the fljB, fljA, and hin genes. Nevertheless, 13 (14.5%) of them were positive for these last three genes, revealing monophasic strains named "inconsistent" as previously described. All nonmotile 1,4,[5],12:-:- strains had the fliC, fljA, fljB, and hin genes and the fliC gene was detected in 88% of monophasic S.1,4,[5],12:-:1,2 strains. The combination of the seven markers detection enables to recognize eight different genotypes within the S.1,4,[5],12:i:- collection, among which the Spanish and the U.S. clones previously described could be distinguished and assigned to a genotype. Based on this molecular approach, 71% of the French S.1,4,[5],12:i:- collection belonged to the Spanish clone, whereas only 2% were assigned to the U.S. clone. This study highlights the usefulness of these molecular markers and genotypes for identifying lineages, especially among the epidemiologically important monophasic S.1,4,[5],12:i:- variant.

CRISPR typing and subtyping for improved laboratory surveillance of Salmonella infections

Laboratory surveillance systems for salmonellosis should ideally be based on the rapid serotyping and subtyping of isolates. However, current typing methods are limited in both speed and precision. Using 783 strains and isolates belonging to 130 serotypes, we show here that a new family of DNA repeats named CRISPR (clustered regularly interspaced short palindromic repeats) is highly polymorphic in Salmonella. We found that CRISPR polymorphism was strongly correlated with both serotype and multilocus sequence type. Furthermore, spacer microevolution discriminated between subtypes within prevalent serotypes, making it possible to carry out typing and subtyping in a single step. We developed a high-throughput subtyping assay for the most prevalent serotype, Typhimurium. An open web-accessible database was set up, providing a serotype/spacer dictionary and an international tool for strain tracking based on this innovative, powerful typing and subtyping tool.

Phenotypic and molecular characterization of human salmonella enterica serovar 4,[5],12:i:- isolates in Slovakia

Forty-three epidemiologically unrelated emerging Salmonella enterica subsp. enterica serovar 4,[5],12:i:- strains isolated during the period 2009-2010 in Slovakia were characterized by phenotypic and genotypic methods. Thirty-one isolates (72.1%) expressed resistance to ampicillin, streptomycin, sulfizoxazole, and tetracycline [R-type ASSuT]. The majority of the strains belonged to both definitive phage types DT193 (30.2%) and U311 (27.9%). Other phage types identified were U302 (6.9%), DT18 (4.7%), and DT194 (2.3%). Twelve strains (27.9%) were not typeable. Pulsed-field gel electrophoresis analysis identified three closely related major banding profiles (X1, X1a, and X2), suggesting the similarity and close epidemiological relationship between S. enterica serovar 4,[5],12:i:- strains. In two isolates with R-type ASSuT, phage type NT and in one isolate with R-type ACROSSuSxTTTMPNA, phage type DT193 class 1 integrons were found encoding bla(PSE-1) and dfrA, aadA1, respectively.

Different mutations in the oafA gene lead to loss of O5-antigen expression in Salmonella enterica serovar Typhimurium

AIMS

To analyse genetic changes in the oafA gene explaining the loss of O5-antigen expression in Salmonella Typhimurium and Salm. 4,[5],12:i:-.

METHODS AND RESULTS

The oafA gene in 52 O5-antigen-negative and 77 O5-antigen-positive Salm. Typhimurium (N = 47) and Salm. 4,[5],12:i:- (monophasic Salm. Typhimurium strains, N = 82) was investigated by a combination of PCR screening and DNA sequencing to identify mutations leading to the suppression of the O5-antigen. Various DNA sequence changes within the open reading frame (ORF) of oafA in O5-antigen-negative strains could be identified. In 77% of the O5-antigen-negative strains, a 7-bp deletion of a duplicated sequence within the functional oafA gene led to a frameshift in the ORF. In four strains, an IS4 element and in two, an IS1 element was inserted at different positions. Four other strains carried at different positions single base pair substitutions causing a premature stop codon. Finally, in two strains, a deletion of the oafA 3'end of undetermined size was responsible for the lack of O5-antigen expression. In none of the strains investigated, the complete ORF of oafA was deleted. Primers were designed and used to detect the most prominent variants.

CONCLUSIONS

O5-antigen-negative Salm. Typhimurium and Salm. 4,[5],12:i:- strains carry an oafA pseudogene caused by different genetic events indicating that there is a selection for oafA mutations leading to the loss of O5-antigen expression.

SIGNIFICANCE AND IMPACT OF THE STUDY

The loss of O5-antigen expression may be an example of a common evolutionary mechanism to escape host defence or to adapt to environmental changes. The data are the basis for the development of diagnostic PCR assays for the differentiation of O5-antigen-positive and O5-antigen-negative Salm. Typhimurium and its monophasic (Salm. 4,[5],12:i-) strains.