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

Introduction

Salmonella enterica subspecies I serovar 4,[5],12:i:- (Salmonella I 4,[5],12:i:-) is currently one of the top five serovars associated with human salmonellosis in the United States (CDC, 2018b; Marder et al., 2018). Salmonella I 4,[5],12:i:- with resistance to ampicillin, streptomycin, sulfonamides, and tetracycline (ASSuT) is of particular importance because of its relatively recent emergence as a major source of multidrug resistant infections.

The National Antibiotic Resistance Monitoring System (NARMS) first detected an increase in ASSuT-resistant Salmonella I 4,[5],12:i:- infections in the United States when the percentage of these clinical isolates rose from 1.4% of all human Salmonella I 4,[5],12:i:- isolates in 2009 to nearly 17% in 2010. This upward trend continued in subsequent years, with the percentage increasing to 18.3% in 2011, 26.5% in 2012, 46.5% in 2013, 42.7% in 2014, and 59.1% in 2015. Among nontyphoidal Salmonella clinical isolates tested by NARMS in 2015, 5.0% (118/2364) were resistant to ASSuT; 74.6% of these were Salmonella I 4,[5],12:i:-. Historically the majority of nontyphoidal Salmonella isolates in the United States that were at least ASSuT-resistant were also resistant to chloramphenicol; that resistance profile has shown a steady decline (CDC, 2018a). Similar findings have been reported by the Canadian Integrated Program on Antimicrobial Resistance Surveillance (Mulvey et al., 2013).

Although the sources of sporadic human infections with ASSuT-resistant Salmonella I 4,[5],12:i: in the United States are not known, outbreaks have been attributed to a variety of transmission routes and sources. These include exposure to live animal markets, contact with livestock (cattle, pigs, and goats), pets, and animal feed and the consumption of beef, pork and poultry products (Grass et al., 2014; Imanishi et al., 2014).

European countries identified a marked increase in human ASSuT-resistant Salmonella I 4,[5],12:i:- infections and detection in swine and pork in the years predating the U.S. emergence (Bone et al., 2010; Hopkins et al., 2010; Barco et al., 2014). Strains isolated from swine, pork and humans in Europe were found to be highly related, suggesting transmission along the food chain (Hauser et al., 2010). The strain was also isolated from cattle in European countries with human infections attributed to the consumption of beef (Raguenaud et al., 2010). The University of Minnesota and its collaborators compared the whole genome sequences of Salmonella I 4,[5],12:i:- clinical isolates recovered from livestock (mainly swine) in the U.S. Midwest in 2014–2016, other livestock, food, and humans in the United States and Europe. The researchers concluded that many of the U.S. isolates recovered in 2014–2016 were part of the emerging ASSuT-resistant Salmonella I 4,[5],12:i:- clade first reported in Europe (Elnekave et al., 2018).

To provide further insights into possible meat and poultry sources of human infections with ASSuT-resistant Salmonella I 4,[5],12:i:-, this report describes the isolates derived from various meat and poultry and cecal content sampling programs.

Materials and Methods

A key component of the U.S. Department of Agriculture, Food Safety and Inspection Service's (FSIS) public health mission is the sampling and testing of regulated products for microbiological contaminants. FSIS conducts Salmonella testing on a broad array of domestically produced and imported products. FSIS characterizes its Salmonella isolates from meat, poultry and egg samples and assists other agencies, per request. The various sampling programs provide an important source of data on Salmonella associated with meat, poultry, and egg products. United States Department of Agriculture (USDA) laboratories have characterized the antimicrobial susceptibility of Salmonella food isolates since the initiation of NARMS in 1997. Currently the FSIS Eastern Laboratory conducts antimicrobial susceptibility testing (AST) on all Salmonella isolates recovered from FSIS-regulated product sampling.

Results

Discussion

Cautious interpretation of data presented in this report is warranted, due to changes in the type and number of samples collected in the various commodities over time. However, the broad scope of sampling over time of meat and poultry products and cecal contents provides a unique opportunity for descriptive analysis. Notable variations in sampling include suspension of routine sampling of hog and beef carcasses in 2011, with sampling pork products and chicken parts beginning in 2015. In 2013, FSIS announced a change in Salmonella sampling from a set-based approach to a routine sampling model which was implemented in a staggered fashion in 2014 and 2015 (FSIS, 2016a). The small number of tests in some commodities in certain years and risk-based testing make exploration of trends and sources difficult. However, these recent additions to FSIS' sampling programs are improving our insight into the presence of ASSuT-resistant Salmonella I 4,[5],12:i:- within FSIS-regulated products and animal sources.

Based on our review, Salmonella I 4,[5],12:i:- appears to be an established serovar in many livestock and poultry species in the U.S. ASSuT-resistant Salmonella I 4,[5],12:i:- has been detected in FSIS-regulated products at low levels in all major food animals and associated meat and poultry products, with percent recovery consistently the highest in swine and turkey samples. Since the cecal sampling program was initiated in 2013 and the FSIS Exploratory Raw Pork sampling project was initiated in 2015, Salmonella I 4,[5],12:i:- has been isolated from swine and pork products. The number of ASSuT-resistant Salmonella I 4,[5],12:i:- turkey product isolates recovered since 2015 highlights that commodity as a potential new source of concern. Variations in recovery rates geographically may be influenced by regional variations in animal production volume and production practices.

PFGE pattern JPXX01.1314 is the most commonly exhibited PFGE pattern in ASSuT-resistant Salmonella I 4,[5],12:i:- isolates in both humans and from meat and poultry. However multiple PFGE patterns are seen among isolates with some additional PFGE patterns in common between human and food isolates (Table 6). Thus, this report focuses on ASSuT-resistant isolates regardless of PFGE pattern. With the FSIS Eastern Laboratory transition to whole genome sequencing of its Salmonella isolates, sequence data would be available for a future analysis which could further elucidate the potential associations between human and food ASSuT-resistant isolates.

Epidemiologic linkages between Salmonella I 4,[5],12:i:- illnesses and vehicles during outbreak investigations have generally been inconclusive due to multiple factors including lack of case-patient exposure information, multiple reported exposures, cross-contamination issues at the point of service, and lack of similar or “like” product for testing (Grass et al., 2014). A large pansusceptible outbreak was linked to poultry pot pies in 2007 (Mody et al., 2014). An ASSuT-resistant Salmonella I 4,[5],12:i:- outbreak investigation in Washington state in 2015 identified the consumption of pork from roaster pigs (primarily at “pig roasts”) as the source of infections (CDC, 2015). In 2016 a foodborne disease investigation linked ASSuT-resistant Salmonella I 4,[5],12:i:- illnesses to chicken (rotisserie chicken products) consumption (FSIS, 2018). Variation in consumption patterns and handling practices involving different types of meat and poultry products may partly explain variations in human exposure. Though pork is considered an important source of ASSuT-resistant Salmonella I 4,[5],12:i:- foodborne infections in the United States, food handling issues (e.g., cross-contamination and under-cooking) may also lead to other commodities, such as poultry and beef, being the vehicle in foodborne outbreaks. Additionally, there is evidence that Salmonella enterica serovar Typhimurium strains may have enhanced biofilm formation capabilities (Stepanovic et al., 2004), therefore increasing the potential for cross-contamination-associated illnesses. An additional source of human infection may be from direct animal contact, as illustrated from the NARMS cecal isolate findings.

Interagency collaboration is ongoing to identify sources of human infections to focus efforts targeting at-risk populations, strategies for food safety interventions, consumer and industry education, and actions which enhance food safety from farm to table. Epidemiological studies are needed to identify risk factors along the food to table continuum which has enhanced the spread of this MDR Salmonella strain and to identify risk management options which help to halt its spread. It is important to continually assess the impact of the FDA Feed Directive and other regulations on specific antimicrobial use and changes in antimicrobial resistance seen in Salmonella strains in animal production units.

FSIS food safety research priorities include studies to identify unique attributes of pathogen outbreak strains that may increase the probability of foodborne illness. These types of studies are needed to identify genotypic and phenotypic attributes (e.g., virulence, increased resistance to biocides, acids, heat, pressure pasteurization, biofilm formation, etc.) which have conferred selection advantages to this serovar which may have facilitated its rapid spread. In the United Kingdom this serovar has developed some adaptive mechanisms, such as resistance to heavy metals (copper and zinc), which allow it to grow and proliferate in swine herds even when some other Salmonella serovars do not normally persist (Petrovska et al., 2016). There appears to be a strong association between decreased susceptibility to heavy metals and antimicrobial resistance among Salmonella serovars isolated from swine, swine feed, and barn floors in the United States (Medardus et al., 2014). Characterization of outbreak strains may provide insights into mechanisms that contribute to the survival of the pathogen to commonly used processes in FSIS-regulated establishments, mechanisms that affect the severity of illness in humans, and antibiotic resistance in outbreak strains.

Conclusions

In addition to its public health importance, ASSuT-resistant Salmonella I 4,[5],12:i:- represents a concern for animal health. There has been a notable increase in the occurrence of Salmonella I 4,[5],12:i:- in U.S. swine (Hong et al., 2016; USAHA, 2016). There has also been an increased frequency of isolation of multi-drug resistant Salmonella I 4,[5],12:i:- from swine with histologic lesions consistent with salmonellosis in the United States (USAHA, 2016). Inoculation of swine with a ASSuT-resistant Salmonella I 4,[5],12:i:- isolate with PFGE pattern JPXX01.1314 associated with a multistate pork outbreak resulted in colonization of porcine intestinal tissues and fecal shedding and transient clinical disease (Shippy et al., 2018). The frequency of fecal shedding and transient illness in swine could account for the spread of this strain through swine populations.

A 12-month study of swine herds in Australia noted that Salmonella I 4,[5],12:i:- was one of several serovars that persisted within the herds and was found among each production stage following disease outbreaks. Higher Salmonella I 4,[5],12:i:- specific shedding rates or longer duration of shedding in weaners and finishing swine indicated that high pathogen load at slaughter may be an important pathway of Salmonella I 4,[5],12:i:- into the human food chain. This has implications for on-farm management and the application and targeting control measures both at slaughter and processing establishments (Weaver et al., 2016).

Control measures on the farm, during slaughter and processing, and during food handling are needed to reduce spread of infection to humans via the food chain. Improved surveillance and collaboration between USDA agencies, State colleagues and industry on research and epidemiological studies will enhance our understanding of this pathogen and aid in the identification of feasible and effective farm to table interventions to prevent or reduce illness.