Prevalence and genomic investigation of Salmonella isolates recovered from animal food-chain in Xinjiang, China
Graphical abstract
Introduction
Salmonella spp. are important foodborne pathogens worldwide contaminating a wide range of animal-borne products, including meat and meat products. Salmonella strains growing in animal farms frequently cross-contaminate animal carcasses during slaughtering operations before being transmitted to humans via the food-chain (Bonardi, 2017; Z. Jiang et al., 2019, Liu et al., 2020). In fact, previous studies have reported the high contamination of meat products with Salmonella strains (Ed-Dra et al., 2017, Yang et al., 2019). Therefore, the consumption of contaminated meat and meat products may lead to severe cases of salmonellosis, characterized by self-limited gastroenteritis in immunocompetent adults and invasive infections, particularly in immunocompromised patients (Elbediwi et al., 2020, Xu et al., 2020a, Yue, 2016).
Diarrheal and invasive non-typhoidal Salmonella infections were classified among the major foodborne diseases worldwide (Kirk et al., 2015). In fact, it is estimated that Salmonella strains were responsible for about 180 million (9%) of the diarrheal illnesses that occur globally each year, and caused about 298,000 deaths which represent 41% of all diarrheal disease-associated deaths (Besser, 2018). In the United States, it is estimated that non-typhoidal Salmonella were responsible for about one million cases of foodborne illnesses each year, with 19,586 hospitalizations and 378 deaths (Scallan et al., 2011). In the European Union, 91,662 confirmed human salmonellosis cases were reported during the year 2017, with an incidence rate of 19.7 cases per 100,000 populations (EFSA & ECDC, 2018). In China, Salmonella was classified among the major foodborne pathogens, causing n foodborne outbreaks (Paudyal et al., 2018, Zhou et al., 2020). Currently, Salmonella remains an important foodborne pathogen worldwide, presenting a major threat to public health with a significant economic burden (EFSA & ECDC, 2018, Kirk et al., 2015, Pan et al., 2019).
The use of antibiotics for treatment or prevention of bacterial infection in both human and animal fields has increased significantly during past decades. However, the overuse and misuse of antibiotics have led to the selection or accumulation of antimicrobial resistance in numerous bacterial species, especially those belonging to the Enterobacteriaceae family (Ed-Dra et al., 2019, Qiao et al., 2018, Sampaio and Gales, 2016). Consequently, the emergence of antibiotic-resistant bacteria has reached different corners of life, including humans, animals, environments, and food-chains (Elbediwi et al., 2019, Paudyal and Yue, 2019, Qiao et al., 2018). In fact, the World Health Organization classified antimicrobial resistance as a global public health crisis that must be managed with the utmost urgency (WHO, 2017). Importantly, surveillance data based on the epidemiological investigations demonstrated a dramatic increase in overall antimicrobial resistance of Salmonella strains since the early 1990s. This resistance was firstly linked to penta-resistant S. Typhimurium DT104 and then to the appearance of Salmonella strains resistant to the 3rd generation cephalosporin and quinolone (Eller et al., 2013; H. X. Jiang et al., 2014, Le Hello, 2014, Su et al., 2004). Recently, numerious studies reported the emergence of colistin resistance in different Salmonella serovars (Biswas et al., 2019, Elbediwi et al., 2020, Elbediwi et al., 2020, Lima et al., 2019). The high spreading of antimicrobial resistant Salmonella strains in food products is a serious problem for public health worldwide and the multidrug resistant strains originated from food products could be transmitted to humans leading to adverse outcomes.
Surveillance of Salmonella along the food-chain has a major concern for public health; in fact, conventional various labor intensive methods have been used to evaluate the antimicrobial resistance, virulence, plasmids profiles as well as the discrimination of isolates when an outbreak occurs (Ed-Dra et al., 2018, Murgia et al., 2015, Skyberg et al., 2006), which requires long-time and sometimes includes bias assessments for the choice of the particular method. In most of the cases, the results lose the value for a comparative purpose among relevant studies. Recently, the development in sequencing technologies stimulated the use of whole genome sequencing (WGS) as one-step approach for an unbiased understanding of serovars, antimicrobial resistance, virulence genes, plasmid types, multi-locus sequence types, and importantly, for an early recognition of emerging threats that could be responsible for severe humans and/or animal infections (Köser et al., 2014, Liu et al., 2020, Thomas et al., 2017, Viana et al., 2020, Xu et al., 2020a, Yu et al., 2020).
Xinjiang is considered the largest Chinese Autonomous Region with a superficial of about 1.6 million km2. In Xinjiang, animal husbandry is considered the major activity of the local population, and animal-borne foods have taken a principal place in the local diet. In fact, animal-borne foods have been known as a major vehicle for foodborne pathogen transmission, including Salmonella. So far, studies investigated the prevalence of Salmonella in animal food-chain in Xinjiang are very limited (Yue et al., 2020). In this study, we investigated the prevalence and antimicrobial resistance of Salmonella isolates in animal farms, slaughterhouses, and food markets. Moreover, genomic sequences of 103 strains were conducted in order to produce a streamlined study of serovars, antimicrobial and virulence genes, plasmid types, multi-locus sequence types, and allelic types.
Section snippets
Sample collection and isolation of Salmonella strains
Between 2016 and 2019, a total of 25 visits were conducted for the isolation of Salmonella strains from five regions (Changji, Korla, Shihezi, Urumqi, and Ili) of Xinjiang Autonomous Region. A total of 2408 samples were collected, including 1060 from farms (stool, feed, skin, and environment), 864 from slaughterhouses (carcass, meat, and internal organs), and 484 from markets (meat sample). The isolation of Salmonella was performed according to the methods described previously (Z. Jiang et al.,
Prevalence of Salmonella isolates
The prevalence of Salmonella isolates in the food chain in Xinjiang province is summarized in Table 3. A total of 314 Salmonella isolates were recovered from 2408 samples (13.04%). According to sampling sites, Salmonella was more prevalent in samples collected from farms (19.73%; 209/1060), followed by markets (8.26%; 40/484) and slaughterhouses (7.52%; 65/864) (Fig. 1A). However, considering the source of the samples, Salmonella was more prevalent in sheep/goat (16.58%; 157/947) followed by
Discussion
Salmonella is a major food-borne pathogen worldwide, causing a serious risk for public health. Meat and meat products were considered as the principal agent that carries Salmonella to humans. Generally, Salmonella contaminate meat products in different food-chain processing points, including breeding on farms, slaughtering operations, transport, and sale in different sites and areas (Ed-Dra et al., 2017; Z. Jiang et al., 2019, Jiang et al., 2020, Liu et al., 2020, Xu et al., 2020b).
Conclusion
This study provided first picture about the prevalence of Salmonella in the animal food chain in Xinjiang province, in China, and demonstrated the use of whole-genome sequencing as a cost-effective method for epidemiological analysis of Salmonella isolates, by the prediction of serovars, MLST patterns, antimicrobial resistance genes, plasmids and virulence genes implicated in virulence and pathogenicity determinants. We reported the high prevalence of MDR Salmonella in the analyzed samples
Funding
This work was supported by the National Program on Key Research Project of China (2018YFD0500504; 2019YFE0103900; 2017YFC1600103) as well as the European Union's Horizon 2020 Research and Innovation Programme under Grant Agreement No. 861917 – SAFFI, Zhejiang Provincial Natural Science Foundation of China (LR19C180001) and Opening Fund of Key Laboratory of microorganism technology and bioinformatics research of Zhejiang Province (2017E10010).
Ethics Statements
No ethical approval was deemed required for the experiments conducted in current study. Oral permission was obtained from all the farmers and slaughterhouse managers before the samplings.
Author Contributions
YL and JJ collected the samples. YL, JJ, LNX and QG conducted the lab analysis. AE and XML analyzed the genomic data. AE, YL and XP did the data analysis, produced the figures and prepared a draft. MY and GY conceived the project and provided critical comments for the draft. All the authors have read and agreed to the manuscript.
Declaration of Competing Interest
There are no conflicts of interest to declare.
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These authors have contributed equally to this work.