Abstract
Pig is usually the carrier of Salmonella and Staphylococcus aureus, and can transmit the bacteria along the pork production chain to cause severe public health problems. In this study, we investigated the prevalence of Salmonella and S. aureus in fattening pigs in Hubei Province, China. The overall prevalence of Salmonella in rectal swab among 896 samples from 22 farms was 17.30%, and that of S. aureus in nasal swab among 814 samples from 20 farms was 28.26%. Antimicrobial resistance (AMR) analysis showed that 95.33% of the Salmonella strains exhibited resistance to more than three classes of antimicrobial agents tested. The highest resistance proportions were for chloramphenicol (100%), sulfamethoxazole/trimethoprim (SXT) (100%), and tetracycline (TET) (93.46%), while the lowest proportions were for cefotaxime (37.38%), gentamicin (GEN) (34.58%), and ciprofloxacin (24.30%). On the other hand, 98.42% of the S. aureus strains were resistant to more than three classes of antimicrobial agents tested. The most common resistance among the S. aureus strains was against SXT (100.00%), followed by TET (98.43%), erythromycin (91.34%), and clindamycin (91.34%), while the lowest frequent resistances were against GEN (34.65%) and oxacillin (16.54%). The prevalence and AMR of Salmonella and S. aureus exhibited an obvious diversity among different pig farms. Our results provided the epidemiological data for risk analysis of foodborne bacteria and AMR in pig farms.
Introduction
Foodborne diseases are global public health problems. Both Salmonella and Staphylococcus aureus are important zoonotic and foodborne pathogens. Salmonella is prevalent in food-producing animals and can spread along the whole pork production chain, which can cause fever, vomiting, abdominal pain, diarrhea, and even death in human.1,2 S. aureus can contaminate meat products and then produce different enterotoxins, which can lead to such diseases as diarrhea, vomiting, and dehydration in human. 3 Moreover, S. aureus can infect human with compromised immune system, causing infections ranging from local infections to life-threatening invasive diseases. 4
Pigs are asymptomatic carriers and disseminators that can spread pathogens such as Salmonella and S. aureus from pig farms to slaughterhouses.5–7 However, the presence of foodborne bacterial pathogens in nonclinical pigs in farms is generally overlooked. The epidemiological investigation on prevalence of Salmonella and S. aureus in intensive pig farms in Hubei Province, a major pig breeding province in China, is still scarce.
Antimicrobials are often used for the prevention and treatment of diseases in animal breeding. Global consumption of antimicrobial drugs for food animals was estimated to reach 20,235 tons by 2030. 8 China is the largest consumer of veterinary antibiotics in the world. In 2013, about 8,424 tons of 36 common antibiotics were used in China. 9 Immoderate use of antimicrobial drugs contributes to the emergence of resistant bacteria, 10 which can lead to longer course of disease, higher mortality, and more serious economic losses. 11 China had gradually reduced the use of veterinary antibiotics since 2017, and plans to withdraw all growth-promoting antimicrobials in livestock breeding industry after 2020. 12
Our previous studies during 2016–2018 showed that there was 19.54% (927/4,744) prevalence of Salmonella 13 and 17.45% (824/4,723) prevalence of S. aureus (data not published) in pork samples collected from Wuhan city, Hubei province, China. This study was designed to investigate the prevalence of Salmonella and S. aureus in 22 representative fattening pig farms in Hubei Province in 2019. Moreover, the resistance to different antimicrobials was analyzed using both bacteria as indicators among different farms. These results provided the fundamental data for the risk analysis of foodborne bacterial contamination and antimicrobial resistance (AMR) in pig farms in China.
Materials and Methods
Sample collection
Basing on the intensive breeding system with a similar number of pigs in all farms in Hubei Province, 22 representative farms were selected and a sampling program was formulated (Fig. 1). About 30 nonclinical pigs were selected to sample from each farm. The rectal swab and nasal swab samples were collected from each animal with sterile cotton swabs soaked in buffered peptone water medium (BPW) and 10% NaCl soybean-casein digest broth, respectively, and then were quickly transferred into sterile tubes with the relative medium. The animal study was approved by the Scientific Ethics Committee of Huazhong Agricultural University (the approval number: HZAUSW-2016-016).

Distribution of sampling and monitoring of intensive breeding farms in Hubei Province, China. The sampled area is marked in gray, and the black dots indicate the location of the pig farms.
Bacterial isolation and identification
The methods for the isolation and identification of Salmonella were modified according to the Chinese National Food Safety Standard GB 4789.4-2016. 14 The rectal swab samples were transferred to a 10 mL sterile centrifuge tube containing 5 mL of BPW, and pre-enriched for 18 hours at 37°C with shaking at a speed of 180 r/min. One milliliter of pre-enrichment BPW solution was transferred into 10 mL of selective tetrathionate broth (TTB) medium, and incubated for 18 hours at 37°C with shaking. Genomic DNA extracted from the enriched TTB medium was used for amplifying the stn gene for initial PCR screening. 15
The positive bacterial enrichment solution was streaked on the selective bismuth sulfite agar plate, and was incubated for 48 hours at 37°C. The typical colonies on the chromogenic medium were inoculated with nutrient agar plate and cultured for 24 hours at 37°C. The positive colonies were further identified by PCR amplification of stn gene.
The methods for the isolation and identification of S. aureus were modified according to the Chinese National Food Safety Standard GB 4789.10-2016. 16 Each nasal swab sample was transferred into a 10 mL sterile centrifuge tube containing 5 mL of 10% NaCl soybean-casein digest broth and incubated for 18 hours at 37°C with shaking. The enrichment solution with flocculent precipitation was streaked on the Baird-Parker (BP) agar plate and incubated for 48 hours at 37°C. The typical colonies were selected and cultured in LB medium at 37°C for 5 hours with shaking. The positive colonies were identified by PCR amplification of femB gene. 17
Antimicrobial susceptibility testing
The minimal inhibitory concentrations of antimicrobials were determined using the broth microdilution method according to the guidelines of the Clinical and Laboratory Standards Institute. 18 Escherichia coli ATCC 25922 and S. aureus ATCC 25923 were used as quality controls. A total of 10 classes of antibiotics were selected, which represented the major classes of antimicrobial agents important for both veterinary and human medicine.
The following antimicrobial agents were used for Salmonella: amoxicillin/clavulanic acid (AMC), ampicillin (AMP), chloramphenicol (CHL), ciprofloxacin (CIP), cefotaxime (CTX), gentamicin (GEN), sulfamethoxazole/trimethoprim (SXT), and tetracycline (TET). SXT, erythromycin (ERY), TET, clindamycin (CLI), CHL, CIP, GEN, and oxacillin (OXA) were used for S. aureus. The resistance breakpoints were defined according to CLSI guidelines (M100; CLSI 2017) (Table 1). The isolates resistant to at least one antimicrobial agent showed AMR and those resistant to three or more drugs showed multidrug resistance (MDR).
Category of Antibiotics and Minimal Inhibitory Concentration Breakpoints in Antimicrobial Susceptibility Testing in This Study
AMC, amoxicillin/clavulanic acid; AMP, ampicillin; CHL, chloramphenicol; CIP, ciprofloxacin; CLI, clindamycin; CTX, cefotaxime; ERY, erythromycin; GEN, gentamicin; OXA, oxacillin; SXT, sulfamethoxazole/trimethoprim; TET, tetracycline.
The breakpoints for clinical and intermediate resistance are defined according to CLSI guidelines (2017). CLSI, Clinical and Laboratory Standards Institute; MIC, minimum inhibitory concentration.
S: sensitive; I: intermediate; R: resistance.
—, analysis not performed.
MIC, minimal inhibitory concentration.
Statistical analysis
All statistical analyses were performed using SPSS 20.0.0 software (SPSS, Inc., Chicago, IL). Ninety-five percent confidence intervals were calculated using the method described by Ross. 19 The statistical significance between percentages of different groups was compared using the chi-squared test (χ 2 ) (SPSS, crosstable), and p-value <0.05 was taken as significantly different.
Results
Prevalence of Salmonella and S. aureus in pig farms
As shown in Fig. 1 and Table 2, 22 representative pig farms in Hubei Province were subject to sampling from March to November in 2019. Salmonella was detected from all the 22 pig farms, except the farm CH-2. A total of 155 individual Salmonella isolates were recovered from 896 rectal swab samples with the overall prevalence of 17.30%. The prevalence of Salmonella in different farms ranged from 3.33% to 70.00%, with the highest in the farm ZYL and the lowest in the farms NZ and WJ.
Prevalence of Salmonella and S. aureus in Pig Farms in Hubei Province
The samples for the isolation of Salmonella and S. aureus were collected from 22 and 20 pig farms during 2019, respectively.
—, samples not collected.
CI, confidence interval.
On the other hand, a total of 230 S. aureus isolates were recovered from 814 nasal swab samples with the overall prevalence of 28.26%. S. aureus was detected from all the 20 farms where the nasal swab samples were collected. The prevalence of S. aureus in different farms ranged from 3.45% to 60.00%, with the highest in the farm NZ. There was a relatively low prevalence of both Salmonella (6.67%) and S. aureus (3.45%) in the farm JJY.
Antimicrobial susceptibility testing
A total of 107 Salmonella strains were subject to testing for the susceptibility to 8 antimicrobials (Table 3). All the Salmonella strains were resistant to at least 1 antimicrobial agent tested, among which 102 strains (95.33%) exhibited MDR, including 56 strains (52.34%) resistant to 3–5 antimicrobials and 46 strains (42.99%) resistant to 6–8 antimicrobials.
Antimicrobial Resistance of the Salmonella Isolates from Different Pig Farms
Number of resistant strains/number of tested strains; the superscript with different capital letter (A, B, C, and D) indicated significant difference (p < 0.05).
—, rectal swabs not collected in the farm.
All the Salmonella isolates exhibited the resistance to CHL and SXT, with the resistance proportion (100%) significantly higher than the other six antimicrobials (p < 0.05). There were 100 (93.46%), 86 (80.37%), and 67 (62.62%) isolates resistant to TET, AMP, and AMC, respectively. The proportions of isolates resistant to CTX (37.38%, 40/107), GEN (34.58%, 37/107), and CIP (24.30%, 26/107) were significantly lower than those resistant to the other five antimicrobials (p < 0.05). The Salmonella strains resistant to AMP, CHL, SXT, and TET were detected in all the 21 positive farms, and the strains resistant to AMC, CTX, GEN, and CIP were detected in 19, 15, 11, and 11 pig farms, respectively.
A total of 127 S. aureus strains were tested for the susceptibility to 8 antimicrobials (Table 4). All the S. aureus strains were resistant to at least 1 antimicrobial agent tested, among which 124 strains (97.64%) exhibited MDR, including 43 strains (33.86%) resistant to 3–5 antimicrobials and 81 stains (63.78%) resistant to 6–8 antimicrobials.
Antimicrobial Resistance of the S. aureus Isolates from Different Pig Farms
Number of resistant strains/number of tested strains; The superscript with different capital letter (A, B, C, D, and E) indicated significant difference (p < 0.05).
—, nasal swabs not collected in the farm.
The proportion of resistant S. aureus strains was the highest in SXT (100%, 127/127), followed by TET (98.43%, 125/127), ERY (91.34%, 116/127), CLI (91.34%, 116/127), CHL (74.80%, 95/127), and CIP (62.99%, 80/127). The lowest resistance proportions were in GEN (34.65%, 44/127) and OXA (16.54%, 21/127). The resistance proportions of SXT and TET were significantly higher than the other six drugs (p < 0.05), and the resistance proportion of OXA was significantly lower compared with the other seven drugs (p < 0.05). The proportion of isolates resistant to GEN was significantly higher than that resistant to OXA (p < 0.05), but significantly lower than that resistant to the other six drugs (p < 0.05). The S. aureus strains resistant to CHL and CIP were detected in all the 20 positive farms, except the farm JJY, and the strains resistant to GEN and OXA were detected in 15 and 10 farms, respectively.
Discussion
Epidemiological investigation of foodborne pathogens in pig farms is necessary to ensure the sanitary and safety during the whole pork production chain. Compared with free-range pigs, the prevalence of bacterial pathogens in intensive pig farms is higher because of the higher risk of spreading bacteria between pigs through direct contact. 7 Pigs carrying bacterial pathogens are important sources of contamination at slaughterhouses. 20 Prevention and control of pig contamination by foodborne pathogens are of critical importance to reduce the risk of pork contamination and the emergence of foodborne diseases in human. 21
A 2014–2016 meta-analysis demonstrated high frequencies of Salmonella in diarrhea pig farms in 26 provinces in China. 22 Another study found that the prevalence of Salmonella in healthy pigs from 16 provinces, from 2013 to 2017, in China was only 2.3%. 23 In this study, the overall prevalence of Salmonella in fattening pigs of different intensive farms was 17.30%, lower than previous results in provinces of Sichuan (24.11%) and Henan (19.46%) in China, but higher than that in Shandong province (11.11%).24–26 High prevalence of Salmonella in pig farms was also reported in other countries such as Southern Brazil (13.84%), Japan (19.46%), Canada (37.30%), and Argentina (41.50%), which differed from the study in Korea (5.09%).6,27–30
In this study, Salmonella was detected in 95.45% of the farms (21/22), higher than the overall proportion of Salmonella-positive farms (37.80%) in Spain. 31 High frequencies of Salmonella from the farms ZYL (70.00%), MS (55.00%), and YHB (50.00%) may be caused by poor sanitary and biosecurity measures. Moreover, S. aureus was detected in all the pig farms tested and the overall prevalence from nasal swab samples was 28.26%, significantly higher than that reported in Chongqing city, China (10.09%), 32 and in other countries such as Morocco (9.97%). 33
The farms NZ (60.00%), WJ (56.67%), and ZJC (40.00%) showed the highest prevalence of S. aureus. Farm environment and contact between pigs may be the key factors for the spread of S. aureus.34,35 Interestingly, the prevalence of S. aureus was also higher in the farms with higher Salmonella prevalence such as XNXA, YHB, and ZYL, but the prevalence of Salmonella was generally lower in the farms with higher S. aureus prevalence such as NZ and WJ. The reasons for the difference are worthy of analyzing in further studies.
AMR is a growing global threat. Many countries have restricted or prohibited the use of some antibiotics in food-producing animals, especially those critically important antimicrobials for human medicine. 36 The widespread use of antibiotics in livestock can lead to the emergence of resistant bacteria, which may pose serious threats to animal and human health. MDR Salmonella and oxacillin-resistant S. aureus had been isolated in pig and pork samples, so it is of great significance to detect and evaluate the resistant bacteria in pig farms.13,37 In this study, the tested Salmonella isolates were mainly resistant to sulfonamides, phenylpropanols, TETs, penicillins, and β-lactam/β-lactamase inhibitors combinations. High resistance proportions to these antibiotics were also reported in Salmonella strains recovered from pork in Wuhan city and from pig farms in Henan province.13,38
Cephalosporins and fluoroquinolones are the preferred antibiotics for the treatment of bacterial infections; therefore, the resistance of Salmonella to these antibiotics increased. 39 The proportions of Salmonella strains resistant to both classes of antimicrobials in this study were higher than that reported in other studies.5,40 Combined with our previous research, the resistance of GEN showed a downward trend from 2008 to 2019, and the reason may be due to the decreased application of aminoglycosides in pig husbandry and veterinary practice. 40
In this study, S. aureus isolates exhibited an MDR proportion of 98.42%. Moreover, high resistance proportions of S. aureus were for sulfonamides, TETs, lincosamides, and macrolides, which was in agreement with the previous studies in Ghana, Morocco, and Korea.30,33,41 The lowest resistance proportion was for OXA (19.69%), and the OXA-resistant strains were detected in 10 pig farms. Other studies also revealed consistent evidence of methicillin-resistant S. aureus in herds (55.3%) raised with antibiotics. 42 As early as 2002, CHL had been banned in food animals. 43 However, in this study, the resistance proportion of CHL was as high as 100.00% and 74.80% for Salmonella and S. aureus, respectively. The reason may be due to the frequent use of CHL or its similar drugs in some pig farms, so it must be strengthened for reasonable use and monitoring of antimicrobial drugs. A serious resistance threat had been also reported in other bacteria such as E. coli in China. 44
Environment is a potential source for the spread of resistant bacteria. 45 In this study, all drinking water samples were negative for Salmonella and S. aureus. However, Salmonella was detected in the feed of the farms SP, NZ, and WJ, and the strains recovered from feed and anal swabs in same farms shared the same AMR patterns, suggesting that Salmonella could be transmitted through feed. The results are consistent with the previous study. 46 Feed must be prevented from Salmonella contamination after feed processing, and disinfection procedures should be improved. 47
In summary, our results provide epidemiological data for the risk analysis of Salmonella and S. aureus in Chinese pig farms, and also identify both bacteria as indicator for the monitoring of farm management levels and AMR risks. The prevalence and AMR of Salmonella and S. aureus exhibited an obvious diversity among pig farms. Therefore, it will be very useful to collect enough background information of the farms in the further study, so as to find the proper management measures to reduce the risk of bacterial infection and AMR.
Ethics Statements
Studies involving animal subjects
The animal study was reviewed and approved by the Scientific Ethics Committee of Huazhong Agricultural University (the approval number: HZAUSW-2016-016). Written informed consent was obtained from the owners for the participation of their animals in this study.
Studies involving human subjects
No human studies are presented in this article.
Inclusion of identifiable human data
No potentially identifiable human image or data is presented in this study.
Data availability statement
The original contributions presented in the study are included in the article/supplementary materials; further inquiries can be directed to the corresponding author/s.
Footnotes
Acknowledgments
The official veterinarian of the Agricultural Law Enforcement Inspection Team of Hubei Province and the farmers should be acknowledged for their assistance in the sampling work.
Authors' Contributions
Z.X., X.C., C.Y., H.C., and W.T. performed the experiments and conceptualized the structure of the article. S.L., X.M., Q.H., Z.X., X.C., and Z.Z. designed research and analyzed the data. S.L., X.M., and Q.H. reviewed the drafts of the article. Z.X. and X.C. were responsible for the data interpretation and critically revised the article. All authors contributed to the article and approved the submitted version.
Disclosure Statement
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Funding Information
This work was supported by the National Key Research and Development Program of China [2018YFD0500500], and the Joint Funds of the National Natural Science Foundation of China (NSFC) [Grant No. 8161101134].
