Antimicrobial resistance and genomic characteristics of Salmonella from broilers in Shandong Province

Comprehensive epidemiological profiling of poultry-derived Salmonella spp. in Shandong, China, 2019-2022: a longitudinal study of prevalence, antibiotic resistances, virulence factors and molecular characteristics

Salmonella spp., as a major foodborne pathogen, pose significant threats to public health globally and has been an important zoonotic contamination for poultry industry that should receive increasing attentions. This study aimed to comprehensively investigate the prevalence, antimicrobial resistances, virulence factors, and plasmid types of Salmonella isolates collected from chickens, ducks, and geese across eight cities in Shandong between 2019 and 2022. Out of 300 samples, 53 Salmonella strains (17.67%) were isolated, with varied prevalence from 8.33% to 25.00% in different cities of Shandong. A total of seven serotypes were identified among the 53 Salmonella isolates, wherein the S. Enteritidis (45.28%), S. Pullorum (22.64%) and S. Typhimurium (16.98%) were identified as the most prevalent. Whole-genome sequencing analysis revealed that ST11, ST92, and ST19 were the predominant sequence types for S. Enteritidis, S. Pullorum, and S. Typhimurium, respectively. Phylogenetic analysis indicated that potential clonal spread of S. Enteritidis, S. Pullorum, and S. Typhimurium occurred across different regions, particularly the evidences supported that the S. Typhimurium isolates were dispersed in a cross-species manner. Finally, the phenotypic and genotypic profiling of antibiotic resistance among the isolates revealed that these isolates were multidrug resistant with corresponding antibiotic resistance genes (ARGs) including bla TEM, aac, aph, tet(A), and tet(B) to confer them with resistances to commonly-used veterinary drugs such as β-lactams, quinolones, macrolides. To sum, this study provides valuable insights into the current epidemiology of Salmonella in poultry industry in one of the biggest provinces in China, and shedding the light on the urgent necessity for further approaches to prevent and decontaminate such MDR Salmonella in livestock under One Health concept.

Genotypic and phenotypic characterization of antimicrobial resistance in Salmonella strains isolated from both No-Antibiotics-Ever (NAE) and conventional broiler complexes

Antimicrobial resistance is a serious global public health concern that could endanger the efficacy of antibiotics used for the treatment of diseases in humans, animals, and plants. The objective of this study was to characterize the antimicrobial resistance (AMR) pattern of Salmonella strains isolated from different stages of both No-Antibiotics-Ever (NAE) and conventional integrated broiler complexes. ResFinder was used to identify AMR genes from whole genome sequences while the phenotypic resistance of 14 different antibiotics was determined using broth microdilution method. Odds ratio and 95 % confidence limits were calculated using multivariate logistic regression for different complexes and stages of broiler production (α = 0.05). The major AMR genes identified were aac(6')-Iaa, aph(6)-Id, aph(3″)-Ib, blaCARB-2, sul1, tet(A), tet(B), tet(G), floR, fosA7, gyrA, and parC. The phenotypic results showed that 58 % (49/85) of isolates were resistant to at least one antibiotic class (AOR), 24 % (20/85) of isolates were resistant to at least two or more classes of antibiotics (ATR) and 6 % (5/85) of isolates were multi-drug resistant (MDR). In terms of 14 different antibiotics tested, 41 %, 39 %, 6 %, 5 % and 2 % of isolates were resistant to sulfisoxazole, tetracycline, nalidixic acid, ampicillin and ciprofloxacin respectively. Interestingly, 80 % (32/40) of Kentucky isolates showed phenotypic resistance to either tetracycline or sulfisoxazole or both. In addition, the odds of ATR Salmonella detection were 7 times (1.37 - 43.45; 95 % CL) more likely in the isolates from NAE complex as compared to conventional broiler complex (p = 0.0233). Overall, drug-resistant Salmonella were present within and surroundings of poultry production and poultry product that could potentially contaminate the final raw product. It may lead to complicated antimicrobial therapy during foodborne infections in consumers.

Phenotypic and WGS-derived antibiotic resistance patterns of Salmonella Enteritidis isolates from retail meat and environment during 2014 to 2019 in China

The emergence of multidrug-resistant (MDR) Salmonella Enteritidis has highlighted the importance of regularly monitoring for the occurrence of antibiotic-resistant strains. The current study combined phenotyping analysis and whole-genome-sequencing (WGS) to investigate the associations between the antibiotic-resistant phenotypes (ARPs) and genetic characteristics determinants in 95 Salmonella Enteritidis isolates from retail meat and environmental samples in China (2014-2019). Phenotypic analyses revealed that 70 isolates (73.68%) were MDR with 12 distinct resistance patterns. Most MDR strains (81.43%) had NAL-AMP-FIS-STR ± TET profiles, showing a fluctuating trend from 2015 to 2019, likely influenced by tetracycline withdrawal management. WGS identified four types of mutations in the gyrA gene were associated with nalidixic acid resistance. The co-carrying of bla TEM, sul2 and aph(6)-Id/aph(3″)-Ib was likely mediated by an X1-type plasmid, corresponding to resistance against ampicillin, sulfisoxazole, and streptomycin. Combining phenotypic analyses and WGS data, the 31 sequenced strains were primarily divided into two clusters, with most epidemic resistant strains in the largest cluster A. Identical ARP patterns observed across different sample types, regions, and isolation years but clustering together in cluster A suggested potential cross-contamination within the retail chain. Cluster B exhibited more diverse resistance patterns and genetic characteristics. Notably, three isolates in cluster B require special mention: a monophasic strain resistant to eight antibiotics, a strain exhibiting highly heteroresistance, and a strain with additional exotoxin genes. These results highlight the importance of ongoing surveillance and the utility of WGS to track and understand antibiotic resistance in Salmonella Enteritidis.

Antimicrobial Resistance Genes and Clonal Relationships of Duck-Derived Salmonella in Shandong Province, China in 2023

Salmonella is a major threat to both human and animal health. However, the diversity and antibiotic resistance of animal-derived Salmonella and their association with human infections remain largely unexplored. In this study, Salmonella strains were isolated, identified, and sequenced from dead embryos and cloacal swab samples obtained from 278 large-scale duck farms in 11 cities in Shandong Province. The results show that a total of 57 Salmonella strains were isolated, with the dominant sequence types (ST) being ST17 (15/57) and ST19 (9/57), while the dominant serotypes were S. Indiana (15/57) and S. Typhimurium (11/57). Furthermore, genomic analysis has revealed the presence of prevalent antibiotic resistance genes (ARGs), which are often associated with co-transfer mechanisms. Over 52.63% of the strains were observed to carry two or more ARGs, especially one Salmonella strain that carried twenty-eight distinct ARGs. Furthermore, core genome multilocus sequence typing analysis (cgMLST) indicated that the 57 Salmonella strains may have a close relationship, which could be clonally transmitted among different cities. The results demonstrated a close relationship between the Salmonella strains identified in diverse geographical regions, suggesting that these strains may have been widely disseminated through clonal transmission. The mutation analysis reveals significant mutations at parC (T57S), gyrA (S83F), parC (S80R), gyrA (D87N), and gyrA (S83Y). These findings emphasize the necessity for monitoring and controlling Salmonella infections in animals, as they may serve as a reservoir for ARGs with the potential to affect human health or even be the source of pathogens that infect humans.

Serotype Distribution and Antimicrobial Resistance of Salmonella Isolates from Poultry Sources in China

BACKGROUND

Salmonella is an important zoonotic pathogen, of which poultry products are important reservoirs. This study analyzed the prevalence, antimicrobial resistance, and characterization of Salmonella from broiler and laying hen sources in China.

METHODS

A total of 138 (12.27%) strains of Salmonella were isolated from 1125 samples from broiler slaughterhouses (20.66%, 44/213), broiler farms (18.21%, 55/302), and laying hen farms (6.39%, 39/610). Multiplex PCR was used to identify the serotypes. Antibiotic susceptibility testing to a set of 21 antibiotics was performed and all strains were screened by PCR for 24 selected antimicrobial resistance genes (ARGs). In addition, 24 strains of Salmonella were screened out by whole-genome sequencing together with 65 released Salmonella genomes to evaluate phylogenetic characteristics, multilocus sequence typing (MLST), and plasmid carriage percentages.

RESULTS

A total of 11 different serotypes were identified, with the dominance of S. Enteritidis (43/138, 31.16%), S. Newport (30/138, 21.74%), and S. Indiana (19/138, 13.77%). The results showed that S. Enteritidis (34.34%, 34/99) and S. Newport (51.28%, 20/39) were the dominant serotypes of isolates from broilers and laying hens, respectively. The 138 isolates showed the highest resistance to sulfisoxazole (SXZ, 100%), nalidixic acid (NAL, 54.35%), tetracycline (TET, 47.83%), streptomycin (STR, 39.86%), ampicillin (AMP, 39.13%), and chloramphenicol (CHL, 30.43%), while all the strains were sensitive to both tigacycline (TIG) and colistin (COL). A total of 45.65% (63/138) of the isolates were multidrug-resistant (MDR) strains, and most of them (61/63, 96.83%) were from broiler sources. The results of PCR assays revealed that 63.77% of the isolates were carrying the quinolone resistance gene qnrD, followed by gyrB (58.70%) and the trimethoprim resistance gene dfrA12 (52.17%). Moreover, a total of thirty-four ARGs, eighty-nine virulence genes, and eight plasmid replicons were detected in the twenty-four screened Salmonella strains, among which S. Indiana was detected to carry the most ARGs and the fewest plasmid replicons and virulence genes compared to the other serotypes.

CONCLUSIONS

This study revealed a high percentage of multidrug-resistant Salmonella from poultry sources, stressing the importance of continuous monitoring of Salmonella serotypes and antimicrobial resistance in the poultry chain, and emergency strategies should be implemented to address this problem.

Pathogenicity of Multidrug-Resistant Salmonella typhimurium Isolated from Ducks

Salmonella typhimurium (S. typhimurium) is one of the most common Salmonella serotypes in epidemiological surveys of poultry farms in recent years. It causes growth retardation, mortality, and significant economic losses. The extensive use of antibiotics has led to the emergence of multi-drug resistance (MDR) in Salmonella, which has become a significant global problem and long-term challenge. In this study, we investigated the prevalence and features of S. typhimurium strains in duck embryos and cloacal swabs from large-scale duck farms in Shandong, China, including drug resistance and virulence genes and the pathogenicity of an S. typhimurium strain by animal experiment. The results demonstrated that a total of 8 S. typhimurium strains were isolated from 13,621 samples. The drug resistance results showed that three of the eight S. typhimurium strains were MDR with the dominant resistance profile of CTX-DX-CTR-TE-AMX-AMP-CAZ. In particular, the virulence genes invA, hilA, pefA, rck, and sefA showed high positive rates. Based on the analysis of the biological characteristics of bacterial biofilm formation and mobility, a strain of S. typhimurium with the strongest biofilm formation ability, designated 22SD07, was selected for animal infection experiments with broiler ducklings. The results of animal experiments demonstrated that infection with 22SD07 reduced body weight and bursa index but increased heart and liver indexes compared to the control group. Histological examination revealed desquamation of the intestinal villous epithelium, the presence of large aggregates of lymphocytes, and a decrease in goblet cells following infection. Furthermore, the expression of IL-10 was significantly increased in the liver at 3 dpi, while TNF-α was significantly increased in the spleen at 7 dpi. The above results indicate that S. typhimurium may pose a potential threat to human health through the food chain. This helps us to understand the frequency and characteristics of S. typhimurium in duck farms and emphasizes the urgent need to strengthen and implement effective continuous monitoring to control its infection and transmission.

Prevalence and transmission of extensively drug-resistant Salmonella enterica serovar Kentucky ST198 based on whole-genome sequence in an intensive laying hen farm in Jiangsu, China

Salmonella, which is widely distributed in nature, is an important zoonotic pathogen affecting humans, livestock, and other animals. Salmonella infection not only hinders the development of livestock and poultry-related industries but also poses a great threat to human health. In this study, we collected 1,537 samples including weak chicks, dead embryos, fecal samples and environmental samples from 2020 to 2023 (for a period of 1 to 2 months per year) to keep a long-term monitor the prevalence of Salmonella in an intensive laying hen farm, 105 Salmonella strains were isolated with an isolation rate of 6.83% (105/1,537). It revealed a significant decrease in prevalence rates of Salmonella over time (P < 0.001). Before 2020, the predominant serotype was S. Enteritidis. S. Kentucky was first detected in November 2020 and its proportion was gradually found to exceed that of S. Enteritidis since then. S. Kentucky isolates were distributed in various links of the four regions in the poultry farm. A total of 55 S. Kentucky strains, were assigned to ST198 based on whole genome sequencing. Among them, 54 strains were resistant to 12 to 16 antibiotics, indicating that they were extensively drug-resistant (XDR). Seventeen antimicrobial resistance genes were detected in 55 S. Kentucky isolates. For most of these isolates, antibiotic resistance phenotypes were concordant with their genotypes. All S. Kentucky strains isolated from this farm in 2020 to 2023 showed a high similarity based on their core-genome SNP-based phylogeny. The traceability analysis revealed that S. Kentucky was introduced to the farm through newly purchased flocks. The long-term existence of XDR S. Kentucky ST198 poses a substantial risk because of the multiage management and circulation of workers in this poultry farm. Thus, this study is the first to report extensively drug-resistant S. Kentucky ST198 detected in this intensive poultry farm in China.