Core genome sequence analysis to characterize <i>Salmonella enterica</i> serovar Rissen ST469 from a swine production chain

Salmonella enterica subsp. enterica serotype Rissen is the predominant serotype found in Thai pork production and can be transmitted to humans through contamination of the food chain. This study was conducted to investigate the genetic relationships between serovar Rissen isolates from all levels of the pork production chain and evaluate the ability of the in silico antimicrobial resistance (AMR) genotypes to predict the phenotype of serovar Rissen. A total of 38 serovar Rissen isolates were tested against eight antibiotic agents by a disk diffusion method and the whole genomes of all isolates were sequenced to detect AMR genetic elements using the ResFinder database.A total of 86.84% of the isolates were resistant to tetracycline, followed by ampicillin (78.96%) and sulfonamide-trimethoprim (71.05%). Resistance to more than one antimicrobial agent was observed in 78.95% of the isolates, with the most common pattern showing resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide-trimethoprim, and tetracycline. The results of genotypic AMR indicated that 89.47% of the isolates carried tet(A), 84.22% carried blaTEM-1B, 78.95% carried sul3, and 78.95% carried dfrA12. The genotypic prediction of phenotypic resistance resulted in a mean sensitivity of 97.45% and specificity of 75.48%. Analysis by core genome multilocus sequence typing (cgMLST) demonstrated that the Salmonella isolates from various sources and different locations shared many of the same core genome loci. This implies that serovar Rissen has infected every stage of the pork production process and that contamination can occur in every part of the production chain

Identification of Streptococcus suis carriage in healthy pigs in Chiang Mai, Thailand

Streptococcus suis (S. suis) belongs to the critical streptococcal swine pathogens affecting financial losses in pig production globally and being concerned as a zoonotic bacterial that causes a severe invasive disease emerging in pigs and humans. Serotype 2 is considered the major serotype and is the most pathogenic S. suis obtained from human cases, and the healthy pigs are known as the major reservoir of S. suis. In this cross-sectional study, S. suis prevalence was conducted in live pigs from 111 farms across Chiang Mai, Thailand. S. suis carriage rate and serotypes were determined from the bacteriological and multiplex PCR method from tonsil swab samples. We found that 18.2% (138/760) of tonsil swab samples and 54.1% (60/111) of pig farms were positive to S. suis, and only one (0.72%) from 138 isolates was identified as serotype 9. Meanwhile, all the remains were identified as non-serotype ½/1/2/7/9/14 strains. In addition, there was an independent relation between age-ranged, farm types, and production systems with S. suis-positive rates at the farm level. The results indicate that both intensive and smallholder production systems can generally be the source of S. suis carriage. Therefore, implementing good husbandry practices and S. suis-infection predisposing factors limiting that appropriate for each farm type is essential to minimize the opportunities of S. suis outbreak in humans

Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis

Some of the most common infectious diseases are caused by bacteria that naturally colonise humans asymptomatically. Combating these opportunistic pathogens requires an understanding of the traits that differentiate infecting strains from harmless relatives. Staphylococcus epidermidis is carried asymptomatically on the skin and mucous membranes of virtually all humans but is a major cause of nosocomial infection associated with invasive procedures. Here we address the underlying evolutionary mechanisms of opportunistic pathogenicity by combining pangenome-wide association studies and laboratory microbiology to compare S. epidermidis from bloodstream and wound infections and asymptomatic carriage. We identify 61 genes containing infection-associated genetic elements (k-mers) that correlate with in vitro variation in known pathogenicity traits (biofilm formation, cell toxicity, interleukin-8 production, methicillin resistance). Horizontal gene transfer spreads these elements, allowing divergent clones to cause infection. Finally, Random Forest model prediction of disease status (carriage vs. infection) identifies pathogenicity elements in 415 S. epidermidis isolates with 80% accuracy, demonstrating the potential for identifying risk genotypes pre-operatively.Peer reviewe

Quantification of contamination levels and particular risk of Salmonella spp. in pigs in slaughterhouses in Chiang Mai and Lamphun provinces, Thailand

Salmonella spp. is one of the important foodborne pathogens, and the slaughtering process is recognized as a potential point of contamination and the spread of the pathogens. The three objectives of this study are first, to quantify the contamination levels of Salmonella spp. in pig skins and carcasses, second, to evaluate the outcomes from different pig supply sources and different practices at three critical steps (scalding, splitting, and washing) for Salmonella spp. contamination, and third, to assess risk of Salmonella spp. contamination in pork products after slaughtering level. The study was performed in three representative slaughterhouses in Chiang Mai and Lamphun provinces, Thailand. Investigation conducted from May 2013 through October 2013 found the overall prevalence and contamination levels mean to be 11.85% and 0.34 MPN/cm2, respectively. There was no statistically significant in Salmonella spp. prevalence and contamination levels detected with different patterns at the slaughterhouses which were supplied pigs from either co-operative or integrated farms. Factors found to reduce Salmonella spp. loads on carcasses included good practices, e.g., regular changing of water in the scalding tank after each batch and the use of chlorine in the washing step. Risk of Salmonella spp. contamination of pork products at the final stage of slaughtering was nearly 10%. Good practices and proper hygiene measures should be applied to minimize the risk of Salmonella spp. exposure in the slaughtering line, which can reduce the contamination pressure downstream at retail shops as well as for end consumers

Molecular evidence for cross boundary spread of Salmonella spp. in meat sold at retail markets in the middle Mekong basin area

Background The surrounding areas of the middle Mekong basin, particularly along the border between Thailand and Lao People’s Democratic Republic (Lao PDR), are high-risk areas for many livestock-associated foodborne illnesses, especially salmonellosis. This study aimed to determine the prevalence and characteristics of Salmonella spp. contamination in pork, beef and chicken meats sold at retail markets in the Thailand-Laos border area surrounding the Thai-Lao Friendship Bridge I from January to May 2019. We focused on the prevalent serotypes, antimicrobial susceptibility profiles and the multilocus sequence type (MLST) genotypes of the collected Salmonella strains. Results From a total of 370 meat samples collected, 63% were positive for Salmonella, with the prevalence of 73%, 60% and 56% from pork, beef and chicken meat samples, respectively. Of all the positive samples, 53 serotypes were identified. Of these, Salmonella enterica serovar London accounted for the majority (27%), followed by serovars Corvallis (14%), and Rissen (6%). Resistance against tetracycline was found at the highest frequency (50%), followed by ampicillin (35%) and sulfamethoxazole-trimethoprim (28%). MLST revealed no evidence of shared genetic relatedness of Salmonella at retail sites among Thailand-Laos border zone. However, a diverse range of Salmonella genotypes were spread over the area. Besides, the persistence of the residential pathogen and sharing of the supply route within-country can be inferred. Conclusions Given the high levels of contamination of retail meats, regular disinfecting of all working areas and quality control checking at pre-retail stage must be applied to reduce the transmission of Salmonella and other foodborne pathogens to consumers. The findings of this study will make a significant contribution to the current understanding of Salmonella epidemiology to enhance food security in the region

Class 1 integrons characterization and multilocus sequence typing of Salmonella spp. from swine production chains in Chiang Mai and Lamphun provinces, Thailand

Pigs and pork products are well known as an important source of Salmonella, one of the major zoonotic foodborne pathogens. The emergence and spread of antimicrobial resistance is becoming a major public health concern worldwide. Integrons are genetic elements known to have a role in the acquisition and expression of genes conferring antibiotic resistance. This study focuses on the prevalence of class 1 integrons-carrying Salmonella, the genetic diversity of strains of those organisms obtained from swine production chains in Chiang Mai and Lamphun provinces, Thailand, using multilocus sequence typing (MLST) and comparison of genetic diversity of sequence types of Salmonella from this study with pulsotypes identified in previous study. In 175 Salmonella strains, the overall prevalence of class 1 integrons-carrying-Salmonella was 14%. The gene cassettes array pattern “dfrA12-orfF-aadA2” was the most frequently observed. Most of the antimicrobial resistance identified was not associated with related gene cassettes harbored by Salmonella. Six sequence types were generated from 30 randomly selected strains detected by MLST. Salmonella at the human-animal-environment interface was　confirmed. Linkages both in the farm to slaughterhouse contamination route and the horizontal transmission of resistance genes were demonstrated. To reduce this problem, the use of antimicrobials in livestock should be controlled by veterinarians. Education and training of food handlers as well as promotion of safe methods of food consumption are important avenues for helping seventyprevent foodborne illness

Core genome sequence analysis to characterize <i>Salmonella enterica</i> serovar Rissen ST469 from a swine production chain

Salmonella enterica subsp. enterica serotype Rissen is the predominant serotype found in Thai pork production and can be transmitted to humans through contamination of the food chain. This study was conducted to investigate the genetic relationships between serovar Rissen isolates from all levels of the pork production chain and evaluate the ability of the in silico antimicrobial resistance (AMR) genotypes to predict the phenotype of serovar Rissen. A total of 38 serovar Rissen isolates were tested against eight antibiotic agents by a disk diffusion method and the whole genomes of all isolates were sequenced to detect AMR genetic elements using the ResFinder database.A total of 86.84% of the isolates were resistant to tetracycline, followed by ampicillin (78.96%) and sulfonamide-trimethoprim (71.05%). Resistance to more than one antimicrobial agent was observed in 78.95% of the isolates, with the most common pattern showing resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide-trimethoprim, and tetracycline. The results of genotypic AMR indicated that 89.47% of the isolates carried tet(A), 84.22% carried blaTEM-1B, 78.95% carried sul3, and 78.95% carried dfrA12. The genotypic prediction of phenotypic resistance resulted in a mean sensitivity of 97.45% and specificity of 75.48%. Analysis by core genome multilocus sequence typing (cgMLST) demonstrated that the Salmonella isolates from various sources and different locations shared many of the same core genome loci. This implies that serovar Rissen has infected every stage of the pork production process and that contamination can occur in every part of the production chain

Comparative Phenotypic and Genotypic Characterization of <i>Salmonella</i> spp. in Pig Farms and Slaughterhouses in Two Provinces in Northern Thailand

<div><p><i>Salmonella</i> spp. are an important group of bacterial zoonotic pathogens which can cause acute food-borne diseases in humans. Pork products are the main source of salmonellosis, but the origins and transmission routes of the disease have not been clearly determined. The purpose of this study was to characterize <i>Salmonella</i> spp. isolated in pig production lines both from pig farms and from slaughterhouses in Chiang Mai and Lamphun provinces in northern Thailand. The study focuses on the association among serotypes, antimicrobial resistance patterns and Pulse Field Gel Electrophoresis (PFGE) patterns to investigate possible sources of infection and to provide information which could help strengthen salmonellosis control programs in the region. A total of 86 strains of <i>Salmonella</i> comprising five majority serotypes were identified. Antibiotic resistance to tetracycline was found to be the most prevalent (82.56%) followed by ampicillin (81.40%) and streptomycin (63.95%). Seven clusters and 28 fingerprint-patterns generated by PFGE were identified among strains recovered from various locations and at different times, providing information on associations among the strains as well as evidence of the existence of persistent strains in some areas. Study results suggest that <i>Salmonella</i> control programs should be implemented at slaughterhouse production lines, including surveillance to insure good hygiene practices, in addition to regular monitoring of large populations of farm animals.</p></div

Antibiotic resistance ability of individual <i>Salmonella</i> strains by production levels.

<p>Antibiotic abbreviation: ampicillin (AMP); amoxicillin-clavulanic acid (AUG); chloramphenicol (C); ciprofloxacin (CIP); cefotaxime (CTX); nalidixic acid (NA); norfloxacin (NOR); streptomycin (S); sulfamethoxazole-Trimethoprim (SXT); tetracycline (TE).</p