Genomic diversity of class I integrons from antimicrobial resistant strains of Salmonella Typhimurium isolated from livestock, poultry and humans

Antimicrobial Resistance Profiles and Molecular Characteristics of Extended-Spectrum β-Lactamase-Producing Salmonella enterica Serovar Typhimurium Isolates from Food Animals During 2010-2021 in South Korea

Extended-spectrum β-lactamase (ESBL)-producing Salmonella is emerging as a worldwide public health concern. In this study, we aimed to investigate the antimicrobial resistance profiles and molecular characteristics of ESBL-producing Salmonella enterica serovar Typhimurium (S. Typhimurium). We obtained a total of 995 S. Typhimurium isolates from the feces and carcasses of pigs (n = 678), chickens (n = 202), and cattle (n = 115) during 2010-2021 in Korea. We found that 35 S. Typhimurium isolates (3.5%) showed resistance to ceftiofur: pigs (51.4%, 18/35) and cattle (42.9%, 15/35). All of the ceftiofur-resistant S. Typhimurium isolates demonstrated multidrug resistance. Moreover, ceftiofur-resistant S. Typhimurium isolates displayed significantly higher rates of resistance to chloramphenicol and trimethoprim/sulfamethoxazole than ceftiofur-susceptible S. Typhimurium isolates (p < 0.05). The ceftiofur-resistant S. Typhimurium isolates produced four different CTX-M-type β-lactamase, comprising blaCTX-M-55 in the majority (51.4%, 18/35), followed by blaCTX-M-65 (28.6%, 10/35), blaCTX-M-14 (17.1%, 6/35), and blaCTX-M-1 (2.9%, 1/35). Among the 35 ceftiofur-resistant S. Typhimurium isolates, 16 blaCTX-M-55-positive isolates and one blaCTX-M-1-positive isolate were transferred to recipient Escherichia coli RG488 by conjugation. The predominantly found transposable units were blaCTX-M-55-orf477 (45.7%, 16/35), followed by blaCTX-M-65-IS903 (28.6%, 10/35) and blaCTX-M-14-IS903 (17.1%, 6/35). Ceftiofur-resistant S. Typhimurium represented 19 types, with types P1-19 (22.9%, 8/35) and P12-34 (22.9%, 8/35) making up the majority and being found in most farms nationwide. Sequence types (STs) were different by animal species: ST19 (48.6%, 17/35) and ST34 (42.9%, 15/35) were mostly found STs in pigs and cattle, respectively. These findings showed that food animals, especially pigs and cattle, act as reservoirs of blaCTX-M-harboring S. Typhimurium that can potentially be spread to humans.

In Silico Detection of Integrons and Their Relationship with Resistance Phenotype of Salmonella Isolates from a Brazilian Pork Production Chain

The pork production chain is an important reservoir of antimicrobial resistant bacteria. This study identified and characterized integrons in Salmonella isolates from a Brazilian pork production chain and associate them with their antibiotic resistance pattern. A total of 41 whole-genome sequencing data of nontyphoidal Salmonella were analyzed using PlasmidSPAdes and IntegronFinder software. Nine isolates (21.9%) had some integrons identified (complete and/or incomplete). Six complete class 1 integrons were found, with streptomycin resistance genes (aadA1, aadA2) alone or downstream of a trimethoprim resistance gene (dfrA1, dfrA12), and some also containing resistance genes for sulfonamides (sul1, sul3) and chloramphenicol (cmlA1). Class 2 integron was detected in only one isolate, containing dfrA1-sat2-aadA1 gene cassettes. Five isolates harbored CALINs-clusters attC but lacking integrases-with antimicrobial resistance genes typically found in integron structures. In all, integrons were observed among four serotypes: Derby, Bredeney, Panama, and monophasic var. Typhimurium I 4,[5],12:i:-. The association of integrons with antibiotic resistance phenotype showed that these elements were predominantly identified in multidrug resistance isolates, and six of the seven gentamicin-resistant isolates had integrons. So, surveillance of integrons in Salmonella should be performed to identify the potential for the spread of antimicrobial resistance genes among bacteria.

Antibiotic Resistance Profile of Salmonella sp. Isolates from Commercial Laying Hen Farms in Central-Western Brazil

Microbial resistance to antibiotics poses a significant threat to both human and animal health, necessitating international efforts to mitigate this issue. This study aimed to assess the resistance profiles of Salmonella sp. isolates and identify the presence of intl1, sul1, and blaTEM resistance genes within antigenically characterized isolates, including Agona, Livingstone, Cerro, Schwarzengrund, Salmonella enterica subsp. enterica serotype O:4.5, Anatum, Enteritidis, Johannesburg, Corvallis, and Senftenberg. These isolates underwent susceptibility testing against 14 antibiotics. The highest resistance percentages were noted for sulfamethoxazole (91%), sulfonamides (51%), and ceftiofur (28.9%), while no resistance was observed for ciprofloxacin. Salmonella Johannesburg and Salmonella Corvallis showed resistance to one antibiotic, whereas other serovars were resistant to at least two. Salmonella Schwarzengrund exhibited resistance to 13 antibiotics. The intl1 gene was detected in six out of the ten serovars, and the sul1 gene in three, always co-occurring with intl1. The blaTEM gene was not identified. Our findings highlight the risk posed by the detected multiple resistances and genes to animal, human, and environmental health. The multidrug resistance, especially to third-generation cephalosporins and fluoroquinolones, highlights the need for stringent monitoring of Salmonella in laying hens. The potential of the environment, humans, eggs, and their products to act as vectors for antibiotic resistance represents a significant concern for One Health.

Whole-Genome Sequencing Analysis of Non-Typhoidal Salmonella Isolated from Breeder Poultry Farm Sources in China, 2020-2021

Non-typhoidal salmonellosis is a dangerous foodborne disease that causes enormous economic loss and threatens public health worldwide. The consumption of food, especially poultry or poultry products, contaminated with non-typhoidal Salmonella (NTS) is the main cause of human salmonellosis. To date, no research has identified the molecular epidemiological characteristics of NTS strains isolated from breeder chicken farms in different provinces of China. In our study, we investigated the antimicrobial resistance, phylogenetic relationships, presence of antimicrobial resistance and virulence genes, and plasmids of NTS isolates recovered from breeder chicken farms in five provinces of China between 2020 and 2021 by using a whole-genome sequencing (WGS) approach and phenotypic methods. All sequenced isolates belonged to six serovars with seven sequence types. Nearly half of the isolates (44.87%) showed phenotypic resistance to at least three classes of antimicrobials. Salmonella enterica serotype Kentucky harbored more antimicrobial resistance genes than the others, which was highly consistent with phenotypic resistance. Furthermore, the carried rate of 104 out of 135 detected virulence genes was 100%. Overall, our WGS results highlight the need for the continuous monitoring of, and additional studies on, the antimicrobial resistance of NTS.

Combined metabolomics and transcriptomics analysis reveals the mechanism of antibiotic resistance of Salmonella enterica serovar Typhimurium after acidic stress

Drug-resistant Salmonella is widely distributed in the meat production chain, endangering food safety and public health. Acidification of meat products during processing can induce acid stress, which may alter antibiotic resistance. Our study investigated the effects of acid stress on the antibiotic resistance and metabolic profile of Salmonella Typhimurium, and explored the underlying mechanisms using metabolomic and transcriptomic analysis. We found that acid-stressed 14028s was more sensitive to small molecule hydrophobic antibiotics (SMHA) while more resistant to meropenem (MERO). Metabolomic analysis revealed that enhanced sensitivity to SMHA was correlated with increased purine metabolism and tricarboxylic acid cycle. Transcriptomic analysis revealed the downregulation of chemotaxis-related genes, which are also associated with SMHA sensitivity. We also found a significant downregulation of the ompF gene, which encodes a major outer membrane protein OmpF of Salmonella. The decreased expression of OmpF porin hindered the influx of MERO, leading to enhanced resistance of the bacteria to the drug. Our findings contribute to greatly improve the understanding of the relationship between Salmonella metabolism, gene expression, and changes in drug resistance after acid stress, while providing a structural framework for exploring the relationship between bacterial stress responses and antibiotic resistance.

The phenotypic and genotypic antimicrobial resistance patterns of Salmonella isolated from chickens and meat at poultry slaughterhouses in Japan and Thailand

Background and Aim

Poultry meat is a popular food consumed globally. However, poultry farming is a source of Salmonella contamination which causes human salmonellosis. This study aimed to estimate the prevalence and antimicrobial resistance (AMR) of Salmonella among chickens and meat at poultry slaughterhouses in province study areas in Thailand and Japan.

Materials and Methods

Chicken meat and feces samples were collected in Thailand and Japan. In Nakhon Ratchasima Province, Thailand, 558 samples were obtained from slaughterhouses from January 2021 to March 2022. In Gifu Prefecture, Japan, 140 samples (70 each of intestinal contents and meat) were purchased from slaughterhouses from June to October 2022. For Salmonella detection, the samples were cultivated according to the International Organization for Standardization 6579:2002/AMD 1:2007 method and confirmed using polymerase chain reaction (PCR) and agglutination tests for serotyping. Isolated Salmonella were tested for AMR to nine antibiotics using the disk diffusion method. Selected phenotypic multidrug-resistant (MDR) isolates were evaluated for AMR genes (AMRGs) using PCR.

Results

Salmonella prevalence from chickens and meat at slaughterhouses in Thailand and Japan was 41.2% and 40.7%, respectively. All the Salmonella isolates in Japan were serotyped as Schwarzengrund, and no Salmonella isolates were resistant to the nine antibiotics tested. In contrast, most of the Thai Salmonella isolates from chicken cloacal swabs and meat were resistant to doxycycline (78.3%) and colistin (63.5%). The prevalence of MDR Salmonella (MDRS) in chickens and meat from Thailand and Japan was 29.1% (67/230) and 0% (0/57), respectively. However, the most frequent AMRGs found in MDRS in Thailand were extended-spectrum beta-lactamase-Temoneira (ESBL-TEM) (45.1%). All isolated Salmonella from Japan revealed a class 1 integron gene (Int-1).

Conclusion

Phenotypic MDRS isolates from Thailand showed the greatest correlation to AMRG and ESBL-TEM. Although there were no phenotypic AMR Salmonella isolates found in Japan, they can be found associated with Int-1, which may carry other AMRGs within the gene cassettes.

Prevalence of Multidrug-Resistant Salmonella enterica Serovars in Buffalo Meat in Egypt

The current study aimed to investigate the presence of Salmonella spp. prevalence in buffalo meat in Egypt, along with studying the antimicrobial susceptibility of the recovered isolates. Salmonella spp. was detected in 25% of tested buffalo meat. A total of 53 (100%) isolates were genetically verified by PCR as Salmonella, based on the detection of the invA gene. The stn and hilA genes were detected in 71.7% (38/53), and 83.0% (44/53) of the recovered isolates, respectively. Salmonella Enteritidis (11/53; 20.7%) was the most commonly isolated serovar, followed by S. Typhimurium (9/53; 17%), S. Montevideo (6/53; 11.3%), meanwhile, S. Chester, S. Derby, S. Papuana, and S. Saintpaul were the least commonly identified serovars (a single strain for each; 1.9%). Among the 16 antimicrobials tested, amikacin, imipenem, gentamicin, cefotaxime, meropenem, ciprofloxacin, and enrofloxacin were the most effective drugs, with bacterial susceptibility percentages of 98.1%, 94.3%, 92.5%, 86.8%, 83.0%, 73.6%, and 69.8%, respectively. Meanwhile, the least effective ones were erythromycin, streptomycin, clindamycin, cefepime, and nalidixic acid, with bacterial resistance percentages of 100%, 98.1%, 88.7%, 77.4%, and 66%, respectively. Interestingly, the high contamination level of Egyptian buffalo meat with multidrug-resistant Salmonella (79.2%; 42/53) can constitute a problem for public health. Therefore, programs to control Salmonella contamination are needed in Egypt.

Molecular Detection of Integrons, Colistin and β-lactamase Resistant Genes in Salmonella enterica Serovars Enteritidis and Typhimurium Isolated from Chickens and Rats Inhabiting Poultry Farms

The rapid growth of multidrug-resistant Salmonella is a global public health concern. The aim of this study was to detect integrons, colistin and β-lactamase resistance genes in Salmonella enteritidis and typhimurium. A total of 63 isolates of S. enteritidis (n = 18) and S. typhimurium (n = 45) from fecal samples of layers and rats at chicken farms were screened for antibiotic resistant genes. Conventional PCR was performed for the detection of integrons (classes 1, 2, and 3), colistin (mcr-1-5) and β-lactamase (bla_CTX-M, bla_CTX-M-1, bla_CTX-M-2, bla_CTX-M-9, bla_CTX-M-15, bla_TEM, bla_SHV, and bla_OXA) resistant genes. Of these isolates, 77% and 27% of S. typhimurium and S. enteritidis harboured the mcr-4 encoded gene for colistin, respectively. The prevalence of class 1 integrons for S. typhimurium and S. enteritidis was 100% for each serovar, while for class 2 integrons of S. typhimurium and S. enteritidis it was 49% and 33% respectively, while class 3 integron genes was not detected. Our study also detected high levels of β-lactamase encoding genes (bla gene), namely bla_CTX-M, bla_CTX-M-1, bla_CTX-M-9 and bla_TEM from both S. typhimurium and S. enteritidis. This, to our knowledge, is the first report of mcr-4 resistance gene detection in Salmonella serovars in South Africa. This study also highlights the importance of controlling rats at poultry farms in order to reduce the risk of transmission of antibiotic resistance to chickens and eventually to humans.

Salmonella Vaccine Vector System for Foot-and-Mouth Disease Virus and Evaluation of Its Efficacy with Virus-Like Particles

Foot-and-mouth disease virus (FMDV) causes a highly contagious and devastating disease in livestock animals and has a great potential to cause severe economic loss worldwide. The major antigen of FMDV capsid protein, VP1, contains the major B-cell epitope responsible for effectively eliciting protective humoral immunity. In this study, irradiated Salmonella Typhimurium (KST0666) were used as transgenic vectors containing stress-inducible plasmid pRECN-VP1 to deliver the VP1 protein from FMDV-type A/WH/CHA/09. Mice were orally inoculated with ATOMASal-L3 harboring pRECN-VP1, and FMDV virus-like particles, where (VLP_FMDV)-specific humoral, mucosal, and cellular immune responses were evaluated. Mice vaccinated with attenuated Salmonella (KST0666) expressing VP1 (named KST0669) showed high levels of VLP-specific IgA in feces and IgG in serum, with high FMDV neutralization titer. Moreover, KST0669-vaccinated mice showed increased population of IFN-γ (type 1 T helper cells; Th1 cells)-, IL-5 (Th2 cells)-, and IL-17A (Th17 cells)-expressing CD4⁺ as well as activated CD8⁺ T cells (IFN-γ⁺CD8⁺ cells), detected by stimulating VLP_FMDV. All data indicate that our Salmonella vector system successfully delivered FMDV VP1 to immune cells and that the humoral and cellular efficacy of the vaccine can be easily evaluated using VLP_FMDV in a Biosafety Level I (BSL1) laboratory.