Antimicrobial Resistance, Virulence Genes, and Genetic Diversity of Salmonella enterica Isolated from Sausages

Epidemiology and antimicrobial resistance of Salmonella serovars Typhimurium and 4,[5],12:i- recovered from hospitalized patients in China

Global emergence of multidrug-resistant (MDR) Salmonella enterica serovar Typhimurium is a continuing challenge for modern healthcare. However, the knowledge, regarding the epidemiology of salmonellosis caused by the monophasic variant S. 4,[5],12:i:- in hospitalized patients, is limited in China. To bridge this gap, we carried out a retrospective study to determine the antimicrobial resistance, trends, and risk factors of S. Typhimurium and S. 4,[5],12:i:- (n = 329) recovered from patients in Zhejiang province between 2011 and 2019. The results showed that 90.57% (298/329) of the isolates were MDR; among them, 48.94% (161/329) and 12.46% (41/329) were phenotypically resistant to cephalosporins and fluoroquinolones, respectively, which are the drugs of choice used to treat salmonellosis in clinics. Additionally, we observed a higher incidence of infections among the young population (<5 years old). Notably, the higher prevalence of ST34 (sequence type 34) isolates, especially after 2014, with MDR (57.05%, 170/298) phenotype, and incidence of ST34 isolates co-harbouring mcr-1 (mobile colistin resistance gene) and blaCTX-M-14 (β-lactamase gene) suggest an association between STs and drug resistance. Together, the increasing prevalence of MDR ST34 calls for enhanced monitoring strategies to mitigate the spread and dissemination of MDR clones of S. Typhimurium and S. 4,[5],12:i-. Our study provides improved knowledge about non-typhoid Salmonella (NTS) infections, which could help in the effective recommendation of antimicrobials in hospitalized patients.

Serotype Distribution, Antimicrobial Resistance, Virulence Genes, and Genetic Diversity of Salmonella spp. Isolated from small-scale Leafy Green Vegetable Supply Chains in South Africa

Salmonella have been implicated in foodborne disease outbreaks globally and is a pressing concern in the South African small-scale sector due to inadequate hygiene standards and limited regulatory oversight, leading to a higher risk of foodborne diseases. By investigating irrigation water and leafy green vegetables produced by small-scale growers and sold through unregulated supply chains, this study was able to determine the presence, serotype distribution, virulence gene profiles, antibiotic resistance, and genetic diversity of Salmonella isolated from these sources. From 426 samples, 21 Salmonella-positive samples were identified, providing 53 Salmonella isolates. Of these, six different Salmonella serotypes and sequence types (STs) were identified, including Salmonella II 42:r: ST1208 (33.96%; n = 18), Salmonella Enteritidis: ST11 (22.64%; n = 12), Salmonella II 42:z29: ST4395 (16.98%; n = 9), Salmonella Havana: ST1524 (15.09%; n = 8), Salmonella Typhimurium: ST19 (9.43%; n = 5), and Salmonella IIIb 47:i:z: ST7890 (1.89%; n = 1). A total of 92.45% of the isolates were found to be multidrug-resistant, showing high rates of resistance to aztreonam (88.68%; n = 47), ceftazidime (86.79%; n = 46), nalidixic acid (77.36%; n = 41), cefotaxime (75.47%; n = 40), cefepime (71.70%; n = 38), and streptomycin (69.81%; n = 37). All isolates possessed the aac(6')-Iaa antimicrobial resistance gene, with a range of between 9 and 256 virulence genes. Eleven cluster patterns were observed from Enterobacterial Repetitive Intergenic Consensus sequence analyses, demonstrating high diversity among the Salmonella spp., with water and fresh produce isolates clustering, suggesting water as a potential contamination source. Plasmid replicon types were identified in 41.51% (n = 22) of the isolates, including Col(pHAD28) in Salmonella Havana (5.66%; n = 3), Col156 in Salmonella II 42:z29:- (1.89%; n = 1) and both IncFIB(S) and IncFII(S) in Salmonella Enteritidis (22.64; n = 12), Salmonella Typhimurium (9.43%; n = 5), and Salmonella Havana (1.89%; n = 1). This study highlights the presence of multidrug-resistant and multivirulent Salmonella spp. in the small-scale leafy green vegetable supply chains, underscoring the need for the development of a "fit-for-purpose" food safety management system within this system.

Assessment of stn, sipB and sopB Virulence Genes in Various Salmonella Serovars

Salmonella is a zoonotic bacterium that is considered to be one of the most common causes of foodborne infections worldwide. Bearing in mind the genes involved in its virulence, identifying these genes can enable experts to better understand bacterial pathogenicity, which could subsequently help develop more efficient means to control and prevent infections. This study aimed to analyze stn, sipB, and sopB genes in various Salmonella serovars. To carry out this study, 103 Salmonella serovars were extracted from livestock, poultry, and humans from existing samples at the Department of Microbiology of the Razi Serum and Vaccine Research Institute in Karaj, Iran. These samples were cultured in selection and differential media, and their serovars were identified using specific antibodies based on Kaufman-White Tables. Utilizing PCR and specific primers, stn, sopB, and sipB genes were detected among these serovars. In this investigation, the most common human serovars were Salmonella paratyphi A, Salmonella paratyphi B, and Salmonella enteritidis; the most common serovars among livestock consisted of Salmonella dublin and Salmonella typhimurium and the most common Salmonella serovars among poultry consisted of Salmonella infantis and Salmonella enteritidis. The results of PCR on stn, sipB, and sopB genes demonstrated segments with 617bp, 875 bp, and 220 bp on agar gel, respectively. Based on the obtained findings, stn, sipB, and sopB genes were detected in 96.11%, 99.02%, and 98.05% of Salmonella serovars, respectively. Considering the fact that the aforementioned genes play significant roles in bacterial virulence, they can be used to develop diagnostic ELISA kits and recombinant vaccines.

Epidemiological and clinicopathological findings in 15 fatal outbreaks of salmonellosis in dairy calves and virulence genes in the causative Salmonella enterica Typhimurium and Dublin strains

Salmonella enterica is a major food-borne pathogen that affects cattle-rearing systems worldwide. Little information is available on the epidemiology and pathology of salmonellosis and the virulence genes (VGs) carried by Salmonella in spontaneous outbreaks in cattle. We describe epidemiological findings in 15 fatal outbreaks of salmonellosis in Uruguayan dairy farms and the age, clinical signs, and pathology in 20 affected calves. We also describe the serotypes and frequencies of 17 VGs in the causative Salmonella strains and explore their associations with epidemiological, clinical, and pathological findings. Salmonella Typhimurium and Dublin were identified in 11/15 and 4/15 outbreaks, respectively. The most frequent reason for consultation was digestive disease (8 outbreaks caused by S. Typhimurium), followed by sudden death (4 outbreaks, 3 caused by S. Dublin). Morbidity, mortality, and lethality ranged 4.8-100%, 3.8-78.9%, and 10-100%, without significant differences between serotypes. Diarrhea, the most common clinical sign (14 cases), was associated with the Typhimurium serotype (OR = 26.95), especially in ≤ 30-day-old calves with fibrinous enteritis as the main autopsy finding. The Dublin serotype affected ≥ 50-day-old calves and was associated with fibrinosuppurative splenitis (p = 0.01) and tubulointerstitial nephritis (OR = 48.95). The chances of the Dublin serotype increased significantly with age. There was low variability of VG across serotypes. The pefA gene was associated with the Typhimurium serotype (OR = 21.95), macroscopic enteritis (p = 0.03), and microscopic fibrinosuppurative splenitis (p = 0.04). Understanding the epidemiology, pathology, and virulence of S. enterica at the farm level is key to delineating prevention and control strategies to mitigate its impact on animal and human health.

Molecular Detection of Virulence Factors in Salmonella serovars Isolated from Poultry and Human Samples

Salmonellosis is a common infectious disease in humans caused by Salmonella spp., which in recent years has shown an increase in its incidence, with products of avian origin being a common source of transmission. To present a successful infective cycle, there are molecular mechanisms such as virulence factors that provide characteristics that facilitate survival, colonization, and damage to the host. According to this, the study aims to characterize the virulence factors of Salmonella spp. strains isolated from broilers (n = 39) and humans (n = 10). The presence of 24 virulence genes was evaluated using end-point PCR. All the strains of Salmonella spp. isolated from broiler chickens revealed presence of 7/24 (29, 16%) virulence genes (lpfA, csgA, sitC, sipB, sopB, sopE, and sivH). Regarding the strains isolated from cases of gastroenteritis in humans, all strains contained (14/24, 58, 33%) virulence genes (lpfA, csgA, pagC, msgA, spiA, sitC, iroN, sipB, orgA, hilA, sopB, sifA, avrA, and sivH). In summary, the presence of virulence genes in different strains of Salmonella isolated from broilers and humans could be described as bacteria with potential pathogenicity due to the type and number of virulence genes detected. These findings are beneficial for the pathogenic monitoring of Salmonella in Colombia.

Prevalence, antimicrobial resistance and virulence genes of Salmonella serovars isolated from humans and animals

We investigated the prevalence, antimicrobial susceptibility, antimicrobial resistance and virulence genes of Salmonella isolates recovered from humans and different species of animals. Out of 1231 samples, 88 (7.15%) Salmonella isolates were obtained, among which 21 (23.86%) belonged to Salmonella enterica subsp. enterica sero var. Weltevreden, 22 (25%) to S. Enteritidis, 16 (18.2%) to S. Typhi and 14 (15.9%) to S. Newport; 7 (7.95%) isolates were untypable. Among the 88 isolates, 65.90% showed resistance to gentamicin, 61.36% to tetracycline, 61.18% to cefotaxime, 48.86% to trimethoprim, 45.45% to ampicillin, 11.36% to ceftriaxone, 10.22% to chloramphenicol and 7.95% each to ciprofloxacin and cefepime. Most of the isolates were susceptible, with a low MIC (≤ 0.25 μg/ml) value, to cefepime, cefotaxime, ciprofloxacin, ceftriaxone and co-trimoxazole and with a moderate MIC (0.5-4 μg/ml) to ampicillin, tetracycline, gentamicin and chloramphenicol. The resistance genes bla_TEM, tetA and dfrA12 were most prevalent, irrespective of the host of origin of the isolates. While invA was used for molecular detection of Salmonella, other virulence genes, viz. sipA, sipB, sipC, stn and pagN, were also detected in all Salmonella isolates. A total of 38.64% isolates were multidrug-resistant (MDR), and various virulence genes were present among the isolated serovars. This study highlights the importance of continuous monitoring and surveillance for pathogenic Salmonella and their potential risks to both humans and animals.

Phenotypic and Genotypic Characterization of Salmonella Isolates Recovered from Foods Linked to Human Salmonellosis Outbreaks in Minas Gerais State, Brazil

ABSTRACT

Salmonella is one of the primary pathogens that causes foodborne diseases worldwide. In the present study, we characterized Salmonella isolates recovered from foods linked to human salmonellosis outbreaks in Minas Gerais, Brazil, from 2003 to 2017. Serotype, antimicrobial susceptibility, presence of virulence genes, and genetic polymorphism as determined by repetitive element sequence-based PCR were determined for 70 Salmonella isolates. Thirteen Salmonella serotypes were identified, and the most prevalent were Enteritidis and Typhimurium, comprising 52 (74.3%) of the 70 isolates. Sixty-five (92.8%) of the isolates were resistant to at least 1 of the 15 antimicrobials tested. Ten isolates (14.2%) had a multidrug resistance phenotype. Isolates were screened for 16 virulence genes, which were found in 75.7 to 100% of the isolates. A statistical difference was found among Salmonella serotypes in the presence of the sipB, sopE, lfpA, sefA, and spvC genes. Based on their DNA fingerprints, 40 isolates of Salmonella Enteritidis from 16 outbreaks were separated into 14 groups and 12 isolates of Salmonella Typhimurium were separated into 6 groups. These serological patterns were similar to those reported by public health centers worldwide. Of concern is the high prevalence among the isolates in this study of both virulence genes and resistance to antimicrobials, especially to critically important drugs. Special attention should be given to Salmonella Enteritidis. Although the genomes of these Salmonella isolates were relatively variable, high genetic similarity was observed among them, and some had identical fingerprints. These results support the hypothesis of clonal circulation of Salmonella isolates causing human infections in Minas Gerais.

HIGHLIGHTS

Antibiotic Resistance Development in Animal Production: A Cross-Sectional Study

Background

In recent years, an increase in the development of antimicrobial-resistant pathogens especially foodborne zoonotic bacteria has been observed. As a result, crude mortality rates are increasing due to those resistant bacteria in both human and animal populations, particularly in developing countries like Tanzania where the risk of infection is high due to poor biosecurity measures, close animal–human interactions, and extensive use of antimicrobials for animal productions. One of those zoonotic bacterial pathogens, which commonly contaminates food, is Salmonella.

Methodology

A cross-sectional study was carried out on samples collected from diarrheic sheep, to assess the level of antibiotic resistance of Salmonella. From 165 fecal samples, 80 of which were tested positive for Salmonella. The antibiotic resistance level of Salmonella isolates was conducted by the Kirby-Bauer disc diffusion method using ten commonly used antibiotics in the study area.

Results

Out of 80 Salmonella positive samples, all (100%) of them were resistant to amoxicillin and ampicillin while sixty-eight (85%), 68 (85%), and 60 (75%) isolates were susceptible to gentamicin, ciprofloxacin, and kanamycin, respectively. Thirty (37.5%) Salmonella isolates were resistant to both trimethoprim and tetracycline and 25% of the isolates were resistant to both doxycycline and chloramphenicol while 12.5% of the isolates were resistant to nalidixic acid.

Conclusion

This study revealed that the Salmonella isolates of diarrheic sheep developed a wide range of resistance to different antibiotics. Further studies and integrative approaches in a one health framework among animal–human and environmental health professionals are recommended for the mitigation of health risks arising from antibiotic-resistant zoonotic pathogens like Salmonella.

Comprehensive Evaluation on the Use of Thymus vulgaris Essential Oil as Natural Additive against Different Serotypes of Salmonella enterica

Essential oils were proposed as natural additives to ensure food safety and quality in a more sustainable approach. The chemical composition of Thymus vulgaris essential oil (TV-EO) collected from Morocco, its antioxidant and antimicrobial activity against different serotypes of Salmonella enterica subsp. enterica was investigated. A mathematical model was implemented to predict the Salmonella behavior when exposed to TV-EO. In situ antimicrobial activity and sensory influence were tested in minced poultry meat experimentally contaminated with Salmonella and treated with TV-EO. Hydrodistillation was used to extract TV-EO, and gas chromatography-mass spectrometry (GC-MS) analysis found thymol as the most representative compound. Results of the antioxidant activity showed an IC50 of 0.29 ± 0.04 mg/mL, EC50 of 0.74 ± 0.08 mg/mL, and RC50 of 0.59 ± 0.06 mg/mL. All the Salmonella strains were susceptible to TV-EO with performing results for the disc diffusion method (inhibition diameters ranged between 24 ± 0.4 mm and 32 ± 0.6 mm), determination of minimum inhibitory concentration (MIC; 0.5%) and minimum bactericidal concentration (MBC; 1%), sublethal-injured cells (7.99 ± 0.08%), in situ activity (growth inhibition after 3 days), and meat sensory preservation (up to 1 week). The implemented mathematical model well fitted the Salmonella growth curve. TV-EO with significant antioxidant and antibacterial activities was suitable to ensure food safety and quality consistent with the new sustainable trends in the food field.

Genomic investigation of antimicrobial resistance determinants and virulence factors in Salmonella enterica serovars isolated from contaminated food and human stool samples in Brazil

This study investigated the antimicrobial resistance determinants, virulence factors and identified serovars in 37 Salmonella enterica strains isolated from human stool and contaminated foods linked to outbreaks that occurred in Brazil over 7 years using whole genome sequencing (WGS). Phylogenetic analysis of selected serovars (S. Typhimurium, S. Infantis, S. London, and S. Johannesburg) was performed. Ten distinct serovars were identified and, 51% of the tested strains (n = 19) showed disagreement with the previous conventional serotyping. The antimicrobial resistance (AMR) determinants or plasmids varied among the strains. Resistome analysis revealed the presence of resistance genes to aminoglycosides [aac (6')-laa, aph (3″)-lb, aph (6)-ld, aadA1 and aadA2], sulfonamides (sul1), trimethoprin (dfrA8), fosfomycin (fosA7) and tetracyclines (tetA, tetB, tetC), as well as point mutations in parC (T57S) and gyrA (S83F). Plasmidome showed the presence of IncHI2, IncHI2A, IncFIB (S), IncFII (S), IncI1 and p0111 plasmids. Eight Salmonella pathogenicity islands and up to 102 stress and/or virulence genes were identified in the evaluated genomes. Virulence genes of K88 fimbrial adhesin were first reported in S. enterica (S. Pomona, S. Bredeney and S. Mbandaka strains). pilW gene was first identified in S. Pomona. Phylogenetic analysis showed that some serovars circulated in Brazil for decades, primarily within the poultry production chain. Findings highlighted the virulence and AMR determinants in strains that may lead to recurring food outbreaks.

Prevalence and genomic investigation of Salmonella isolates recovered from animal food-chain in Xinjiang, China

Salmonella is a major foodborne pathogen worldwide, causing serious cases of morbidity and mortality due to the consumption of contaminated foods. Animal-borne foods were considered the main source of transferring Salmonella to humans; however, route surveillance by genomic platforms along the food-chain is limited in China. Here, we proceeded to the application of whole genome sequencing in the epidemiological analysis of Salmonella isolated along the food-chain in Xinjiang, China. A total of 2408 samples were collected from farms, slaughterhouses, and markets, and subjected to the isolation of Salmonella strains. 314 (13.04%) of the samples were positive for Salmonella. Phenotypic antimicrobial resistance was conducted by the broth dilution method using 14 antimicrobial agents belonging to ten classes for all 314 isolates. A selection of representative 103 isolates was subjected to whole-genome sequencing for understanding the Salmonella diversity, including serovars, antimicrobial and virulence genes, plasmid types, multi-locus sequence types, and allelic types. We found that S. Agona was the dominant serovar and O:4(B) was the dominant serogroup. The dominant genotype was ST13 and each serovar has a unique MLST pattern. Plasmids prediction reported Col(MGD2)_1 and Col(Ye4449)_1 as the dominant plasmids, in addition to the detection of IncFII(S)_1 and IncFIB(S)_1 carried by all S. Enteritidis isolates. Importantly, virulence genes prediction showed the presence of cdtB gene encoding typhoid toxins, spv genes, and pef gene cluster encoding fimbriae in the genomes of S. Indiana and S. Enteritidis. Phenotypic antimicrobial resistance identified 92.04% of the sampled isolates as multi-drug resistance (MDR), with high resistance to tetracycline (78.03%; 245/314), amoxicillin/ clavulanic acid (75.80%; 238/314), and ampicillin (70.70%; 222/314). Together, we firstly reported the prevalence of MDR Salmonella isolates harboring critical virulence factors transmission via animal-borne food-chain in Xinjiang, hence route surveillance by whole-genome sequencing platform could facilitate recognition and project early warning for the emerging MDR clones along the food-chain.

Chemical composition, antioxidant capacity and antibacterial action of five Moroccan essential oils against Listeria monocytogenes and different serotypes of Salmonella enterica

Essential oils (EOs) obtained from aromatic plants are rich in natural components with interesting antimicrobial effects. The aim of this study was to evaluate the chemical composition of EOs extracted from Origanum majorana (OM-EO), Mentha suaveolens (MS-EO), Rosmarinus officinalis (RO-EO), Salvia officinalis (SO-EO) and Mentha pulegium (MP-EO). Their antioxidant properties and antibacterial activity against Listeria monocytogenes and different serotypes of Salmonella enterica subsp. enterica were also studied. The EOs were extracted from plants by hydro-distillation and their chemical composition was determined by GC-MS. Terpinen-4-ol, 1,8-Cineole, Camphor, Limonene and Cinerone were the main chemical components found in OM-EO, RO-EO, SO-EO, MP-EO and MS-EO, respectively. To the best of our knowledge, Limonene and Cinerone were reported, for the first time, as the major components of MP-EO and MS-EO. Moreover, our results showed that MS-EO had the best antioxidant activity with an IC₅₀ of 0.78 ± 0.05 mg/mL, EC₅₀ of 1.53 ± 0.07 mg/mL, and RC₅₀ of 0.98 ± 0.04 mg/mL, and the higher antibacterial activity using microdilution broth method with MIC of 0.5% for Salmonella and 0.25% for L. monocytogenes, while OM-EO had the best antibacterial activity using disc diffusion method (inhibition diameters ranged between 15.3 ± 0.3 mm and 18.5 ± 0.3 mm for Salmonella and between 20.1 ± 0.2 mm and 25.4 ± 0.4 mm for L. monocytogenes). However, OM-EO and MS-EO present the higher percentage of sub-lethally injured cells against S. enterica (5.50 ± 0.11%) and L. monocytogenes (5.23 ± 0.07%), respectively. From this study, we can conclude that the investigated EOs are rich in components with interesting antibacterial activity and they could be applied in food preparations as natural preservatives to extend the shelf life of food products and to inhibit the growth of food-borne pathogens.

Occurrence of oxytetracycline residues in milk samples from Palakkad, Kerala, India

Background and Aim

Food of animal origin such as milk is vital for nutritional security and should be free of any antibiotic residues due to its public health significance. We designed a study aiming to determine the occurrence of antibiotic residues and in further levels of oxytetracycline residues in pooled raw milk samples from Palakkad district, Kerala.

Materials and Methods

We collected pooled raw milk samples were collected from Alathur, Chittoor, and Palakkad blocks of Palakkad district, Kerala. A total of 215 samples were screened for antibiotic residues by microbial inhibition assay (MIA) and the positive samples were subjected to enzyme-linked immunosorbent assay (ELISA) to determine oxytetracycline residues, this was further confirmed using high-performance liquid chromatography (HPLC).

Results

We found that out of the 215 pooled raw milk samples screened for antibiotic residues using MIA, 22 samples (10.23%) were positive for antibiotic residues from Palakkad, Kerala. Out of these 22 samples, five (2.33%) were positive for oxytetracycline residues. We further calculated the mean concentration of oxytetracycline residues in these five samples and estimated it to be 201.00±41.25 ng/mL and 272.11±53.21 ng/mL using ELISA and HPLC, respectively. On analyzing these five samples, we found that four samples (1.86%) exceeded the maximum residue limits level of 100 ng/mL for oxytetracycline residues in milk as specified by Codex Alimentarius Commission/Food Safety and Standards Authority of India (FSSAI).

Conclusion

This study revealed that the occurrence of oxytetracycline residues in pooled raw milk samples in the Palakkad district of Kerala. Hence, there is a need for surveillance and monitoring of antibiotic residues in milk due to its impact on public health to ensure consumer safety.