Genotypic virulence profiles and associations in Salmonella isolated from meat samples in wet markets and abattoirs of Metro Manila, Philippines

Development of a closed-tube, calcein-based loop-mediated isothermal amplification assay to detect Salmonella spp. in raw meat samples

Foodborne pathogens compromise food safety and public health, and Salmonella spp. are among the major pathogenic bacteria that cause outbreaks worldwide. Proper surveillance through timely and cost-effective detection methods across the food animal production chain is crucial to prevent Salmonella outbreaks and agricultural losses. Traditional culture methods are labor- and resource-intensive, with lengthy turnaround times. Meanwhile, conventional molecular tools, such as PCR and qPCR, are expensive and require technical skills and equipment. Loop-mediated isothermal amplification (LAMP) is a simple, rapid, inexpensive, highly sensitive, and specific molecular assay that does not require expensive equipment. Hence, this study developed and optimized a closed-tube, calcein-based LAMP assay to detect Salmonella using the invA gene and performed evaluation and validation against conventional PCR. The LAMP assay showed high specificity and sensitivity. It showed 10-fold higher sensitivity than conventional PCR, at <1 ng/μL DNA concentrations. Meanwhile, for CFU/mL, LAMP assay showed 1000-fold higher sensitivity than conventional PCR at 4.8 × 103 cells/mL than 4.8 × 107 cells/mL, respectively. For parallel testing of 341 raw meat samples, after conventional culture enrichment (until Rappaport-Vassiliadis broth), the optimized LAMP assay showed 100% detection on all samples while conventional PCR showed 100%, 99.04%, and 96.64% for raw chicken, beef, and pork samples, respectively. Meanwhile, a shortened enrichment protocol involving 3-h incubation in buffered peptone water only, showed lower accuracy in tandem with the optimized LAMP assay ranging from 55 to 75% positivity rates among samples. These suggest that the optimized LAMP assay possesses higher sensitivity over conventional PCR for invA gene detection when coupled with conventional enrichment culture methods. Hence, this assay has potential as a powerful complementary or alternative Salmonella detection method to increase surveillance capacity and protect consumer food safety and public health worldwide.

Genomic analysis of Salmonella enterica from Metropolitan Manila abattoirs and markets reveals insights into circulating virulence and antimicrobial resistance genotypes

The integration of next-generation sequencing into the identification and characterization of resistant and virulent strains as well as the routine surveillance of foodborne pathogens such as Salmonella enterica have not yet been accomplished in the Philippines. This study investigated the antimicrobial profiles, virulence, and susceptibility of the 105 S. enterica isolates from swine and chicken samples obtained from slaughterhouses and public wet markets in Metropolitan Manila using whole-genome sequence analysis. Four predominant serovars were identified in genotypic serotyping, namely, Infantis (26.7%), Anatum (19.1%), Rissen (18.1%), and London (13.3%). Phenotypic antimicrobial resistance (AMR) profiling revealed that 65% of the isolates were resistant to at least one antibiotic, 37% were multidrug resistant (MDR), and 57% were extended-spectrum β-lactamase producers. Bioinformatic analysis revealed that isolates had resistance genes and plasmids belonging to the Col and Inc plasmid families that confer resistance against tetracycline (64%), sulfonamide (56%), and streptomycin (56%). Further analyses revealed the presence of 155 virulence genes, 42 of which were serovar-specific. The virulence genes primarily code for host immune system modulators, iron acquisition enzyme complexes, host cell invasion proteins, as well as proteins that allow intracellular and intramacrophage survival. This study showed that virulent MDR S. enterica and several phenotypic and genotypic AMR patterns were present in the food chain. It serves as a foundation to understand the current AMR status in the Philippines food chain and to prompt the creation of preventative measures and efficient treatments against foodborne pathogens.

Occurrence, genetic diversity and resistance profiles of Salmonella enterica from Brazilian sausages collected at production facilities

This study aimed to investigate the occurrence and the genetic diversity of Salmonella enterica subsp. enterica in sausages from Southern Brazil, evaluate virulence genes and determine the phenotypic and genotypic basis of antimicrobial and sanitizer resistance. Salmonella was detected in sausage samples with an overall prevalence of 5.5%. The prevalent serovars were S. Infantis and S. Rissen. Pulsed-field gel electrophoresis (PFGE) analysis yielded nine distinct PFGE profiles, and some of them were recurrently recovered in the same establishment on different dates. Among tested isolates, 28.5% showed resistance to at least one antimicrobial agent and a multidrug-resistance (MDR) profile was observed in 21.4%. Resistance occurred most frequently to ampicillin, sulfonamide, trimethoprim/sulfamethoxazole, and trimethoprim. Regarding the genotypic antimicrobial resistance profile, S. Schwarzengrund carried tet(B), strA, strB, and sul2 genes. Benzalkonium chloride and chlorhexidine were more effective than peracetic acid and sodium hypochlorite, showing lower minimum inhibitory concentration values. Six Salmonella serovars were found, demonstrating a potential risk of salmonellosis associated with consuming this food. Salmonella carrying virulence genes, MDR profile, and tolerance to sanitizers is a public health concern and a challenge for the food industry, suggesting that new strategies should be developed to control this pathogen.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-023-05809-w.

Physiological characteristics and virulence gene composition of selected serovars of seafood-borne Salmonella enterica

Background and Aim: All serotypes of Salmonella enterica are considered potentially pathogenic. However, the non-typhoidal Salmonella (NTS) serotypes vary considerably in terms of pathogenicity and the severity of infections. Although diverse serotypes of NTS have been reported from tropical seafood, their sources, physiological characteristics, and virulence potentials are not well understood. This study aimed to compare the physiological characteristics of selected serovars of Salmonella from seafood and investigate possible variations in the distribution of known genes within the pathogenicity islands. Materials and Methods: A series of biochemical tests, including carbohydrate fermentation and amino acid decarboxylation tests were performed to physiologically compare the isolates. The genetic characterization with respect to putative virulence genes was done by screening for genes associated with Salmonella pathogenicity island (SPI) I– V, as well as the toxin- and prophage-associated genes by polymerase chain reaction. Results: Irrespective of serotypes, all the isolates uniformly harbored the five SPIs screened in this study. However, some virulence genes, such as the avrA, sodC, and gogB were not detected in all Salmonella isolates. The biochemical profiles of Salmonella serotypes were highly conserved except for variations in inositol fermentation and citrate utilization. All the isolates of this study were weak biofilm formers on polystyrene surfaces. Conclusion: The pathogenicity profiles of environmental NTS isolates observed in this study suggest that they possess the virulence machinery necessary to cause human infections and therefore, urgent measures to contain Salmonella contamination of seafood are required to ensure the safety of consumers. Keywords: biofilm, invasion, non-typhoidal Salmonella, Salmonella pathogenicity islands, seafood, virulence.