In‐house validation of real‐time PCR methods for detecting the INV A and TTR genes of Salmonella spp. in food

Broiler litter moisture and trace metals contribute to the persistence of Salmonella strains that harbor large plasmids carrying siderophores

Broiler litter sampling has proven to be an effective method for determining the Salmonella status of a broiler chicken flock and understanding the ecology of Salmonella prior to harvest. In this study, we investigated the ecology of Salmonella within the litter (n = 224) from two commercial broiler houses in the United States. We employed culture enrichment methods and quantitative polymerase chain reaction to determine the prevalence and load of Salmonella and utilized antimicrobial susceptibility testing and whole-genome sequencing (WGS) to characterize select isolates. Additionally, we applied machine learning algorithms and in vitro experiments to identify environmental selective pressures that may contribute to the persistence of Salmonella in litter. Our findings indicate that the prevalence and abundance of Salmonella in broiler litter are influenced by the downtime between flocks as well as by the flock raised on the litter. A Decision Tree Classifier model developed demonstrated that the moisture in the caked part of litter was the most influential environmental parameter for predicting the prevalence of viable Salmonella. WGS analysis revealed that Typhimurium, Infantis, and Kentucky strains that harbored large self-conjugative plasmids encoding fitness factors for iron siderophore production were the dominant Salmonella population found in litter, and exposure to iron-limiting and copper-enriched culture media affected Salmonella growth. Our results suggest that trace metals may select for siderophores harbored on plasmids, and interventions that reduce litter moisture can potentially curtail the persistence of Salmonella in pre-harvest environments.IMPORTANCEBroiler chicken meat is the most consumed protein worldwide, and global poultry imports are projected to reach 17.5 million tons by 2031. To raise billions of chickens, litter is reused multiple times by the top global producers and exporters of chicken (Brazil and the United States). Chickens are in continuous contact with litter and depend on it for warmth and coprophagy. Consequently, litter serves as a major route for pathogens such as Salmonella to infect chickens, making it crucial to understand the environmental and genetic selective pressures that might explain why certain Salmonella strains persist on broiler farms more than others. In this study, we demonstrated that Salmonella strains that harbored siderophores on large conjugative plasmids persisted in litter and suggested that reducing litter moisture would significantly control Salmonella prevalence. However, a complete eradication of persisting Salmonella strains will require novel, innovative, and multifaceted approaches.

Whole-genome sequence of Salmonella enterica subsp. diarizonae serovar 17: l,v:z: a new serovar isolated from a nose-horned viper in Republic of Serbia

We report the draft genome sequence of Salmonella enterica subsp. diarizonae serovar 17: l,v:z isolated from a nose-horned viper (Vipera ammodytes) in Republic of Serbia which might be considered a new serovar of Salmonella.

Evaluating Commercial Loop-Mediated Isothermal Amplification Master Mixes for Enhanced Detection of Foodborne Pathogens

Loop-mediated isothermal amplification, LAMP, is nowadays the most popular isothermal nucleic acid amplification technique, and as such, several commercial, ready-to-use master mixes have flourished. Unfortunately, independent studies to determine their performance are limited. The current study performed an independent evaluation of the existing ready-to-use commercial LAMP master mixes WarmStart® LAMP Kit, LavaLAMP™ DNA Master Mix, Saphir Bst Turbo GreenMaster, OptiGene Fast Master Mix ISO-004, and SynLAMP Mix. To reduce bias, three different genes, namely ttr (Salmonella spp.), rfbE (E. coli O157), and hly (Listeria monocytogenes), were targeted. The comparison was based on amplification speed, performance with decreasing DNA concentrations, and the effect of five typical LAMP reaction additives (betaine, DMSO, pullulan, TMAC, and GuHCl). Significant differences were observed among the different master mixes. OptiGene provided the fastest amplification and showed less detrimental effects associated with the supplements evaluated. Out of the chemicals tested, pullulan provided the best results in terms of amplification speed. It is noteworthy that the different additives impacted the master mixes differently. Overall, the current study provides insights into the performance of commercial LAMP master mixes, which can be of value for the scientific community to better select appropriate reagents when developing new methods.

Independent evaluation of a DNA microarray system for Salmonella detection in ground beef

A new DNA microarray test kit has been developed to detect foodborne pathogens in various food matrices. This study focuses on evaluating the PathogenDx microarray-based system to detect Salmonella in ground beef and verify critical parameters that could interfere with the method's effectiveness, such as enrichment incubation time, ground beef fat content, inclusivity, exclusivity, and analytical sensitivity. Sample preparation protocols were evaluated at 6, 8, 12, 18, and 24 h enrichment times at varying bacterial levels to identify optimal conditions to detect the invA gene using the PathogenDx microarray. An 8 h enrichment step was selected based on 100% detection when initial inoculum levels were ≥5 CFU/g, and fractional detection was achieved when the concentration was as low as 1 CFU/g. Thus, the detection of Salmonella using the PathogenDx microarray system can be conducted in 12.5 h, including sample preparation, labeling PCR, hybridization, and analysis. Regarding fat content, there was no significant difference in detection rates of PathogenDx protocol among the highest and lowest commercially sold lean-to-fat ratios of ground beef. Inclusivity and exclusivity experiments showed that Salmonella was correctly identified 100% of the time. Using the ground beef matrix, PathogenDx method is comparable to the United States Department of Agriculture's Microbiology Laboratory Guidebook methodology for detection, which correctly identified Salmonella in 100% of the samples. Salmonella was detected between 93.33 and 100% when ground beef was inoculated with 1 and 5 CFU/g, respectively.

Whole genome sequencing and protein structure analyses of target genes for the detection of Salmonella

Rapid and sensitive detection of Salmonella is a critical step in routine food quality control, outbreak investigation, and food recalls. Although various genes have been the targets in the design of rapid molecular detection methods for Salmonella, there is limited information on the diversity of these target genes at the level of DNA sequence and the encoded protein structures. In this study, we investigated the diversity of ten target genes (invA, fimA, phoP, spvC, and agfA; ttrRSBCA operon including 5 genes) commonly used in the detection and identification of Salmonella. To this end, we performed whole genome sequencing of 143 isolates of Salmonella serotypes (Enteritidis, Typhimurium, and Heidelberg) obtained from poultry (eggs and chicken). Phylogenetic analysis showed that Salmonella ser. Typhimurium was more diverse than either Enteritidis or Heidelberg. Forty-five non-synonymous mutations were identified in the target genes from the 143 isolates, with the two most common mutations as T ↔ C (15 times) and A ↔ G (13 times). The gene spvC was primarily present in Salmonella ser. Enteritidis isolates and absent from Heidelberg isolates, whereas ttrR was more conserved (0 non-synonymous mutations) than ttrS, ttrB, ttrC, and ttrA (7, 2, 2, and 7 non-synonymous mutations, respectively). Notably, we found one non-synonymous mutation (fimA-Mut.6) across all Salmonella ser. Enteritidis and Salmonella ser. Heidelberg, C → T (496 nt postion), resulting in the change at AA 166 position, Glutamine (Q) → Stop condon (TAG), suggesting that the fimA gene has questionable sites as a target for detection. Using Phyre² and SWISS-MODEL software, we predicted the structures of the proteins encoded by some of the target genes, illustrating the positions of these non-synonymous mutations that mainly located on the α-helix and β-sheet which are key elements for maintaining the conformation of proteins. These results will facilitate the development of sensitive molecular detection methods for Salmonella.

Advancement in Salmonella Detection Methods: From Conventional to Electrochemical-Based Sensing Detection

Large-scale food-borne outbreaks caused by Salmonella are rarely seen nowadays, thanks to the advanced nature of the medical system. However, small, localised outbreaks in certain regions still exist and could possess a huge threat to the public health if eradication measure is not initiated. This review discusses the progress of Salmonella detection approaches covering their basic principles, characteristics, applications, and performances. Conventional Salmonella detection is usually performed using a culture-based method, which is time-consuming, labour intensive, and unsuitable for on-site testing and high-throughput analysis. To date, there are many detection methods with a unique detection system available for Salmonella detection utilising immunological-based techniques, molecular-based techniques, mass spectrometry, spectroscopy, optical phenotyping, and biosensor methods. The electrochemical biosensor has growing interest in Salmonella detection mainly due to its excellent sensitivity, rapidity, and portability. The use of a highly specific bioreceptor, such as aptamers, and the application of nanomaterials are contributing factors to these excellent characteristics. Furthermore, insight on the types of biorecognition elements, the principles of electrochemical transduction elements, and the miniaturisation potential of electrochemical biosensors are discussed.