Evolution and Ecology of Salmonella

An RNase III-processed sRNA coordinates sialic acid metabolism of Salmonella enterica during gut colonization

Sialic acids derived from colonic mucin glycans are crucial nutrients for enteric bacterial pathogens like Salmonella. The uptake and utilization of sialic acid in Salmonella depend on coordinated regulons, each activated by specific metabolites at the transcriptional level. However, the mechanisms enabling crosstalk among these regulatory circuits to synchronize gene expression remain poorly understood. Here, we identify ManS, a small noncoding RNA derived from the 3' UTR of STM1128 mRNA transcribed from a Salmonella enterica-specific genetic locus, as an important posttranscriptional regulator coordinating sialic acid metabolism regulons. ManS is primarily processed by RNase III and, along with its parental transcripts, is specifically activated by N-acetylmannosamine (ManNAc), the initial degradation product of sialic acid. We found that the imperfect stem-loop structure at the 5' end of ManS allows RNase III to cleave in a noncanonical manner, generating two functional types of ManS with the assistance of RNase E and other RNases: short isoforms with a single seed region that regulate the uptake of N-acetylglucosamine, an essential intermediate in sialic acid metabolism; and long isoforms with an additional seed region that regulate multiple genes involved in central and secondary metabolism. This sophisticated regulation by ManS significantly impacts ManNAc metabolism and S. enterica's competitive behavior during infection. Our findings highlight the role of sRNA in coordinating transcriptional circuits and advance our understanding of RNase III-mediated processing of 3' UTR-derived sRNAs, underscoring the important role of ManNAc in Salmonella adaptation within host environments.

Prophage-mediated genome differentiation of the Salmonella Derby ST71 population

Although Salmonella Derby ST71 strains have been recognized as poultry-specific by previous studies, multiple swine-associated S. Derby ST71 strains were identified in this long-term, multi-site epidemic study. Here, 15 representative swine-associated S. Derby ST71 strains were sequenced and compared with 65 (one swine-associated and 64 poultry-associated) S. Derby ST71 strains available in the NCBI database at a pangenomic level through comparative genomics analysis to identify genomic features related to the differentiation of swine-associated strains and previously reported poultry-associated strains. The distribution patterns of known Salmonella pathogenicity islands (SPIs) and virulence factor (VF) encoding genes were not capable of differentiating between the two strain groups. The results demonstrated that the S. Derby ST71 population harbours an open pan-genome, and swine-associated ST71 strains contain many more genes than the poultry-associated strains, mainly attributed to the prophage sequence contents in the genomes. The numbers of prophage sequences identified in the swine-associated strains were higher than those in the poultry-associated strains. Prophages specifically harboured by the swine-associated strains were found to contain genes that facilitate niche adaptation for the bacterial hosts. Gene deletion experiments revealed that the dam gene specifically present in the prophage of the swine-associated strains is important for S. Derby to adhere onto the host cells. This study provides novel insights into the roles of prophages during the genome differentiation of Salmonella.

Salmonella Genomics in Public Health and Food Safety

The species Salmonella enterica comprises over 2,600 serovars, many of which are known to be intracellular pathogens of mammals, birds, and reptiles. It is now apparent that Salmonella is a highly adapted environmental microbe and can readily persist in a number of environmental niches, including water, soil, and various plant (including produce) species. Much of what is known about the evolution and diversity of nontyphoidal Salmonella serovars (NTS) in the environment is the result of the rise of the genomics era in enteric microbiology. There are over 340,000 Salmonella genomes available in public databases. This extraordinary breadth of genomic diversity now available for the species, coupled with widespread availability and affordability of whole-genome sequencing (WGS) instrumentation, has transformed the way in which we detect, differentiate, and characterize Salmonella enterica strains in a timely way. Not only have WGS data afforded a detailed and global examination of the molecular epidemiological movement of Salmonella from diverse environmental reservoirs into human and animal hosts, but they have also allowed considerable consolidation of the diagnostic effort required to test for various phenotypes important to the characterization of Salmonella. For example, drug resistance, serovar, virulence determinants, and other genome-based attributes can all be discerned using a genome sequence. Finally, genomic analysis, in conjunction with functional and phenotypic approaches, is beginning to provide new insights into the precise adaptive changes that permit persistence of NTS in so many diverse and challenging environmental niches.

Salmonella Virulence and Immune Escape

Salmonella genus represents the most common foodborne pathogens causing morbidity, mortality, and burden of disease in all regions of the world. The introduction of antimicrobial agents and Salmonella-specific phages has been considered as an effective intervention strategy to reduce Salmonella contamination. However, data from the United States, European countries, and low- and middle-income countries indicate that Salmonella cases are still a commonly encountered cause of bacterial foodborne diseases globally. The control programs have not been successful and even led to the emergence of some multidrug-resistant Salmonella strains. It is known that the host immune system is able to effectively prevent microbial invasion and eliminate microorganisms. However, Salmonella has evolved mechanisms of resisting host physical barriers and inhibiting subsequent activation of immune response through their virulence factors. There has been a high interest in understanding how Salmonella interacts with the host. Therefore, in the present review, we characterize the functions of Salmonella virulence genes and particularly focus on the mechanisms of immune escape in light of evidence from the emerging mainstream literature.

The diversity, evolution and ecology of Salmonella in venomous snakes

BACKGROUND

Reptile-associated Salmonella bacteria are a major, but often neglected cause of both gastrointestinal and bloodstream infection in humans globally. The diversity of Salmonella enterica has not yet been determined in venomous snakes, however other ectothermic animals have been reported to carry a broad range of Salmonella bacteria. We investigated the prevalence and diversity of Salmonella in a collection of venomous snakes and non-venomous reptiles.

METHODOLOGY/PRINCIPLE FINDINGS

We used a combination of selective enrichment techniques to establish a unique dataset of reptilian isolates to study Salmonella enterica species-level evolution and ecology and used whole-genome sequencing to investigate the relatedness of phylogenetic groups. We observed that 91% of venomous snakes carried Salmonella, and found that a diverse range of serovars (n = 58) were carried by reptiles. The Salmonella serovars belonged to four of the six Salmonella enterica subspecies: diarizonae, enterica, houtanae and salamae. Subspecies enterica isolates were distributed among two distinct phylogenetic clusters, previously described as clade A (52%) and clade B (48%). We identified metabolic differences between S. diarizonae, S. enterica clade A and clade B involving growth on lactose, tartaric acid, dulcitol, myo-inositol and allantoin.

SIGNIFICANCE

We present the first whole genome-based comparative study of the Salmonella bacteria that colonise venomous and non-venomous reptiles and shed new light on Salmonella evolution. Venomous snakes examined in this study carried a broad range of Salmonella, including serovars which have been associated with disease in humans such as S. Enteritidis. The findings raise the possibility that venomous snakes could be a reservoir for Salmonella serovars associated with human salmonellosis.

Inactivation of Salmonella enterica and spoilage microorganisms in orange juice treated with dimethyl dicarbonate (DMDC)

Salmonella enterica is the pertinent pathogen associated with orange juice products that have resulted in numerous foodborne outbreaks. Although fresh orange juice typically has a pH below 4.0, which inhibits most pathogen growth, S. enterica can survive at low pH for extended periods. Additionally, fresh juice contains spoilage microorganisms such as natural yeasts and molds, which can grow at low pH, and may cause fermentation and product spoilage if left untreated. Numerous Salmonella outbreaks linked to fresh orange juice, as well as the burden of product spoilage, have generated increased demand for alternative, non-thermal treatments that can ensure pathogen- and spoilage-free products. In this study, the effect of dimethyl dicarbonate (DMDC) on pathogen and spoilage microorganism inactivation in orange juice has been investigated with two experiments. First, pasteurized orange juice was inoculated with approximately 10⁶-10⁷ CFU/ml of five serotypes of S. enterica per ml and treated with DMDC to test the effectiveness of inactivation against Salmonella. For the fungal spoilage microorganism study, fresh orange juice was held at room temperature to increase natural yeast and mold count to roughly 10⁵-10⁶ CFU/ml, followed with treatment with DMDC. DMDC at two concentrations (172 and 200 ppm) was used, and the tests were carried out at ambient (21 °C ± 3 °C) and refrigeration (4 °C) temperatures. There was a >5-log reduction of Salmonella at 4 °C after 24 h at both 172 and 200 ppm of DMDC. For the treatment of fungal spoilage microorganisms, a nearly 5 and 4 log reduction of yeasts and molds was observed at ambient temperature and 4 °C, respectively. These results suggest that DMDC is most effective for use under the 4 °C holding conditions to inactivate S. enterica, and should be coupled with an additional preservative system for fungal spoilage control to produce safe orange juice that retains fresh quality.

Genetic Adaptation to Growth Under Laboratory Conditions in Escherichia coli and Salmonella enterica

Experimental evolution under controlled laboratory conditions is becoming increasingly important to address various evolutionary questions, including, for example, the dynamics and mechanisms of genetic adaptation to different growth and stress conditions. In such experiments, mutations typically appear that increase the fitness under the conditions tested (medium adaptation), but that are not necessarily of interest for the specific research question. Here, we have identified mutations that appeared during serial passage of E. coli and S. enterica in four different and commonly used laboratory media and measured the relative competitive fitness and maximum growth rate of 111 genetically re-constituted strains, carrying different single and multiple mutations. Little overlap was found between the mutations that were selected in the two species and the different media, implying that adaptation occurs via different genetic pathways. Furthermore, we show that commonly occurring adaptive mutations can generate undesired genetic variation in a population and reduce the accuracy of competition experiments. However, by introducing media adaptation mutations with large effects into the parental strain that was used for the evolution experiment, the variation (standard deviation) was decreased 10-fold, and it was possible to measure fitness differences between two competitors as small as |s| < 0.001.