Molecular insights into farm animal and zoonotic Salmonella infections

A new Salmonella enterica serovar that was isolated from a wild sparrow presents a distinct genetic, metabolic and virulence profile

Salmonella enterica is a ubiquitous and clinically-important bacterial pathogen, able to infect and cause different diseases in a wide range of hosts. Here, we report the isolation and characterization of a new S. enterica serovar (13,23:i:-; S. Tirat-Zvi), belonging to the Havana supper-lineage that was isolated from a wild house sparrow (Passer domesticus) in Israel. Whole genome sequencing and complete assembly of its genome indicated a plasmid-free, 4.7 Mb genome that carries the Salmonella pathogenicity islands 1-6, 9, 19 and an integrative and conjugative element (ICE), encoding arsenic resistance genes. Phenotypically, S. Tirat-Zvi isolate TZ282 was motile, readily formed biofilm, more versatile in carbon source utilization than S. Typhimurium and highly tolerant to arsenic, but impaired in host cell invasion. In-vivo infection studies indicated that while S. Tirat-Zvi was able to infect and cause an acute inflammatory enterocolitis in young chicks, it was compromised in mice colonization and did not cause an inflammatory colitis in mice compared to S. Typhimurium. We suggest that these phenotypes reflect the distinctive ecological niche of this new serovar and its evolutionary adaptation to passerine birds, as a permissive host. Moreover, these results further illuminate the genetic, phenotypic and ecological diversity of S. enterica pathovars.

Characterization of Salmonella enterica Biofilms and Antibiofilm Effect of Carvacrol and 2-Aminobenzimidazole

Biofilm-associated foodborne Salmonella infections in poultry have become increasingly challenging for veterinarians, particularly in developing countries, and warrant thorough investigation. We assessed the biofilm-forming tendency of poultry isolates of Salmonella enterica, namely Salmonella Typhimurium (n = 23), Salmonella Infantis (n = 28), and Salmonella Heidelberg (n = 18), in nutrient-rich Rappaport-Vassiliadis Soya (RVS) peptone broth and nutrient-deficient diluted Tryptone Soya Broth (TSB). Seven of the tested isolates exhibited moderate biofilm formation in diluted TSB, whereas two showed such formation in RVS. In addition, the Congo red agar assay revealed curli and cellulose production in seven isolates. Fourteen specific biofilm-associated genes were analyzed identifying sdiA and seqA to be the most prevalent (100%), and glyA the least prevalent (69.5%). The prevalence of the genes bcsA and csgA was significantly lower in moderate and weak biofilm formers, respectively, as compared with nonbiofilm formers in RVS peptone broth. Furthermore, the compounds carvacrol and 2-aminobenzimidazole (2-ABI) effectively inhibited biofilm formation by Salmonella serovars in RVS peptone and TSB media, respectively. Whereas the antibiofilm activity of 2-ABI against Salmonella has not been reported previously, we determined its most effective concentration at 1.5 mM among tested antibiofilm treatments. These findings indicate that Salmonella strains prevalent in poultry farms have the potential to form biofilms, and the tested compounds should be further explored as supportive or alternative antimicrobials.

A comparison of methods to detect low levels of Salmonella enterica in surface waters to support antimicrobial resistance surveillance efforts performed in multiple laboratories

Developing effective and sensitive detection methods for antimicrobial resistant Salmonella enterica from surface water is a goal of the National Antimicrobial Resistance Monitoring System (NARMS). There are no specified methods for recovery of S. enterica in surface waters in the U.S. A multi-laboratory evaluation of four methods - bulk water enrichment (BW), vertical Modified Moore Swab (VMMS), modified Standard Method 9260.B2 (SM), and dead-end ultrafiltration (DEUF) - was undertaken to recover S. enterica from surface water. In Phase 1, one-liter volumes of water were collected from the same site on five different dates. Water was shipped and analyzed at four different laboratory locations (A, B, C, and D) for recovery of 1) inoculated fluorescent S. Typhimurium strain (ca. 30 CFU/L) and 2) Salmonella present in the water sampled. At each location, BW, VMMS, or SM recovery was performed on five separate 1 L water samples. Twenty 1 L water samples were subjected to each recovery method, and overall, sixty 1 L samples were assayed for Salmonella. Inoculated, fluorescent Salmonella Typhimurium and environmental Salmonella spp. were recovered from 65 % (39/60) and 45 % (27/60) of water samples, respectively. BW, VMMS, and SM recovered fluorescent S. Typhimurium from 60 %, 60 %, and 75 % of inoculated samples, respectively. Analysis by Chi-squared test determined laboratory location had a significant (p < 0.05) effect on fluorescent S. Typhimurium recovery compared to method or date of water collection. In Phase 2, recovery of inoculated fluorescent S. Typhimurium from 1 L samples by SM and DEUF was compared at laboratory locations B and D. SM and DEUF recovered fluorescent S. Typhimurium from 100 % (20/20) and 95 % (19/20) of inoculated water samples, respectively; laboratory location (p > 0.05) did not affect Salmonella recovery. Uniform laboratory methodology and training should be prioritized in conducting Salmonella recovery from surface water in laboratories.

Genomic and phenotypic comparison of two variants of multidrug-resistant Salmonella enterica serovar Heidelberg isolated during the 2015-2017 multi-state outbreak in cattle

Salmonella enterica subspecies enterica serovar Heidelberg (Salmonella Heidelberg) has caused several multistate foodborne outbreaks in the United States, largely associated with the consumption of poultry. However, a 2015-2017 multidrug-resistant (MDR) Salmonella Heidelberg outbreak was linked to contact with dairy beef calves. Traceback investigations revealed calves infected with outbreak strains of Salmonella Heidelberg exhibited symptoms of disease frequently followed by death from septicemia. To investigate virulence characteristics of Salmonella Heidelberg as a pathogen in bovine, two variants with distinct pulse-field gel electrophoresis (PFGE) patterns that differed in morbidity and mortality during the multistate outbreak were genotypically and phenotypically characterized and compared. Strain SX 245 with PFGE pattern JF6X01.0523 was identified as a dominant and highly pathogenic variant causing high morbidity and mortality in affected calves, whereas strain SX 244 with PFGE pattern JF6X01.0590 was classified as a low pathogenic variant causing less morbidity and mortality. Comparison of whole-genome sequences determined that SX 245 lacked ~200 genes present in SX 244, including genes associated with the IncI1 plasmid and phages; SX 244 lacked eight genes present in SX 245 including a second YdiV Anti-FlhC(2)FlhD(4) factor, a lysin motif domain containing protein, and a pentapeptide repeat protein. RNA-sequencing revealed fimbriae-related, flagella-related, and chemotaxis genes had increased expression in SX 245 compared to SX 244. Furthermore, SX 245 displayed higher invasion of human and bovine epithelial cells than SX 244. These data suggest that the presence and up-regulation of genes involved in type 1 fimbriae production, flagellar regulation and biogenesis, and chemotaxis may play a role in the increased pathogenicity and host range expansion of the Salmonella Heidelberg isolates involved in the bovine-related outbreak.

Curcumin and carvacrol mediated photodynamic inactivation with 405 nm light emitting diodes (LEDs) on Salmonella Enteritidis

Photodynamic inactivation (PDI) has a potential application for food preservation that can minimize food pathogens posing risks to consumer health. This study aimed to evaluate the antibacterial activity of 405 nm light-emitting diodes (LEDs) illumination in the presence of carvacrol and curcumin against Salmonella Enteritidis and S. Enteritidis PT4 at different temperatures (4 °C, 25 °C and 37 °C) and time parameters (15 min, 30 min and 45 min) in the illumination system. Compared to their individual treatment, the decrease in the bacterial population was stronger in bacteria treated with LEDs + carvacrol or LEDs + curcumin. Co-application of carvacrol or curcumin with LEDs at 37 °C showed strong antibacterial activity against both bacteria depending on the application time. Co-application at 37 °C for 45 min completely inhibited the growth of S. Enteritidis. LEDs, curcumin, carvacrol applications alone or LEDs + curcumin, LEDs + carvacrol applications caused a decrease in bacterial population in proportion to the increase in the storage temperature and application times. These results showed that carvacrol or curcumin potentiates LEDs illumination therapy against both bacteria. Future studies on adapting the PDI system to control bacteria in a variety of foods may help develop novel strategies to fight against foodborne bacterial pathogens.

Longitudinal Assessment of Prevalence and Incidence of Salmonella and Escherichia coli O157 Resistance to Antimicrobials in Feedlot Cattle Sourced and Finished in Two Different Regions of the United States

The objective was to investigate the influence of cattle origin and region of finishing on the prevalence of Salmonella, Escherichia coli O157:H7, and select antimicrobial resistance in E. coli populations. Yearling heifers (n = 190) were utilized in a 2 × 2 factorial arrangement. After determining fecal Salmonella prevalence, heifers were sorted into one of four treatments: heifers originating from South Dakota (SD) and finished in SD (SD-SD); heifers originating from SD and finished in Texas (SD-TX); heifers originating from TX and finished in SD (TX-SD); and heifers originating from TX and finished in TX (TX-TX). Fecal, pen, and water scum line samples were collected longitudinally throughout the study; hide swab and subiliac lymph node (SLN) samples were collected at study end. A treatment × time interaction was observed (p ≤ 0.01) for fecal Salmonella prevalence, with prevalence being greatest for TX-TX and TX-SD heifers before transport. From day (d) 14 through study end, prevalence was greatest for TX-TX and SD-TX heifers compared with SD-SD and TX-SD heifers. Salmonella prevalence on hides were greater (p ≤ 0.01) for heifers finished in TX compared with SD. Salmonella prevalence in SLN tended (p = 0.06) to be greater in TX-TX and SD-TX heifers compared with TX-SD and SD-SD. Fecal E. coli O157:H7 prevalence had a treatment × time interaction (p = 0.04), with SD-TX prevalence being greater than TX-SD on d 56 and SD-SD and TX-TX being intermediate. A treatment × time interaction was observed for fecal trimethoprim-sulfamethoxazole-resistant and cefotaxime-resistant E. coli O157:H7 prevalence (p ≤ 0.01). Overall, these data suggest that the region of finishing influences pathogenic bacterial shedding patterns, with the initial 14 d after feedlot arrival being critical for pathogen carriage.

From Eberthella typhi to Salmonella Typhi: The Fascinating Journey of the Virulence and Pathogenicity of Salmonella Typhi

Salmonella Typhi (S. Typhi), the invasive typhoidal serovar of Salmonella enterica that causes typhoid fever in humans, is a severe threat to global health. It is one of the major causes of high morbidity and mortality in developing countries. According to recent WHO estimates, approximately 11-21 million typhoid fever illnesses occur annually worldwide, accounting for 0.12-0.16 million deaths. Salmonella infection can spread to healthy individuals by the consumption of contaminated food and water. Typhoid fever in humans sometimes is accompanied by several other critical extraintestinal complications related to the central nervous system, cardiovascular system, pulmonary system, and hepatobiliary system. Salmonella Pathogenicity Island-1 and Salmonella Pathogenicity Island-2 are the two genomic segments containing genes encoding virulent factors that regulate its invasion and systemic pathogenesis. This Review aims to shed light on a comparative analysis of the virulence and pathogenesis of the typhoidal and nontyphoidal serovars of S. enterica.

Europium Nanoparticle-Based Lateral Flow Strip Biosensors Combined with Recombinase Polymerase Amplification for Simultaneous Detection of Five Zoonotic Foodborne Pathogens

The five recognized zoonotic foodborne pathogens, namely, Listeria monocytogenes, Staphylococcus aureus, Streptococcus suis, Salmonella enterica and Escherichia coli O157:H7, pose a major threat to global health and social-economic development. These pathogenic bacteria can cause human and animal diseases through foodborne transmission and environmental contamination. Rapid and sensitive detection for pathogens is particularly important for the effective prevention of zoonotic infections. In this study, rapid and visual europium nanoparticle (EuNP)-based lateral flow strip biosensors (LFSBs) combined with recombinase polymerase amplification (RPA) were developed for the simultaneous quantitative detection of five foodborne pathogenic bacteria. Multiple T lines were designed in a single test strip for increasing the detection throughput. After optimizing the key parameters, the single-tube amplified reaction was completed within 15 min at 37 °C. The fluorescent strip reader recorded the intensity signals from the lateral flow strip and converted the data into a T/C value for quantification measurement. The sensitivity of the quintuple RPA-EuNP-LFSBs reached a level of 10¹ CFU/mL. It also exhibited good specificity and there was no cross-reaction with 20 non-target pathogens. In artificial contamination experiments, the recovery rate of the quintuple RPA-EuNP-LFSBs was 90.6-101.6%, and the results were consistent with those of the culture method. In summary, the ultrasensitive bacterial LFSBs described in this study have the potential for widespread application in resource-poor areas. The study also provides insights in respect to multiple detection in the field.

Symbiotic bacteria stabilize the intestinal environment by producing phenylpropanoids

Salmonella enterica serovar Enteritidis (S. Enteritidis) can colonize in the intestinal tract of chickens and transmit to humans. In order to decrypt the mechanism of avian resistance to S. Enteritidis, we utilized two China local chicken breeds to generate the reciprocal crosses (the Cross and the Reverse-cross). The two lines of hybrids were orally inoculated with S. Enteritidis at 2-day old and sampled at 3 days post-inoculation. Along the analysis direction of multi-omics, differential metabolites, functional pathways and correlated microbes, we found that 12 species of microbes thrived upon S. Enteritidis challenge and probably contributed to the intestinal stability in the Cross by enhancing the production of phenylpropanoids. Our findings can help to understand the symbiotic and resistant mechanisms derived from the intestinal microbiota.

The World of Organoids: Gastrointestinal Disease Modelling in the Age of 3R and One Health with Specific Relevance to Dogs and Cats

One Health describes the importance of considering humans, animals, and the environment in health research. One Health and the 3R concept, i.e., the replacement, reduction, and refinement of animal experimentation, shape today’s research more and more. The development of organoids from many different organs and animals led to the development of highly sophisticated model systems trying to replace animal experiments. Organoids may be used for disease modelling in various ways elucidating the manifold host–pathogen interactions. This review provides an overview of disease modelling approaches using organoids of different kinds with a special focus on animal organoids and gastrointestinal diseases. We also provide an outlook on how the research field of organoids might develop in the coming years and what opportunities organoids hold for in-depth disease modelling and therapeutic interventions.

Genomic Characterization of Salmonella Typhimurium Isolated from Guinea Pigs with Salmonellosis in Lima, Peru

Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) is one of the most important foodborne pathogens that infect humans globally. The gastrointestinal tracts of animals like pigs, poultry or cattle are the main reservoirs of Salmonella serotypes. Guinea pig meat is an important protein source for Andean countries, but this animal is commonly infected by S. Typhimurium, producing high mortality rates and generating economic losses. Despite its impact on human health, food security, and economy, there is no genomic information about the S. Typhimurium responsible for the guinea pig infections in Peru. Here, we sequence and characterize 11 S. Typhimurium genomes isolated from guinea pigs from four farms in Lima-Peru. We were able to identify two genetic clusters (HC100_9460 and HC100_9757) distinguishable at the H100 level of the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing (HierCC-cgMLST) scheme with an average of 608 SNPs of distance. All sequences belonged to sequence type 19 (ST19) and HC100_9460 isolates were typed in silico as monophasic variants (1,4,[5],12:i:-) lacking the fljA and fljB genes. Phylogenomic analysis showed that human isolates from Peru were located within the same genetic clusters as guinea pig isolates, suggesting that these lineages can infect both hosts. We identified a genetic antimicrobial resistance cassette carrying the ant(3)-Ia, dfrA15, qacE, and sul1 genes associated with transposons TnAs3 and IS21 within an IncI1 plasmid in one guinea pig isolate, while antimicrobial resistance genes (ARGs) for β-lactam (blaCTX-M-65) and colistin (mcr-1) resistance were detected in Peruvian human-derived isolates. The presence of a virulence plasmid highly similar to the pSLT plasmid (LT2 reference strain) containing the spvRABCD operon was found in all guinea pig isolates. Finally, seven phage sequences (STGP_Φ1 to STGP_Φ7) were identified in guinea pig isolates, distributed according to the genetic lineage (H50 clusters level) and forming part of the specific gene content of each cluster. This study presents, for the first time, the genomic characteristics of S. Typhimurium isolated from guinea pigs in South America, showing particular diversity and genetic elements (plasmids and prophages) that require special attention and also broader studies in different periods of time and locations to determine their impact on human health.

Molecular Epidemiology and Virulence of Non-Typhoidal Salmonella in Armenia

In this work, we analysed human isolates of nontyphoidal Salmonella enterica subsp. enterica (NTS), which were collected from salmonellosis cases in Armenia from 1996 to 2019. This disease became a leading food-borne bacterial infection in the region, with the younger age groups especially affected. The isolates were characterised by serotyping, Enterobacterial Repetitive Intergenic Consensus (ERIC-PCR) typing, and whole genome sequencing (WGS). The main serotypes were S. Typhimurium, S. Enteritidis, and S. Arizonae. ERIC-PCR indicated a high degree of clonality among S. Typhimurium strains, which were also multidrug-resistant and produced extended spectrum beta-lactamases. During the study period, the frequency of S. Typhimurium and S. Arizonae isolations decreased, but with the increase in S. Enteritidis and other NTS. A total of 42 NTS isolates were subjected to WGS and explored for virulence-related traits and the corresponding genetic elements. Some virulence and genetic factors were shared by all NTS serotypes, while the main differences were attributed to the serotype-specific diversity of virulence genes, SPIs, virulence plasmids, and phages. The results indicated the variability and dynamics in the epidemiology of salmonellosis and a high virulence potential of human NTS isolates circulating in the region.

Differences between the global transcriptomes of Salmonella enterica serovars Dublin and Cerro infecting bovine epithelial cells

Background

The impact of S. enterica colonization in cattle is highly variable and often serovar-dependent. The aim of this study was to compare the global transcriptomes of highly pathogenic bovine-adapted S. enterica serovar Dublin and the less pathogenic, bovine-adapted, serovar Cerro during interactions with bovine epithelial cells, to identify genes that impact serovar-related outcomes of S. enterica infections in dairy animals.

Result

Bovine epithelial cells were infected with S. enterica strains from serovars Dublin and Cerro, and the bacterial RNA was extracted and sequenced. The total number of paired-end reads uniquely mapped to non-rRNA and non-tRNA genes in the reference genomes ranged between 12.1 M (Million) and 23.4 M (median: 15.7 M). In total, 360 differentially expressed genes (DEGs) were identified with at least two-fold differences in the transcript abundances between S. Dublin and S. Cerro (false discovery rate ≤ 5%). The highest number of DEGs (17.5%, 63 of 360 genes) between the two serovars were located on the genomic regions potentially associated with Salmonella Pathogenicity Islands (SPIs). DEGs potentially located in the SPI-regions that were upregulated (≥ 2-fold) in the S. Dublin compared with S. Cerro included: 37 SPI-1 genes encoding mostly Type 3 Secretion System (T3SS) apparatus and effectors; all of the six SPI-4 genes encoding type I secretion apparatus (siiABCDEF); T3SS effectors and chaperone (sopB, pipB, and sigE) located in SPI-5; type VI secretion system associated protein coding genes (sciJKNOR) located in SPI-6; and T3SS effector sopF in SPI-11. Additional major functional categories of DEGs included transcription regulators (n = 25), amino acid transport and metabolism (n = 20), carbohydrate transport and metabolism (n = 20), energy production and metabolism (n = 19), cell membrane biogenesis (n = 18), and coenzyme transport and metabolism (n = 15). DEGs were further mapped to the metabolic pathways listed in the KEGG database; most genes of the fatty acid β-oxidation pathway were upregulated/uniquely present in the S. Dublin strains compared with the S. Cerro strains.

Conclusions

This study identified S. enterica genes that may be responsible for symptomatic or asymptomatic infection and colonization of two bovine-adapted serovars in cattle.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08725-z.

Characterization of Salmonella enterica Contamination in Pork and Poultry Meat from São Paulo/Brazil: Serotypes, Genotypes and Antimicrobial Resistance Profiles

Salmonellosis is a zoonosis of major relevance to global public health. Here we present the assessment of Salmonella enterica contamination in pork and poultry meat sold at retail markets in São Paulo, Brazil. A total of 780 meat samples (386 poultry meat and 394 pork samples) were collected from 132 markets. From these, 57 samples (7.3%) were positive for S. enterica isolation, including 32 (8.3%) poultry meat and 25 (6.3%) pork samples. S. enterica isolates were further characterized for serotyping, antimicrobial resistance and genotyping by amplified fragment length polymorphism and pulsed field gel electrophoresis. Antimicrobial resistance analysis demonstrated two main profiles: pork isolates were more resistant to macrolides, β-lactams, tetracycline, phenicols, and fluoroquinolones, and poultry meat isolates presented higher resistance to fluoroquinolones, sulfonamides, tetracycline, and β-lactams. A total of 72.4% of poultry meat isolates were identified as S. Heidelberg, while most of pork isolates were S. Typhimurium (31.7%) and S. Give (16.7%). Genotyping resulted in most clusters consisting exclusively of pork or poultry meat, no cross-contamination was detected, and a tendency to differentiate isolates according to their serotypes and markets of origin. High resistance rates to critically important antimicrobials reinforce the importance of controlling Salmonella contamination in meat production chains.

Salmonella Typhimurium and inflammation: a pathogen-centric affair

Microbial infections are controlled by host inflammatory responses that are initiated by innate immune receptors after recognition of conserved microbial products. As inflammation can also lead to disease, tissues that are exposed to microbial products such as the intestinal epithelium are subject to stringent regulatory mechanisms to prevent indiscriminate signalling through innate immune receptors. The enteric pathogen Salmonella enterica subsp. enterica serovar Typhimurium, which requires intestinal inflammation to sustain its replication in the intestinal tract, uses effector proteins of its type III secretion systems to trigger an inflammatory response without the engagement of innate immune receptors. Furthermore, S. Typhimurium uses a different set of effectors to restrict the inflammatory response to preserve host homeostasis. The S. Typhimurium-host interface is a remarkable example of the unique balance that emerges from the co-evolution of a pathogen and its host.

Salmonella in Swine: Prevalence, Multidrug Resistance, and Vaccination Strategies

An estimated 1.3 million Salmonella infections and 420 deaths occur annually in the United States, with an estimated economic burden of $3.7 billion. More than 50% of US swine operations test positive for Salmonella according to the National Animal Health Monitoring System, and 20% of Salmonella from swine are multidrug resistant (resistant to ≥3 antimicrobial classes) as reported by the National Antimicrobial Resistance Monitoring System. This review on Salmonella in swine addresses the current status of these topics by discussing antimicrobial resistance and metal tolerance in Salmonella and the contribution of horizontal gene transfer. A major challenge in controlling Salmonella is that Salmonella is a foodborne pathogen in humans but is often a commensal in food animals and thereby establishes an asymptomatic reservoir state in such animals, including swine. As food animal production systems continue to expand and antimicrobial usage becomes more limited, the need for Salmonella interventions has intensified. A promising mitigation strategy is vaccination against Salmonella in swine to limit animal, environmental, and food contamination. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Trend of Salmonella enterica occurrence and serotypes in Sardinian pig slaughterhouses

The aim of this study was to evaluate Salmonella prevalence and serotypes in four Sardinian pig slaughterhouses. Moreover, a population study was conducted with pulsed field gel electrophoresis (PFGE). The results were compared with previous investigations carried out during years 2008 and 2014. A total of 147 samples were collected, 117 from slaughtered pigs (lymph nodes, colon content and carcass surface) and 30 from the slaughterhouse environment (surfaces in contact and not in contact with meat). Salmonella was isolated from 3.4% pig samples and was not detected from environmental samples. Comparing the results with those of previous investigations, occurrence showed a sharp decrease through the years in both animals (18.8% in 2008, 10% in 2014 and 3.4% in 2020) and environmental samples (34.1% in 2008, 3.7 in 2014, and 0% in 2020). At the same time, prevalence of carriers (pigs positive at lymph nodes and/or colon content level) showed a reduction through the years and was always lower in animals coming from local farms rather than those coming from other European Member States, probably indicating the role of stressful factors as transport in increasing Salmonella susceptibility and shedding. Salmonella serotypes were monophasic Typhimurium, Rissen and Muenchen. Overall, 13 different Salmonella serotypes were identified during the three surveys with the most prevalent being serotypes often isolated from slaughtered pigs and during human salmonellosis cases: S. Derby and S. Typhimurium in 2008, S. Anatum and S. Rissen in 2014, monophasic S. Typhimurium in 2020. Population study with pulsed field gel electrophoresis showed a high similarity between Salmonella strains belonging to the same serotype. The results of the investigations showed a decrease of Salmonella occurrence during twelve years in Sardinia, probably due to the improvement in the application of correct GMPs and GHPs at slaughterhouse and also to a reduction of the rate of carrier pigs at farm level.

Genomic signatures of adaptation to natural settings in non-typhoidal Salmonella enterica Serovars Saintpaul, Thompson and Weltevreden

Salmonella enterica is a pathogenic bacterium responsible for intestinal illness and systemic diseases such as typhoid and paratyphoid fevers. Among clinical manifestation classification, non-typhoidal Salmonella is mainly known as foodborne pathogen associated with the consumption of fecal contaminated food and water. Even though Salmonella hosts include humans and warm-blooded animals, it has been found in non-host environments as river water where the bacteria use different strategies to fitness the environment persisting and establishment. Now with the availability of WGS and bioinformatics tools, we can explore bacterial genomes with higher resolution to increase our understanding of specific genetic signatures among environmental and clinical isolates, being the goal of this work. Pangenome construction allowed the detection of specific environmental and clinical gene clusters related to metabolism and secretion systems as the main signature respectively. Specifically, D-galactonate degradation pathway was observed mainly in environmental genomes while T3SS and flagellum genes were detected for all clinical but not for all environmental isolates. Gene duplication and pseudogenes accumulation were detected as the main adaptation strategy for environmental isolates; thus, isolation source may play an important role in genome plasticity, conferring a selective advantage to survive and persist for environmental Salmonella isolates. Intact prophage sequences with cargo genes were observable for both isolation sources playing an important role in virulence contribution.

Distribution and Antibiotic Resistance Profiles of Salmonella enterica in Rural Areas of North Carolina After Hurricane Florence in 2018

In this study, water samples were analyzed from a rural area of North Carolina after Hurricane Florence in 2018 and the distribution of the ttrC virulence gene of Salmonella enterica were investigated. We also examined the distribution of culturable S. enterica and determined their antibiotic resistance profiles. Antibiotic resistance genes (ARGs) in the classes of aminoglycoside, beta-lactam, and macrolide-lincosamide-streptogramin B (MLSB) were targeted in this study. The ttrC gene was detected in 23 out of 25 locations. There was a wider and higher range of the ttrC gene in flooded water versus unflooded water samples (0-2.12 × 105 copies/L vs. 0-4.86 × 104 copies/L). Culturable S. enterica was isolated from 10 of 25 sampling locations, which was less prevalent than the distribution of the ttrC gene. The antibiotic resistance profiles were not distinct among the S. enterica isolates. The aminoglycoside resistance gene aac(6')-Iy had the highest relative abundance (around 0.05 copies/16S rRNA gene copy in all isolates) among all ARGs. These findings suggested that the 2018 flooding event led to higher copy numbers of the ttrC genes of S. enterica in some flooded water bodies compared to those in unflooded water bodies. The high ARG level and similar ARG profiles were observed in all S. enterica isolates from both flooded and unflooded samples, suggesting that the antibiotic resistance was prevalent in S. enterica within this region, regardless of flooding.

Bacteriophage as an alternative to prevent reptile-associated Salmonella transmission

Salmonellosis is a major global public health issue; its most common infection, gastroenteritis, accounts for approximately 90 million illnesses and 150,000 mortalities per year. Eradicating salmonellosis requires surveillance, prevention and treatment, entailing large expenditures. However, it is difficult to control Salmonella transmission because it occurs via multiple routes; exotic reptiles are a reservoir of Salmonella and comprise one such route. As the popularity of exotic pets and animal exhibition has increased, human encounters with reptiles have also increased. As a result, reptile-associated salmonellosis (RAS) has been recognized as an emerging disease. The development of antimicrobial resistance in RAS-causing Salmonella sp. requires alternatives to antibiotics. In this study, bacteriophages have been established as an alternative to antibiotics because only target bacteria are lysed; thus, they are promising biocontrol agents. Here, bacteriophage pSal-SNUABM-02, which infects and lyses reptile Salmonella isolates, was isolated and characterized. The morphology, host range, growth traits and stability of the phage were investigated. The phage was assigned to Myoviridae and was stable in the following conditions: pH 5-9, 4-37°C, and ultravioletA/ultravioletB (UVA/UVB) exposure. Salmonella clearance efficacy was tested using planktonic cell lysis activity and biofilm degradation on polystyrene 96-well plates and reptile skin fragments. The phage exhibited vigorous lysis activity against planktonic cells. In in vitro biofilm degradation tests on reptile skin and polystyrene plates, both low- and high-concentration phage treatments lowered bacterial cell viability by approximately 2.5-3 log colony-forming units and also decreased biomass. Thus, bacteriophages are a promising alternative to antibiotics for the prevention and eradication of RAS.

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.

Identification of Natural Mutations Responsible for Altered Infection Phenotypes of Salmonella enterica Clinical Isolates by Using Cell Line Infection Screens

The initial steps of Salmonella pathogenesis involve adhesion to and invasion into host epithelial cells. While well-studied for Salmonella enterica serovar Typhimurium, the factors contributing to this process in other, host-adapted serovars remains unexplored. Here, we screened clinical isolates of serovars Gallinarum, Dublin, Choleraesuis, Typhimurium, and Enteritidis for adhesion to and invasion into intestinal epithelial cell lines of human, porcine, and chicken origins. Thirty isolates with altered infectivity were used for genomic analyses, and 14 genes and novel mutations associated with high or low infectivity were identified. The functions of candidate genes included virulence gene expression regulation and cell wall or membrane synthesis and components. The role of several of these genes in Salmonella adhesion to and invasion into cells has not previously been investigated. The genes dksA (encoding a stringent response regulator) and sanA (encoding a vancomycin high-temperature exclusion protein) were selected for further analyses, and we confirmed their roles in adhesion to and invasion into host cells. Furthermore, transcriptomic analyses were performed for S Enteritidis and S Typhimurium, with two highly infective and two marginally infective isolates for each serovar. Expression profiles for the isolates with altered infection phenotypes revealed the importance of type 3 secretion system expression levels in the determination of an isolate's infection phenotype. Taken together, these data indicate a new role in cell host infection for genes or gene variants previously not associated with adhesion to and invasion into the epithelial cells.IMPORTANCESalmonella is a foodborne pathogen affecting over 200 million people and resulting in over 200,000 fatal cases per year. Its adhesion to and invasion into intestinal epithelial cells represent one of the first and key steps in the pathogenesis of salmonellosis. Still, around 35 to 40% of bacterial genes have no experimentally validated function, and their contribution to bacterial virulence, including adhesion and invasion, remains largely unknown. Therefore, the significance of this study is in the identification of new genes or gene allelic variants previously not associated with adhesion and invasion. It is well established that blocking adhesion and/or invasion would stop or hamper bacterial infection; therefore, the new findings from this study could be used in future developments of anti-Salmonella therapy targeting genes involved in these key processes. Such treatment could be a valuable alternative, as the prevalence of antibiotic-resistant bacteria is increasing very rapidly.

Molecular Screening of Salmonella sp. from fecal sample of Sparrows (Passer domesticus) in Yogyakarta, Indonesia

Wild birds is one of the reservoir agent of some of various zoonotic diseases. The study was aim to see the potential of sparrow as the reservoir agent of Salmonella sp. using polymerase chain reaction (PCR) method. We detected the invA gene of Salmonella sp. from faecal sample of sparrows (Passer domesticus) in local area of Yogyakarta, Indonesia. A total of 30 faecal dropping samples were collected from sparrows. DNA was extracted from the faecal samples, then amplified by PCR for the target genes. The amplicons were electrophorized to see the visualization of DNA on the agarose gel. The result showed the prevalence of the positive result of Salmonella sp. was 3,3%. The study indicated that sparrows can spread zoonotic pathogens and this necessitates monitoring for the epidemiologic status of these pathogens among birds, also applying the appropriate intervention measures to prevent the transmission of zoonotic diseasesfrom birds to humans.

Transcriptional response of blood leukocytes from turkeys challenged with Salmonella enterica serovar Typhimurium UK1

Non-typhoidal Salmonella is one of the most common causes of bacterial foodborne disease and consumption of contaminated poultry products, including turkey, is one source of exposure. Minimizing Salmonella colonization of commercial turkeys could decrease the incidence of Salmonella-associated human foodborne illness. Understanding host responses to these bacteria is critical in developing strategies to minimize colonization and reduce food safety risk. In this study, we evaluated bacterial load and blood leukocyte transcriptomic responses of 3-week-old turkeys challenged with the Salmonella enterica serovar Typhimurium (S. Typhimurium) UK1 strain. Turkeys (n = 8/dose) were inoculated by oral gavage with 10⁸ or 10¹⁰ colony forming units (CFU) of S. Typhimurium UK1, and fecal shedding and tissue colonization were measured across multiple days post-inoculation (dpi). Fecal shedding was 1-2 log₁₀ higher in the 10¹⁰ CFU group than the 10⁸ CFU group, but both doses effectively colonized the crop, spleen, ileum, cecum, colon, bursa of Fabricius and cloaca without causing any detectable clinical signs in either group of birds. Blood leukocytes were isolated from a subset of the birds (n = 3-4/dpi) both pre-inoculation (0 dpi) and 2 dpi with 10¹⁰ CFU and their transcriptomic responses assayed by RNA-sequencing (RNA-seq). At 2 dpi, 647 genes had significant differential expression (DE), including large increases in expression of immune genes such as CCAH221, IL4I1, LYZ, IL13RA2, IL22RA2, and ACOD1. IL1β was predicted as a major regulator of DE in the leukocytes, which was predicted to activate cell migration, phagocytosis and proliferation, and to impact the STAT3 and toll-like receptor pathways. These analyses revealed genes and pathways by which turkey blood leukocytes responded to the pathogen and can provide potential targets for developing intervention strategies or diagnostic assays to mitigate S. Typhimurium colonization in turkeys.

Antimicrobial resistance and molecular characterization of Salmonella enterica serovar Corvallis isolated from human patients and animal source foods in China

In this study, 205 Salmonella enterica serovar Corvallis strains were obtained from humans and foods from Guangdong, Guangxi, and Shanghai in China from 2009 to 2017 to assess drug resistance and molecular epidemiology. These isolates displayed high rates of resistance to sulfisoxazole (94.15%) and tetracycline (77.56%). Surprisingly, the rate of resistance to ciprofloxacin reached 21.46%. Moreover, 63.9% of the strains displayed multidrug resistance. Detection of quinolone genes showed that 97.56% of the strains had single mutations (T57S) in parC. The plasmid-mediated quinolone resistance (PMQR) genes qnrS, aac(6')-Ib-cr, and qnrB, were also detected. The extended spectrum β-lactamase (ESBLS) gene that was most common among the isolates was bla_TEM-1 (18.05%). These S. Corvallis isolates are the first to date, that have been reported to possess bla_CTX-M-55 or bla_NDM-5. Additionally, 95.61% of isolates were biofilm producers. The streptomycin resistance rate was higher in strong biofilm producers (87.50%) than in moderate (37.93%) and weak (26.49%) biofilm producers. Pulsed-field gel electrophoresis (PFGE) showed that some strains from different sources had the same genotype. These isolates may be transmitted to humans through food and therefore the monitoring of these isolates should be strengthened in China.

Molecular characterization of antimicrobial resistance and enterobacterial repetitive intergenic consensus-PCR as a molecular typing tool for Salmonella spp. isolated from poultry and humans

Background and Aim:

Salmonella spp. are one of the most important food-borne pathogens in the world, emerging as a major public health concern. Moreover, multidrug-resistant (MDR) strains have been isolated from salmonellosis outbreaks, which compromise its treatment success. This study was conducted to characterize the phenotypic and genotypic antibiotic resistance profile of Salmonella strains isolated from broilers and humans from the regions of Tolima and Santander (Colombia).

Materials and Methods:

Salmonella spp. strains (n=49) were confirmed through molecular detection by amplification of the invA gene. Phenotypic antibiotic resistance was determined by the automated method and the agar diffusion method, and the presence of resistance genes was evaluated by PCR. Genotypic characterization was conducted using the enterobacterial repetitive intergenic consensus (ERIC)-PCR method, from which a dendrogram was generated and the possible phylogenetic relationships were established.

Results:

Salmonella isolates were classified as MDR strains exhibiting resistance to four antibiotic classes, penicillins, aminoglycosides, sulfonamides, and cephalosporins, and the human strains were resistant to gentamicin. At the genotypic level, the isolates contained the genes bla_CMY2, bla_CTX-M, bla_PSE-1, bla_TEM, aadA1, srtB, dfrA1, sul2, and floR. The genotyping results obtained by ERIC-PCR allowed the grouping of strains according to the source of isolation.

Conclusion:

The Salmonella spp. strains exhibited resistance to multiple antibiotics, as well as multiple genes associated with them, and the ERIC-PCR method was a technique that was helpful in generating clusters with biological significance.

Comparative Genomic Analysis of 450 Strains of Salmonella enterica Isolated from Diseased Animals

Salmonella is a leading cause of bacterial infections in animals and humans. We sequenced a collection of 450 Salmonella strains from diseased animals to better understand the genetic makeup of their virulence and resistance features. The presence of Salmonella pathogenicity islands (SPIs) varied by serotype. S. Enteritidis carried the most SPIs (n = 15), while S. Mbandaka, S. Cerro, S. Meleagridis, and S. Havana carried the least (n = 10). S. Typhimurium, S. Choleraesuis, S. I 4,5,12:i:-, and S. Enteritidis each contained the spv operon on IncFII or IncFII-IncFIB hybrid plasmids. Two S. IIIa carried a spv operon with spvD deletion on the chromosome. Twelve plasmid types including 24 hybrid plasmids were identified. IncA/C was frequently associated with S. Newport (83%) and S. Agona (100%) from bovine, whereas IncFII (100%), IncFIB (100%), and IncQ1 (94%) were seen in S. Choleraesuis from swine. IncX (100%) was detected in all S. Kentucky from chicken. A total of 60 antimicrobial resistance genes (ARGs), four disinfectant resistances genes (DRGs) and 33 heavy metal resistance genes (HMRGs) were identified. The Salmonella strains from sick animals contained various SPIs, resistance genes and plasmid types based on the serotype and source of the isolates. Such complicated genomic structures shed light on the strain characteristics contributing to the severity of disease and treatment failures in Salmonella infections, including those causing illnesses in animals.

Development of Salmonella Enteritidis vaccine candidate based on streptomycin independent suppressor and metabolic drift rifampicin resistance-attenuating markers

Salmonella is one of the most frequent food-borne pathogens and remains public health threat globally. The control of Salmonella in poultry, the main reservoir of non-typhoidal salmonellae, is a fundamental approach to ensure the safety of poultry products for human consumption. In the present study, a new live attenuated Salmonella enterica serovar Enteritidis vaccine candidate containing three attenuating markers based on streptomycin-independent (Sm-id) suppressor, and metabolic drift antibiotic resistance (MD- “res”) was developed. The streptomycin dependent (Smd) mutants were derived from Salmonella Enteritidis wild-type strain using streptomycin. Then the Sm-id mutants were derived from the isolated Smd mutants and designated “Smd→Sm-id”. A third MD- “res” marker was generated from Smd→Sm-id using rifampicin (Rif) and designated “Smd→Sm-id→Rif”. The colony sizes of these mutants were stable after more than 50 serial passages on blood agar; reversion to virulence can be almost excluded. The safety and efficacy of Smd→Sm-id and Smd→Sm-id→Rif were evaluated in one-day-old commercial layer chicks. Both mutants proved to be safe in terms of clinical signs, mortalities, lesion scores of visceral organs and rapid clearance when administered orally at a dose of 10⁸ colony forming unit (CFU), whereas birds inoculated with 10⁸ CFU Salmonella Enteritidis wild-type strain showed diarrhea, mortalities (3/40) and necrosis in liver and spleen. Chickens vaccinated with the developed mutants showed no seroconversion; however, wild-type strain induced a significant seroconversion at 3-week-postvaccination (wpv). The developed mutants protected chickens against challenge with 10⁸ CFU of Salmonella Enteritidis wild-type strain at 3-wpv. Vaccinated birds showed neither clinical signs nor mortalities during two-week post-challenge. In addition, the challenge strain could not be detected in pooled liver and spleen samples (0/5) at 7^th day post-inoculation (dpi). However, non-vaccinated challenged birds showed diarrhea and the challenge strain was re-isolated from pooled liver and spleen samples (3/5) at 7^th dpi. In conclusion, the developed mutants are safe and fully protected immunized chickens following heterologous challenge. It is obvious that the genetic characterization of these mutants and evaluation of different vaccination regimes are still in demand.

Emerging Meat Processing Technologies for Microbiological Safety of Meat and Meat Products

A consumer trend toward convenient, minimally processed meat products has exerted tremendous pressure on meat processors to ensure the safety of meat and meat products without compromising product quality and the meeting of consumer demands. This has led to challenges in developing and implementing novel processing technologies as the use of newer technologies may affect consumer choices and opinions of meat and meat products. Novel technologies adopted by the meat industry for controlling foodborne pathogens of significant public health implications, gaps in the technologies, and the need for scaling up technologies that have been proven to be successful in research settings or at the pilot scale will be discussed. Novel processing technologies in the meat industry warrant microbiological validation prior to becoming commercially viable options and enacting infrastructural changes. This review presents the advantages and shortcomings of such technologies and provides an overview of technologies that can be successfully implemented and streamlined in existing processing environments.

Translocation of Orally Inoculated Salmonella Following Mild Immunosuppression in Holstein Calves and the Presence of the Salmonella in Ground Beef Samples

The objective of this study was to determine if immunosuppression through daily dexamethasone (DEX) infusion altered Salmonella translocation from the gastrointestinal tract. Weaned Holstein steers (n = 20; body weight [BW] = 102 ± 2.7 kg) received DEX (n = 10; 0.5 mg/kg BW) or saline (control [CON]; n = 10;) for 4 days (from day -1 to 2) before oral inoculation of naldixic acid-resistant Salmonella enterica Typhimurium (SAL; 3.4 × 10⁶ colony-forming units [CFU]/animal) on day 0. Fecal swabs were obtained daily, and blood was collected daily for hematology. At harvest (day 5), ileum, cecal fluid, lymph nodes (ileocecal, mandibular, popliteal, and subscapular), and synovial (stifle, coxofemoral, and shoulder) samples were collected for isolation of the inoculated strain of SAL. White blood cell (WBC) and neutrophil concentrations were elevated (p < 0.01) in DEX calves following each administration event. Following inoculation, 100% of DEX calves shed the experimental strain of SAL for all 5 days, 90% of CON calves shed from day 1 to 3, and 100% of CON calves shed from day 4 to 5. Greater (p < 0.01) concentrations of SAL were quantified from the cecum of DEX calves (3.86 ± 0.37 log CFU/g) compared with CON calves (1.37 ± 0.37 log CFU/g). There was no difference in SAL concentrations between DEX and CON calves in ileal tissue (p = 0.07) or ileocecal (p = 0.57), mandibular (p = 0.12), popliteal (p = 0.99), or subscapular (p = 0.83) lymph nodes. Of the stifle samples collected, 3.3% were positive for SAL, highlighting a contamination opportunity during hindquarter breakdown. While more research is needed to elucidate the interactions of immunosuppression and pathogen migration patterns, these data confirm that orally inoculated SAL can translocate from the gastrointestinal tract and be harbored in atypical locations representing a food safety risk.

IPEC-1 variable immune response to different serovars of Salmonella enterica subsp. enterica

Salmonella is a genus of Gram-negative bacteria in the Enterobacteriaceae family causing various illnesses. The ability of the different serovars of Salmonella enterica subsp. enterica to infect a host and to induce pathology relies in part on their cellular and molecular interactions with the intestinal epithelium. In the current study, an in vitro approach using non-polarized or polarized IPEC-1 porcine intestinal epithelial cells were used in order to assess the relation between adhesion, invasion, and induction of the immune response as a function of the serotype of Salmonella. Five serovars, Choleraesuis (host-adapted), Typhimurium (ubiquitous), Typhisuis (host-restricted), which are relevant for pig infection, and Dublin and Gallinarum, which are host-restricted or host-adapted, were studied. A strong variation was observed in the percentages of adhesion and invasion amongst the S. enterica serovars used to interact with the non-polarized and polarized cells. Subsequently, differences were identified between serovars in terms of immune response induced. Serovars Typhimurium and Typhisuis induced a strong innate immune response four and half hours after the beginning of cell stimulation while Choleraesuis, Gallinarum, and Dublin did not. A strong inflammatory response could limit the spread of the porcine serovars to the gut while, with a weak response, bacteria may not be constrained by the immune response enabling severe systemic diseases. Different repertoires of adhesion factors and of secreted protein effectors between Salmonella serovars interacting with IPEC-1 cells probably explains the differences in their early pathogenic behaviours.

Complete Genome Sequence of Multidrug-Resistant Salmonella enterica Serovar I 4,[5],12:i:- 2015 U.S. Pork Outbreak Isolate USDA15WA-1

The genome of a multidrug-resistant (MDR) Salmonella enterica subsp. enterica serovar I 4,[5],12:i:- isolate from the 2015 U.S. pork outbreak was sequenced. The complete nucleotide sequence of USDA15WA-1 is 5,031,277 bp, including Salmonella genomic island 4 encoding tolerance to multiple metals and an MDR module inserted in the fljB region.

Sources of human infection by Salmonella enterica serotype Javiana: A systematic review

Non-typhoidal Salmonella (NTS) infection is one of the major causes of diarrheal disease throughout the world. In recent years, an increase in human S. Javiana infection has been reported from the southern part of the United States. However, the sources and routes of transmission of this Salmonella serotype are not well understood. The objective of this study was to perform a systematic review of the literature to identify risk factors for human S. Javiana infection. Using PRISMA guidelines, we conducted a systematic search in Web of Science, PubMed, and the Morbidity and Mortality Weekly Report (MMWR). Searches returned 63 potential articles, of which 12 articles met all eligibility criteria and were included in this review. A review of the literature indicated that both food and non-food (such as animal contact) exposures are responsible for the transmission of S. Javiana infection to humans. Consumption of fresh produce (tomatoes and watermelons), herbs (paprika-spice), dairy products (cheese), drinking contaminated well water and animal contact were associated with human S. Javiana infections. Based on the findings of this study, control of human S. Javiana infection should include three factors, (a) consumption of drinking water after treatment, (b) safe animal contact, and (c) safe food processing and handling procedures. The risk factors of S. Javiana infections identified in the current study provide helpful insight into the major vehicles of transmission of S. Javiana. Eventually, this will help to improve the risk management of this Salmonella serotype to reduce the overall burden of NTS infection in humans.

Global disease burden of pathogens in animal source foods, 2010

Animal source foods (ASF) such as dairy, eggs, fish and meat are an important source of high-quality nutrients. Lack of ASF in diets can result in developmental disorders including stunting, anemia, poor cognitive and motor development. ASF are more effective in preventing stunting than other foods and promoting ASF consumption in low- and middle-income countries could help improve health, particularly among pregnant women and young children. Production and consumption of ASF are, however, also associated with potential food safety risks. Strengthening of food control systems, informed by quantitative assessments of the disease burden associated with ASF is necessary to meet global nutrition goals. We present the human disease burden associated with 13 pathogens (bacteria and parasites) in ASF, based on an analysis of global burden of foodborne disease (FBD) estimates of the WHO Foodborne Disease Burden Epidemiology Reference Group (FERG). The FBD burden of these pathogens was combined with estimates of the proportion of disease transmitted by eight main groups of ASF. Uncertainty in all estimates was accounted for by Monte Carlo simulation. In 2010, the global burden of ASF was 168 (95% uncertainty interval (UI 137-219) Disability Adjusted Life Years (DALYs) per 100,000 population, which is approximately 35% of the estimated total burden of FBD. Main pathogens contributing to this burden included non-typhoidal Salmonella enterica, Taenia solium, and Campylobacter spp. The proportion of FBD burden associated with ASF varied considerably between subregions and between countries within subregions. Likewise, the contribution of different pathogens and ASF groups varied strongly between subregions. Pathogens with a localized distribution included T. solium and fishborne trematodes. Pathogens with a global distribution included non-typhoidal S. enterica, Campylobacter spp., Toxoplasma gondii, and Mycobacterium bovis. Control methods exist for many hazards associated with ASF, and their implementation is linked to economic development and effective food safety systems.

A review of Salmonella enterica with particular focus on the pathogenicity and virulence factors, host specificity and antimicrobial resistance including multidrug resistance

Salmonella genus represents the most common foodborne pathogens frequently isolated from food-producing animals that is responsible for zoonotic infections in humans and animal species including birds. Thus, Salmonella infections represent a major concern to public health, animals, and food industry worldwide. Salmonella enterica represents the most pathogenic specie and includes > 2600 serovars characterized thus far. Salmonella can be transmitted to humans along the farm-to-fork continuum, commonly through contaminated foods of animal origin, namely poultry and poultry-related products (eggs), pork, fish etc. Some Salmonella serovars are restricted to one specific host commonly referred to as "host-restricted" whereas others have broad host spectrum known as "host-adapted" serovars. For Salmonella to colonize its hosts through invading, attaching, and bypassing the host's intestinal defense mechanisms such as the gastric acid, many virulence markers and determinants have been demonstrated to play crucial role in its pathogenesis; and these factors included flagella, capsule, plasmids, adhesion systems, and type 3 secretion systems encoded on the Salmonella pathogenicity island (SPI)-1 and SPI-2, and other SPIs. The epidemiologically important non-typhoidal Salmonella (NTS) serovars linked with a high burden of foodborne Salmonella outbreaks in humans worldwide included Typhimurium, Enteritidis, Heidelberg, and Newport. The increased number of NTS cases reported through surveillance in recent years from the United States, Europe and low- and middle-income countries of the world suggested that the control programs targeted at reducing the contamination of food animals along the food chain have largely not been successful. Furthermore, the emergence of several clones of Salmonella resistant to multiple antimicrobials worldwide underscores a significant food safety hazard. In this review, we discussed on the historical background, nomenclature and taxonomy, morphological features, physical and biochemical characteristics of NTS with a particular focus on the pathogenicity and virulence factors, host specificity, transmission, and antimicrobial resistance including multidrug resistance and its surveillance.

Persistent Infection and Long-Term Carriage of Typhoidal and Nontyphoidal Salmonellae

The ability of pathogenic bacteria to affect higher organisms and cause disease is one of the most dramatic properties of microorganisms. Some pathogens can establish transient colonization only, but others are capable of infecting their host for many years or even for a lifetime. Long-term infection is called persistence, and this phenotype is fundamental for the biology of important human pathogens, including Helicobacter pylori, Mycobacterium tuberculosis, and Salmonella enterica Both typhoidal and nontyphoidal serovars of the species Salmonella enterica can cause persistent infection in humans; however, as these two Salmonella groups cause clinically distinct diseases, the characteristics of their persistent infections in humans differ significantly. Here, following a general summary of Salmonella pathogenicity, host specificity, epidemiology, and laboratory diagnosis, I review the current knowledge about Salmonella persistence and discuss the relevant epidemiology of persistence (including carrier rate, duration of shedding, and host and pathogen risk factors), the host response to Salmonella persistence, Salmonella genes involved in this lifestyle, as well as genetic and phenotypic changes acquired during prolonged infection within the host. Additionally, I highlight differences between the persistence of typhoidal and nontyphoidal Salmonella strains in humans and summarize the current gaps and limitations in our understanding, diagnosis, and curing of persistent Salmonella infections.

High-levels of resistance to quinolone and cephalosporin antibiotics in MDR-ACSSuT Salmonella enterica serovar Enteritidis mainly isolated from patients and foods in Shanghai, China

In this study, 2887 Salmonella strains were mainly obtained from patients and foods in Shanghai from 2006 to 2014 in order to assess the susceptibility to 16 antibiotics. Among them, 3.8% (110/2887) S. Enteritidis isolates were shown to have an ACSSuT (ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline) resistance pattern. The resistance genes of ACSSuT included sul2 (74.55%), flo (67.27%), tetA (49.09%), and aph(3)-IIa (46.36%). In addition, class 1 integron profiles were detected in 9 isolates, and 55.6% (5/9) were shown to carry resistant genes against aminoglycosides and sulfonamides. Moreover, these isolates had a high rate of resistance to nalidixic acid (95.29%), cefotaxime (70.64%), cefepime (58.72%), and ceftazidime (48.62%). Detection of quinolone genes showed that 93.64% (103/110) of the strains had gyrA single mutations (D87G, D87Y, D87N, S83Y, and S83F), where D87G was the dominant mutation in 55.45% isolates. 19.1% (21/110) isolates carried plasmid-mediated quinolone resistance (PMQR) genes (qnrB and aac(6')-Ib-cr), and the most prevalent was qnrB. Furthermore, we also detected ESBLS genes. The most common were bla_CTX-M-55 (57.27%) followed by bla_TEM (23.6%) and bla_OXY (4.55%). Mart, prot6E, steB, fimA, and sopE2 genes (100%) were the most in these isolates. The strains in the dominant PFGE profiles of G1 were all co-resistant to quinolones, cephalosporins, and ACSSuT, and were isolated from different sources. This suggests that existence of these genes lead to the emergence of high-levels of resistance to quinolone and cephalosporin in these ACSSuT resistance pattern isolates. And these isolates are transmitted between humans and food.

Adhesion of Salmonella to Pancreatic Secretory Granule Membrane Major Glycoprotein GP2 of Human and Porcine Origin Depends on FimH Sequence Variation

Bacterial host tropism is a primary determinant of the range of host organisms they can infect. Salmonella serotypes are differentiated into host-restricted and host-adapted specialists, and host-unrestricted generalists. In order to elucidate the underlying molecular mechanisms of host specificity in Salmonella infection, we investigated the role of the intestinal host cell receptor zymogen granule membrane glycoprotein 2 (GP2), which is recognized by FimH adhesin of type 1 fimbriae found in Enterobacteriaceae. We compared four human and two porcine GP2 isoforms. Isoforms were expressed in Sf9 cells as well as in one human (HEp-2) and one porcine (IPEC-J2) cell line. FimH genes of 128 Salmonella isolates were sequenced and the 10 identified FimH variants were compared regarding adhesion (static adhesion assay) and infection (cell line assay) using an isogenic model. We expressed and characterized two functional porcine GP2 isoforms differing in their amino acid sequence to human isoforms by approximately 25%. By comparing all isoforms in the static adhesion assay, FimH variants were assigned to high, low or no-binding phenotypes. This FimH variant-dependent binding was neither specific for one GP2 isoform nor for GP2 in general. However, cell line infection assays revealed fundamental differences: using HEp-2 cells, infection was also FimH variant-specific but mainly independent of human GP2. In contrast, this FimH variant dependency was not obvious using IPEC-J2 cells. Here, we propose an alternative GP2 adhesion/infection mechanism whereby porcine GP2 is not a receptor that determined host-specificity of Salmonella. Salmonella specialists as well as generalists demonstrated similar binding to GP2. Future studies should focus on spatial distribution of GP2 isoforms in the human and porcine intestine, especially comparing health and disease.

Porcine Response to a Multidrug-Resistant Salmonella enterica serovar I 4,[5],12:i:- Outbreak Isolate

Salmonella enterica serovar I 4,[5],12:i:- has emerged as a common nontyphoidal Salmonella serovar to cause human foodborne illness. An interesting trait of serovar I 4,[5],12:i:- is that it only expresses the fliC gene for bacterial motility (i.e., monophasic), while most Salmonella strains alternately express two flagellin genes (fliC and fljB). The goal of this study was to characterize the porcine response following inoculation with a multidrug-resistant (MDR) serovar I 4,[5],12:i:- isolate associated with a multistate pork outbreak to determine if the increased prevalence of serovar I 4,[5],12:i:- in swine is due to enhanced pathogenicity. Pigs were inoculated and subsequently evaluated for the ability of the isolate to colonize intestinal tissues, cause clinical symptoms, induce an immune response, and alter the fecal microbiota over a 7-day period. Pigs exhibited a significant increase in rectal temperature (fever) (p < 0.01) and fecal moisture content (diarrhea) (p < 0.05) at 2 days postinoculation (d.p.i.) compared with preinoculation (day 0). Serum analyses revealed significantly increased interferon-gamma (IFN-γ) levels at 2 (p ≤ 0.0001) and 3 (p < 0.01) d.p.i. compared with day 0, and antibodies against Salmonella lipopolysaccharide (LPS) were present in all pigs by 7 d.p.i. Serovar I 4,[5],12:i:- colonized porcine intestinal tissues and was shed in the feces throughout the 7-day study. Analysis of the 16S rRNA gene sequences demonstrated that the fecal microbiota was significantly altered following MDR serovar I 4,[5],12:i:- inoculation, with the largest shift observed between 0 and 7 d.p.i. Our data indicate that the pork outbreak-associated MDR serovar I 4,[5],12:i:- isolate induced transient clinical disease in swine and perturbed the gastrointestinal microbial community. The porcine response to MDR serovar I 4,[5],12:i:- is similar to previous studies with virulent biphasic Salmonella enterica serovar Typhimurium, suggesting that the absence of fljB does not substantially alter acute colonization or pathogenesis in pigs.

Quantifying the Survival of Multiple Salmonella enterica Serovars In Vivo via Massively Parallel Whole-Genome Sequencing To Predict Zoonotic Risk

Salmonella enterica is an animal and zoonotic pathogen of worldwide importance. Salmonella serovars that differ in their host and tissue tropisms exist. Cattle are an important reservoir of human nontyphoidal salmonellosis, and contaminated bovine peripheral lymph nodes enter the food chain via ground beef. The relative abilities of different serovars to survive within the bovine lymphatic system are poorly understood and constrain the development of control strategies. This problem was addressed by developing a massively parallel whole-genome sequencing method to study mixed-serovar infections in vivo. Salmonella serovars differ genetically by naturally occurring single nucleotide polymorphisms (SNPs) in certain genes. It was hypothesized that these SNPs could be used as markers to simultaneously identify serovars in mixed populations and quantify the abundance of each member in a population. The performance of the method was validated in vitro using simulated pools containing up to 11 serovars in various proportions. It was then applied to study serovar survival in vivo in cattle challenged orally with the same 11 serovars. All the serovars successfully colonized the bovine lymphatic system, including the peripheral lymph nodes, and thus pose similar risks of zoonosis. This method enables the fates of multiple genetically unmodified strains to be evaluated simultaneously in a single animal. It could be useful in reducing the number of animals required to study mixed-strain infections and in testing the cross-protective efficacy of vaccines and treatments. It also has the potential to be applied to diverse bacterial species which possess shared but polymorphic alleles.

IMPORTANCE While some Salmonella serovars are more frequently isolated from lymph nodes rather than the feces and environment of cattle, the relative abilities of serovars to survive within the lymphatic system of cattle remain ill defined. A sequencing-based method which used available information from sequenced Salmonella genomes to study the dynamics of mixed-serovar infections in vivo was developed. The main advantages of the method include the simultaneous identification and quantification of multiple strains without any genetic modification and minimal animal use. This approach could be used in vaccination trials or in epidemiological surveys where an understanding of the dynamics of closely related strains of a pathogen in mixed populations could inform the prediction of zoonotic risk and the development of intervention strategies.

Two consecutive large outbreaks of Salmonella Muenchen linked to pig farming in Germany, 2013 to 2014: Is something missing in our regulatory framework?

In 2013, raw pork was the suspected vehicle of a large outbreak (n = 203 cases) of Salmonella Muenchen in the German federal state of Saxony. In 2014, we investigated an outbreak (n = 247 cases) caused by the same serovar affecting Saxony and three further federal states in the eastern part of Germany. Evidence from epidemiological, microbiological and trace-back investigations strongly implicated different raw pork products as outbreak vehicles. Trace-back analysis of S. Muenchen-contaminated raw pork sausages narrowed the possible source down to 54 pig farms, and S. Muenchen was detected in three of them, which traded animals with each other. One of these farms had already been the suspected source of the 2013 outbreak. S. Muenchen isolates from stool of patients in 2013 and 2014 as well as from food and environmental surface swabs of the three pig farms shared indistinguishable pulsed-field gel electrophoresis patterns. Our results indicate a common source of both outbreaks in the primary production of pigs. Current European regulations do not make provisions for Salmonella control measures on pig farms that have been involved in human disease outbreaks. In order to prevent future outbreaks, legislators should consider tightening regulations for Salmonella control in causative primary production settings.

Characterization of a Multidrug-Resistant Salmonella enterica Serovar Heidelberg Outbreak Strain in Commercial Turkeys: Colonization, Transmission, and Host Transcriptional Response

In recent years, multidrug-resistant (MDR) Salmonella enterica serovar Heidelberg (S. Heidelberg) has been associated with numerous human foodborne illness outbreaks due to consumption of poultry. For example, in 2011, an MDR S. Heidelberg outbreak associated with ground turkey sickened 136 individuals and resulted in 1 death. In response to this outbreak, 36 million pounds of ground turkey were recalled, one of the largest meat recalls in U.S. history. To investigate colonization of turkeys with an MDR S. Heidelberg strain isolated from the ground turkey outbreak, two turkey trials were performed. In experiment 1, 3-week-old turkeys were inoculated with 10⁸ or 10¹⁰ CFU of the MDR S. Heidelberg isolate, and fecal shedding and tissue colonization were detected following colonization for up to 14 days. Turkey gene expression in response to S. Heidelberg exposure revealed 18 genes that were differentially expressed at 2 days following inoculation compared to pre-inoculation. In a second trial, 1-day-old poults were inoculated with 10⁴ CFU of MDR S. Heidelberg to monitor transmission of Salmonella from inoculated poults (index group) to naive penmates (sentinel group). The transmission of MDR S. Heidelberg from index to sentinel poults was efficient with cecum colonization increasing 2 Log10 CFU above the inoculum dose at 9 days post-inoculation. This differed from the 3-week-old poults inoculated with 10¹⁰ CFU of MDR S. Heidelberg in experiment 1 as Salmonella fecal shedding and tissue colonization decreased over the 14-day period compared to the inoculum dose. These data suggest that young poults are susceptible to colonization by MDR S. Heidelberg, and interventions must target turkeys when they are most vulnerable to prevent Salmonella colonization and transmission in the flock. Together, the data support the growing body of literature indicating that Salmonella establishes a commensal-like condition in livestock and poultry, contributing to the asymptomatic carrier status of the human foodborne pathogen in our animal food supply.

Characterization of Integrons and Resistance Genes in Salmonella Isolates from Farm Animals in Shandong Province, China

A total of 154 non-duplicate Salmonella isolates were recovered from 1,105 rectal swabs collected from three large-scale chicken farms (78/325, 24.0%), three large-scale duck farms (56/600, 9.3%) and three large-scale pig farms (20/180, 11.1%) between April and July 2016. Seven serotypes were identified among the 154 isolates, with the most common serotype in chickens and ducks being Salmonella enteritidis and in pigs Salmonella typhimurium. Antimicrobial susceptibility testing revealed that high antimicrobial resistance rates were observed for tetracycline (72.0%) and ampicillin (69.4%) in all sources. Class 1 integrons were detected in 16.9% (26/154) of these isolates and contained gene cassettes aadA2, aadA1, drfA1-aadA1, drfA12-aadA2, and drfA17-aadA5. Three β-lactamase genes were detected among the 154 isolates, and most of the isolates carried blaTEM-1(55/154), followed by blaPSE-1(14/154) and blaCTX-M-55 (11/154). Three plasmid-mediated quinolone resistance genes were detected among the 154 isolates, and most of the isolates carried qnrA (113/154), followed by qnrB (99/154) and qnrS (10/154). Fifty-four isolates carried floR among the 154 isolates. Multilocus sequence typing (MLST) analysis showed that nine sequence types (STs) were identified; ST11 was the most frequent genotype in chickens and ducks, and ST19 was identified in pigs. Our findings indicated that Salmonella was widespread, and the overuse of antibiotics in animals should be reduced considerably in developing countries.

Antimicrobial resistance and typing of Salmonella isolated from street vended foods and associated environment

The present study was carried out to find out the occurrence and types of Salmonella present in street vended foods and associated environment, and their resistance pattern against various antibiotics. About 1075 street vended food and associated environment samples were processed for isolation and confirmation of different Salmonella spp. by targeting gene specific invA gene and serotype specific Sdf I, Via B and Spy genes by PCR. Selected Salmonella isolates were screened for antibiotic resistance by using Baeur-Kirby disk diffusion test. Out of 1075 samples, only 31 (2.88%) isolates could be amplified the invA gene of which 19 could be recovered from meat vendors; 8 from egg vendors while remaining 4 from milk vendors. Though, majority of Salmonella recovered from raw foods the ready-to-eat food like chicken gravy and rasmalai also showed its presence which pose a serious public health threat. Overall, 19, 6 and 1 isolates of S. Typhimurium, S. Enteritidis and S. Typhi could be detected by PCR while remaining 5 isolates could not be amplified suggesting other type of Salmonella. Selected Salmonella isolates were completely resistance to Oxacillin (100%) followed by Cefoxitin (30.43%) and Ampicillin (26.10%). Thus, it is observed that the street vended foods of animal origin and associated environment play an important role in transmission of food borne pathogens including Salmonella.

Recombinant Salmonella expressing SspH2-EscI fusion protein limits its colonization in mice

Background

Activation of inflammasome contributes to the clearance of intracellular bacteria. C-terminus of E. coli EscI protein can activate NLRC4 (NLR family, CARD domain containing-4) inflammasome in macrophages. The purpose of this study was to determine if activation of NLRC4 inflammasome by EscI can reduce the colonization of Salmonella in mice.

Results

A recombinant S. typhimurium strain expressing fusion protein of the N-terminal SspH2 (a Salmonella type III secretion system 2 effector) and C-terminal EscI was constructed and designated as X4550(pYA3334-SspH2-EscI). In vitro assay showed that X4550(pYA3334-SspH2-EscI) significantly enhanced IL-1β and IL-18 secretion (P < 0.05) and pyroptotic cell death of mouse peritoneal macrophages, compared with those infected with control strain, X4550(pYA3334-SspH2). In vivo studies showed that colonization of X4550(pYA3334-SspH2-EscI) in both spleen and liver were significantly lower than that of X4550(pYA3334-SspH2) (P < 0.05). The bacterial counts of X4550(pYA3334-SspH2-EscI) in mice decreased, while those of X4550(pYA3334-SspH2) increased over the time after infection. Additionally, X4550(pYA3334-SspH2-EscI) induced a less pathological alteration in spleen and liver than X4550(pYA3334-SspH2).

Conclusion

Fusion protein SspH2-EscI may be translocated into macrophages and activate NLRC4 inflammasome, which limits Salmonella colonization in spleen and liver of mice.

Prevalence of Salmonella enterica and Shiga toxin-producing Escherichia coli in zoo animals from Chile

Salmonella (S.) enterica and Shiga toxin-producing Escherichia coli (STEC) are foodborne pathogens. Here, we report the prevalence of S. enterica and STEC in feces of 316 zoo animals belonging to 61 species from Chile. S. enterica and STEC strains were detected in 7.5% and 4.4% of animals, respectively. All Salmonella isolates corresponded to the serotype Enteritidis. To the best of our knowledge, this is the first report of S. Enteritidis in the culpeo fox (Lycalopex culpaeus), black-capped capuchin (Sapajus apella) and Peruvian pelican (Pelecanus thagus) and the first STEC report in Thomson's gazelle (Eudorcas thomsonii).

Immunometabolic Phenotype Alterations Associated with the Induction of Disease Tolerance and Persistent Asymptomatic Infection of Salmonella in the Chicken Intestine

The adaptation of Salmonella enterica to the eukaryotic host is a key process that enables the bacterium to survive in a hostile environment. Salmonella have evolved an intimate relationship with its host that extends to their cellular and molecular levels. Colonization, invasion, and replication of the bacteria in an appropriate host suggest that modification of host functions is central to pathogenesis. Intuitively, this subversion of the cell must be a complex process, since hosts are not inherently programmed to provide an environment conducive to pathogens. Hosts have evolved countermeasures to pathogen invasion, establishment, and replication through two types of defenses: resistance and tolerance. Resistance functions to control pathogen invasion and reduce or eliminate the invading pathogen. Research has primarily concentrated on resistance mechanisms that are mediated by the immune system. On the other hand, tolerance is mediated by different mechanisms that limit the damage caused by a pathogen’s growth without affecting or reducing pathogen numbers or loads. The mechanisms of tolerance appear to be separated into those that protect host tissues from the virulence factors of a pathogen and those that limit or reduce the damage caused by the host immune and inflammatory responses to the pathogen. Some pathogens, such as Salmonella, have evolved the capacity to survive the initial robust immune response and persist. The persistent phase of a Salmonella infection in the avian host usually involves a complex balance of protective immunity and immunopathology. Salmonella is able to stay in the avian ceca for months without triggering clinical signs. Chronic colonization of the intestinal tract is an important aspect of persistent Salmonella infection because it results in a silent propagation of bacteria in poultry stocks due to the impossibility to isolate contaminated animals. Data from our lab promote the hypothesis that Salmonella have evolved a unique survival strategy in poultry that minimizes host defenses (disease resistance) during the initial infection and then exploits and/or induces a dramatic immunometabolic reprogramming in the cecum that alters the host defense to disease tolerance. Unfortunately, this disease tolerance results in the ongoing human food safety dilemma.