Association of Virulence and Antibiotic Resistance in Salmonella-Statistical and Computational Insights into a Selected Set of Clinical Isolates

Isolation and characterization of a novel bacteriophage ST1749 and its effectiveness against Vibrio parahaemolyticus and Salmonella spp

Bacteriophages are extensively employed across various fields, including medicine, veterinary medicine, the food industry, agriculture, biotechnology, and pharmacy, owing to their numerous advantages. These advantages include rapid clearance of pathogens, self-propagation at the infection site, host specificity, potential for genetic modification, ease of isolation, stability, and low production costs. This study isolated a bacteriophage from shrimp pond wastewater in the Mekong Delta region. The bacteriophage was identified as a lytic bacteriophage belonging to the genus Bruyoghevirus, class Caudoviricetes, with the ability to effectively lyse three bacterial strains: V. parahaemolyticus, Salmonella enteritidis, and Salmonella typhimurium. Growth curve analysis revealed variations in the latency period and the number of phages produced during the life cycle across all three hosts. Bacteriophage Produced 117, 176, and 52 PFU/cell against V. parahaemolyticus, S. enteritidis, and S. typhimurium, respectively. Phage ST1749 demonstrated activity across a broad range of temperatures (-20 °C to 70 °C) and pH levels (2 to 10), with optimal stability observed at pH 5 to 7. Furthermore, phage ST1749 exhibited biofilm-degrading and lytic capabilities against the three bacterial strains studied. These findings suggest that phage ST1749 has the potential to serve as a biocontrol agent for treating infections caused by antibiotic-resistant bacteria.

Impact on Human Health of Salmonella spp. and Their Lipopolysaccharides: Possible Therapeutic Role and Asymptomatic Presence Consequences

Epidemiologically, one of the most important concerns associated with introducing Salmonella spp. into the environment and food chain is the presence of asymptomatic carriers. The oncogenic and oncolytic activity of Salmonella and their lipopolysaccharides (LPSs) is important and research on this topic is needed. Even a single asymptomatic dose of the S. Enteritidis LPS (a dose that has not caused any symptoms of illness) in in vivo studies induces the dysregulation of selected cells and bioactive substances of the nervous, immune, and endocrine systems. LPSs from different species, and even LPSs derived from different serotypes of one species, can define different biological activities. The activity of low doses of LPSs derived from three different Salmonella serotypes (S. Enteritidis, S. Typhimurium, and S. Minnesota) affects the neurochemistry of neurons differently in in vitro studies. Studies on lipopolysaccharides from different Salmonella serotypes do not consider the diversity of their activity. The presence of an LPS from S. Enteritidis in the body, even in amounts that do not induce any symptoms of illness, may lead to unknown long-term consequences associated with its action on the cells and biologically active substances of the human body. These conclusions should be important for both research strategies and the pharmaceutical industry &.

Nucleotide sequence variants, gene expression and serum profile of immune and antioxidant markers associated with bacterial diarrhea susceptibility in Barki lambs

BACKGROUND

Despite the fact that diarrhea is more accurately described as a clinical symptom than a disease. Diarrhea is one of the most important issues in ovine medicine, particularly in lambs, and because of high morbidity and mortality rate, sluggish growth performance, and veterinary costs, it is believed to be a major source of economic loss. Salmonella and enterotoxigenic Escherichia coli are the most common and commercially significant agents responsible for diarrhea.

OBJECTIVE

The objective of this study was to monitor the nucleotide sequence variations, gene expression, serum inflammatory and oxidative stress biomarkers in diarrheic lambs. Another aim was to identify different pathotypes and virulence genes of Salmonella and E. coli causing diarrhea.

METHODOLOGY

Blood samples were taken from 50 Barki who were diarrheal and 50 who appeared to be healthy, and then divided in 3 portions, with EDTA added to the first part for CBC, DNA and RNA extraction. The second sample received 5000 I.U. of heparin calcium, and a clean plain tube was used for the third component. The second and third sections were centrifuged to extract serum and plasma until the biochemical and immunological analysis was completed. Fecal samples were collected for bacteriological examination, and the bacteria were identified by PCR analysis. PCR-DNA sequencing was conducted for immune (SELL, JAK2, SLC11A1, IL10, FEZF1, NCF4, LITAF, SBD2, NFKB, TNF-α, IL1B, IL6, LGALS, and CATH1), antioxidant (SOD1, CAT, GPX1, GST, Nrf2, Keap1, HMOX1, and NQO1), and GIT health (CALB1, GT, and MUC2) genes in healthy and diarrheic lambs.

RESULTS

Virulent genetic markers of pathogenic characteristics of E. coli (astA, Vt2e (Stx2e), CFA/I, groES and luxS) and Salmonella (invA, SopB, bcfC and avrA) were detected in all diarrheic lambs. PCR-DNA sequencing of immune, antioxidant and intestinal health genes found eleven single nucleotide polymorphisms (SNPs) linked to either diarrhea resistance or susceptibility in Barki lambs. Transcript levels of immune, antioxidant, and GIT health (CALB1, GT, and MUC2) genes varied between healthy and diarrheic lambs. Nucleotide sequence variation of the genes under inquiry between reference sequences in GenBank and those of the animals under investigation verified all identified SNPs. Significant (P = 0.001) erythrocytosis, neutrophilic leukocytosis, with lymphocytopenia were observed in diarrheic lambs. Significant (P = 0.001) increases in serum IL-1α, IL-1β, IL-6, TNF-α (90.5 ± 1.7, 101.8 ± 1.7, 72.3 ± 6.6, 71.26 ± 4.89 Pg/ml, respectively), serum Fb, Cp, Hp, SAA (230.7 ± 12.4 mg/dl, 6.5 ± 0.07 mg/dl, 2.5 ± 0.09 g/dl, 7.4 ± 0.4 mg/L, respectively), free radicals (MDA, NO), cortisol (6.91 ± 0.18 μg/dl) and growth hormone, with significant (P = 0.001) decreases in serum IL-10 (81.71 ± 1.05 Pg/ml), antioxidants (CAT, GPx), insulin, triiodothyronine (T3) and thyroxine (T4) in diarrheic lambs.

CONCLUSIONS

The study's findings provided credence to the theory that marker-assisted selection (MAS) could be used to predict and prevent diarrhea in Barki sheep by selecting lambs based on SNPs in genes linked to inflammation, antioxidants, and intestinal health. In order to establish an efficient management protocol and determine the most susceptible risk period for disease occurrence, gene expression profiles of the genes under investigation, pro-inflammatory cytokines and acute phase proteins may also be utilized as proxy biomarkers for lamb enteritis.

Clinical Outcomes of Patients With Nontyphoidal Salmonella Infections by Isolate Resistance-Foodborne Diseases Active Surveillance Network, 10 US Sites, 2004-2018

BACKGROUND

Nontyphoidal Salmonella causes an estimated 1.35 million US infections annually. Antimicrobial-resistant strains are a serious public health threat. We examined the association between resistance and the clinical outcomes of hospitalization, length-of-stay ≥3 days, and death.

METHODS

We linked epidemiologic data from the Foodborne Diseases Active Surveillance Network with antimicrobial resistance data from the National Antimicrobial Resistance Monitoring System (NARMS) for nontyphoidal Salmonella infections from 2004 to 2018. We defined any resistance as resistance to ≥1 antimicrobial and clinical resistance as resistance to ampicillin, azithromycin, ceftriaxone, ciprofloxacin, or trimethoprim-sulfamethoxazole (for the subset of isolates tested for all 5 agents). We compared outcomes before and after adjusting for age, state, race/ethnicity, international travel, outbreak association, and isolate serotype and source.

RESULTS

Twenty percent of isolates (1105/5549) had any resistance, and 16% (469/2969) had clinical resistance. Persons whose isolates had any resistance were more likely to be hospitalized (31% vs 28%, P = .01) or have length-of-stay ≥3 days (20% vs 16%, P = .01). Deaths were rare but more common among those with any than no resistance (1.0% vs 0.4%, P = .01). Outcomes for patients whose isolates had clinical resistance did not differ significantly from those with no resistance. After adjustment, any resistance (adjusted odds ratio 1.23, 95% confidence interval 1.04-1.46) remained significantly associated with hospitalization.

CONCLUSIONS

We observed a significant association between nontyphoidal Salmonella infections caused by resistant pathogens and likelihood of hospitalization. Clinical resistance was not associated with poorer outcomes, suggesting that factors other than treatment failure (eg, strain virulence, strain source, host factors) may be important.

Genotyping virulence and resistance profiles in salmonella isolated from diarrheic children in Nairobi city, Kenya

Aim

To characterize salmonella virulent and antibiotic resistance genes in children with diarrhea in Nairobi city, Kenya.

Background

Salmonella species carry virulent genes whose expression correlate with severity of salmonellosis. Effective treatment of salmonellosis by antibiotics is threatened by expression of antibiotic resistant genes.

Methods

In a cross-sectional study, a total of 374 children below five years of age presenting with diarrhea at Mbagathi County Hospital were recruited. Stool microbiology test was used to detect Salmonella species. Polymerase chain reaction was employed to detect virulent and antibiotic resistant genes.

Results

Salmonella species was isolated in 9 (2.4%) children. A total of 9 (100.0%), 7 (77.8%), 9 (100.0%) and 6 (66.6%) of the isolates harbored invA, Hila, sopB, and Stn virulent genes, respectively. None (0.0%) of the isolates was resistant to gentamycin but 7 (77.8%), 7 (77.8%), 9 (100.0%), 8 (88.9%), 7 (77.8%), 6 (66.7%) and 5 (55.6%) of Salmonella species were resistant to ampicillin, ceftriaxone, streptomycin, ciprofloxacin, chloramphenicol, erythromycin, and tetracycline, respectively. Ampicillin (citm), ceftriaxone (bla CMY), streptomycin (aadA1), gentamycin (aac(3)-IV), ciprofloxacin (qnr), chloramphenicol (catA1), erythromycin (ereA), and tetracycline (tetA) resistant gene was detected in 6 (85.7%), 6 (85.7%), 9 (100.0%), 8 (100.0%), 6 (85.7%), 6 (100.0%), and 5 (100.0%) of Salmonella isolates which were phenotypic resistant to ampicillin, ceftriaxone, streptomycin, ciprofloxacin, chloramphenicol, erythromycin and tetracycline, respectively.

Conclusion

Salmonella species expressing virulent and antibiotic resistant genes is an important cause of gastroenteritis in children in Kenya.

Salmonella typhimurium targeting with monoclonal antibodies prevents infection in mice

Salmonella is a prevalent foodborne and waterborne pathogens threating global public health and food safety. Given the diversity of Salmonella serotypes and the emergence of antibiotic-resistant strains, there is an urgent need for the development of broadly protective therapies. This study aims to prepare monoclonal antibodies (Mabs) with broad reactivity against multi-serotype Salmonella strains, potentially offering cross-protection. We prepared two Mabs F1D4 and B7D4 against protein FliK and BcsZ, two potential vaccine candidates against multi-serotype Salmonella. The two Mabs belonging to IgG1 isotype exhibited high titers of 1:256,000 and 1:512,000 respectively, as well as broad cross-reactivity against 28 different serotypes of Salmonella strains with percentages of 89.29% and 92.86%, correspondingly. Neutralizing effects of the two Mabs on Salmonella growth, adhesion, invasion and motility was evaluated in vitro using bacteriostatic and bactericidal activity with and without complement and bacterial invasion inhibition assay. Additionally, cytotoxicity assays, animal toxicity analyses, and pharmacokinetic evaluations demonstrated the safety and sustained effectiveness of both Mabs. Furthermore, F1D4 or B7D4-therapy in mice challenged with S. Typhimurium LT2 exhibited milder organs damage and lower Salmonella colonization, as well as the higher relative survival of 86.67% and 93.33% respectively. This study produced two broadly reactive and potential cross protective Mabs F1D4 and B7D4, which offered new possibilities for immunotherapy of salmonellosis.

Assessment of the prevalence, serotype, and antibiotic resistance pattern of Salmonella enterica in integrated farming systems in the Maryland-DC area

Implementation of organic/pasture farming practices has been increasing in the USA regardless of official certification. These practices have created an increasingly growing demand for marketing safe products which are produced through these systems. Products from these farming systems have been reported to be at greater risk of transmitting foodborne pathogens because of current trends in their practices. Salmonella enterica (SE) is a ubiquitous foodborne pathogen that remains a public health issue given its prevalence in various food products, but also in the environment and as part of the microbial flora of many domestic animals. Monitoring antibiotic resistance and identifying potential sources contamination are increasingly important given the growing trend of organic/pasture markets. This study aimed to quantify prevalence of SE at the pre- and post-harvest levels of various integrated farms and sites in Maryland-Washington D.C. area, as well as identify the most prevalent serovars and antibiotic resistance patterns. Samples from various elements within the farm environment were collected and screened for SE through culture and molecular techniques, which served to identify and serotype SE, using species and serovar-specific primers, while antibiotic resistance was evaluated using an antibiogram assay. Results showed a prevalence of 7.80% of SE pre-harvest and 1.91% post-harvest. These results also showed the main sources of contamination to be soil (2.17%), grass (1.28%), feces (1.42%) and unprocessed produce (1.48%). The most commonly identified serovar was Typhimurium (11.32%) at the pre-harvest level, while the only identified serovar from post-harvest samples was Montevideo (4.35%). With respect to antibiotic resistance, out of the 13 clinically relevant antibiotics tested, gentamycin and kanamycin were the most effective, demonstrating 78.93 and 76.40% of isolates, respectively, to be susceptible. However, ampicillin, amoxicillin and cephradine had the lowest number of susceptible isolates with them being 10.95, 12.36, and 9.83%, respectively. These results help inform farms striving to implement organic practices on how to produce safer products by recognizing areas that pose greater risks as potential sources of contamination, in addition to identifying serotypes of interest, while also showcasing the current state of antibiotic efficacy and how this can influence antibiotic resistance trends in the future.

Virulence and antimicrobial resistance profiles of Salmonella enterica isolated from foods, humans, and the environment in Mexico

Salmonella enterica genotypic and phenotypic characteristics play an important role in its pathogenesis, which could be influenced by its origin. This study evaluated the association among the antimicrobial resistance, virulence, and origin of circulating S. enterica strains in Mexico, isolated from foods, humans, and the environment. The antimicrobial susceptibility to fourteen antibiotics by the Kirby-Bauer method (n = 117), and the presence of thirteen virulence genes by multiplex PCR (n = 153) and by sequence alignments (n = 2963) were evaluated. In addition, a set of S. enterica isolates from Mexico (n = 344) previously characterized according to their genotypic and phenotypic print was included to increase the coverage of the association analysis. Strains with the presence of sopE and strains with the absence of sspH1 were significantly associated with multidrug-resistant (MDR) phenotypes (p < 0.05). The origin of the strains had significant associations with the antimicrobial profiles and some virulence genes (hilA, orgA, sifA, ssaQ, sseL, sspH1, pefA, and spvC) (p < 0.05). Animal-origin food isolates showed the highest frequency of MDR (57.2 %), followed by human isolates (30.0 %). Also, sspH1, pefA, and spvC were found in major frequency in human (32.4 %, 31.0 %, 31.7 %) and animal-origin foods (41.6 %, 10.6 %, 10.6 %) isolates. The findings highlighted that antimicrobial profiles and specific virulence genes of S. enterica strains are related to their origin. Similar genotypic and phenotypic characteristics between human and animal-origin foods isolates were found, suggesting that animal-origin foods isolates are the most responsible for human cases. The revealed associations can be used to improve risk estimation assessments in national food safety surveillance programs.

Study of Virulence Genes, Antimicrobial Resistance, and Genetic Relatedness of Foodborne Salmonella Isolates from Tunisia

ABSTRACT

Nontyphoidal Salmonella strains are among the major foodborne pathogens with emerging multidrug-resistant phenotypes. In this study, antimicrobial susceptibility testing of a collection of Salmonella isolates (n = 54) recovered from poultry and bivalve molluscs was performed. The study also investigated profiling of virulence and resistance genes as well as phylogenetic relationships through pulsed-field gel electrophoresis (PFGE) and enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprinting. Results revealed the presence of multiple virulence genes among Salmonella isolates. Salmonella intestinal infection A (siiA), Salmonella outer protein (sopB and sopE), putative 4-hydroxybutyrate coenzyme A transferase (cat2), Salmonella atypical fimbria C (safC), and Salmonella Enteritidis fimbria B (sefB) were present in most (83.32 to 100%) of the isolates, whereas the remaining tested genes (Salmonella plasmid virulence [spvC and spvB]), and the sopE gene, were exclusively detected within the serotype Enteritidis. The highest resistance rates were observed for oxacillin (94.4%), ampicillin (37%), and nalidixic acid (27.7%), followed by cefotaxime and amoxicillin-clavulanic acid (14.8%), trimethoprim-sulfamethoxazole (9.3%), and ciprofloxacin (5.5%). The results indicate that the Salmonella Enteritidis serotype possessed the widest range of virulence determinants and increasing levels of resistance. Such high-risk clones should be particularly controlled in Tunisia. Overall, increased resistance and virulence confer a selective advantage for the evolution of these bacteria and represent an alarming problem for global public health. The genetic study via PFGE and ERIC-PCR showed the high diversity of the clonal origins of these bacteria and the sources of contamination and revealed the great capacity of Salmonella to diversify within food-producing animals.

HIGHLIGHTS

Tracking the Transmission of Antimicrobial-Resistant Non-O157 Escherichia coli and Salmonella Isolates at the Interface of Food Animals and Fresh Produce from Agriculture Operations Using Whole-Genome Sequencing

An increasing number of outbreaks are caused by foodborne pathogens such as Escherichia coli and Salmonella, which often harbor antimicrobial resistance (AMR) genes. We previously demonstrated the transmission of pathogens from animal operations to produce fields on sustainable farms, which illustrated an urgent need to develop and implement novel prevention methods and remediation practices such as the vegetative buffer zone (VBZ) to prevent this movement. The focus of this study was to use whole-genome sequencing (WGS) to characterize the AMR, virulence, and single-nucleotide polymorphism profile of 15 Salmonella and 128 E. coli isolates collected from small-scale dairy and poultry farms on a research station in North Carolina. Phenotypically, seven E. coli and three Salmonella isolates displayed resistance to antibiotics such as tetracycline (n = 4), ampicillin (n = 4), nalidixic acid (n = 3), chloramphenicol (n = 2), sulfisoxazole (n = 1), and streptomycin (n = 1). A single E. coli isolate was found to be resistant to five different antibiotic class types and possessed the bla_TEM-150 resistance gene. Virulence genes that facilitate toxin production and cell invasion were identified. Mauve analysis of the E. coli isolates identified seven clusters (dairy-six and poultry-one) indicating that transmission is occurring from animal operations to fresh produce fields and the surrounding environment when the VBZ is denudated. This suggests that the VBZ is a useful barrier to reducing the transmission of enteric pathogens in agricultural systems. Our study demonstrates the prevalence of AMR and virulence genes on small-scale sustainable farms and highlights the advantage of using WGS to assess the impact of the VBZ to reduce the transmission of E. coli and Salmonella.

Salmonella Yoruba: a rare serotype revealed through genomic sequencing along the farm-to-fork continuum of an intensive poultry farm in KwaZulu-Natal, South Africa

Salmonella enterica is a zoonotic pathogen of worldwide public health importance. We characterised Salmonella isolates from poultry along the farm-to-fork continuum using whole genome sequencing (WGS) and bioinformatics analysis. Three multilocus sequence types (MLSTs), i.e., ST15 (1.9%), ST152 (5.9%) and ST1316 (92.2%) and three serotypes, i.e., S. Heidelberg (1.9%), Kentucky (5.9%) and Yoruba (92.2%) were detected. The rare serotype, S. Yoruba, was detected among the farm and abattoir isolates and contained resistance and virulence determinants. Resistome analysis revealed the presence of the aac(6')-Iaa gene associated with aminoglycoside resistance, a single point mutation in the parC gene associated with fluoroquinolone and quinolone resistance, and a single isolate contained the fosA7 gene responsible for fosfomycin resistance. No antibiotic resistance genes (ARGs) were identified for isolates phenotypically non-susceptible to azithromycin, cephalosporins, chloramphenicol and nitrofurantoin and resistance was thought to be attributable to other resistance mechanisms. The fully susceptible profiles observed for the wastewater isolates suggest that the poultry environment may receive antibiotic-resistant strains and resistance determinants from poultry with the potential of becoming a pathway of Salmonella transmission along the continuum. Six plasmids were identified and were only carried by 92.2% of the S. Yoruba isolates in varying combinations. Four plasmids were common to all S. Yoruba isolates along the continuum; isolates from the litter and faeces on the farm contained two additional plasmids. Ten Salmonella pathogenicity islands (SPIs) and 177 virulence genes were identified; some were serotype-specific. Phylogenetic analysis of S. Heidelberg and Kentucky showed that isolates were related to animal and human isolates from other countries. Phylogenetic analysis among the S. Yoruba isolates revealed four clades based on the isolate sources along the farm-to-fork continuum. Although the transmission of Salmonella strains along the farm-to-fork continuum was not evident, pathogenic, resistant Salmonella present in the poultry production chain poses a food safety risk. WGS analysis can provide important information on the spread, resistance, pathogenicity, and epidemiology of isolates and new, rare or emerging Salmonella strains to develop intervention strategies to improve food safety.

Application of a High-Throughput Targeted Sequence AmpliSeq Procedure to Assess the Presence and Variants of Virulence Genes in Salmonella

We have developed a targeted, amplicon-based next-generation sequencing method to detect and analyze 227 virulence genes (VG) of Salmonella (AmpliSeq_{Salm_227VG}) for assessing the pathogenicity potential of Salmonella. The procedure was developed using 80 reference genomes representing 75 epidemiologically-relevant serovars associated with human salmonellosis. We applied the AmpliSeq_{Salm_227VG} assay to (a) 35 previously characterized field strains of Salmonella consisting of serovars commonly incriminated in foodborne illnesses and (b) 34 Salmonella strains with undisclosed serological or virulence attributes, and were able to divide Salmonella VGs into two groups: core VGs and variable VGs. The commonest serovars causing foodborne illnesses such as Enteritidis, Typhimurium, Heidelberg and Newport had a high number of VGs (217–227). In contrast, serovars of subspecies not commonly associated with human illnesses, such as houtenae, arizonae and salame, tended to have fewer VGs (177–195). Variable VGs were not only infrequent but, when present, displayed considerable sequence variation: safC, sseL, sseD, sseE, ssaK and stdB showed the highest variation and were linked to strain pathogenicity. In a chicken infection model, VGs belonging to rfb and sse operons showed differences and were linked with pathogenicity. The high-throughput, targeted NGS-based AmpliSeq_{Salm_227VG} procedure provided previously unknown information about variation in select virulence genes that can now be applied to a much larger population of Salmonella for evaluating pathogenicity of various serovars of Salmonella and for risk assessment of foodborne salmonellosis.