Whole genome sequencing analysis of Salmonella enterica serovar Weltevreden isolated from human stool and contaminated food samples collected from the Southern coastal area of China

Myocarditis associated with Salmonella enterica serovar Weltevreden gastroenteritis in medical practitioner; case report from South India

Salmonella enterica serovar Weltevreden, a non-typhoidal serovar, has emerged as a significant foodborne pathogen, particularly in Southeast Asian countries. While it is commonly associated with gastroenteritis and foodborne outbreaks, it can also lead to invasive infections in immunocompromised adults and neonates. This case report presents a rare instance of myocarditis associated with Salmonella Weltevreden gastroenteritis in a 43-year-old healthy male physician from South India. The patient had a month-long history of intermittent fever, which worsened 2 days before admission, along with myalgia and headache. A day after the admission the patient developed diarrhea. Upon investigation, stool culture revealed Salmonella enterica serovar Weltevreden. Notably, the patient had a genetic predisposition to inflammatory bowel disease and reported recent use of nonsteroidal anti-inflammatory drugs, which may have increased his susceptibility to non-typhoidal Salmonella infection. The patient also developed myocarditis, making this the first reported case of Weltevreden-associated myocarditis in the region. Antimicrobial susceptibility testing indicated ciprofloxacin susceptibility, an increasingly rare finding, as most reported serovar Weltevreden cases exhibit ciprofloxacin resistance. The patient recovered following treatment with ciprofloxacin and was discharged with instructions for follow-up. This case highlights the need for heightened awareness of the potential for non-typhoidal Salmonella infections to cause systemic manifestations, even in individuals without major underlying comorbidities. Continuous monitoring of antimicrobial resistance patterns and strict food safety measures are essential to control outbreaks of these emerging pathogens.

Salmonella Weltevreden lung abscess and empyema without preceding gastrointestinal symptoms: an emerging pathogen in Australia?

Non-typhoidal Salmonella lung infections are rare and are usually confined to immunocompromised hosts. Previous case reports have found that usually patients have either gastroenteritis or bacteraemia in addition to pulmonary involvement. We present the first known reported case of a Salmonella Weltevreden lung abscess and empyema in an immunocompetent patient without gastroenteritis. Despite the use of antimicrobials active against the pathogen, the patient needed surgical intervention to achieve adequate source control. While S. Weltevreden has previously been associated with returned travellers, especially from Southeast Asia, its incidence in Queensland is now increasing. Therefore, it is important for clinicians to be aware of its potential severity as well as the range of presentations.

Whole-Genome Sequencing Analysis of Antimicrobial Resistance, Virulence Factors, and Genetic Diversity of Salmonella from Wenzhou, China

Salmonella species are important foodborne pathogens worldwide. Salmonella pathogenicity is associated with multiple virulence factors and enhanced antimicrobial resistance. To determine the molecular characteristics and genetic correlations of Salmonella, 24 strains of Salmonella isolated from different sources (raw poultry, human stool, and food) in the Wenzhou area were investigated to determine the distribution of antimicrobial resistance and virulence determinants using whole-genome sequencing (WGS). Aminoglycoside resistance genes were detected in all samples. Over half of the samples found antimicrobial resistance genes (ARGs) and point mutations for several clinically frequently used antibiotic, beta-lactams, tetracyclines, and quinolones. Of these strains, 62.5% were predicted to be multidrug-resistant (MDR). The quinolone-modifying enzyme gene aac(6')-Ib-cr, detected in five samples (S1-S4 and S10), was located on integrons. The analysis of Salmonella pathogenicity island (SPI) profiles suggests that serotypes with close genetic relationships share the same distribution of virulence factors, revealing a link between genotype and SPI profiles. cgMLST analysis indicated that five isolates S14-S18 were closely related to strains originating from the United Kingdom, suggesting that they may share a common origin. Data from this study may enrich the molecular traceability database for Salmonella and provide a basis for effective public health policies.

Foodborne Outbreak by Salmonella enterica Serovar Weltevreden in West Bengal, India

Foodborne gastroenteritis outbreaks owing to Salmonella enterica serovar Weltevreden (Salmonella Weltevreden) represent a significant global public health problem. In the past two decades, Salmonella Weltevreden has emerged as a dominant foodborne pathogen, especially in South-East Asian countries. This report describes a community foodborne outbreak of gastroenteritis caused by Salmonella Weltevreden in August 2022 following consumption of panipuri from a street vendor in the Polba block in Hooghly district, West Bengal, India. This food item was consumed by 185 people, of whom 129 had acute watery diarrhea with other clinical symptoms and 65 of them were admitted to different District hospitals for treatment. Stool specimens collected from hospitalized cases were positive for S. enterica, and further serotyped as Salmonella Weltevreden. All the Salmonella Weltevreden strains possessed the Salmonella pathogenicity islands associated genes (invA/E, orgA, ttrc, ssaQ, mgtC, misL, spi4D), the enterotoxin (stn), and hyperinvasive locus gene (hilA). Except erythromycin, all the strains were susceptible for commonly used antimicrobials in the treatment of diarrhea. The XbaI-based pulsed-field gel electrophoresis analysis indicated that all the isolates responsible for the recent outbreak were similar, but diverged from other Salmonella Weltevreden that were previously reported in West Bengal. This report indicates that foodborne infection is a major public health concern in India and demands to strengthen capacity-building measures at the local health care levels for linking causative agents of outbreaks.

SW16-7, a Novel Ackermannviridae Bacteriophage with Highly Effective Lytic Activity Targets Salmonella enterica Serovar Weltevreden

Salmonella enterica serovar Weltevreden is a foodborne pathogen commonly transmitted through fresh vegetables and seafood. In this study, a lytic phage, SW16-7, was isolated from medical sewage, demonstrating high infectivity against S. Weltevreden, S. London, S. Meleagridis, and S. Give of Group O:3. In vitro inhibition assays revealed its effective antibacterial effect for up to 12 h. Moreover, analysis using the Comprehensive Antibiotic Resistance Database (CARD) and the Virulence Factor Database (VFDB) showed that SW16-7's genome does not contain any virulence factors or antibiotic resistance genes, indicating its potential as a promising biocontrol agent against S. Weltevreden. Additionally, a TSP gene cluster was identified in SW16-7's genome, with TSP1 and TSP2 showing a high similarity to lysogenic phages ε15 and ε34, respectively, in the C-terminal region. The whole-genome phylogenetic analysis classified SW16-7 within the Ackermannviridae family and indicated a close relationship with Agtrevirus, which is consistent with the ANI results.

Genomic Characterization of Salmonella enterica serovar Weltevreden Associated with Human Diarrhea

Salmonella Weltevreden is an emerging pathogen associated with human diarrhea, and knowledge of the genomics and epidemiology of this serovar is still limited. In this study, we performed whole-genome sequencing of 96 S. Weltevreden isolates recovered from diarrheal patients and 62 isolates from food animals in China between 2006 and 2017. Together, with an additional 199 genome sequences of S. Weltevreden published in NCBI, we performed an analysis on all 357 S. Weltevreden genome sequences. Our results demonstrated that the majority of S. Weltevreden from diarrheal patients from China (97.92%, 94/96) and the other regions in the world (94.97%, 189/199) identified in this study were sequence type (ST) 365. The remaining types were ST3771 (n = 3), ST22 (n = 1), ST155 (n = 1), and ST684 (n = 1). In addition, ST365 was also widely recovered from animals, food, and environmental samples in different regions of the world. Phylogenetic analysis and pulsed-field gel electrophoresis (PFGE) revealed that S. Weltevreden from diarrheal patients was closely related to those recovered from food and environmental specimens. We also showed that S. Weltevreden did not exhibit severe antimicrobial resistance profiles, suggesting administering antibiotics is still effective for controlling the agent. Interestingly, we found that S. Weltevreden strains carried a number of virulence factor genes, and a 100.03-kb IncFII(S) type plasmid was widely distributed in S. Weltevreden strains. Elimination of this plasmid decreased the bacterial capacity to infect both Caco-2 cells and C57BL/6 mice, suggesting the importance of this plasmid for bacterial virulence. Our results contribute to the understanding of the epidemiology and virulence of S. Weltevreden. IMPORTANCE Salmonella Weltevreden is a pathogen associated with human diarrheal diseases found across the globe. However, knowledge of the genomics and epidemiology of this pathogen is still limited. In this study, we found S. Weltevreden sequence type (ST) 365 is commonly recovered from diarrheal patients in China and many other regions of the world, and there is no major difference between the Chinese isolates and the global isolates at the phylogenetic level. We also demonstrated that ST365 was widely recovered from animal, food, and environmental samples collected in different, global regions. Importantly, we discovered an IncFII(S) type plasmid commonly carried by S. Weltevreden strains of human, animal, and food origins, and this plasmid is likely to contribute to the bacterial pathogenesis. These findings enhance our understanding of the emergence of S. Weltevreden involved in diarrheal outbreaks and the global spread of S. Weltevreden strains.

Prevalence, antimicrobial resistance and virulence genes of Salmonella serovars isolated from humans and animals

We investigated the prevalence, antimicrobial susceptibility, antimicrobial resistance and virulence genes of Salmonella isolates recovered from humans and different species of animals. Out of 1231 samples, 88 (7.15%) Salmonella isolates were obtained, among which 21 (23.86%) belonged to Salmonella enterica subsp. enterica sero var. Weltevreden, 22 (25%) to S. Enteritidis, 16 (18.2%) to S. Typhi and 14 (15.9%) to S. Newport; 7 (7.95%) isolates were untypable. Among the 88 isolates, 65.90% showed resistance to gentamicin, 61.36% to tetracycline, 61.18% to cefotaxime, 48.86% to trimethoprim, 45.45% to ampicillin, 11.36% to ceftriaxone, 10.22% to chloramphenicol and 7.95% each to ciprofloxacin and cefepime. Most of the isolates were susceptible, with a low MIC (≤ 0.25 μg/ml) value, to cefepime, cefotaxime, ciprofloxacin, ceftriaxone and co-trimoxazole and with a moderate MIC (0.5-4 μg/ml) to ampicillin, tetracycline, gentamicin and chloramphenicol. The resistance genes bla_TEM, tetA and dfrA12 were most prevalent, irrespective of the host of origin of the isolates. While invA was used for molecular detection of Salmonella, other virulence genes, viz. sipA, sipB, sipC, stn and pagN, were also detected in all Salmonella isolates. A total of 38.64% isolates were multidrug-resistant (MDR), and various virulence genes were present among the isolated serovars. This study highlights the importance of continuous monitoring and surveillance for pathogenic Salmonella and their potential risks to both humans and animals.

Clinically healthy household dogs and cats as carriers of multidrug-resistant Salmonella enterica with variable R plasmids

Introduction. Antimicrobial resistance (AMR) is a One Health issue concerning humans, animals and the environment and a unified One Health approach is required to contain this problematic issue. Dogs and cats are popular pet animals and are known to carry many bacterial pathogens that are of public health importance, including Salmonella . However, data on AMR in companion animals is limited.

Gap statement. Scant AMR data from bacteria originating from companion animals limits an accurate assessment of the impacts of pet-animal-related AMR on public health.

Purpose. This study aimed to phenotypically and genetically investigate AMR in Salmonella isolated from pet dogs and cats in Thailand.

Methodology. Salmonella enterica were isolated from pet dogs (n=159) and cats (n=19) in Thailand between 2016 and 2019. All isolates were serotyped. Phenotypic and genotypic antimicrobial resistance was examined. PCR-based replicon typing, replicon sequence typing and plasmid multilocus sequence typing were conducted to characterize plasmids.

Results. Seventy-seven serovars were identified, with serovars Weltevreden (9.6%) and Stockholm (9.0%) the most common. Most of the isolates (34.3%) were multidrug-resistant. The serovar Stockholm was an ESBL-producer and carried the β-lactamase genes bla TEM-1 and bla CTX-M-55. The plasmid-mediated quinolone resistance (PMQR) gene, qnrS, was also detected (10.1%). Class 1 integrons carrying the dfrA12-aadA2 cassette array were most frequent (45.9%). Five plasmid replicon types as IncA/C (0.6%), N (1.1%), IncFIIA (28.7%), IncHI1 (2.2%), and IncI1 (3.4%) were identified. Based on the pMLST typing scheme (n=9), plasmids were assigned into five different STs including IncA/C-ST6 (n=1), IncH1-ST16 (n=4), IncI1-ST3 (n=1), IncI1-ST60 (n=1) and IncI1-ST136 (n=1). The ST 16 of IncHI1 plasmid was a novel plasmid ST. Subtyping F-type plasmids using the RST scheme (n=9) revealed four different combinations of replicons including S1:A-:B- (n=4), S1:A-:B22 (n=2), S3:A-:B- (n=1) and S-:A-:B47 (n=1).

Conclusions. Our findings highlight the role of clinically healthy household dogs and cats as carriers of AMR Salmonella strains with different R plasmid. The implementation of AMR phenotypes instigation and genotypic monitoring and surveillance programmes in companion animals are imperative as integral components of the One Health framework.

Evaluation of Antibiotic Resistance of Salmonella Serotypes and Whole-Genome Sequencing of Multiresistant Strains Isolated from Food Products in Russia

Food products may be a source of Salmonella, one of the main causal agents of food poisoning, especially after the emergence of strains resistant to antimicrobial preparations. The present work dealt with investigation of the occurrence of resistance to antimicrobial preparations among S. enterica strains isolated from food. The isolates belonged to 11 serovars, among which Infantis (28%), Enteritidis (19%), and Typhimurium (13.4%) predominated. The isolates were most commonly resistant to trimethoprim/sulfamethoxazole (n = 19, 59.38%), cefazolin (n = 15, 46.86%), tetracycline (n = 13, 40.63%), and amikacin (n = 9, 28.13%). Most of the strains (68.75%) exhibited multiple resistance to commonly used antibiotics. High-throughput sequencing was used to analyse three multidrug-resistant strains (resistant to six or more antibiotics). Two of them (SZL 30 and SZL 31) belonged to S. Infantis, while one strain belonged to S. Typhimurium (SZL 38). Analysis of the genomes of the sequenced strains revealed the genes responsible for antibiotic resistance. In the genomes of strains SZL 30 and SZL 31 the genes of antibiotic resistance were shown to be localized mostly in integrons within plasmids, while most of the antibiotic resistance genes of strain SZL 38 were localized in a chromosomal island (17,949 nt). Genomes of the Salmonella strains SZL 30, SZL 31, and SZL 38 were shown to contain full-size pathogenicity islands: SPI-1, SPI-2, SPI-4, SPI-5, SPI-9, SPI-11, SPI-13, SPI-14, and CS54. Moreover, the genome of strain SZL 38 was also found to contain the full-size pathogenicity islands SPI-3, SPI-6, SPI-12, and SPI-16. The emergence of multidrug-resistant strains of various Salmonella serovars indicates that further research on the transmission pathways for these genetic determinants and monitoring of the distribution of these microorganisms are necessary.

Presence of Tetracycline and Sulfonamide Resistance Genes in Salmonella spp.: Literature Review

Tetracyclines and sulfonamides are broad-spectrum antibacterial agents which have been used to treat bacterial infections for over half a century. The widespread use of tetracyclines and sulfonamides led to the emergence of resistance in a diverse group of bacteria. This resistance can be studied by searching for resistance genes present in the bacteria responsible for different resistance mechanisms. Salmonella is one of the leading bacteria causing foodborne diseases worldwide, and its resistance to tetracyclines and sulfonamides has been widely reported. The literature review searched the Virtual Health Library for articles with specific data in the studied samples: the resistance genes found, the primers used in PCR, and the thermocycler conditions. The results revealed that Salmonella presented high rates of resistance to tetracycline and sulfonamide, and the most frequent samples used to isolate Salmonella were poultry and pork. The tetracycline resistance genes most frequently detected from Salmonella spp. were tetA followed by tetB. The gene sul1 followed by sul2 were the most frequently sulfonamide resistance genes present in Salmonella. These genes are associated with plasmids, transposons, or both, and are often conjugative, highlighting the transference potential of these genes to other bacteria, environments, animals, and humans.

Integrated Whole-Genome Sequencing Infrastructure for Outbreak Detection and Source Tracing of Salmonella enterica Serotype Enteritidis

As an important foodborne pathogen, Salmonella enterica serotype Enteritidis is recognized as one of the most common causes of human salmonellosis globally. Outbreak detection for this highly homogenous serotype, however, has remained challenging. Rapid advances in sequencing technologies have presented whole-genome sequencing (WGS) as a significant advancement for source tracing and molecular typing of foodborne pathogens. A retrospective analysis was conducted using Salmonella Enteritidis isolates (n = 65) from 11 epidemiologically confirmed outbreaks and a collection of contemporaneous sporadic isolates (n = 258) during 2007-2017 to evaluate the performance of WGS in delineating outbreak-associated isolates. Whole-genome single-nucleotide polymorphism (SNP)-based phylogenetic analysis revealed well-supported clades in concordance with epidemiological evidence and pairwise distances of ≤3 SNPs for all outbreaks. WGS-based framework of outbreak detection was thus proposed and applied prospectively to investigate isolates (n = 66) from nine outbreaks during 2018-2019. We further demonstrated the superior discriminatory power and accuracy of WGS to resolve and delineate outbreaks for pragmatic food source tracing. The proposed integrated WGS framework is the first in China for Salmonella Enteritidis and has the potential to serve as a paradigm for outbreak detection and source tracing of Salmonella throughout the stages of food production, as well as expanded to other foodborne pathogens.

Antibiotic Resistance in Salmonella Typhimurium Isolates Recovered From the Food Chain Through National Antimicrobial Resistance Monitoring System Between 1996 and 2016

Salmonella is a major foodborne pathogen which causes widespread contamination and infection worldwide. Salmonella Typhimurium is one of the leading serovars responsible for human and animal salmonellosis, globally. The increasing rate of antibiotic resistance in Salmonella Typhimurium poses a significant global concern, and an improved understanding of the distribution of antibiotic resistance patterns in Salmonella Typhimurium is essential for choosing the suitable antibiotic for the treatment of infections. To evaluate the roles of animal and human in antibiotic resistance dissemination, this study aims to categorize 11,447 S. Typhimurium strains obtained across the food-chain, including food animals, retail meats and humans for 21 years in the United States by analyzing minimum inhibitory concentrations (MICs) values for 27 antibiotics. Random Forest Algorithm and Hierarchical Clustering statistics were used to group the strains according to their minimum inhibitory concentration values. Classification and Regression Tree analysis was used to identify the best classifier for human- and animal-populations’ isolates. We found the persistent population or multi-drug resistant strains of S. Typhimurium across the four time periods (1996∼2000, 2001∼2005, 2006∼2010, 2011∼2016). Importantly, we also detected that there was more diversity in the MIC patterns among S. Typhimurium strains isolated between 2011 and 2016, which suggests significant emergence of diversified multi-drug resistant strains. The most frequently observed (43%) antibiotic resistance patterns found in S. Typhimurium were tetra-resistant pattern ASSuT (ampicillin, streptomycin, sulfonamides, and tetracycline) and the penta-resistant pattern ACSSuT (ampicillin, chloramphenicol, streptomycin, sulfonamides, and tetracycline). Animals (mainly swine and bovine) are the major source for these two frequently found antibiotic resistance patterns. The occurrence of antibiotic resistant strains from humans and chicken is alarming. Strains were mostly susceptible to fluoroquinolones. Together, this study helped in understanding the expansion of dynamics of antibiotic resistance of S. Typhimurium and recommended fluoroquinolones as a possible treatment options against S. Typhimurium infection.

Characterization of Salmonella enterica serovars recovered from meat products legally and illegally imported into the EU reveals the presence of multiresistant and AmpC-producing isolates

BACKGROUND

Food products of animal origin brought into the EU from third countries, both legally and illegally, can harbor foodborne pathogens such as Salmonella enterica. In this study, we examined five S. enterica isolates recovered either from legally imported chicken meat (n = 3) or from meat products confiscated from air travel passengers arriving in Germany (n = 2). The isolates were serotyped and further characterized by antimicrobial susceptibility testing, PCR-detection and sequencing of genes associated with antimicrobial resistances, and macrorestriction analysis. Transferability of resistance to third-generation cephalosporins was assessed by conjugation experiments and the plasmids tested for their incompatibility groups.

RESULTS

The three isolates from legal imports were identified as S. Heidelberg or as non-flagellated. All three isolates were identified as AmpC producers carrying bla CMY-2 and as non-susceptible to ciprofloxacin. They were additionally resistant to tetracycline and sulfamethoxazole. The bla CMY-2-carrying plasmids were transferable by conjugation and belonged to incompatibility groups IncI1 or IncA/C. The two isolates from illegally imported meat belonged to the serovars Infantis or Weltevreden. The former was phenotypically resistant to five classes of antimicrobial agents while the S. Weltevreden isolate was fully susceptible to all agents tested.

CONCLUSION

The results of this study demonstrate that meat products imported from third countries, both legally and illegally, can harbor multiresistant Salmonella enterica. Consequently, these imports could constitute a source for the dissemination of antimicrobial resistant isolates, including those resistant to third-generation cephalosporins and fluoroquinolones.

Fluoroquinolone resistance in Salmonella: insights by whole-genome sequencing

Fluoroquinolone (FQ)-resistant Salmonella spp. were listed by the WHO in 2017 as priority pathogens for which new antibiotics were urgently needed. The overall global burden of Salmonella infections is high, but differs per region. Whereas typhoid fever is most prevalent in South and South-East Asia, non-typhoidal salmonellosis is prevalent across the globe and associated with a mild gastroenteritis. By contrast, invasive non-typhoidal Salmonella cause bloodstream infections associated with high mortality, particularly in sub-Saharan Africa. Most Salmonella strains from clinical sources are resistant to first-line antibiotics, with FQs now being the antibiotic of choice for treatment of invasive Salmonella infections. However, FQ resistance is increasingly being reported in Salmonella, and multiple molecular mechanisms are already described. Whole-genome sequencing (WGS) is becoming more frequently used to analyse bacterial genomes for antibiotic-resistance markers, and to understand the phylogeny of bacteria in relation to their antibiotic-resistance profiles. This mini-review provides an overview of FQ resistance in Salmonella, guided by WGS studies that demonstrate that WGS is a valuable tool for global surveillance.