Genomic Characterization of Endemic and Ecdemic Non-typhoidal Salmonella enterica Lineages Circulating Among Animals and Animal Products in South Africa

Whole genome analysis of Salmonella Gallinarum strains isolated from a fowl typhoid outbreak in southern Brazil

1. Salmonella Gallinarum strains isolated from a southern Brazil fowl typhoid outbreak were subjected to phenotypic and genotypic analyses to identify genetic elements that could improve prevention and control strategies.2. Whole-genome sequencing revealed the presence of the aac(6')-Iaa gene, conferring aminoglycoside resistance, along with novel chromosomal point mutations, including the first detection of parE p.S451F in Salmonella Gallinarum.3. Additionally, IncFII(S) plasmid replicons, Salmonella pathogenicity islands and 105 virulence genes associated with cell adhesion, invasion and antimicrobial peptide resistance were identified.4. These findings shed light on the molecular mechanisms of fowl typhoid and provide crucial insights into emerging antimicrobial resistance and virulence factors.

R programming environment in wildlife: Are Veterinary Sciences at the same level than other research areas?

The computing environment has revolutionized the management and analysis of data in sciences during the last decades. This study aimed to evaluate the use of R software in research articles addressing the study of wildlife worldwide, particularly focusing on the research area "Veterinary Sciences". For this purpose, a systematic review mainly performed in the Web of Science database was conducted. Out of a total of 509 articles reviewed, our results show an increasing trend of the number of publications using the R software over time, as well as a wide geographical distribution at a global scale, particularly in North America, Europe, Australia and China. Most publications were categorized in research areas related to "Biological Sciences", while a minority of them was included in "Veterinary Sciences" (5.9%; 30/509). About the species groups assessed, many articles evaluated a single species group (96.5%), being mammals (50.7%) and birds (14.8%) the most studied ones. The present study showed a high variety of R-packages used in the publications reviewed, all of them related to data analysis, the study of genetic/phylogenetic information and graphical representation. Interestingly, the common use of packages between different research areas is indicative of the high interest of using R software in scientific articles. Our study points the R software as an open-source programming language that allows to support research addressing the study of wildlife, becoming a key software for many research areas, including "Veterinary Sciences". However, an in-depth methodological description about the use of R software in publications to improve the tracking, reproducibility and transparency is encouraged.

Egg-associated Salmonella enterica serovar Enteritidis: comparative genomics unveils phylogenetic links, virulence potential, and antimicrobial resistance traits

Salmonella enterica serovar Enteritidis (SE) remains a frequent cause of foodborne illnesses associated with the consumption of contaminated hen eggs. Such a food-pathogen association has been demonstrated epidemiologically, but the molecular basis for this association has not been explored. Comparative genomic analysis was implemented to decipher the phylogenomic characteristics, antimicrobial resistance, and virulence potential of eggs-associated SE. Analyzing 1,002 genomes belonging to 841 sequence types of food-isolated SE strains suggests a high genomic similarity within the egg-related lineage, which is phylogenetically close to SE strains isolated from poultry but is different from those isolated from beef. Core genome- and single nucleotide polymorphism (SNP)-based phylogeny of 74 SE strains of egg origin showcased two distinct sublineages. Time-scaled phylogeny supported the possibility of a common ancestor of egg-related SE lineages. Additionally, genome mining revealed frequent antibiotic resistance due to the presence of aac(6')-Iaa and mdsAB encoded on the genomes of egg-associated SE strains. For virulence gene profiling, 103-113 virulence determinants were identified in the egg-associated SE, which were comparable to 112 determinants found in human-associated SE, emphasizing the capacity of egg-associated strains to infect humans and cause diseases. The findings of this study proved the genomic similarity of egg-associated SE strains, and these were closely related to poultry strains. The egg-associated strains also harbor virulence genes equivalent to those found in human-associated SE strains. The analysis provided critical insights into the genetic structure, phylogenomics, dynamics of virulence, and antibiotic resistance of Salmonella Enteritidis, circulating in eggs and emphasizing the necessity of implementing anti-Salmonella intervention strategies, starting at the production stage of the poultry supply chain.

Prevalence of Salmonella species and factors associated with contamination of mechanically recovered poultry meat imported into South Africa, 2016-2017

Background and Aim

Mechanically recovered meat (MRM) products have been linked to outbreaks of human salmonellosis. However, no studies have investigated the prevalence of Salmonella species in MRM products in South Africa despite the products being imported. Therefore, this study aimed to estimate the prevalence and factors associated with Salmonella spp. contamination of mechanically recovered poultry meat (MRPM) imported into South Africa.

Materials and Methods

This study used secondary data of MRPM consignments imported through a port entry into South Africa from May 2016 to December 2017. Crude and factor-specific proportions of Salmonella positive MRPM and their 95% confidence intervals were calculated. A logistic regression model was used to assess the association among country, season, importer, year, and MRPM Salmonella status.

Results

A total of 8127 MRPM consignments were imported. Seventeen percentages (17.18%, 985/5733) of consignments tested positive for Salmonella species and only 364 isolates were serotyped. Salmonella Heidelberg (73.90%, 269/364) was the most common serotype followed by Salmonella Infantis (6.59%, 24/364), Salmonella Salamae (4.67%, 17/364), and Salmonella Schwarzengrund (3.57%, 13/364). The odds of a consignment testing positive for Salmonella spp. was higher among consignments from country-B (Odds Ratio [OR]: 3.958, p < 0.0001) compared to "All others." The odds of testing positive for Salmonella were also higher among consignments imported in autumn (OR: 1.488, p < 0.0001) but lower among those imported in spring (OR: 0.767, p = 0.0004) and summer (OR: 0.843, p < 0.0001) when compared to the winter season. Consignments imported in 2016 compared to 2017 were 1.563 times (p < 0.0001) as likely to test positive for a Salmonella species.

Conclusion

Salmonella species were reported in MRPM consignments in this study with Salmonella Heidelberg being the most common serotype. Furthermore, some Salmonella serotypes reported in this study have been implicated in foodborne disease outbreaks. Country of origin, season, and year of importation were significantly associated with the odds of a consignment testing positive for Salmonella species.

A multidrug-resistant Salmonella enterica Typhimurium DT104 complex lineage circulating among humans and cattle in the USA lost the ability to produce pertussis-like toxin ArtAB

Salmonella enterica subsp. enterica serotype Typhimurium definitive type 104 (DT104) can infect both humans and animals and is often multidrug-resistant (MDR). Previous studies have indicated that, unlike most S . Typhimurium, the overwhelming majority of DT104 strains produce pertussis-like toxin ArtAB via prophage-encoded genes artAB . However, DT104 that lack artAB have been described on occasion. Here, we identify an MDR DT104 complex lineage circulating among humans and cattle in the USA, which lacks artAB (i.e. the ‘U.S. artAB -negative major clade’; n =42 genomes). Unlike most other bovine- and human-associated DT104 complex strains from the USA (n =230 total genomes), which harbour artAB on prophage Gifsy-1 (n =177), members of the U.S. artAB -negative major clade lack Gifsy-1, as well as anti-inflammatory effector gogB . The U.S. artAB -negative major clade encompasses human- and cattle-associated strains isolated from ≥11 USA states over a 20-year period. The clade was predicted to have lost artAB , Gifsy-1 and gogB circa 1985–1987 (95 % highest posterior density interval 1979.0–1992.1). When compared to DT104 genomes from other regions of the world (n =752 total genomes), several additional, sporadic artAB , Gifsy-1 and/or gogB loss events among clades encompassing five or fewer genomes were observed. Using phenotypic assays that simulate conditions encountered during human and/or bovine digestion, members of the U.S. artAB -negative major clade did not differ from closely related Gifsy-1/artAB /gogB -harbouring U.S. DT104 complex strains (ANOVA raw P >0.05); thus, future research is needed to elucidate the roles that artAB , gogB and Gifsy-1 play in DT104 virulence in humans and animals.

Whole-genome sequencing and phylogenetic analysis capture the emergence of a multi-drug resistant Salmonella enterica serovar Infantis clone from diagnostic animal samples in the United States

Introduction

Salmonella enterica is a major cause of foodborne illness in the United States. A multi-drug resistant (MDR) emergent Salmonella Infantis (ESI) with a megaplasmid (pESI) was first identified in Israel and Italy and subsequently reported worldwide. The ESI clone carrying an extended spectrum β-lactamase blaCTX-M-65 on a pESI-like plasmid and a mutation in the gyrA gene has recently been found in the United States in poultry meat.

Methods

We analyzed the phenotypic and genotypic antimicrobial resistance, genomics and phylogeny of 200 S. infantis isolates from animal diagnostic samples.

Results

Of these, 33.5% were resistant to at least one antimicrobial and 19.5% were multi-drug resistant (MDR). Eleven isolates from different animal sources were phenotypically and genetically similar to the ESI clone. These isolates had a D87Y mutation in the gyrA gene conferring reduced susceptibility to ciprofloxacin and harbored a combination of 6-10 resistance genes: blaCTX-M-65, aac(3)-IVa, aadA1, aph(4)-Ia, aph(3')-Ia, floR, sul1, dfrA14, tetA, and fosA. These 11 isolates carried class I and class II integrons and three virulence genes: sinH, involved in adhesion and invasion, ybtQ and ybtP, associated with iron transport. These isolates were also closely related to each other (separated by 7 to 27 SNPs) and phylogenetically related to the ESI clone recently found in the U.S.

Discussion

This dataset captured the emergence of the MDR ESI clone in multiple animal species and the first report of a pESI-like plasmid in isolates from horses in the U.S.

What is the Source of Infections Causing Invasive Nontyphoidal Salmonella Disease?

Invasive nontyphoidal Salmonella (iNTS) disease is a clinical condition distinct from Salmonella gastroenteritis. With an overall case-fatality rate of 14.5%, iNTS remains a major cause of morbidity and mortality, particularly in sub-Saharan Africa. However, the sources of infections that lead to cases of iNTS remain unclear. Broadly, there are 2 hypotheses as to the source of infections: (i) transmission from a zoonotic reservoir, similar to other nontyphoidal salmonelloses; or (ii) person-to-person transmission. Here we review several recent studies that have asked, "What is the source of infections causing invasive nontyphoidal Salmonella disease?" Two studies reported isolates in the stool of household members of iNTS cases that were very closely related (<3 single-nucleotide polymorphisms) to the iNTS case isolates; this is consistent with the hypothesis of person-to-person transmission, but infection from a common source (eg, a foodstuff) cannot be excluded. On the other hand, thorough investigations of the domestic environment of iNTS cases and the food pathway found only a single iNTS-associated Salmonella Enteritidis isolate. Therefore, we recommend that future studies test the hypothesis that iNTS is transmitted between people within the domestic environment. Further studies of food and water pathways are also warranted.

Evaluation of Genomic Typing Methods in the Salmonella Reference Laboratory in Public Health, England, 2012-2020

We aim to provide an evidence-based evaluation of whole genome sequence (WGS) methods, employed at the Salmonella reference laboratory in England, in terms of its impact on public health and whether these methods remain a fit for purpose test under UKAS ISO 15189. The evaluation of the genomic methods were mapped against the value of detecting microbiological clusters to support the investigation of food-borne outbreaks of Salmonella in England between 2012-2020. The analysis of WGS with both SNP- and allelic-based methods provided an unprecedented level of strain discrimination and detection of additional clusters when comparing to all of the previous typing methods. The robustness of the routine genomic sequencing at the reference laboratory ensured confidence in the microbiological identifications, even in large outbreaks with complex international food distribution networks. There was evidence that the phylogeny derived from the WGS data can be used to inform the provenance of strains and support discrimination between domestic and non-domestic transmission events. Further insight on the evolutionary context of the emerging pathogenic strains was enabled with a deep dive of the phylogenetic data, including the detection of nested clusters. The public availability of the WGS data linked to the clinical, epidemiological and environmental context of the sequenced strains has improved the trace-back investigations during outbreaks. The global expansion in the use of WGS-based typing in reference laboratories has shown that the WGS methods are a fit for purpose test in public health as it has ensured the rapid implementation of interventions to protect public health, informed risk assessment and has facilitated the management of national and international food-borne outbreaks of Salmonella.

Review of major meat-borne zoonotic bacterial pathogens

The importance of meat-borne pathogens to global disease transmission and food safety is significant for public health. These pathogens, which can cause a variety of diseases, include bacteria, viruses, fungi, and parasites. The consumption of pathogen-contaminated meat or meat products causes a variety of diseases, including gastrointestinal ailments. Humans are susceptible to several diseases caused by zoonotic bacterial pathogens transmitted through meat consumption, most of which damage the digestive system. These illnesses are widespread worldwide, with the majority of the burden borne by developing countries. Various production, processing, transportation, and food preparation stages can expose meat and meat products to bacterial infections and/or toxins. Worldwide, bacterial meat-borne diseases are caused by strains of Escherichia coli, Salmonella, Listeria monocytogenes, Shigella, Campylobacter, Brucella, Mycobacterium bovis, and toxins produced by Staphylococcus aureus, Clostridium species, and Bacillus cereus. Additionally, consuming contaminated meat or meat products with drug-resistant bacteria is a severe public health hazard. Controlling zoonotic bacterial pathogens demands intervention at the interface between humans, animals, and their environments. This review aimed to highlight the significance of meat-borne bacterial zoonotic pathogens while adhering to the One Health approach for creating efficient control measures.

Resistome and virulome diversity of foodborne pathogens isolated from artisanal food production chain of animal origin in the Mediterranean region

The aim of the present study was to investigate the resistome and virulome diversity of 43 isolates of Listeria monocytogenes, Salmonella enterica and S. aureus collected from artisanal fermented meat and dairy products and their production environments in Portugal, Spain, Italy and Morocco. After DNA extraction, genomes were sequenced, and de novo assembled. Genetic relationships among genomes were investigated by SNP calling and in silico 7- loci MLST. Genomes of the same species belonged to different ST-types demonstrating the circulation of different clones in in the same artisanal production plant. One specific clone included genomes of S. Paratyphi B belonging to ST43 and repeatedly isolated for more than a year in an artisanal sausage production plant. No genomes but three (belonging to Salmonella enterica), were predicted as multiresistant to different antimicrobials classes. Regarding virulence, genomes of L. monocytogenes belonging to ST1, ST3 and ST489, as well as genomes of S.enterica enterica (ST43, ST33, ST314, ST3667, ST1818, ST198) and ST121 S. aureus were predicted as virulent and hypervirulent. The occurrence of virulent and hypervirulent L. monocytogenes, Salmonella enterica and S. aureus strains in artisanal fermented meat and dairy productions as well as in their finished products suggests the need for a specific focus on prevention and control measures able to reduce the risk of these biological hazards in artisanal food productions.

Investigation of the Genes Involved in the Outbreaks of Escherichia coli and Salmonella spp. in the United States

Salmonella spp. and Escherichiacoli (E. coli) are two of the deadliest foodborne pathogens in the US. Genes involved in antimicrobial resistance, virulence, and stress response, enable these pathogens to increase their pathogenicity. This study aims to examine the genes detected in both outbreak and non-outbreak Salmonella spp. and E. coli by analyzing the data from the National Centre for Biotechnology Information (NCBI) Pathogen Detection Isolates Browser database. A multivariate statistical analysis was conducted on the genes detected in isolates of outbreak Salmonella spp., non-outbreak Salmonella spp., outbreak E. coli, and non-outbreak E. coli. The genes from the data were projected onto a two-dimensional space through principal component analysis. Hierarchical clustering was then used to quantify the relationship between the genes in the dataset. Most of the outlier genes identified in E. coli isolates are virulence genes, while outlier genes identified in Salmonella spp. are mainly involved in stress response. Gene epeA, which encodes a high-molecular-weight serine protease autotransporter of Enterobacteriaceae (SPATE) protein, along with subA and subB that encode cytotoxic activity, may contribute to the pathogenesis of outbreak E. coli. The iro operon and ars operon may play a role in the ecological success of the epidemic clones of Salmonella spp. Concurrent relationships between esp and ter operons in E. coli and pco and sil operons in Salmonella spp. are found. Stress-response genes (asr, golT, golS), virulence gene (sinH), and antimicrobial resistance genes (mdsA and mdsB) in Salmonella spp. also show a concurrent relationship. All these findings provide helpful information for experiment design to combat outbreaks of E. coli and Salmonella spp.