Distribution and factors associated with Salmonella enterica genotypes in a diverse population of humans and animals in Qatar using multi-locus sequence typing (MLST)

Multi-locus sequence typing, antimicrobials resistance and virulence profiles of Salmonella enterica isolated from bovine carcasses in Minas Gerais state, Brazil

The aim of this study was to identify virulence and antimicrobial resistance profiles and determine the sequence type (ST) by multilocus sequence typing (MLST) of Salmonella enterica isolates from bovine carcasses from slaughterhouse located in Minas Gerais state, Brazil, and its relationship with bovine isolates obtained on the American continent based on sequence type profile. The MLST results were compared with all Salmonella STs associated with cattle on American continent, and a multi-locus sequence tree (MS tree) was built. Among the 17 S. enterica isolates, five ST profiles identified, and ST10 were the most frequent, grouping seven (41.2%) isolates. The isolates presented 11 different profiles of virulence genes, and six different antibiotics resistance profiles. The survey on Enterobase platform showed 333 Salmonella STs from American continent, grouped into four different clusters. Most of the isolates in the present study (13/17), were concentrated in a single cluster (L4) composed by 74 STs. As a conclusion, five different STs were identified, with ST10 being the most common. The isolates showed great diversity of virulence genes and antibiotics resistance profiles. Most of the isolates of this study were grouped into a single cluster composed by 74 STs formed by bovine isolates obtained on the American continent.

Rodent-Related Zoonotic Pathogens at the Human-Animal-Environment Interface in Qatar: A Systematic Review and Meta-Analysis

Rodents are one of the most diversified terrestrial mammals, and they perform several beneficial activities in nature. These animals are also important as carriers of many pathogens with public health importance. The current systematic review was conducted to formulate a true depiction of rodent-related zoonoses in Qatar. Following systematic searches on PubMed, Scopus, Science Direct, and Web of Science and a screening process, a total of 94 published articles were selected and studied. The studied articles reported 23 rodent-related zoonotic pathogens that include nine bacterial, eleven parasitic, and three viral pathogens, from which the frequently reported pathogens were Mycobacterium tuberculosis (32 reports), Escherichia coli (23), and Salmonella spp. (16). The possible pathway of entry of the rodent-borne pathogens can be the land port, seaports, and airport of Qatar through carrier humans and animals, contaminated food, and agricultural products. The pathogens can be conserved internally by rodents, pets, and livestock; by agricultural production systems; and by food marketing chains. The overall estimated pooled prevalence of the pathogens among the human population was 4.27% (95%CI: 4.03–4.51%; p < 0.001) with significant heterogeneity (I² = 99.50%). The top three highest prevalent pathogens were M.tuberculosis (30.90%; 22.75–39.04%; p < 0.001; I² = 99.70%) followed by Toxoplasma gondii (21.93%; 6.23–37.61%; p < 0.001; I² = 99.30%) and hepatitis E virus (18.29%; 11.72–24.86%; p < 0.001; I² = 96.70%). However, there is a knowledge gap about the listed pathogens regarding the occurrence, transmission pathways, and rodent role in transmission dynamics at the human–animal–environment interface in Qatar. Further studies are required to explore the role of rodents in spreading zoonotic pathogens through the One Health framework, consisting of zoologists, ecologists, microbiologists, entomologists, veterinarians, and public health experts in this country.

Genomic investigation of antimicrobial resistance determinants and virulence factors in Salmonella enterica serovars isolated from contaminated food and human stool samples in Brazil

This study investigated the antimicrobial resistance determinants, virulence factors and identified serovars in 37 Salmonella enterica strains isolated from human stool and contaminated foods linked to outbreaks that occurred in Brazil over 7 years using whole genome sequencing (WGS). Phylogenetic analysis of selected serovars (S. Typhimurium, S. Infantis, S. London, and S. Johannesburg) was performed. Ten distinct serovars were identified and, 51% of the tested strains (n = 19) showed disagreement with the previous conventional serotyping. The antimicrobial resistance (AMR) determinants or plasmids varied among the strains. Resistome analysis revealed the presence of resistance genes to aminoglycosides [aac (6')-laa, aph (3″)-lb, aph (6)-ld, aadA1 and aadA2], sulfonamides (sul1), trimethoprin (dfrA8), fosfomycin (fosA7) and tetracyclines (tetA, tetB, tetC), as well as point mutations in parC (T57S) and gyrA (S83F). Plasmidome showed the presence of IncHI2, IncHI2A, IncFIB (S), IncFII (S), IncI1 and p0111 plasmids. Eight Salmonella pathogenicity islands and up to 102 stress and/or virulence genes were identified in the evaluated genomes. Virulence genes of K88 fimbrial adhesin were first reported in S. enterica (S. Pomona, S. Bredeney and S. Mbandaka strains). pilW gene was first identified in S. Pomona. Phylogenetic analysis showed that some serovars circulated in Brazil for decades, primarily within the poultry production chain. Findings highlighted the virulence and AMR determinants in strains that may lead to recurring food outbreaks.

Isolation and characterization of Salmonella in pork samples collected from retail and wholesale markets in each season from 2016 to 2018 in Wuhan, China

AIMS

To investigate the prevalence and characteristics of Salmonella in pork on sale in Wuhan, Central China.

METHODS AND RESULTS

A total of 4744 pork samples were collected from retail or wholesale markets in each season from 2016 to 2018. The samples showed an overall Salmonella prevalence of 19·54% (927/4744), among which the samples collected in 2017 (21·67%, 428/1975) possessed a significantly higher prevalence than those collected in 2016 (18·61%, 209/1123) (P = 0·047) or 2018 (17·51%, 290/1656) (P = 0·002), and the samples collected in winter showed the lowest prevalence (15·86%, 177/1116). The Salmonella prevalence was significantly higher among samples from retail markets (25·68%, 283/1102) than wholesale markets (17·68%, 644/3642) (P = 0·000). Antimicrobial resistance of 922 Salmonella strains was tested by determining the minimal inhibitory concentrations using a broth microdilution method. The strains revealed that 98·92% (912/922) were resistant to at least one of the antimicrobial agents, and 80·04% (738/922) were resistant to three or more antimicrobials (MDR). Resistance to sulfamethoxazole/trimethoprim (89·91%), tetracycline (87·20%) and ampicillin (71·69%) was predominant. The proportion of MDR strains in 2017 (93·62%, 396/423) was significantly higher than that in 2016 (63·16%, 132/209) (P = 0·000) or 2018 (69·66%, 202/290) (P = 0·000). No significant difference was observed in the proportions of MDR strains between wholesale markets (76·07%, 213/280) and retail markets (80·53%, 517/642) (P = 0·075). Multi-locus sequence typing for 554 of the isolates revealed 20 different sequence types (STs), among which ST40 (38·27%, 212/554), ST34 (18·41%, 102/554) and ST469 (14·46%, 79/554) were dominant.

CONCLUSIONS

A high risk of Salmonella prevalence and antimicrobial resistance was observed in pork in Wuhan. The risk varies between different sampling years, seasons and market types.

SIGNIFICANCE AND IMPACT OF THE STUDY

Providing baseline data on Salmonella contamination in pork on sale in Central China.

Incidence and Characterization of Salmonella Isolates From Raw Meat Products Sold at Small Markets in Hubei Province, China

Salmonella is a leading cause of foodborne disease and is often associated with the consumption of foods of animal origin. In this study, sixty-six Salmonella isolates were obtained from 631 raw meat samples purchased at small retail suppliers in Hubei Province, China. The most prevalent Salmonella serotypes were Thompson (18.2%) and Agona (13.6%). Frequent antimicrobial resistance was observed for the sulfonamides (43.9%), tetracycline (43.9%), and the β-lactams amoxicillin and ampicillin (36.4% for each). Interestingly, a high incidence of resistance to cephazolin was observed in strains of the most common serotype, S. Thompson. Class I integrons were found in 27.3% (18/66) of the isolates and five of these integrons contained different gene cassettes (aacA4C-arr-3-dfr2, dfrA12-aadA21, aadA2, dfrA12-aadA2, dfr17-aadA5). Additional antimicrobial resistance genes, including bla _TEM-1, bla _CTX-M-65, bla _CTX-M-15, qnrB, and qnrS, were also identified among these Salmonella isolates. Results of replicon typing and conjugation experiments revealed that an integron with qnrB and bla _CTX-M-15 genes was present on incH12 mobile plasmid in S. Thompson strain. Multilocus sequence typing (MLST) analysis revealed 32 sequence types, indicating that these isolates were phenotypically and genetically diverse, among which ST26 (18.2%) and ST541 (12.1%) were the predominant sequence types. The integrons, along with multiple antimicrobial resistance genes on mobile plasmids, are likely contributors to the dissemination of multidrug resistance in Salmonella.

Childhood Diarrhoea in the Eastern Mediterranean Region with Special Emphasis on Non-Typhoidal Salmonella at the Human⁻Food Interface

Diarrhoeal disease is still one of the most challenging issues for health in many countries across the Eastern Mediterranean region (EMR), with infectious diarrhoea being an important cause of morbidity and mortality, especially in children under five years of age. However, the understanding of the aetiological spectrum and the burden of enteric pathogens involved in diarrhoeal disease in the EMR is incomplete. Non-typhoidal Salmonella (NTS), the focus of this review, is one of the most frequently reported bacterial aetiologies in diarrhoeal disease in the EMR. Strains of NTS with resistance to antimicrobial drugs are increasingly reported in both developed and developing countries. In the EMR, it is now widely accepted that many such resistant strains are zoonotic in origin and acquire their resistance in the food-animal host before onward transmission to humans through the food chain. Here, we review epidemiological and microbiological aspects of diarrhoeal diseases among children in the EMR, with emphasis on the implication and burden of NTS. We collate evidence from studies across the EMR on the zoonotic exposure and antimicrobial resistance in NTS at the interface between human and foods of animal origin. This review adds to our understanding of the global epidemiology of Salmonella with emphasis on the current situation in the EMR.

Molecular Detection and Epidemiological Features of Selected Bacterial, Viral, and Parasitic Enteropathogens in Stool Specimens from Children with Acute Diarrhea in Thi-Qar Governorate, Iraq

Knowledge of etiology causes of diarrheal illness is essential for development and implementation of public health measures to prevent and control this disease syndrome. There are few published studies examining diarrhea in children aged <5 years in Iraq. This study aims to investigate the occurrences and epidemiology of selected bacterial (Salmonella spp. and Campylobacter spp.), viral (adenovirus, norovirus GI and GII, and astrovirus), and parasitic (Entamoeba spp. and Giardia spp.) agents in stool samples from 155 child diarrheal cases enrolled between March and August 2017, in a hospital-based cross-sectional study in Thi-Qar, southeastern Iraq. Using molecular techniques and sequence-based characterization, adenovirus was the most frequently detected enteropathogen (53/155 (34.2%)), followed by Salmonella spp. (23/155 (14.8%)), Entamoeba spp. (21/155 (13.5%)), and Campylobacter spp. (17/155 (10.9%)). Mixed infection with Salmonella spp. and Campylobacter spp. was evident, and the same was revealed between various enteric viruses, particularly adenovirus and norovirus. The most frequent co-infection pattern was between adenovirus and Campylobacter spp., in seven cases (7/155 (4.5%)). Whole-genome sequencing-derived typing data for Salmonella isolates (n = 23) revealed that sequence type 49 was the most prevalent in this sample set (15/23 (65.2%)). To the best of our knowledge, this study provides the first report on detection and identification of floR, bla_CARB-2, and mphA antimicrobial resistance genes in Salmonella isolated from children in the Middle East region. Logistic regression analysis pointed to few enteropathogen-specific correlations between child age, household water source, and breastfeeding patterns in relation to the outcome of detection of individual enteropathogens. This study presents the first published molecular investigation of multiple enteropathogens among children <5 years of age in Iraq. Our data provide supporting evidence for planning of childhood diarrhea management programs. It is important to build on this study and develop future longitudinal case-control research in order to elaborate the epidemiology of enteropathogens in childhood diarrhea in Iraq.

Non-typhoidal Salmonella blood stream infection in Kuwait: Clinical and microbiological characteristics

Non-typhoidal Salmonella (NTS) bacteremia is a significant cause of morbidity and mortality worldwide. It is considered to be an emerging and neglected tropical disease in Africa. We studied this in two tertiary hospitals–Al Farwaniya and Al Amiri–in Kuwait, a subtropical country, from April 2013-May 2016. NTS bacteremia was present in 30 of 53,860 (0.75%) and 31 of 290,36 (1.33%) blood cultures in the two hospitals respectively. In Al Farwaniya hospital, one-third of the patients were from some tropical developing countries of Asia. About 66% of all patients (40/61) had diarrhea, and of these, 65% had the corresponding blood serovar isolated from stool culture. A few patients had Salmonella cultured from urine. Patients were either young or old. Most of the patients had co-morbidities affecting the immune system. Two patients each died in both hospitals. The number of different serovars cultured in each hospital was 13, and most infections were due to S. Enteritidis (all sequence type [ST]) 11) and S. Typhimurium (all ST19) except in a subgroup of expatriate patients from tropical developing countries in Al Farwaniya hospital. About a quarter of the isolates were multidrug-resistant. Most patients were treated with a cephalosporin with or without other antibiotics. S. Enteritidis and S. Typhimurium isolates were typed by pulsed field-gel electrophoresis (PFGE) and a selected number of isolates were whole-genome sequenced. Up to four different clades were present by PFGE in either species. Whole-genome sequenced isolates showed antibiotic-resistance genes that showed phenotypic correlation, and in some cases, phenotypes showed absence of specific genes. Whole-genome sequenced isolates showed presence of genes that contributed to blood-stream infection. Phylogeny by core genome analysis showed a close relationship with S. Typhimurium and S. Enteritidis from other parts of the world. The uniqueness of our study included the finding of a low prevalence of infection, mortality and multidrug-resistance, a relatively high prevalence of gastrointestinal infection in patients, and the characterization of selected isolates of S. Typhimurium and S. Enteritidis serovars by whole-genome sequencing that shed light on phylogeny, virulence and resistance. Similarities with studies from developing countries especially Africa included infection in patients with co-morbidities affecting the immune system, predominance of S. Typhimurium and S. Enteritidis serovars and presence of drug-resistance in isolates.

Salmonella organisms are classified into typhoidal Salmonella (causing enteric fever) and non-typhoidal Salmonella (NTS) (causing infections other than enteric fever). Apart from causing other infections, NTS causes blood-stream infection (bacteremia and septicemia). NTS blood stream infection (NTS-BI) is considered to be an emerging and neglected tropical disease in Africa. It causes a very high morbidity and mortality in Africa. The individuals affected in Africa are children, malnourished people, patients with malaria or HIV etc. These conditions affect the immune system and make them vulnerable to infection with NTS. In these patients, diarrheal disease due to NTS is rare. The majority of infections are due to two types of NTS: Typhimurium and Enteritidis. There is a very high prevalence of multidrug-resistance in NTS making the infection difficult to treat. NTS-BI is also present in other parts of the world including developed countries albeit at a lower prevalence. Kuwait is a high-income, subtropical country in transition (from a developing to developed country), located in the Middle East. We studied NTS-BI in Al Farwaniya and Al Amiri hospitals in Kuwait during April 2013 to May 2016. Out of nearly 30,000 to more than 50,000 blood cultures done in these hospitals, NTS was present in 0. 75 to 1.33% of blood cultures, representing a very small proportion of blood cultures, unlike in Africa. This showed that 31 patients in Al Farwaniya hospital and 30 patients in Al Amari hospital had NTS-BI. Most of these patients had underlying illnesses such as diabetes, lung infection, cancer etc. that affect the immune system, as in Africa. Many patients also had diarrheal disease caused by the same NTS that caused blood stream infection, unlike in Africa. Only two patients in each hospital died, a low mortality, unlike in Africa. The majority of the isolates belonged to Typhimurium and Enteritidis as in Africa. Even though resistance to drugs was a problem, about quarter of the isolates only were multidrug-resistant, a lower prevalence compared to in Africa. In Kuwait, we performed a detailed genetic study of a selected number of Typhimurium and Enteritidis isolates by a modern technique called whole genome sequencing. This revealed genetic determinants encoding drug-resistance and virulence causing blood-stream infection. This type of study was not performed in African isolates. Thus, our study revealed similarities and differences with studies of NTS-BI in Africa.

Foodborne disease and food control in the Gulf States

Gulf States in the Middle East have had to change rapidly from subsidence herding, farming and fishing communities to modern states through the exploitation of revenue-generating petroleum products. Fresh water is an even more precious commodity than oil today as this is seen as a rapidly diminishing resource through over use of aquifers with scarce and unpredictable rainfall not replenishing the needs of these countries which increasing rely on reverse-osmosis (RO) desalination of seawater but at a cost in terms of energy. Recycling of waste water and sewage is carried out and used to water urban landscaping and some crops, but there are risks of the presence of pathogens. Much food today is imported to satisfy the requirements of expanding populations, especially foreign workers on temporary visas who make up more than half the residents in many of these Gulf States. Despite limited published data on Gulf States regarding enteric and foodborne diseases and their prevention and control, profiles emerge that can describe the current situation and some future directions. Gastrointestinal diseases, such as typhoid, cholera, and amebic dysentery can be brought into these countries through workers returning from endemic regions, and also through refugees from conflict-torn neighboring countries. However, some diseases are endemic like brucellosis and fatal illnesses from the newly identified Middle East Respiratory Corona Virus (MERS-CoV) associated with camels. In the 1990s, coalition troops stationed during the Gulf War brought in external suppliers and caterers, but using local products like chickens with troops occasionally suffering from infections. The hot climate, particularly in summer, can allow rapid growth of pathogens in foods, especially where refrigeration is not available as in home-prepared lunches by workers and during transportation of foods across traffic-congested cities. One of the biggest concerns for Saudi Arabia is the health oversight of millions during the annual Hajj, and despite much care over restriction of infected pilgrims and care of food, occasional outbreaks have been reported. Government agencies are particularly concerned about restaurant food and try and follow up on complaints of customers but rarely are agents identified; those that have include Salmonella, Bacillus cereus and Staphylococcus aureus. Implicated foods include ethnic products such as Turkish menu items and shawarma. Local culture may play a role in allowing growth of pathogens such as serving women after men at weddings. However, deaths that have been attributed to microbial sources may have been caused by illegal use of pesticides such as aluminum phosphide. Severe penalties have been applied to owners and staff implicated in outbreaks including fines, jail sentences and deportations, which are not typical of Western nations. However, some agencies have initiatives to help educate and train foreign workers in several languages. Foodborne disease surveillance systems are generally not adequate though some countries have initiated modernization of inspection approaches and laboratories. Consumer surveys show that residents have some knowledge of foodborne disease but this could be improved especially for women who do most of the shopping and food preparation in homes. Agencies are increasing directing campaigns for general food safety in their populations, and as long as resources are available, food control is likely to improve over time in Gulf States which is good news for visitors, expatriate workers and citizens alike.

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Water availability, geographic and political overview of each of the Gulf States.

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Gastrointestinal and foodborne diseases affecting citizens and expatriate workers.

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Relevant research and government policies and actions to reduce foodborne disease.