Poultry as a possible source of non-typhoidal Salmonella enterica serovars in humans in Bangladesh

Is There a Shift in Salmonella Diversity Among Poultry in Northern India?

The present study was conducted to determine the serotype diversity of Salmonella among poultry in northern India. A total of 101 poultry droppings from 30 farms in the Jammu and Kashmir union territory were analyzed. Nineteen isolates of Salmonella were obtained, and these belonged to four serotypes: Salmonella enterica enterica serotype Kentucky (n = 3), Salmonella enterica enterica serotype Infantis (n = 5), Salmonella enterica enterica serotype Agona (n = 4), and Salmonella enterica enterica serotype Typhimurium (n= 7). The study has isolated some Salmonella serotypes that are infrequently reported in India. Some of the isolated serotypes are reported to be endemic for human nontyphoidal salmonellosis cases in the region. Whether this indicates a shift in the serotype pattern in poultry in the region needs to be investigated further. Nevertheless, the study clearly indicates the risk of foodborne salmonellosis associated with consumption of contaminated poultry and poultry products in the region.

Genome-wide analysis provides a deeper understanding of the population structure of the Salmonella enterica serotype Paratyphi B complex in Bangladesh

The Salmonella enterica serotype Paratyphi B complex causes a wide range of diseases, from gastroenteritis to paratyphoid fever, depending on the biotypes Java and sensu stricto. The burden of Paratyphi B biotypes in Bangladesh is still unknown, as these are indistinguishable by Salmonella serotyping. Here, we conducted the first whole-genome sequencing (WGS) study on 79 Salmonella isolates serotyped as Paratyphi B that were collected from 10 nationwide enteric disease surveillance sites in Bangladesh. Placing these in a global genetic context revealed that these are biotype Java, and the addition of these genomes expanded the previously described PG4 clade containing Bangladeshi and UK isolates. Importantly, antimicrobial resistance (AMR) genes were scarce amongst Bangladeshi S. Java isolates, somewhat surprisingly given the widespread availability of antibiotics without prescription. This genomic information provides important insights into the significance of S. Paratyphi B biotypes in enteric disease and their implications for public health.

Multilocus sequence typing of multidrug-resistant Salmonella strains circulating in poultry farms of Bangladesh

Salmonella is one of the most important foodborne zoonotic pathogens, and becoming multidrug-resistant (MDR), which represents a serious public health concern worldwide. This study aimed to identify the circulating MDR strains of Salmonella through cutting edge molecular techniques including gene specific PCR, RAPD-PCR, ribosomal gene sequencing, and multilocus sequence types (MLST) in the poultry industry of Bangladesh. Two hundred Salmonella isolates were retrieved from 154 samples comprising droppings (n = 60), cloacal swabs (n = 60), feeds (n = 14), feeding water (n = 14), and handler's swab (n = 6) from 14 commercial layer farms of Bangladesh. The isolates were confirmed as Salmonella through invA gene specific PCR, and further genotyping was done by RAPD-PCR, and 16S rRNA sequencing. The isolates were distributed into 18 different genotypes according to RAPD typing. The phylogenetic analysis identified three diverging phylogroups such as S. enterica Litchfield, S. enterica Enteritidis and S. enterica Kentucky with 11, 8, and 6 strains, respectively. The in vitro antibiogram profiling the Salmonella isolates through disc diffusion method using 13 commercially available antibiotics revealed highest resistance against doxycycline (91.5%) followed by tetracycline and ampicillin (86.0%, in each), and 72.0% isolates as MDR, being resistant to ≥ 5 antibiotics. The MLST typing was carried out based on the PCR amplification of seven housekeeping genes (aroC, hisD, hemD, purE, secA, thrA, and dnaN). MLST typing also revealed three sequence types (STs) such as ST11, ST198, and ST214 in these isolates, and eBURST analysis showed ST11 as the founder genotype. The three STs were highly resistant to tetracyclines and quinolone group of antibiotics, and all of the isolates harboring S. enterica Litchfield showed the highest resistance. Circulating common MLSTs with MDR properties in different farms confirmed the possibility of a common route of intra-farm transmission. We report for the first time of the association serovar Litchfield (ST11) in avian salmonellosis with MDR properties which is an urgent public health concern in Bangladesh.

Genomic Characterization of Antimicrobial Resistance in Food Chain and Livestock-Associated Salmonella Species

Simple Summary

In the era of the COVID-19 global pandemic, antimicrobial resistance is looming as an imminent threat and challenge to human public health. Antimicrobial resistance is a major global threat of increasing concern to human and animal health. It also has implications for both food safety and food security and the economic well-being of millions of humans. Among other zoonotic infectious diseases, antimicrobial resistance in food chain and livestock-associated pathogens such as Salmonella is of great concern. In the present study, the genomic characterization of antimicrobial resistance in food chain and livestock-associated Salmonella was summarized. Several antimicrobial resistance determinants were reported in Salmonella isolated from food chain animals and livestock. Monitoring of antimicrobial resistance in Salmonella in livestock and food chain animals through genomic characterization is significant to control and protect humans from the threat of antimicrobial resistance. Salmonella, a foodborne zoonotic enterobacterium species can transmit antimicrobial resistance from the microbiome of animals to humans. This study summarizes the genomic characterization of antimicrobial resistance in Salmonella species with special focus on resistance against carbapenems and colistin which are the last resort antibiotics used against infections caused by multidrug resistant bacteria. The present review aims to draw attention to prudent use of antibiotics, a good example of the One Health concept.

Abstract

The rising trend of antimicrobial resistance (AMR) by foodborne bacteria is a public health concern as these pathogens are easily transmitted to humans through the food chain. Non-typhoid Salmonella spp. is one of the leading foodborne pathogens which infect humans worldwide and is associated with food and livestock. Due to the lack of discovery of new antibiotics and the pressure exerted by antimicrobial resistance in the pharmaceutical industry, this review aimed to address the issue of antibiotic use in livestock which leads to AMR in Salmonella. Much attention was given to resistance to carbapenems and colistin which are the last-line antibiotics used in cases of multi drug resistant bacterial infections. In the present review, we highlighted data published on antimicrobial resistant Salmonella species and serovars associated with livestock and food chain animals. The importance of genomic characterization of carbapenem and colistin resistant Salmonella in determining the relationship between human clinical isolates and food animal isolates was also discussed in this review. Plasmids, transposons, and insertion sequence elements mediate dissemination of not only AMR genes but also genes for resistance to heavy metals and disinfectants, thus limiting the therapeutic options for treatment and control of Salmonella. Genes for resistance to colistin (mcr-1 to mcr-9) and carbapenem (blaVIM-1, blaDNM-1, and blaNDM-5) have been detected from poultry, pig, and human Salmonella isolates, indicating food animal-associated AMR which is a threat to human public health. Genotyping, plasmid characterization, and phylogenetic analysis is important in understanding the epidemiology of livestock-related Salmonella so that measures of preventing foodborne threats to humans can be improved.

Major zoonotic diseases of public health importance in Bangladesh

Zoonotic diseases cause repeated outbreaks in humans globally. The majority of emerging infections in humans are zoonotic. COVID‐19 is an ideal example of a recently identified emerging zoonotic disease, causing a global pandemic. Anthropogenic factors such as modernisation of agriculture and livestock farming, wildlife hunting, the destruction of wild animal habitats, mixing wild and domestic animals, wildlife trading, changing food habits and urbanisation could drive the emergence of zoonotic diseases in humans. Since 2001, Bangladesh has been reporting many emerging zoonotic disease outbreaks such as nipah, highly pathogenic avian influenza, pandemic H1N1, and COVID‐19. There are many other potential zoonotic pathogens such as Ebola, Middle East respiratory syndrome coronavirus, Kyasanur forest disease virus and Crimean–Congo haemorrhagic fever that may emerge in the future. However, we have a limited understanding of zoonotic diseases’ overall risk in humans and associated factors that drive the emergence of zoonotic pathogens. This narrative review summarised the major emerging, re‐emerging, neglected and other potential zoonotic diseases in Bangladesh and their associated risk factors. Nipah virus and Bacillus anthracis caused repeated outbreaks in humans. More than 300 human cases with Nipah virus infection were reported since the first outbreak in 2001. The highly pathogenic avian influenza virus (H5N1) caused more than 550 outbreaks in poultry, and eight human cases were reported so far since 2007. People of Bangladesh are frequently exposed to zoonotic pathogens due to close interaction with domestic and peri‐domestic animals. The rapidly changing intensified animal–human–ecosystem interfaces and risky practices increase the risk of zoonotic disease transmission. The narrative review's findings are useful to draw attention to the risk and emergence of zoonotic diseases to public health policymakers in Bangladesh and the application of one‐health approach to address this public health threat.

Prevalence of Salmonella enterica on poultry processing equipment after completion of sanitization procedures

Salmonella is a poultry-borne pathogen that causes illness throughout the world. Consequently, it is critical to control Salmonella during the process of converting broilers to poultry meat. Sanitization of a poultry processing facility, including processing equipment, is a crucial control measure that is utilized by poultry integrators. However, prevalence of Salmonella on equipment after sanitization and its potential risk to food safety has not been evaluated thoroughly. Therefore, the objective of this study was to evaluate the persistence of Salmonella on poultry processing equipment before and following cleaning and sanitization procedure. A total of 15 locations within 6 commercial processing plants were sampled at 3 time points: (A) after processing; (B) after cleaning; and (C) after sanitization, on 3 separate visits for a total of 135 samples per plant. Salmonella-positive isolates were recovered from samples using the United States Department of Agriculture MLG 4.09 conventional method. Presumptive Salmonella colonies were subjected to biochemical tests for confirmation. Salmonella isolates recovered after sanitization were serotyped and tested for the presence of specific virulence genes. A completely randomized design with a 6 × 3 × 15 factorial arrangement was utilized to analyze the results for Salmonella prevalence between processing plants. Means were separated using Fishers protected least significant difference when P ≤ 0.05. For Salmonella prevalence between processing plants, differences (P < 0.0001) were observed in the 6 plants tested where the maximum and minimum prevalence was 29.6 and 7.4%, respectively. As expected, there was a difference (P < 0.0001) in the recovery of Salmonella because of sampling time. Salmonella prevalence at time A (36%) was significantly higher, whereas there was no difference between time B (12%) and C (9%). There was a location effect (P < 0.0001) for the prevalence of Salmonella with the head puller, picker, cropper, and scalder having a significantly higher prevalence when compared with several other locations. At sampling time C, a trend toward a difference (P = 0.0899) was observed for Salmonella prevalence between the 6 plants, whereas significant differences were observed because of location (P = 0.0031). Five prominent Salmonella enterica serovars were identified, including Kentucky, Schwarzengrund, Enteritidis, Liverpool, and Typhimurium with S. Kentucky being the most prevalent. PCR analysis of 8 Salmonella virulence genes showed that the invA, sipB, spiA, sseC, and fimA were detected in all isolates, whereas genes carried on plasmids and/or fimbriae varied remarkably among all isolates. This study established Salmonella prevalence and persistence in poultry processing facilities after antimicrobial application through sanitization procedures which could result in contamination of poultry carcasses and food safety risks because of poultry meat.

Serovar diversity of Salmonella among poultry

Background & objectives

Salmonellosis due to the consumption of contaminated poultry products is a well-known public health concern, and assessing the distribution of Salmonella serovars among poultry becomes important for better prevention and control. The objective of the present study was to assess the distribution of Salmonella serovars among poultry.

Methods

The isolates received at National Salmonella and Escherichia Centre during 2011-2016 were subjected to biochemical identification, followed by serological characterization to identify the Salmonella serovars, and the data were presented to exhibit the distribution of Salmonella serovars among poultry.

Results

Salmonella was found to be present in poultry in all the regions included in the study. Salmonella Typhimurium, S. Gallinarum and S. Enteritidis were the most prevalent serovars accounting for 96.2 per cent of isolates. Salmonella was identified in poultry from all major egg-producing and egg-consuming States. Other serovars which were scantly identified included S. Infantis (2.7%), S. Montevideo (0.64%), S. Newport (0.26%) and S. Pullorum (0.13%).

Interpretation & conclusions

Diverse distribution of Salmonella serovars in poultry in India, with known potential to infect human population and/or other poultry flocks, requires urgent nationwide stringent control measures.

A common Salmonella Enteritidis sequence type from poultry and human gastroenteritis in Ibagué, Colombia

Salmonella Enteritidis es una de las mayores causas de salmonelosis en el mundo, siendo los huevos contaminados y la carne de pollo cruda sus principales fuentes de infección. En Ibagué, Colombia, se identificaron los principales serovares circulando en granjas, superficies de huevos y canales de pollo, sin embargo, se desconoce si esos serovares son responsables de gastroenteritis. Objetivo. Evaluar la relación genética entre aislamientos de Salmonella Enteritidis de aves de corral y humanos con gastroenteritis mediante multilocus sequence typing (MLST). Materiales y métodos. Se aisló Salmonella spp., de casos clínicos de gastroenteritis (n=110). Se realizó test de sensibilidad antibiótica, seguido de serotipificación y tipificación por medio de MLST y se comparó S. Enteritidis de humanos frente a S. Enteritidis de granjas ponedoras y de huevo comercializado (n=6). Resultados. Se aislaron 10 cepas de Salmonella spp., a partir de heces de humanos con gastroenteritis. Se obtuvo una prevalencia de Salmonella spp. de 9.09%, siendo S. Enteritidis (n=4), S. Typhymurium (n=2), S. Newport (n=1), S. Grupensis (n=1), S. Uganda (n=1) y S. Braenderup (n=1) los serotipos presentes en pacientes con gastroenteritis. El MLST indico que un tipo de secuencia común (ST11) de S. Enteritidis estuvo presente en todas las tres fuentes y mostraron el mismo patrón de resistencia antibiótica. Conclusión. S. Enteritidis ST11 constituye un vínculo entre el consumo/manipulación de huevos contaminados y gastroenteritis humana en Ibagué. Son necesarios estudios complementarios para conocer si otros serovares de Salmonella aislados de carne de pollo cruda también se asocian con la gastroenteritis humana.

Salmonella enterica serovar Kentucky recovered from human clinical cases in Maryland, USA (2011-2015)

Salmonella Kentucky is among the most frequently isolated S. enterica serovars from food animals in the United States. Recent research on isolates recovered from these animals suggests there may be geographic and host specificity signatures associated with S. Kentucky strains. However, the sources and genomic features of human clinical S. Kentucky isolated in the United States remain poorly described. To investigate the characteristics of clinical S. Kentucky and the possible sources of these infections, the genomes of all S. Kentucky isolates recovered from human clinical cases in the State of Maryland between 2011 and 2015 (n = 12) were sequenced and compared to a database of 525 previously sequenced S. Kentucky genomes representing 12 sequence types (ST) collected from multiple sources on several continents. Of the 12 human clinical S. Kentucky isolates from Maryland, nine were ST198, two were ST152, and one was ST314. Forty-one per cent of isolates were recovered from patients reporting recent international travel and 58% of isolates encoded genomic characteristics similar to those originating outside of the United States. Of the five isolates not associated with international travel, three encoded antibiotic resistance genes conferring resistance to tetracycline or aminoglycosides, while two others only encoded the cryptic aac(6')-Iaa gene. Five isolates recovered from individuals with international travel histories (ST198) and two for which travel was not recorded (ST198) encoded genes conferring resistance to between 4 and 7 classes of antibiotics. Seven ST198 genomes encoded the Salmonella Genomic Island 1 and substitutions in the gyrA and parC genes known to confer resistance to ciprofloxacin. Case report data on food consumption and travel were, for the most part, consistent with the inferred S. Kentucky phylogeny. Results of this study indicate that the majority of S. Kentucky infections in Maryland are caused by ST198 which may originate outside of North America.

Occurrence, antimicrobial resistance and whole-genome sequencing analysis of Salmonella isolates from chicken carcasses imported into Iraq from four different countries

Salmonella is a major cause of human foodborne illnesses worldwide; however, little is known about its occurrence and genomic characteristics in food sources in many developing countries. This study investigates the occurrence, serotypes distribution, antimicrobial resistance, and multilocus sequence types (ST) of Salmonella isolated from 400 imported frozen chicken carcasses sold in the markets of Thi-Qar, south-eastern Iraq. Salmonella was detected in 46 out of 400 tested samples [11.5% (95% confidence interval: 8.5%-15.0%)]. S. Typhimurium was the most abundant (30.4%) among 14 different serotypes recovered from the tested frozen carcasses. Antimicrobial resistance was most frequently detected against tetracycline (84.4%), nalidixic acid (80.4%), streptomycin (69.6%) and trimethoprim/sulfamethoxazole (65.2%). Whole-genome sequencing (WGS) analysis revealed that 18 isolates harbored four β-lactamase resistance genes, with bla_CARB-2 was the most commonly (14/18) detected. It was possible to identify 8 multilocus sequence types from the WGS analysis of 40 out of the 46 Salmonella isolates; with ST-11 (among S. Enteritidis) and ST-19 (among S. Typhimurium) were the most frequently detected. These results add to our understanding of the global epidemiology of Salmonella. Our work stands as one of the first reports on WGS analysis of Salmonella from retail chicken in a Middle-Eastern country. Results from this study could be valuable for guiding an informed import risk analysis aiming at reducing the exposure risk from Salmonella through imported chicken carcasses into Iraq. This work demonstrates the value of WGS as a promising tool for supporting evidence-based food safety hazard characterization.

Infection Dynamics and Antimicrobial Resistance Profile of Salmonella Paratyphi B d-tartrate Positive (Java) in a Persistently Infected Broiler Barn

The infection dynamics of S. Java were examined in three consecutive rearing periods on a broiler farm in Northwestern Germany which had been persistently infected with S. Java for more than five years. The barn was investigated for Salmonella occurrence after cleaning and disinfection to verify the persistent contamination of the broiler house with S. Java before the start of the first rearing cycle. Confirmation of Salmonella absence in day-old chicks (time-point 1) as well as early establishment of infection between days 5-7 (time-point 2) were confirmed by caecal swabs prepared for qPCR and classical microbiological methods. At three time-periods (between days 11-15 (time-point 3), days 25-28 (time-point 4), and days 38-40 (time-point 5)) caecal content was examined for colony forming units (CFU) Salmonella/g. In general, there was an increase in Salmonella Java load at time-point 4 compared to time-points 3 and 5. Therefore, we observed a bell-shaped course of infection resulting in higher rates of Salmonella CFU/g prior to prethinning than at final slaughter. The antimicrobial susceptibility testing revealed resistance to tetracycline, fluorquinolones, trimethoprim, and cefoxitin.

First description of plasmid-mediated quinolone resistance determinants and β-lactamase encoding genes in non-typhoidal Salmonella isolated from humans, one companion animal and food in Romania

BACKGROUND

Gastroenteritis attributable to Salmonella enterica and the continuous increase in antimicrobial resistance of this gut pathogen, which compromises the use of previously effective treatments, is of great concern for public health. This study was conducted in order to investigate the presence of plasmid-mediated quinolone resistance (PMQR) determinants and β-lactamase-encoding genes, in S. enterica, isolated from humans, one companion animal and food. Moreover, the study aimed to identify potential vehicles of transmission of resistant strains to humans, with focus on food products (meat).

METHODS

A total of 20 S. enterica isolates recovered from food (chicken and pork meat), one companion animal and humans (stool samples), were examined for their serotype, antimicrobial susceptibility and the presence of PMQR and β-lactamase-encoding genes. Moreover, the genetic relatedness of nine Salmonella Infantis and ten Salmonella Enteritidis isolates was analyzed by pulsed-field gel electrophoresis (PFGE).

RESULTS

Among all isolates, 15 (75%) were multidrug-resistant (MDR) and the majority of them proved to be resistant to nalidixic acid and fluoroquinolones (FQs) (ciprofloxacin and levofloxacin). Twelve isolates (60%) harboured at least one PMQR gene [qnrA, qnrB, qnrS, aac (6')-Ib-cr or qepA] while seven isolates (35%) carried at least one β-lactamase-encoding gene (bla TEM, bla PSE-1, bla SHV or bla CTX-M). Moreover, two or more PMQR or β-lactamase-encoding genes co-existed in a single S. enterica isolate. A number of nine Salmonella Infantis, as well as the majority of Salmonella Enteritidis isolates analyzed by PFGE proved to be closely related.

CONCLUSIONS

The study demonstrated the co-existence of PMQR and β-lactamase-encoding genes among the Salmonella isolates recovered and confirmed that multiple mechanisms might be involved in the acquisition and spread of resistance determinants. The close genetic relatedness between the clinical and foodborne S. enterica isolates, suggested that chicken meat might be a possible cause of human salmonellosis in our country, during the study period. Results of this study might improve understanding of the antimicrobial resistance mechanisms and transmission dynamics of Salmonella spp. Here, we report for the first time the presence of PMQR and β-lactamase-encoding genes in S. enterica isolates, recovered from humans, one companion animal and food, in Romania.

Salmonella Virchow Infection of the Chicken Elicits Cellular and Humoral Systemic and Mucosal Responses, but Limited Protection to Homologous or Heterologous Re-Challenge

Salmonella enterica serovar Virchow usually causes mild gastroenteritis in humans; however, it is frequently invasive and many isolates are resistant to a broad-range of therapeutic antimicrobials. Poultry meat is considered a major source of human infection. In this study, we characterize the infection biology and immune response to S. Virchow in chickens and determine protection against homologous and heterologous re-challenge, with S. Virchow or S. Typhimurium. Following oral infection of 7-day-old chickens, S. Virchow colonized the gastrointestinal tract and the spleen. Infection elicited an increase in specific IgA, IgG, and IgM antibodies and relative quantitative changes in several leukocyte populations, including CD3, CD4, CD8α, CD8β, MHC II, KuL01, and γδ TCR positive cells, both in the gastrointestinal tract and systemically. Increased expression of pro-inflammatory cytokines IL-1β and IL-6 and the chemokine CXCLi2 was also found. Primary infection with S. Virchow offered limited systemic protection against re-challenge with S. Virchow or S. Typhimurium, but no protection against cecal colonization. In conclusion, S. Virchow exhibits similar infection biology and immune responses in the chicken to that previously described for S. Typhimurium. Unlike S. Typhimurium, S. Virchow infection is poorly protective to homologous and heterologous re-challenge. These findings suggest that S. Virchow is capable of colonizing the chicken well and therefore, presents a risk of entering the food chain in meat production. Furthermore, the development of vaccines that protect effectively against S. Virchow and indeed multivalent vaccines that protect across all Salmonella serogroups in the chicken would appear to remain a challenging proposition.