Occurrence, antimicrobial resistance and whole genome sequence analysis of Salmonella serovars from pig farms in Ilorin, North-central Nigeria

Pathogenicity of Multidrug-Resistant Salmonella typhimurium Isolated from Ducks

Salmonella typhimurium (S. typhimurium) is one of the most common Salmonella serotypes in epidemiological surveys of poultry farms in recent years. It causes growth retardation, mortality, and significant economic losses. The extensive use of antibiotics has led to the emergence of multi-drug resistance (MDR) in Salmonella, which has become a significant global problem and long-term challenge. In this study, we investigated the prevalence and features of S. typhimurium strains in duck embryos and cloacal swabs from large-scale duck farms in Shandong, China, including drug resistance and virulence genes and the pathogenicity of an S. typhimurium strain by animal experiment. The results demonstrated that a total of 8 S. typhimurium strains were isolated from 13,621 samples. The drug resistance results showed that three of the eight S. typhimurium strains were MDR with the dominant resistance profile of CTX-DX-CTR-TE-AMX-AMP-CAZ. In particular, the virulence genes invA, hilA, pefA, rck, and sefA showed high positive rates. Based on the analysis of the biological characteristics of bacterial biofilm formation and mobility, a strain of S. typhimurium with the strongest biofilm formation ability, designated 22SD07, was selected for animal infection experiments with broiler ducklings. The results of animal experiments demonstrated that infection with 22SD07 reduced body weight and bursa index but increased heart and liver indexes compared to the control group. Histological examination revealed desquamation of the intestinal villous epithelium, the presence of large aggregates of lymphocytes, and a decrease in goblet cells following infection. Furthermore, the expression of IL-10 was significantly increased in the liver at 3 dpi, while TNF-α was significantly increased in the spleen at 7 dpi. The above results indicate that S. typhimurium may pose a potential threat to human health through the food chain. This helps us to understand the frequency and characteristics of S. typhimurium in duck farms and emphasizes the urgent need to strengthen and implement effective continuous monitoring to control its infection and transmission.

Unveiling the landscape of resistance against high priority critically important antimicrobials in food-producing animals across Africa: A scoping review

The rapid population growth in Africa is associated with an increasing demand for livestock products which in turn can lead to antimicrobial use. Antimicrobial usage in animals contributes to the emergence and selection of resistant bacteria which constitutes a serious public health threat. This study aims to review and summarize the available information on highest priority critically important antimicrobials (HPCIAs) resistance in livestock production in Africa. This work will help to inform future policies for controlling antimicrobial resistance (AMR) in the food production chain. A scoping review was conducted according to the Cochrane handbook and following PRISMA 2020 guidelines for reporting. Primary research studies published after 1999 and reporting resistance of Escherichia coli, Enterococcus spp, Staphylococcus aureus, Salmonella spp, and Campylobacter spp to HPCIAs in poultry, cattle, pigs, goats, and sheep in Africa were searched in four databases. A total of 312 articles were included in the review. The majority of the studies (40.7) were conducted in North African countries. More than 49.0% of included studies involved poultry and 26.2% cattle. Cephalosporins and quinolones were the most studied antimicrobial classes. Of the bacteria investigated in the current review, E. coli (41.7%) and Salmonella spp (24.9%) represented the most commonly studied. High levels of resistance against erythromycin in E. coli were found in poultry (MR 96.1%, IQR 83.3-100.0%), cattle (MR 85.7%, IQR 69.2-100.0%), and pigs (MR 94.0%, IQR 86.2-94.0%). In sheep, a high level of resistance was observed in E. coli against nalidixic acid (MR 87.5%, IQR 81.3-93.8%). In goats, the low level of sensibility was noted in S. aureus against streptomycin (MR 86.8%, IQR 19.4-99.0%). The study provides valuable information on HPCIAs resistance in livestock production in Africa and highlights the need for further research and policies to address the public health risk of AMR. This will likely require an investment in diagnostic infrastructure across the continent. Awareness on the harmful impact of AMR in African countries is a requirement to produce more effective and sustainable measures to curb AMR.

Epidemiological and Whole Genome Sequencing Analysis of Restaurant Salmonella Enteritidis Outbreak Associated with an Infected Food Handler in Jiangxi Province, China, 2023

In China, Salmonella is one of the most frequent causes of bacterial gastroenteritis, and food handlers in restaurants as an important contaminated source were rarely reported. In May 2023, an outbreak of Salmonella enterica serovar Enteritidis infection in a restaurant in Jiangxi Province, China, was investigated. Cases were interviewed. Stool samples from cases, anal swabs from restaurant employees, suspicious raw food materials, and semifinished food were collected and examined. Pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) were performed to determine the relatedness of the pathogen isolates. Antimicrobial resistance genes and virulence genes of isolates were analyzed by WGS. The antimicrobial profile of the isolates was detected by broth microdilution, which involved 20 different antibiotics. Among the 31 patrons, 26 showed gastrointestinal symptoms. Five Salmonella Enteritidis strains were isolated from patients (2), semifinished food (2), and food handler (1). The results of PFGE and single-nucleotide polymorphism showed that these five isolates were identical clones. These findings demonstrated that this outbreak was a restaurant Salmonella Enteritidis outbreak associated with an infected food handler. The rates of resistance to nalidixic acid and colistin and intermediate resistance to ciprofloxacin were 100%, 80%, and 100%, respectively. These outbreak isolates harbored point mutation gyrA p.D87G. The cause of inconsistency between the genotype and phenotype of resistance was deeply discussed. A total of 107 virulence genes were found in each isolate, with many being associated with Salmonella pathogenicity island (SPI)-1 and SPI-2. As an overlooked contamination source, infected food handlers can easily cause large-scale outbreaks. This outbreak highlighted that the government should enhance the training and supervision of food hygiene and safety for food handlers to prevent foodborne outbreaks.

Rare serovars of non-typhoidal Salmonella enterica isolated from humans, beef cattle and abattoir environments in Nigeria

INTRODUCTION

Salmonella is considered one of the most significant pathogens in public health since it is a bacterium that is frequently linked to food-borne illnesses in humans. Some Salmonella serovars are responsible for outbreaks that are connected to the consumption of animal products. Cattle are connected to humans through a shared environment and the food chain as a significant source of animal protein. In Nigeria, antimicrobial medications are easily accessible for use in food-producing animals. Abattoir environments are reservoirs of foodborne bacteria like non-typhoidal Salmonella enterica (NTS), that have become resistant to antibiotics used for prophylaxis or treatment in animals. This study investigated the prevalence and resistance patterns of Salmonella enterica serovars in abattoir employees, beef cattle and abattoir environments in Abuja and Lagos, Nigeria.

METHODS

A total of 448 samples were collected from healthy personnel, slaughtered cattle, and abattoir environments between May and December 2020. Using Kirby-Bauer disk diffusion method, the resistance profile of NTS isolates were determined. Multidrug resistance (MDR) was considered when NTS was resistant to ≥3 antimicrobial drug classes. We performed phenotypic and genotypic characterizations of all Salmonella isolates including serotyping. Descriptive statistics were used to analyze the data.

RESULTS

Twenty-seven (6%) NTS isolates were obtained. Prevalence of NTS was highest in abattoir environments (15.5%; 9/58), followed by cattle (4.8%;13/272) and abattoir employees (4.2%; 5/118). A high prevalence of resistance was observed for gentamicin (85.2%; 23/27) and tetracycline (77.8%; 21/27). Whole-genome sequencing of 22 NTS showed dissemination of aac(6')-laa (22/22), qnrB19 (1/22), fosA7 (1/22), and tetA (1/22) genes. Serovar diversity of NTS varied with source. S. Anatum, a rare serovar predominated with a prevalence of 18.2% (4/22). Chromosomal point mutations showed ParC T57S substitution in 22 NTS analyzed. Among 22 NTS, 131 mobile genetic elements (MGEs) were detected including insertion sequences (56.5%) and miniature inverted repeats (43.5%). Two integrating MGEs IS6 and IS21 were observed to carry the tetA gene + Incl-1 on the same contig in NTS originating from cattle. Rare serovars namely S. Abony and S. Stormont with MDR phenotypes recovered from cattle and abattoir environments were closely related with a pairwise distance of ≤5 SNPs.

CONCLUSIONS

First report of rare serovars in Nigeria with MDR phenotypes in humans, cattle, and abattoir environments. This study demonstrates the spread of resistance in the abattoir environment possibly by MGEs and emphasizes the importance of genomic surveillance. Beef cattle may be a risk to public health because they spread a variety of rare Salmonella serovars. Therefore, encouraging hand hygiene among abattoir employees while processing beef cattle will further reduce NTS colonization in this population. This requires a One Health collaborative effort among various stakeholders in human health, animal health, and environmental health.

Whole genome sequencing of Salmonella enterica serovars isolated from humans, animals, and the environment in Lagos, Nigeria

BACKGROUND

Salmonella infections remain an important public health issue worldwide. Some serovars of non-typhoidal Salmonella (NTS) have been associated with bloodstream infections and gastroenteritis, especially in children in Sub-Saharan Africa with circulating S. enterica serovars with drug resistance and virulence genes. This study identified and verified the clonal relationship of Nigerian NTS strains isolated from humans, animals, and the environment.

METHODS

In total, 2,522 samples were collected from patients, animals (cattle and poultry), and environmental sources between December 2017 and May 2019. The samples were subjected to a standard microbiological investigation. All the isolates were identified using Microbact 24E, and MALDI-TOF MS. The isolates were serotyped using the Kauffmann-White scheme. Antibiotic susceptibility testing was conducted using the disc diffusion method and the Vitek 2 compact system. Virulence and antimicrobial resistance genes, sequence type, and cluster analysis were investigated using WGS data.

RESULTS

Forty-eight (48) NTS isolates (1.9%) were obtained. The prevalence of NTS from clinical sources was 0.9%, while 4% was recorded for animal sources. The serovars identified were S. Cotham (n = 17), S. Give (n = 16), S. Mokola (n = 6), S. Abony (n = 4), S. Typhimurium (n = 4), and S. Senftenberg (n = 1). All 48 Salmonella isolates carried intrinsic and acquired resistant genes such as aac.6…Iaa, mdf(A), qnrB, qnrB19 genes and golT, golS, pcoA, and silP, mediated by plasmid Col440I_1, incFIB.B and incFII. Between 100 and 118 virulence gene markers distributed across several Salmonella pathogenicity islands (SPIs), clusters, prophages, and plasmid operons were found in each isolate. WGS revealed that strains of each Salmonella serovar could be assigned to a single 7-gene MLST cluster, and strains within the clusters were identical strains and closely related as defined by the 0 and 10 cgSNPs and likely shared a common ancestor. The dominant sequence types were S. Give ST516 and S. Cotham ST617.

CONCLUSION

We found identical Salmonella sequence types in human, animal, and environmental samples in the same locality, which demonstrates the great potential of the applied tools to trace back outbreak strains. Strategies to control and prevent the spread of NTS in the context of one's health are essential to prevent possible outbreaks.

Comprehensive profiling of serotypes, antimicrobial resistance and virulence of Salmonella isolates from food animals in China, 2015-2021

Introduction

Salmonella is a ubiquitous foodborne pathogen and mainly transmitted to human farm-to-fork chain through contaminated foods of animal origin.

Methods

In this study, we investigated the serotypes, antimicrobial resistance and virulence of Salmonella from China.

Results

A total of 617 Salmonella isolates were collected from 4 major food animal species across 23 provi nces in China from 2015-2021. Highest Salmonella prevalence were observed in Guangdong (44.4%) and Sandong (23.7%). Chickens (43.0%) was shown to be the major source of Salmonella contamination, followed by pigs (34.5%) and ducks (18.5%). The number of Salmonella increased significantly from 5.51% to 27.23% during 2015-2020. S. Derby (17.3%), S. Enteritidis (13.1%) and S. Typhimurium (11.4%) were the most common serotypes among 41 serotypes identifiedin this study. Antibiotic susceptibility testing showing that the majority of the Salmonella isolates were resistant to neomycin (99.7%), tetracycline (98.1%), ampicillin (97.4%), sulfadiazine/trimethoprim (97.1%), nalidixic acid (89.1%), doxycycline (83.1%), ceftria xone (70.3%), spectinomycin (67.7%), florfenicol (60.0%), cefotaxime (52.0%) and lomefloxacin (59.8%). The rates of resistance to multiple antibiotics in S. Derby and S.Typhimurium were higher than that in S. Enteritidis. However, the rate of resistance to fosfomycin were observed from higher to lower by S. Derby, S. Enteritidis, and S. Typhimurium. Biofilm formation ability analysis found that 88.49%of the Salmonella were able to produce biofilms, of which 236 Salmonella isolates were strong biofilm producer. Among the 26 types of antibiotics resistance genes (ARGs) were identified in this study, 4 ARGs (tetB,sul2,aadA2, and aph(3')-IIa) were highly prevalent. In addition, 5 β-lactam resistance genes (bla _TEM, bla _SHV, bla _CMY-2, bla _CTX-M, and bla _OXA) and 7 quinolone resistance genes (oqxA, oqxB, qnrB, qnrC, qnrD, qnrS, and qeqA) were detected among these isolates. 12 out of 17 virulence genes selected in this study were commonly presented in the chromosomes of tested isolate, with a detection rate of over 80%, including misL, spiA, stn, pagC, iroN, fim, msgA, sopB, prgH, sitC, ttrC, spaN.

Discussion

This study provided a systematical updating on surveillance on prevalence of Salmonella from food animals in China, shedding the light on continued vigilance for Salmonella in food animals.

Combating the menace of antimicrobial resistance in Africa: a review on stewardship, surveillance and diagnostic strategies

The emergence of antibiotic-resistant pathogens has threatened not only our ability to deal with common infectious diseases but also the management of life-threatening complications. Antimicrobial resistance (AMR) remains a significant threat in both industrialized and developing countries alike. In Africa, though, poor clinical care, indiscriminate antibiotic use, lack of robust AMR surveillance programs, lack of proper regulations and the burden of communicable diseases are factors aggravating the problem of AMR. In order to effectively address the challenge of AMR, antimicrobial stewardship programs, solid AMR surveillance systems to monitor the trend of resistance, as well as robust, affordable and rapid diagnostic tools which generate data that informs decision-making, have been demonstrated to be effective. However, we have identified a significant knowledge gap in the area of the application of fast and affordable diagnostic tools, surveillance, and stewardship programs in Africa. Therefore, we set out to provide up-to-date information in these areas. We discussed available hospital-based stewardship initiatives in addition to the role of governmental and non-governmental organizations. Finally, we have reviewed the application of various phenotypic and molecular AMR detection tools in both research and routine laboratory settings in Africa, deployment challenges and the efficiency of these methods.

Salmonella Typhimurium ST34 Isolate Was More Resistant than the ST19 Isolate in China, 2007 - 2019

To disclose the antimicrobial susceptibility and wide adaptability of commonly occurring genotypes of Salmonella enterica serovar Typhimurium, the antimicrobial resistance and multilocus sequence typing (MLST) profiles of 196 Salmonella Typhimurium isolates (136 from food-producing animals, 19 from environments, 15 from markets, and 26 from humans) in China between 2007 and 2019 were analyzed. Tests of susceptibility to 19 antimicrobial agents using the broth microdilution method showed that 84.7% of the isolates were resistant to at least one antimicrobial. Antimicrobial susceptibility analysis demonstrated that 66.8% of the isolates were multidrug-resistant (MDR) strains, with resistance to three or more antimicrobials. The highest antidrug resistance was to ampicillin, amoxicillin/clavulanic acid, and tetracycline. Three MLST types were detected, and sequence type (ST) 19 was the most common ST. However, ST34 was associated with a higher MDR rate and more complex MDR patterns, than ST19 and ST99, although the exact mechanism has not been reported. Our study highlights the variation of drug resistance and STs from different sources and the association between STs and drug resistance, providing useful information for epidemiological research and developing a public health strategy.