Diversity and antimicrobial susceptibility of Salmonella enterica serovars isolated from pig farms in Ibadan, Nigeria

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.

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.

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

Salmonella enterica is a foodborne pathogen of global public health importance with developing countries mostly affected. Foodborne outbreaks are often attributed to pork consumption and Salmonella contamination of retail pork is directly linked to the Salmonella prevalence on farm. The widespread use of antimicrobials at different steps of swine production can favor resistant strains of Salmonella. The objectives of this study are to characterize the distribution, multilocus sequence typing (MLST), plasmid, virulence profiles and antimicrobial resistance of Salmonella serovars circulating in selected pig farms. Six hundred fecal samples were randomly collected from nine selected farms in Ilorin, Nigeria. Isolates were analyzed by cultural isolation using selective media, conventional biochemical characterization, serotyping, MLST and whole genome sequencing (WGS). Sixteen samples were positive for Salmonella sub-species, comprising of nine serovars. The antimicrobial susceptibility results revealed low-level resistance against 13 antimicrobial agents. Five strains exhibited resistance to nalidixic acid and intermediate resistance to ciprofloxacin with chromosomal (double) mutation at gyrA and parC while four strains possessed single mutation in parC. Salmonella Kentucky showed double mutation each at gyrA and parC. WGS analysis, revealed eight diverse sequence types (STs), the most common STs were ST-321 and ST-19 (n = 4) exhibited by S. Muenster and S. Typhimurium, respectively. Single Nucleotide Polymorphism (SNP)-based phylogeny analysis showed the 16 isolates to be highly related and fell into 8 existing clusters at NCBI Pathogen Detection. Curtailing the spread of resistant strains will require the establishment of continuous surveillance program at the state and national levels in Nigeria. This study provides useful information for further studies on antimicrobial resistance mechanisms in foodborne Salmonella species.

Contamination Status of Salmonella spp., Shigella spp. and Campylobacter spp. in Surface and Groundwater of the Kelani River Basin, Sri Lanka

Waterborne diseases are a global problem that causes more than 2.2 million deaths annually. Therefore, the present study was focused on microbiological contamination of both ground and surface water by means of total coliform, Escherichia coli (E. coli), Salmonella spp., Shigella spp. and Campylobacter spp. Seventy two groundwater and 45 surface water sampling locations were selected to collect water from the head, transitional and meandering regions of the Kelani River Basin for a period of one year (both dry and wet seasons). The results of the study revealed that the entire Kelani River basin was contaminated with total coliform and E. coli bacteria and almost all the sampling locations exceed Sri Lanka Standards Institute (SLSI) guideline value given for drinking water (0 CFU/100 mL). Further, in groundwater, 17 locations were positive for Salmonella spp., whereas only 2 locations were positive for Campylobacter spp. In surface water, 26 and three sampling locations were positive for Salmonella spp. and Campylobacter spp., respectively. In this study, 23 different human pathogenic serovars were isolated and the Salmonella enterica serovar Kentucky was identified as the commonest type. Thus, the result of the study revealed that the consumption of raw water from the Kelani River Basin is unsafe and possible to cause gastrointestinal diseases.

Search for the Occurrence of Clostridium difficile and Clostridium perfringens in Pigs Within Zaria and Environs, in Kaduna State, Nigeria

Animals have been known to be the main study subjects when investigating the epidemiology of zoonotic Gram-positive Clostridium difficile and Clostridium perfringens. This cross-sectional study was aimed at determining the occurrence of C. difficile and C. perfringens in pigs as well as the associated risk factors within Zaria and environs, in Kaduna State of Nigeria. A pre-sampling survey led to the selection of Shika, Samaru and Ungwan Mangu in the pig farming communities of Zaria and environs in Kaduna North as the study sites. Rectal swabs from 132 pigs were obtained and anaerobically cultured in fluid thioglycolate and further grown on reinforced clostridia agar. The colonies obtained were sub-cultured in Clostridium difficile moxalactam norfloxacin agar and reinforced clostridia agar containing egg yolk tellurite. C. difficile was not detected. However, C. perfringens was detected at a prevalence of 16.7 % (22/132). Isolates were tested for their susceptibility to 13 antimicrobials. Only 1 isolate (4.55 %) demonstrated susceptibility to vancomycin, gentamicin, chloramphenicol and erythromycin. Of the bivariate analyses of the risk factors studied, only the type of piggery and pig management were statistically significant (P < 0.05) for C. perfringens. Therefore, it should be recognized that there is a need for pig farmers to be enlightened about this pathogen and its prevention through good management practices and hygiene.

Molecular diversity and antibiotic resistance gene profile of Salmonella enterica serovars isolated from humans and food animals in Lagos, Nigeria

Outbreaks of Salmonellosis remain a major public health problem globally. This study determined the diversity and antibiotic resistance gene profile of Salmonella enterica serovars isolated from humans and food animals. Using standard methods, Salmonella spp. were isolated from fecal samples, profiled for antimicrobial susceptibility and resistance genes. Seventy-one Salmonella isolates were recovered from both humans and food animals comprising cattle, sheep, and chicken. Forty-four serovars were identified, with dominant Salmonella Budapest (31.8%). Rare serovars were present in chicken (S. Alfort, S. Wichita, S. Linton, S. Ealing, and S. Ebrie) and humans (S. Mowanjum, S. Huettwillen, S. Limete, and S. Chagoua). Sixty-eight percent of isolates were sensitive to all test antibiotics, while the highest rate of resistance was to nalidixic acid (16.9%; n = 12), followed by ciprofloxacin (11.3%; n = 8) and tetracycline (9.9%; n = 8). Five isolates (7%) were multidrug-resistant and antimicrobial resistance genes coding resistance to tetracycline (tetA), beta-lactam (bla_TEM), and quinolone/fluoroquinolone (qnrB and qnrS) were detected. Evolutionary analysis of gyrA gene sequences of human and food animal Salmonella isolates revealed variations but are evolutionarily interconnected. Isolates were grouped into four clades with S. Budapest isolate from cattle clustering with S. Budapest isolated from chicken, whereas S. Essen isolated from sheep and chicken was grouped into a clade. Diverse S. enterica serovars with high antibiotic resistance profile are ubiquitous in food animals; hence, there is a need for surveillance and prudent use of antibiotics in human and veterinary medicine.

Antimicrobial Resistance in Food Animals and the Environment in Nigeria: A Review

Antimicrobial resistance (AMR) has emerged as a global health threat, which has elicited a high-level political declaration at the United Nations General Assembly, 2016. In response, member countries agreed to pay greater attention to the surveillance and implementation of antimicrobial stewardship. The Nigeria Centre for Disease Control called for a review of AMR in Nigeria using a “One Health approach”. As anecdotal evidence suggests that food animal health and production rely heavily on antimicrobials, it becomes imperative to understand AMR trends in food animals and the environment. We reviewed previous studies to curate data and evaluate the contributions of food animals and the environment (2000⁻2016) to the AMR burden in Nigeria using a Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) flowchart focused on three areas: Antimicrobial resistance, residues, and antiseptics studies. Only one of the 48 antimicrobial studies did not report multidrug resistance. At least 18 bacterial spp. were found to be resistant to various locally available antimicrobials. All 16 residue studies reported high levels of drug residues either in the form of prevalence or concentration above the recommended international limit. Fourteen different “resistotypes” were found in some commonly used antiseptics. High levels of residues and AMR were found in food animals destined for the human food chain. High levels of residues and antimicrobials discharged into environments sustain the AMR pool. These had evolved into potential public health challenges that need attention. These findings constitute public health threats for Nigeria’s teeming population and require attention.

Antibiotic Resistance in Food Animals in Africa: A Systematic Review and Meta-Analysis

OBJECTIVES

This study critically reviewed the published literature and performed a meta-analysis to determine the overall burden of antibiotic-resistant bacteria in food animals in Africa.

METHODS

English and French published articles indexed in EBSCOhost, PubMed, Web of Science, and African Journals Online were retrieved, with searches being conducted up to August, 2015. Data were pooled and meta-analysis performed using a random-effects model, and the results are described as event rates.

RESULTS

According to the predefined inclusion and exclusion criteria, 17 articles out of the 852 retrieved were eligible for the qualitative and quantitative analysis. The studies included were mainly conducted in Nigeria, with Escherichia coli, Salmonella spp., and Campylobacter spp. being the main bacteria. The pooled estimates showed high level of antibiotic resistance (ABR) (86%; p < 0.001) and multidrug resistance (73%; p = 0.003).

CONCLUSION

Our results suggest that ABR is substantively prevalent and poses a serious threat for food safety and security in Africa. These findings shed light on areas for future research concerning antibiotic-resistant and multidrug-resistant bacteria in food animals as etiological agents of infectious diseases in humans. They further yielded some interesting findings on the burden of ABR that could be useful in developing measures to contain this threat in the farm-to-plate continuum in Africa.

Impact of direct application of biogas slurry and residue in fields: In situ analysis of antibiotic resistance genes from pig manure to fields

Biogas slurry and residue contaminated with antibiotics are widely used as fertilizers in vegetable crop planting. However, their impact on the spreading of antibiotic resistance genes (ARGs) in vegetable fields is still largely unknown. In the present study, antibiotic resistant bacteria (ARB), ARGs and bacterial communities from pig manure to fields were monitored by using viable plate counts, high-throughput fluorescent quantitative PCR (HT-qPCR) and Illumina MiSeq sequencing. Eighty-three ARGs and 3 transposons genes were detected. Anaerobic digestion reduced relative abundance of tetracycline and Macrolide-Lincosamide-Streptogramin (MLSB) resistance genes. However, the number of ARB and the relative abundance of sulfa, aminoglycoside and florfenicol, chloramphenicol, and amphenicol (FCA) resistance genes, respectively, enriched up to 270 times and 52 times in biogas residue. Long-term application of biogas slurry and residue contaminated with antibiotics in fields increased the rate of ARB as well as relative abundance of ARGs and transposons genes. Additionally, bacterial communities significantly differed between the soil treated with biogas slurry and residue and the control sample, especially the phyla Bacteroidetes and Actinobacteria. Based on network analysis, 19 genera were identified as possible hosts of the detected ARGs. Our results provide an important significance for reasonable application of biogas slurry and residue.

Molecular epidemiology of fluoroquinolone resistant Salmonella in Africa: A systematic review and meta-analysis

BACKGROUND

Wide-ranging evidence on the occurrence of fluoroquinolone (FQ) resistance genetic determinants in African Salmonella strains is not available. The main objectives of this study were to assess the heterogeneity, estimate pooled proportions and describe the preponderance of FQ-resistance determinants in typhoidal and non-typhoidal Salmonella (NTS) isolates of Africa.

METHODS

Genetic and phenotypic data on 6103 Salmonella isolates were considered. Meta- and frequency analyses were performed depending on the number of studies by category, number of isolates and risks of bias. A random effects model was used to assess heterogeneity and estimate pooled proportions. Relative and cumulative frequencies were calculated to describe the overall preponderance of FQ-resistance determinants in quinolone resistant isolates.

RESULTS

The pooled proportion of gyrA mutants (Salmonella enterica serovar Typhi, Salmonella enterica serovar Typhimurium, and Salmonella enterica serovar Enteritidis) was estimated at 5.7% (95% Confidence interval (CI) = 2.6, 9.8; Tau squared (T2) = 0.1105), and was higher in S. Typhi than in S. Typhimurium (odds ratio (OR) = 3.3, 95%CI = 2, 5.7). The proportions of each of gyrB and parC mutants, and strains with Plasmid Mediated Quinolone Resistance genes (qnrA, qnrB and qnrS) were low (≤ 0.3%). Overall, 23 mutant serotypes were identified, and most strains had mutations at codons encoding Ser83 and Asp87 of gyrA (82%, 95%CI = 78, 86).

CONCLUSIONS

Mutations at gyrA appear to account for ciprofloxacin non-susceptibility in most clinical Salmonella strains in Africa. The estimates could be harnessed to develop a mismatch-amplification mutation-assay for the detection of FQ-resistant strains in Africa.

Phenotypic and genotypic comparison of salmonellae from diarrhoeic and healthy humans and cattle, Nigeria

The sources and modes of transmission of non-typhoidal Salmonella particularly zoonotic transmission are poorly understood in Africa. This study compared phenotypic and genotypic characteristics of Salmonellae isolated from cattle and humans. Faecal samples of diarrhoeic patients (n = 234), and a healthy population (n = 160), beef cattle at slaughter (n = 250), farms (n = 72) and market (n = 100) were cultured for salmonellae and serotyping and antimicrobial susceptibility were determined. Whole-genome sequence typing (WGST) of selected isolates and bioinformatic analysis were used to identify the multilocus sequence type (MLST), plasmid replicons, antimicrobial resistance genes and genetic relatedness by single nucleotide polymorphism (SNP) analysis. The Salmonella isolates, diarrhoeic patients (n = 17), healthy population (n = 13), cattle (abattoir, n = 67; farms, n = 10; market n = 5), revealed 49 serovars; some serovars were common to humans and cattle. Rare serovars were prevalent: Colindale (cattle and humans); Rubislaw and Bredeney (humans); and Dublin, Give, Eastbourne, Hadar, Marseille, Sundsvall, Bergen, Ekotedo, Carno and Ealing (cattle). The sequence types (ST) include ST 584, ST 198, ST 562 and ST 512 for S. Colindale, S. Kentucky S. Rubislaw and S. Urbana, respectively. Clonal cluster shared by cattle and human WGST isolates was not found. Antimicrobial resistance rates were generally low and towards only chloramphenicol, ampicillin, gentamicin, ciprofloxacin, tetracycline and streptomycin, range 2.7% (chloramphenicol) to 8.9% (streptomycin). Multiply resistant isolates included serovars Kentucky, 4,5,12:i:- and Typhimurium. The study presents a baseline description of the prevalence, serotypes, antimicrobial resistance phenotypes and genetic relatedness of Salmonella isolated from healthy and diarrhoeic humans, and cattle at harvest, on farm and at market. Cattle are a reservoir of diverse salmonellae with shared serovars with humans, but WGST does not support zoonotic transmission. Further study with larger samples is recommended to determine whether epidemiological link exists between cattle and humans.

Investigating Salmonella Eko from Various Sources in Nigeria by Whole Genome Sequencing to Identify the Source of Human Infections

Twenty-six Salmonella enterica serovar Eko isolated from various sources in Nigeria were investigated by whole genome sequencing to identify the source of human infections. Diversity among the isolates was observed and camel and cattle were identified as the primary reservoirs and the most likely source of the human infections.

Fluoroquinolone-Resistant Enteric Bacteria in Sub-Saharan Africa: Clones, Implications and Research Needs

Fluoroquinolones came into widespread use in African countries in the early 2000s, after patents for the first generation of these drugs expired. By that time, quinolone antibacterial agents had been used intensively worldwide and resistant lineages of many bacterial species had evolved. We sought to understand which Gram negative enteric pandemic lineages have been reported from Africa, as well as the nature and transmission of any indigenous resistant clones. A systematic review of articles indexed in the Medline and AJOL literature databases was conducted. We report on the findings of 43 eligible studies documenting local or pandemic fluoroquinolone-resistant enteric clones in sub-Sahara African countries. Most reports are of invasive non-typhoidal Salmonella and Escherichia coli lineages and there have been three reports of cholera outbreaks caused by fluoroquinolone-resistant Vibrio cholerae O1. Fluoroquinolone-resistant clones have also been reported from commensals and animal isolates but there are few data for non-Enterobacteriaceae and almost none for difficult-to-culture Campylobacter spp. Fluoroquinolone-resistant lineages identified in African countries were universally resistant to multiple other classes of antibacterial agents. Although as many as 972 non-duplicate articles refer to fluoroquinolone resistance in enteric bacteria from Africa, most do not report on subtypes and therefore information on the epidemiology of fluoroquinolone-resistant clones is available from only a handful of countries in the subcontinent. When resistance is reported, resistance mechanisms and lineage information is rarely investigated. Insufficient attention has been given to molecular and sequence-based methods necessary for identifying and tracking resistant clones in Africa and more research is needed in this area.