Prevalence and characterization of Salmonella enterica from the feces of cattle, poultry, swine and hedgehogs in Burkina Faso and their comparison to human Salmonella isolates

Prevalence and serotype of poultry salmonellosis in Africa: a systematic review and meta-analysis

RESEARCH HIGHLIGHTS

The pooled sample prevalence of poultry salmonellosis in Africa is high (14.4%).The highest PPE was recorded in meat and meat products.Salmonella serotypes of zoonotic importance were found in all sample types.Salmonella Enteritidis and Typhimurium are common serotypes spreading in Africa.

A Quick Review of the Prevalence of Important Infectious Poultry Diseases all Around the World

The poultry industry is one of the fastest growing industries in the world. Poultry breeding has developed significantly to meet the food needs of the increasing population and it is expected that this growth will continue in the coming years. Prevalent poultry diseases are of great importance as they are responsible for vast economic losses and public health concerns. They also affect the national and international trade of the poultry products. This review will provide a quick and general view of different important poultry diseases for poultry breeders, scientists and decision makers. Based on this review, Campylobacteriosis and infectious bursal disease (IBD) in the Asian continent, and Campylobacteriosis, Newcastle disease (ND) and coccidiosis in the African continent were the most prevalent diseases. In Europe, Campylobacter species and in America, Escherichia coli species are widespread in poultry meat. Infectious Bronchitis (IB) in Europe and Coccidiosis in America were high-incident.

A Systematic review on Prevalence, Serotypes and Antibiotic resistance of Salmonella in Ethiopia, 2010-2022

Background

In Ethiopia, salmonellosis is one of the most common zoonotic and foodborne illnesses. Ethiopia continues to be at risk for its fast-expanding medication resistance. For the development of preventative and control methods, summarized knowledge regarding salmonellosis is necessary. Determining a thorough evaluation of the prevalence, serotypes, and antibiotic resistance of Salmonella in humans and animals from January 1, 2010, to December 30, 2022, in Ethiopia was our goal.

Methods

To find Salmonella related articles that published in English, we used the Google Scholar and PubMed search engines. Three researchers conducted the eligible studies using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) checklist, making sure to include the necessary keywords. If studies were duplicates, incomplete publications, or reported without an antimicrobial test were excluded. Excel 2013 was used to calculate frequencies and tabulate data.

Results

There were a total of 43 investigations from food handlers, diarrhoeic patients, and animals. The prevalence rates ranged from 1% to 10% and 1% to 13% among food handlers and diarrhoea patients, respectively. The highest prevalence was among pigs (41.6%). S. Anatum in animals and S. Typhimurium in people were the predominant serotypes. Amoxicillin and ampicillin were claimed to be 100% resistant in human studies. The highest recorded resistances for ceftriaxone and ciprofloxacin were 16.7% and 100%, respectively. Animal studies revealed that Salmonella resistances to ampicillin, streptomycin and tetracycline were 100%, 90%, 86.4%, respectively. S. Kentucky showed complete resistance to tetracycline, ampicillin, gentamicin, ciprofloxacin, and streptomycin.

Conclusion

The prevalence of Salmonella among asymptomatic food handlers, diarrheal patients and animals were high in Ethiopia. S. Typhimurium that have the zoonotic importance was presented predominantly in human study. High levels of resistances were showed to tetracycline, ampicillin and streptomycin in animal studies. Salmonellosis prevention and control techniques should be strengthened.

Spatiotemporal Distribution of Salmonella enterica in European Hedgehogs in Northern Italy

Growing attention is being given to the European hedgehog (Erinaceus europaeus) because of its synanthropic behaviour and its potential role in harbouring parasites, viruses, fungi and bacteria and disseminating them to several animals and humans. Salmonella are the most frequently detected zoonotic bacteria that hedgehogs could transmit through contaminating water and food sources with faeces. This study aimed to determine the prevalence and distribution of Salmonella spp. in wild hedgehogs in the Emilia-Romagna region (northern Italy). From 2019 to 2022, 212 European hedgehogs that died naturally were tested for Salmonella spp. through culture isolation. Positive samples were subjected to serological typing. A total of 82 samples tested positive for Salmonella spp., with the overall Bayesian posterior estimated prevalence ranging from 35% (95% CI: 23-47%) to a maximum of 45% (95% CI: 31-59%) during the years considered and with an overall prevalence calculated at 39% (95% CI: 33-45%). Salmonella enterica Enteritidis and Veneziana were the most prevalent detected serovars in 65% and 17% of the positive samples, respectively. Since 2021, S. Typhimurium, S. Typhimurium Monofasica, S. Zaiman, S. Hessarek, S. Muenster, S. Isangi serovars, S. enterica subsp. Diarizonae and S. enterica subsp. Houtenae have been detected. These findings show a high prevalence of Salmonella spp. in tested hedgehogs, suggesting an important role of this animal species in the epidemiology of potentially zoonotic serovars circulating in the Emilia-Romagna region.

Knowledge, Attitudes, and Practices Related to Antibiotic Use and Antibiotic Resistance among Poultry Farmers in Urban and Peri-Urban Areas of Ouagadougou, Burkina Faso

Increased use of antibiotics in livestock is a public health concern, as it poses risks of antibiotic residues and antibiotic-resistant pathogens entering the food chains and infecting humans. A cross-sectional survey was conducted on 216 poultry farms to study knowledge, attitudes and practices of poultry farmers on the use of antibiotics in urban and peri-urban areas of Ouagadougou. Results show that only 17.13% (37/216) of farmers attended training on poultry production. Majority of farmers-85.65% (185/216) were not knowledgeable about the rational use of antibiotics. When there was a disease outbreak, 31.98% (63/197) of farmers used veterinary drugs without a prescription and 22.34% (44/197) consulted a community animal health worker. It should also be noted that 79.19% (156/197) of farmers reported using chicken meat as per normal if the bird died during or right after treatment with an antibiotic. Knowledge of rational use of antibiotics was positively influenced by a good attitude adopted by the farmer during the illness of birds and negatively influenced by disease treatment success and high level of education of the farmer. Lack of knowledge about the rational use of antibiotics including their use without a prescription are serious risk factors for the emergence of antimicrobial resistance. Awareness of farmers and other veterinary drug supply chain actors such as drug stockists and animal health workers on best practices in antimicrobial use and promotion of good biosecurity on farms are important to reduce the misuse of antibiotics.

Prevalence and Antimicrobial Resistance of Salmonella in Poultry Products in Central Ethiopia

Salmonellosis is a bacterial infection caused by salmonella, a member of the Enterobacteriaceae family. From December 2021 to May 2021, a cross-sectional study was carried out to isolate Salmonella from poultry farms in the towns of Bishoftu and Adama and to determine the antimicrobial susceptibility frequency of the isolates. A total of 384 samples were tested for the presence of Salmonella, including 259 feces, 56 eggs, and 69 types of meat, using the ISO, 2002 standard procedures. The raw data were organized, coded, and entered into an Excel spreadsheet before being analyzed with STATA via descriptive analysis with chi-square. From 384 collected samples, 62 (16.15%) isolates were obtained, with 9.9%, 3.65, and 2.6% found in feces, eggs, and meat, respectively. Statistically, there was a significant difference between breeds (p value = 0.036). Bovines had the highest prevalence (32.83%), while Saso had the lowest (30.81%). The variation within each sample type, housing condition, and age group was not statistically significant (p value >0.05). Antimicrobial resistance was found in 29 (96.77%) of the isolates. Ampicillin and sulphamethoxazole-trimethoprim were effective against all isolates. Salmonella was isolated from various locations, sample types, ages, and breeds, indicating a wider distribution. Salmonellosis detection isolates suggested that it could be an emerging poultry and public health issue. As a result, future research should concentrate on isolating and identifying salmonella from poultry in backyard systems and comparing it to that of an intensive farm, as well as molecular characterization for serotyping and genetic studies, as well as genes responsible for salmonella pathogenicity and drug resistance.

Genetic Relationship between Salmonella Isolates Recovered from Calves and Broilers Chickens in Kafr El-Sheikh City Using ERIC PCR

A prevalent bacterial intestinal infection with severe economic damage is salmonellosis. Our study was carried out to diagnose Salmonella from chickens and calves, to determine its resistance to antimicrobials' phenotypic and genotypic characterization of integrons and β lactamase genes in the multidrug resistance of different Salmonella serotypes, and to detect the genetic relationship between Salmonella isolates collected from different origins using an ERIC PCR. In total, 200 samples from diseased chicken and diarrheic calves were obtained from 50 various farms from Kafr El-sheikh, Egypt. Salmonella poultry isolates were characterized as S. Typhimurium (3/8), S. Enteritidis (3/8), and S. Kentucky (2/8), but Salmonella isolates from cattle were S. Enteritidis (1/2) and S. Kentucky (1/2). When antibiotic susceptibility testing was completed on all of the isolates, it showed that there was multidrug resistance present (MDR). A PCR was applied for identifying the accompanying class 1 integrons and ESBLs from MDR Salmonella isolates (two isolates of S. Kentucky were divided as one from calf and one from poultry). Our results detected blaTEM and class 1 integron, but were negative for bla IMP, bla VIM, and bla SHV. An ERIC PCR was conducted for understanding the clonal relation between various β-lactamase-producing MDR Salmonella isolates. The same four previously mentioned isolates were also tested. The two isolates of S. Enteritidis isolated from poultry and calves had 100% similarity despite indicating that there were interactions between broilers and calves living on the same farm that caused infection from the same Salmonella strains, while the other two isolates of S. Kentucky showed only 33% serovarities.

Salmonella enterica Newserovar Abeokuta Genome Sequence, Strain OG19FER4 Isolated from Poultry Feed in Nigeria

This report announces the genome of a newly confirmed Salmonella serovar ( Salmonella enterica serovar Abeokuta) that was isolated from a poultry feed sample collected on a farm in Abeokuta, capital of Ogun State in Nigeria. Salmonella Abeokuta has not been identified outside Nigeria, nor does it appear to be a cause for concern for animal and human health.

Salmonella serovars in sheep and goats and their probable zoonotic potential to humans in Suez Canal Area, Egypt

Background

Salmonella is one of the most common and economically important zoonotic pathogens. This study aimed to determine the occurrence of Salmonella serovars in sheep and goats and their probable zoonotic risk to humans in Suez Canal area in Egypt. A total of 320 fecal samples from sheep (n = 120), goats (n = 100), and humans (n = 100) were collected and examined for the presence of Salmonella based on cultural and biochemical characteristics, and serological analysis. Moreover, the virulence of the identified Salmonella isolates was assessed by molecular screening for invA, stn, spvC, and sopB virulence genes using PCR.

Results

Overall, the occurrence of Salmonella in sheep feces (23.3%) was higher than that in goat feces (7%) and human stool (13%) in the study area. The identified isolates belonged to 12 serotypes; ten, five, and eight from sheep, goats, and humans, respectively. The most frequently identified serotypes were S. Typhimurium from sheep feces, and S. Enteritidis from both goat feces and human stool, with four serotypes; S. Typhimurium, S. Enteritidis, S. Dublin and S. Saintpaul, were mutually shared between all of them. Demographic data revealed that diarrheic sheep (85.7%) and goats (25%) had a higher risk for Salmonella fecal carriage than non-diarrheic ones (19.5% and 6.25%, respectively). The prevalence of Salmonella infection in humans in contact with sheep and goats (28%) was significantly higher than its prevalence in people having a history of contact with animals other than sheep and goats (10%) and those having no history of animal contact (7.3%) (χ² = 6.728, P ˂ 0.05). The stn, spvC, and sopB genes were detected in 98.1% of the isolates, with a significant, very strong positive correlation for their mutual presence (P < 0.05). Approximately 40.7% of isolates that carried the invA gene had a non-significant, very weak positive correlation with other virulence genes. The most common genotypic virulence profile for all isolates was stn, spvC, and sopB; however, invA, stn, spvC, and sopB was the frequent virulotype for S. Typhimurium, S. Tsevie, S. Apeyeme, and S. Infantis.

Conclusions

The present study highlights the role of apparently healthy and diarrheic sheep and goats as reservoirs and sources of human infection with virulent Salmonella serovars in the Suez Canal area.

Salmonella Yoruba: a rare serotype revealed through genomic sequencing along the farm-to-fork continuum of an intensive poultry farm in KwaZulu-Natal, South Africa

Salmonella enterica is a zoonotic pathogen of worldwide public health importance. We characterised Salmonella isolates from poultry along the farm-to-fork continuum using whole genome sequencing (WGS) and bioinformatics analysis. Three multilocus sequence types (MLSTs), i.e., ST15 (1.9%), ST152 (5.9%) and ST1316 (92.2%) and three serotypes, i.e., S. Heidelberg (1.9%), Kentucky (5.9%) and Yoruba (92.2%) were detected. The rare serotype, S. Yoruba, was detected among the farm and abattoir isolates and contained resistance and virulence determinants. Resistome analysis revealed the presence of the aac(6')-Iaa gene associated with aminoglycoside resistance, a single point mutation in the parC gene associated with fluoroquinolone and quinolone resistance, and a single isolate contained the fosA7 gene responsible for fosfomycin resistance. No antibiotic resistance genes (ARGs) were identified for isolates phenotypically non-susceptible to azithromycin, cephalosporins, chloramphenicol and nitrofurantoin and resistance was thought to be attributable to other resistance mechanisms. The fully susceptible profiles observed for the wastewater isolates suggest that the poultry environment may receive antibiotic-resistant strains and resistance determinants from poultry with the potential of becoming a pathway of Salmonella transmission along the continuum. Six plasmids were identified and were only carried by 92.2% of the S. Yoruba isolates in varying combinations. Four plasmids were common to all S. Yoruba isolates along the continuum; isolates from the litter and faeces on the farm contained two additional plasmids. Ten Salmonella pathogenicity islands (SPIs) and 177 virulence genes were identified; some were serotype-specific. Phylogenetic analysis of S. Heidelberg and Kentucky showed that isolates were related to animal and human isolates from other countries. Phylogenetic analysis among the S. Yoruba isolates revealed four clades based on the isolate sources along the farm-to-fork continuum. Although the transmission of Salmonella strains along the farm-to-fork continuum was not evident, pathogenic, resistant Salmonella present in the poultry production chain poses a food safety risk. WGS analysis can provide important information on the spread, resistance, pathogenicity, and epidemiology of isolates and new, rare or emerging Salmonella strains to develop intervention strategies to improve food safety.

Resistance Genes, Plasmids, Multilocus Sequence Typing (MLST), and Phenotypic Resistance of Non-Typhoidal Salmonella (NTS) Isolated from Slaughtered Chickens in Burkina Faso

The emergence of antimicrobial-resistant bacteria in developing countries increases risks to the health of both such countries' residents and the global community due to international travel. It is consequently necessary to investigate antimicrobial-resistant pathogens in countries such as Burkina Faso, where surveillance data are not available. To study the epidemiology of antibiotic resistance in Salmonella, 102 Salmonella strains isolated from slaughtered chickens were subjected to whole-genome sequencing (WGS) to obtain information on antimicrobial resistance (AMR) genes and other genetic factors. Twenty-two different serotypes were identified using WGS, the most prevalent of which were Hato (28/102, 27.5%) and Derby (23/102, 22.5%). All strains analyzed possessed at least one and up to nine AMR genes, with the most prevalent being the non-functional aac(6')-Iaa gene, followed by aph(6)-Id. Multi-drug resistance was found genotypically in 36.2% of the isolates for different classes of antibiotics, such as fosfomycin and β-lactams, among others. Plasmids were identified in 43.1% of isolates (44/102), and 25 plasmids were confirmed to carry AMR genes. The results show that chicken can be considered as a reservoir of antibiotic-resistant Salmonella strains. Due to the prevalence of these drug-resistant pathogens and the potential for foodborne illnesses, poultry processing and cooking should be performed with attention to prescribed safe handling methods to avoid cross-contamination with chicken products.

A Public Health Insight into Salmonella in Poultry in Africa: A Review of the Past Decade: 2010-2020

Poultry is a cheap source of animal protein and constituent of diets in Africa. Poultry can serve as a reservoir for Salmonella and cause food-borne infections in humans. This review describes Salmonella contamination of food, poultry, and the farming environment, antimicrobial resistance profiles, and serotypes of Salmonella, as well as the farming systems, antimicrobial use (AMU), hygiene, and husbandry conditions used to rear poultry in Africa. Using the PRISMA (preferred reporting items for systematic reviews and meta-analysis) guidelines, PubMed, Science Direct, and Web of Science databases were searched using a set of predefined keywords. Full-length research articles in English were examined for the period 2010-2020 and relevant information extracted for the narrative synthesis. Of the articles that met the inclusion criteria, 63.1% were conducted on farms and among households, while 36.9% were undertaken at government-controlled laboratories, which quarantine imported birds, processing plants, and retail outlets. The farming systems were intensive, semi-intensive, and extensive. AMU was described in 11.5% of the studies and varied within and across countries. Multidrug-resistant (MDR) Salmonella isolates were detected in 30 studies and the prevalence ranged from 12.1% in Zimbabwe to 100% in Egypt, Ethiopia, Nigeria, Senegal, and South Africa. A total of 226 different Salmonella serotypes were reported. Twenty-four (19.7%) of the studies reported food-borne Salmonella contamination in eggs, poultry, and poultry products at retail outlets and processing plants. The apparent extensive use of antimicrobials and circulation of MDR Salmonella isolates of various serotypes in Africa is a concern. It is important to implement stricter biosecurity measures on farms, regulate the use of antimicrobials and implement surveillance systems, in addition to food safety measures to monitor the quality of poultry and poultry products for human consumption.

Salmonella Salamae and S. Waycross isolated from Nile perch in Lake Victoria show limited human pathogenic potential

Non-enterica subspecies of Salmonella enterica are rarely associated with human infections. Paradoxically, food safety legislations consider the entire genus Salmonella as pathogenic to humans. Globally, large amounts of seafoods are rejected and wasted due to findings of Salmonella. To inform better food safety decisions, we investigated the pathogenicity of Salmonella Salamae 42:r- and Salmonella Waycross isolated from Nile perch from Lake Victoria. Genome-wide analysis revealed absence of significant virulence determinants including on key Salmonella pathogenicity islands in both serovars. In epithelial cells, S. Salamae showed a weak invasion ability that was lower than the invH mutant of S. Typhimiurium used as negative control. Similarly, S. Salamae could not replicate inside macrophages. Moreover, intracellular replication in S. Waycross strains was significantly lower compared to the wild type S. Typhimurium. Our findings suggest a low pathogenicity of S. Salamae reinforcing the existing literature that non-enterica subspecies are avirulent. We propose that food legislations and actions taken on findings of Salmonella are revisited to avoid wasting valuable sea- and other foods.

Development of a Duplex TaqMan Real-Time Polymerase Chain Reaction for Accurate Identification and Quantification of Salmonella Enteritidis from Laboratory Samples and Contaminated Chicken Eggs

Salmonella enteritidis is a major causative agent of foodborne illnesses worldwide. As the traditional serotyping and quantification methods are labor-intensive, time-consuming, and expensive, faster and more convenient molecular diagnostic methods are needed. In this study, we developed and validated a rapid duplex TaqMan real-time polymerase chain reaction (PCR) for the accurate identification and quantification of S. enteritidis. The primers and TaqMan probes were designed based on the S. enteritidis-specific gene lygD and the Salmonella genus-specific gene invA. The melt curve and gel electrophoresis analysis showed that the designed primers had potent specificity for the amplification of lygD and invA. The duplex real-time PCR specifically identified S. enteritidis from a panel of 40 Salmonella strains that represented 29 serovars and 12 non-Salmonella organisms. The duplex real-time PCR assay detected four copies of S. enteritidis DNA per reaction. The intra- and inter- assays indicated a high degree of reproducibility. The real-time PCR could accurately detect and quantify S. enteritidis in chicken organs after Salmonella infection. Furthermore, the assay identified 100% of the S. enteritidis and Salmonella genus isolates from chicken egg samples with superior sensitivity after 6 h of pre-enrichment compared to the traditional culture method. Additionally, the most-probable-number (MPN) combined with qPCR and a shortened incubation time (MPN-qPCR-SIT) method was developed for the population determination of S. enteritidis and compared with various enumeration methods. Thus, we have established and validated a new duplex real-time PCR assay and MPN-qPCR-SIT method for the accurate detection and quantification of S. enteritidis, which could contribute to meeting the need for fast detection and identification in prevention and control measures for food safety.

Molecular Epidemiology of Salmonella enterica in Poultry in South Africa Using the Farm-to-Fork Approach

The presence of the zoonotic pathogen Salmonella in the food supply chain poses a serious public health threat. This study describes the prevalence, susceptibility profiles, virulence patterns, and clonality of Salmonella from a poultry flock monitored over six weeks, using the farm-to-fork approach. Salmonella was isolated using selective media and confirmed to the genus and species level by real-time polymerase chain reaction (RT-PCR) of the invA and iroB genes, respectively. Antimicrobial susceptibility profiles were determined using Vitek-2 and the Kirby–Bauer disk diffusion method against a panel of 21 antibiotics recommended by the World Health Organisation Advisory Group on Integrated Surveillance of Antimicrobial Resistance (WHO-AGISAR). Selected virulence genes were identified by conventional PCR, and clonality was determined using enterobacterial repetitive intergenic consensus PCR (ERIC-PCR). Salmonella was present in 32.1% of the samples: on the farm (30.9%), at the abattoir (0.6%), and during house decontamination (0.6%). A total of 210 isolates contained the invA and iroB genes. Litter, faeces, and carcass rinsate isolates were classified as resistant to cefuroxime (45.2%), cefoxitin (1.9%), chloramphenicol (1.9%), nitrofurantoin (0.4%), pefloxacin (11.4%), and azithromycin (11%). Multidrug resistance (MDR) was observed among 3.8% of the isolates. All wastewater and 72.4% of carcass rinsate isolates were fully susceptible. All isolates harboured the misL, orfL, pipD, stn, spiC, hilA, and sopB virulence genes, while pefA, spvA, spvB, and spvC were absent. In addition, fliC was only present among the wastewater isolates. Various ERIC-PCR patterns were observed throughout the continuum with different subtypes, indicating the unrelated spread of Salmonella. This study concluded that poultry and the poultry environment serve as reservoirs for resistant and pathogenic Salmonella. However, there was no evidence of transmission along the farm-to-fork continuum.

Virulence Gene Profile, Antimicrobial Resistance and Multilocus Sequence Typing of Salmonella enterica Subsp. enterica Serovar Enteritidis from Chickens and Chicken Products

This study was undertaken to determine the virulence, antimicrobial resistance and molecular subtypes of Salmonella in the Central Region of Peninsular Malaysia. A total of 45 Salmonella Enteritidis were detected from live chicken (cloacal swab), and chicken products (fresh and ready-to-eat meat) samples upon cultural isolation and serotyping. Similarly, an antimicrobial susceptibility test based on the Kirby Bauer disk diffusion method as well as antimicrobial resistance AMR genes, virulence determinants and multilocus sequence typing (MLST) typing were conducted after the Whole Genome Sequencing and analysis of the isolates. The results indicate that sequence types ST1925 (63.7%), and ST11 (26.5%) were the predominant out of the seven sequence types identified (ST292, ST329, ST365, ST423 and ST2132). The phenotypic antimicrobial profile corresponds to the genotypic characterization in that the majority of the isolates that exhibited tetracycline, gentamycin and aminoglycoside resistance; they also possessed the tetC and blaTEM β-Lactam resistance genes. However, isolates from cloacal swabs showed the highest number of resistance genes compared to the chicken products (fresh and ready-to-eat meat) samples. Furthermore, most of the virulence genes were found to cluster in the Salmonella pathogenicity island (SPI). In this study, all the isolates were found to possess SPI-1, which codes for the type III secretion system, which functions as actin-binding proteins (SptP and SopE). The virulence plasmid (VP) genes (spvB, spvC) were present in all genotypes except ST365. The findings of this study, particularly with regard to the molecular subtypes and AMR profiles of the Salmonella Enteritidis serotype shows multidrug-resistance features as well as genetic characteristics indicative of high pathogenicity.

Bacteriophages: Combating Antimicrobial Resistance in Food-Borne Bacteria Prevalent in Agriculture

Through recent decades, the subtherapeutic use of antibiotics within agriculture has led to the widespread development of antimicrobial resistance. This problem not only impacts the productivity and sustainability of current agriculture but also has the potential to transfer antimicrobial resistance to human pathogens via the food supply chain. An increasingly popular alternative to antibiotics is bacteriophages to control bacterial diseases. Their unique bactericidal properties make them an ideal alternative to antibiotics, as many countries begin to restrict the usage of antibiotics in agriculture. This review analyses recent evidence from within the past decade on the efficacy of phage therapy on common foodborne pathogens, namely, Escherica coli, Staphylococcus aureus, Salmonella spp., and Campylobacter jejuni. This paper highlights the benefits and challenges of phage therapy and reveals the potential for phages to control bacterial populations both in food processing and livestock and the possibility for phages to replace subtherapeutic usage of antibiotics in the agriculture sector.

Salmonella Genomics in Public Health and Food Safety

The species Salmonella enterica comprises over 2,600 serovars, many of which are known to be intracellular pathogens of mammals, birds, and reptiles. It is now apparent that Salmonella is a highly adapted environmental microbe and can readily persist in a number of environmental niches, including water, soil, and various plant (including produce) species. Much of what is known about the evolution and diversity of nontyphoidal Salmonella serovars (NTS) in the environment is the result of the rise of the genomics era in enteric microbiology. There are over 340,000 Salmonella genomes available in public databases. This extraordinary breadth of genomic diversity now available for the species, coupled with widespread availability and affordability of whole-genome sequencing (WGS) instrumentation, has transformed the way in which we detect, differentiate, and characterize Salmonella enterica strains in a timely way. Not only have WGS data afforded a detailed and global examination of the molecular epidemiological movement of Salmonella from diverse environmental reservoirs into human and animal hosts, but they have also allowed considerable consolidation of the diagnostic effort required to test for various phenotypes important to the characterization of Salmonella. For example, drug resistance, serovar, virulence determinants, and other genome-based attributes can all be discerned using a genome sequence. Finally, genomic analysis, in conjunction with functional and phenotypic approaches, is beginning to provide new insights into the precise adaptive changes that permit persistence of NTS in so many diverse and challenging environmental niches.

Benefits and Risks of Smallholder Livestock Production on Child Nutrition in Low- and Middle-Income Countries

Livestock production may improve nutritional outcomes of pregnant women and children by increasing household income, availability of nutrient-dense foods, and women's empowerment. Nevertheless, the relationship is complex, and the nutritional status of children may be impaired by presence of or proximity to livestock and their pathogens. In this paper, we review the benefits and risks of livestock production on child nutrition. Evidence supports the nutritional benefits of livestock farming through income, production, and women's empowerment. Increasing animal source food consumption requires a combination of efforts, including improved animal management so that herd size is adequate to meet household income needs and consumption and addressing sociocultural and gendered norms. Evidence supports the inclusion of behavior change communication strategies into livestock production interventions to facilitate the sustainability of nutritional benefits over time, particularly interventions that engage women and foster dimensions of women's empowerment. In evaluating the risks of livestock production, evidence indicates that a broad range of enteric pathogens may chronically infect the intestines of children and, in combination with dietary deficits, may cause environmental enteric dysfunction (EED), a chronic inflammation of the gut. Some of the most important pathogens associated with EED are zoonotic in nature with livestock as their main reservoir. Very few studies have aimed to understand which livestock species contribute most to colonization with these pathogens, or how to reduce transmission. Control at the point of exposure has been investigated in a few studies, but much less effort has been spent on improving animal husbandry practices, which may have additional benefits. There is an urgent need for dedicated and long-term research to understand which livestock species contribute most to exposure of young children to zoonotic enteric pathogens, to test the potential of a wide range of intervention methods, to assess their effectiveness in randomized trials, and to assure their broad adaptation and sustainability. This review highlights the benefits and risks of livestock production on child nutrition. In addition to identifying research gaps, findings support inclusion of poor gut health as an immediate determinant of child undernutrition, expanding the established UNICEF framework which includes only inadequate diet and disease.

Prevalence and epidemiological distribution of selected foodborne pathogens in human and different environmental samples in Ethiopia: a systematic review and meta-analysis

Bacterial Foodborne Pathogens (FBP) are the commonest cause of foodborne illness or foodborne diseases (FBD) worldwide. They contaminate food at any stages in the entire food chain, from farm to dining-table. Among these, the Diarrheagenic Escherichia coli (DEC), Non typhoidal Salmonella (NTS), Shigella spp. and Campylobacter spp. are responsible for a large proportion of illnesses, deaths; and, particularly, as causes of acute diarrheal diseases. Though existing studies indicate the problem may be severe in developing countries like Ethiopia, the evidence is commonly based on fragmented data from individual studies. A review of published and unpublished manuscripts was conducted to obtain information on major FBP and identify the gaps in tracking their source attributions at the human, animal and environmental interface. A total of 1753 articles were initially retrieved after restricting the study period to between January 2000 and July 2020. After the second screening, only 51 articles on the humans and 43 on the environmental sample based studies were included in this review. In the absence of subgroups, overall as well as human stool and environmental sample based pooled prevalence estimate of FBP were analyzed. Since, substantial heterogeneity is expected, we also performed a subgroup analyses for principal study variables to estimate pooled prevalence of FBP at different epidemiological settings in both sample sources. The overall random pooled prevalence estimate of FBP (Salmonella, pathogenic Escherichia coli (E. coli), Shigella and Campylobacter spp.) was 8%; 95% CI: 6.5-8.7, with statistically higher (P <  0.01) estimates in environmental samples (11%) than in human stool (6%). The subgroup analysis depicted that Salmonella and pathogenic E. coli contributed to 5.7% (95% CI: 4.7-6.8) and 11.6% (95% CI: 8.8-15.1) respectively, of the overall pooled prevalence estimates of FBD in Ethiopia. The result of meta-regression showed, administrative regional state, geographic area of the study, source of sample and categorized sample size all significantly contributed to the heterogeneity of Salmonella and pathogenic E. coli estimates. Besides, the multivariate meta- regression indicated the actual study year between 2011 and 2015 was significantly associated with the environmental sample-based prevalence estimates of these FBP. This systematic review and meta-analysis depicted FBP are important in Ethiopia though majority of the studies were conducted separately either in human, animal or environmental samples employing routine culture based diagnostic method. Thus, further FBD study at the human, animal and environmental interface employing advanced diagnostic methods is needed to investigate source attributions of FBD in one health approach.

Genome analysis of Salmonella strains isolated from imported frozen fish in Burkina Faso

Purpose

Fish is an excellent source of protein and vitamins for humans, but improperly handled, fish can expose consumers to pathogenic bacteria. This study was aimed to isolate and characterize the genomes of Salmonella strains isolated from imported fish sold in the open market in Ouagadougou.

Methods

One hundred and fifty-nine fish were collected from open markets and were cultured for Salmonella. Antimicrobial susceptibility was determined by broth microdilution. Whole-genome sequencing was done to further study antibiotic resistance genes, plasmid replicons, and MSLT types. Serotyping was done using SeqSero 2.

Result

Out of the 159 fish samples analyzed, 30 (18.9%) were found to be contaminated with Salmonella. Among the isolated Salmonella strains, six different serotypes, Nima, Liverpool, Kokomlemle, Teshie, Derby, and Tennessee, were found using SeqSero2. Salmonella Tennessee was the predominant serotype. All the isolates possessed at least one resistance gene. The aac6-Iaa aminoglycoside resistance gene was the most prevalent gene found in the strains. The gene fosA7 was detected in three strains. All the S. Nima isolates were of Multilocus Sequence Type (MLST) 8086, S. Teshie isolate was ST 530; Liverpool was ST 1959; Derby was ST 7880; Kokomlemle was ST 2696. The Tennessee isolates gave two different STs including ST 8395 and 8398.

Conclusion

The presented results highlight the prevalence of Salmonella on imported fish purchased from the open markets. More attention should be paid regarding fish selling conditions in the country to prevent the potential health risk for consumers.

Genomic Investigation of Salmonella Isolates Recovered From a Pig Slaughtering Process in Hangzhou, China

The pig industry is the principal source of meat products in China, and the presence of pathogens in pig-borne meat is a crucial threat to public health. Salmonella is the major pathogen associated with pig-borne diseases. However, route surveillance by genomic platforms along the food chain is still limited in China. Here, we conducted a study to evaluate the dynamic prevalence of Salmonella in a pig slaughtering process in Hangzhou, Zhejiang Province, China. Fifty-five of 226 (24.37%) samples were positive for Salmonella; from them, 78 different isolates were selected and subjected to whole genome sequencing followed by bioinformatics analyses to determine serovar distribution, MLST patterns, antimicrobial resistance genes, plasmid replicons, and virulence factors. Moreover, phenotypic antimicrobial resistance was performed using the broth dilution method against 14 antimicrobial agents belonging to 10 antimicrobial classes. Our results showed that samples collected from the dehairing area (66.66%) and the splitting area (57.14%) were the most contaminated. Phenotypic antimicrobial resistance classified 67 of 78 isolates (85.90%) as having multidrug resistance (MDR), while the highest resistance was observed in tetracycline (85.90%; 67/78) followed by ampicillin (84.62%; 66/78), chloramphenicol (71.80%; 56/78), and nalidixic acid (61.54%; 48/78). Additionally, serovar prediction showed the dominance of Salmonella Typhimurium ST19 (51.28%; 40/78) among the 78 studied isolates, while plasmid prediction reported the dominance of IncHI2A_1 (20.51%; 16/78), followed by IncX1_1 (17.95%; 14/78) and IncHI2_1 (11.54%; 9/78). Virulence factor prediction showed the detection of cdtB gene encoding typhoid toxins in two Salmonella Goldcoast ST358 and one Salmonella Typhimurium ST19, while one isolate of Salmonella London ST155 was positive for genes encoding for the siderophore “yersiniabactin” and the gene senB encoding for enterotoxin production. From this study, we conclude that pig slaughterhouses are critical points for the dissemination of virulent and multidrug-resistant Salmonella isolates along the food chain which require the implementation of management systems to control the critical points. Moreover, there is an urgent need for the implementation of the whole genome sequencing platform to monitor the emergence of virulent and multidrug-resistant clones along the food chain.

Contamination of street food with multidrug-resistant Salmonella, in Ouagadougou, Burkina Faso

Background

Gastrointestinal infections are a global public health problem. In Burkina Faso, West Africa, exposure to Salmonella through the consumption of unhygienic street food represents a major risk of infection requiring detailed evaluation.

Methods

Between June 2017 and July 2018, we sampled 201 street food stalls, in 11 geographic sectors of Ouagadougou, Burkina Faso. We checked for Salmonella contamination in 201 sandwiches (one per seller), according to the ISO 6579:2002 standard. All Salmonella isolates were characterized by serotyping and antimicrobial susceptibility testing, and whole-genome sequencing was performed on a subset of isolates, to investigate their phylogenetic relationships and antimicrobial resistance determinants.

Results

The prevalence of Salmonella enterica was 17.9% (36/201) and the Salmonella isolates belonged to 16 different serotypes, the most frequent being Kentucky, Derby and Tennessee, with five isolates each. Six Salmonella isolates from serotypes Brancaster and Kentucky were multidrug-resistant (MDR). Whole-genome sequencing revealed that four of these MDR isolates belonged to the emergent S. enterica serotype Kentucky clone ST198-X1 and to an invasive lineage of S. enterica serotype Enteritidis (West African clade).

Conclusion

This study reveals a high prevalence of Salmonella spp. in sandwiches sold in Ouagadougou. The presence of MDR Salmonella in food on sale detected in this study is also matter of concern.

Hedgehogs as a Potential Source of Zoonotic Pathogens-A Review and an Update of Knowledge

Simple Summary

Up to date studies indicate that wild hedgehogs may act as carriers and/or hosts for bacterial, viral, and fungal pathogens with zoonotic potential, posing a significant threat to humans. The same applies to domestic hedgehogs, which are increasingly kept as pets. Considering the potential risk of infection to humans through close contact with hedgehogs or the contaminated environment they inhabit, current data on the prevalence of various zoonotic pathogens in these animals is desirable.

Abstract

Hedgehogs are small insectivorous mammals common across Europe, Asia, and Africa. The increased encroachment of humans into hedgehog habitats has disrupted the human-animal-environment interface. With growing interest in the zoonotic diseases of wildlife species, more studies have been devoted to this subject in the last few years. These papers provide information about known and new emerging diseases. Here we review the current knowledge regarding bacterial, viral, protozoic, and mycotic pathogens with zoonotic potential and assess the importance of hedgehogs as their carriers. Both wild and pet hedgehogs were included in the review. Data from several countries and various hedgehog species were included. The study shows the importance of hedgehogs as carriers of zoonotic diseases and reservoirs of zoonotic pathogens in varied habitats.

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.

Antibiotic resistance of Escherichia coli and Salmonella spp. strains isolated from healthy poultry farms in the districts of Abidjan and Agnibilékrou (Côte d'Ivoire)

Background and Aim

Antimicrobial resistance (AMR) is a serious challenge to animal and human health worldwide. Therefore, this study aims to determine levels and patterns of AMR of Escherichia coli and Salmonella spp. strains isolated from poultry farms in Côte d'Ivoire.

Materials and Methods

A cross-sectional study was conducted in two districts of Côte d'Ivoire with high poultry production: Abidjan and Agnibilékrou. A total of 231 fecal samples were collected in 124 poultry farms in both districts. Enterobacteria were isolated and tested for susceptibility to 14 antimicrobial agents using the disk-diffusion method.

Results

A total of 212 E. coli and 36 Salmonella strains were isolated. In Abidjan, 139 collected samples generated 101 E. coli and 23 Salmonella strains, whereas in Agnibilékrou, 92 collected samples generated 111 E. coli and 13 Salmonella strains. Variable resistance levels were recorded for the antibiotics tested. The resistance prevalence of E. coli and Salmonella, respectively, was high: Doxycycline (98%/94%), sulfonamide (84%/86%), trimethoprim-sulfamethoxazole (80%/41%), and streptomycin (71%/52%). Average resistance rates were recorded for flumequine (38%/66%), ampicillin (49%/33%), amoxicillin (25%/44%), colistin (26%/2%), chloramphenicol (21%/2%), and gentamicin (4%/47%). The antibiotics least affected by resistance were cefuroxime (4%/5%), ceftriaxone (2%/0.00%), and nitrofurantoin (1%/0.00%).

Conclusion

In this study, it was observed that resistance to important antibiotics is emerging in poultry production in Côte d'Ivoire. Policies promoting the rational use of antibiotics should be implemented to manage antibiotic resistance in animal production.

Serotyping of sub-Saharan Africa Salmonella strains isolated from poultry feces using multiplex PCR and whole genome sequencing

Background

Salmonella enterica remains a leading cause of food-borne diseases worldwide. Serotype information is important in food safety and public health activities to reduce the burden of salmonellosis. In the current study, two methods were used to determine serotypes of 111 strains of Salmonella isolated from poultry feces in Burkina Faso. First, Salmonella Multiplex Assay for Rapid Typing (SMART) Polymerase Chain Reaction (PCR) was used to determine the serovars of the S. enterica isolates. Second, serovar prediction based on whole genome sequencing (WGS) data was performed using SeqSero 2.0.

Results

Among the 111 Salmonella isolates, serotypes for 17 (15.31%) isolates were identified based on comparison to a panel of representative SMART codes previously determined for the 50 most common serovars in the United States. Forty-four (44) new SMART codes were developed for common and uncommon serotypes. A total of 105 (94.59%) isolates were serotyped using SeqSero 2.0 for serovar prediction based on WGS data.

Conclusion

We determined that SeqSero 2.0 was more comprehensive for identifying Salmonella serotypes from Burkina Faso than SMART PCR.

DETECTION OF DIARRHEAGENIC ESCHERICHIA COLI IN HUMAN DIARRHEIC STOOL AND DRINKING WATER SAMPLES IN OUAGADOUGOU, BURKINA FASO

Background:

The presence of diarrheagenic Escherichia coli (DEC) in drinking water, is a grave public health problem. This study was aimed at characterization of diarrheagenic Escherichia coli isolated from drinking water and faecal samples from diarrheic patients in Ouagadougou, Burkina Faso.

Materials and Methods:

A total of 242 water samples consisting of 182 potable sachets and 60 from boreholes were collected in the period between October 2018 and April 2019 in the city of Ouagadougou. Faecal samples were also collected from 201 diarrheic patients visiting National Public Health Laboratory for a biological diagnosis by coproculture. The presence of virulence genes associated with DEC was determined by 16-plex polymerase chain reaction from bacteria culture.

Results:

From drinking water, we found 17% (42/242) Escherichia coli isolates in which 1% (2/242) DEC were detected. Among analyzed samples (182 sachet water versus 60 borehole water), the two DEC (01 ETEC and 01 EPEC) were detected in sachet water. DEC were detected in 20% (40/201) of patients. Enteroaggregative Escherichia coli (EAEC) were mostly detected in 10% followed by Enteropathogenic Escherichia coli (EPEC) in 4%, Enteroinvasive Escherichia coli (EIEC) in 2%, and Shiga toxin-producing Escherichia coli (STEC) 0.5%. However, Enterotoxigenic Escherichia coli (ETEC) was not detected alone, but in co-infections with EAEC.

Conclusion:

The present study documented the prevalence of Escherichia coli pathovars associated in patients with diarrhea, and shows that drinking water might be a source of DEC transmission in human.

Survey of Salmonella infections in broiler farms in Iran during 2013-2014: a cross-sectional study

Background and Objectives:

The aim of this study was to determine the prevalence of Salmonella at broiler breeder farms of Iran and investigate the factors underlying salmonellosis in these farms. This is a cross-sectional investigation conducted in 23 provinces of Iran.

Materials and Methods:

Fecal samples were collected from 139 broiler breeder farms in the country and standard bacteriological tests were carried out on the samples for the isolation of Salmonella. The serological tests were then applied for the samples that were positive in the bacteriological test. The information on the sampled farms extracted from the Iran GIS-VET Monitoring and Surveillance System was used for the analysis of the risk factors.

Results:

A total of 11 farms out of the 139 sampled farms were infected with Salmonella with the largest number of infected cases related to Tehran and Fars Provinces.

Conclusion:

The statistical analysis results showed that flocks with older ages and farms with larger number of houses are at greater risk of Salmonella infection.

Extended spectrum beta-lactamase and fluoroquinolone resistance genes among Escherichia coli and Salmonella isolates from children with diarrhea, Burkina Faso

BACKGROUND

The emergence and spread of multidrug-resistant gram-negative bacteria (MDR) has become a major public health concern worldwide. This resistance is caused by enzymes-mediated genes (i.e., extended spectrum beta-lactamases) that are common in certain Enterobacterioceae species. However, the distribution of these genes is poorly documented in Burkina Faso. This study aims to determine the prevalence and distribution of the resistant genes coding for broad spectrum beta-lactamases and quinolones in rural Burkina Faso.

METHODS

Multiplex PCR assays were carried out to detect ESBL-encoding genes, including bla_OXA, bla_TEM, bla_CTX-M, bla_SHV. The assays also assessed the presence of quinolone resistance gene namely qnrA, qnrB and qnrS in the quinolone-resistance DEC and Salmonella strains.

RESULTS

The Extended-Spectrum Beta-Lactamases (ESBL) resistance phenotype was reported in all the E. coli isolates (5/5). Cross-resistance phenotype to quinolones (CRQ) was shown by one Salmonella strain (1/9) and three E. coli (3/5). Cross-resistance phenotypes to fluoroquinolones (CRFQ) were harboured by one Salmonella (1/9) and carbapenemase phenotypes were detected in two E. coli strains (2/5). Whilst the bla_OXA genes were detected in 100% (5/5) of E. coli isolates and in 33.33% (3/9) Salmonella isolates. One strain of E. coli (1/5) harbored the bla_CTX-M gene and the qnrB gene simultaneously.

CONCLUSIONS

This study identified β-lactam (bla) and quinolone resistance (qnr) genes in multidrug-resistant E. coli and Salmonella spp. in rural Burkina Faso. Our finding which highlighted the enterobacteriaceae strains resistance to β-lactams and quinolones are of high interest for adequate management of antimicrobial resistant genes outbreak in Burkina Faso.

Attitudes, practices, and zoonoses awareness of community members involved in the bushmeat trade near Murchison Falls National Park, northern Uganda

The harvest of bushmeat is widespread in the tropics and sub-tropics. Often in these communities, there is a dependence on bushmeat for both food security and basic income. Despite the importance of bushmeat for households worldwide, the practice raises concern for transmission of zoonotic pathogens through hunting, food preparation, and consumption. In Uganda, harvest of wildlife is illegal, but bushmeat hunting, is commonplace. We interviewed 292 women who cook for their households and 180 self-identified hunters from 21 villages bordering Murchison Falls National Park in Uganda to gain insights into bushmeat preferences, opportunity for zoonotic pathogen transmission, and awareness of common wildlife-associated zoonoses. Both hunters and women who cook considered primates to be the most likely wildlife species to carry diseases humans can catch. Among common zoonotic pathogens, the greatest proportions of women who cook and hunters believed that pathogens causing stomach ache or diarrhea and monkeypox can be transmitted by wildlife. Neither women who cook nor hunters report being frequently injury during cooking, butchering, or hunting, and few report taking precautions while handling bushmeat. The majority of women who cook believe that hunters and dealers never or rarely disguise primate meat as another kind of meat in market, while the majority of hunters report that they usually disguise primate meat as another kind of meat. These data play a crucial role in our understanding of potential for exposure to and infection with zoonotic pathogens in the bushmeat trade. Expanding our knowledge of awareness, perceptions and risks enables us to identify opportunities to mitigate infections and injury risk and promote safe handling practices.

Prevalence and risk factors of Salmonella in commercial poultry farms in Nigeria

Salmonella is an important human pathogen and poultry products constitute an important source of human infections. This study investigated prevalence; identified serotypes based on whole genome sequence, described spatial distribution of Salmonella serotypes and predicted risk factors that could influence the prevalence of Salmonella infection in commercial poultry farms in Nigeria. A cross sectional approach was employed to collect 558 pooled shoe socks and dust samples from 165 commercial poultry farms in North West Nigeria. On-farm visitation questionnaires were administered to obtain information on farm management practices in order to assess risk factors for Salmonella prevalence. Salmonella was identified by culture, biotyping, serology and polymerase chain reaction (PCR). PCR confirmed isolates were paired-end Illumina- sequenced. Following de novo genome assembly, draft genomes were used to obtain serotypes by SeqSero2 and SISTR pipeline and sequence types by SISTR and Enterobase. Risk factor analysis was performed using the logit model. A farm prevalence of 47.9% (CI95 [40.3-55.5]) for Salmonella was observed, with a sample level prevalence of 15.9% (CI95 [12.9-18.9]). Twenty-three different serotypes were identified, with S. Kentucky and S. Isangi as the most prevalent (32.9% and 11%). Serotypes showed some geographic variation. Salmonella detection was strongly associated with disposal of poultry waste and with presence of other livestock on the farm. Salmonella was commonly detected on commercial poultry farms in North West Nigeria and S. Kentucky was found to be ubiquitous in the farms.

The Current Status of the Alternative Use to Antibiotics in Poultry Production: An African Perspective

Over the years the growth and health of food-producing animals have been enhanced by the use of antibiotics. These have helped reduce on-farm mortalities, lower incidences of diseases and more importantly improve productivity. Generally, the utilization of antibiotics in feed has been reevaluated since bacterial pathogens have established and shared a variety of antibiotic resistance mechanisms that can easily be spread within microbial communities. Multiple countries have introduced bans or severe restrictions on the non-therapeutic use of antibiotics. This has therefore warranted the urgent need for alternatives. Africa is facing its own challenges as it has been reported to be one of the continents with the highest number of foodborne diseases with approximately 91 million related diseases and 137,000 death per annum. Stakeholder and policy direction has been put in place to curb this escalation; however, the problem persists. The use of alternatives has been recommended and some successfully used in other countries as well as Africa, including pro- and prebiotics and phytochemicals. This then leads to the core aim of this review which is to (1) determine the extent to which antimicrobial-resistant pathogens have affected Africa, (2) assess the current measures put in place by Africa to reduces antimicrobial resistance and finally (3) explore the alternative use of antibiotics in poultry production. Improved sanitary conditions and farm biosecurity are important alternatives that could be adopted by farmers instead of depending on antibiotic drugs for disease control and prevention.

Emerging and re-emerging bacterial zoonoses in Nigeria: current preventive measures and future approaches to intervention

A characteristic of bacterial zoonoses, diseases caused by bacteria that can be transmitted to humans from animals, is a propensity to re-emerge. Several studies demonstrate their ongoing transmission in Nigeria, the most populous country in Africa. However, as local epidemiological data on bacterial zoonoses are inadequate the extent and impact of these infectious diseases is under-reported. Consequently, they are not a targeted priority of national public health policies. This limited recognition is despite indications of their possible roles in the widespread prevalence of non-malarial undifferentiated fever in Nigeria. While a number of animal reservoirs and arthropod vectors have been identified in the transmission routes of these diseases, an escalation of cases of undiagnosed febrile illness highlights the urgent need for a comprehensive assessment of other potential reservoirs, vectors and transmission cycles that may increase the local risk of infection with bacterial zoonoses. Animal health interventions have been proposed as a cost-effective strategy. Here, we present a broad overview of bacterial zoonotic infections of humans in Nigeria in the context of evolving epidemiological patterns. Further, we propose that facilitating the operation of a community-based One Health program is essential to providing the comprehensive epidemiological information that is required to improve prioritization of bacterial zoonoses. This would provide a driver for much needed investment in relevant public health interventions in Africa's most populous country.

Salmonellosis in Hedgehogs

African pygmy hedgehogs are popular pets worldwide. The knowledge and understanding of pet hedgehog common veterinary conditions are increasing as new information and research are published; however, there is still much to learn about this fascinating animal. Salmonella is one of the most common zoonoses worldwide and is naturally isolated from the intestinal tract of many animal species, including hedgehogs. This article discusses the cause, clinical signs, diagnosis, treatment, and prevention of salmonella infection in hedgehogs, primarily focusing on African pygmy hedgehogs, with some reference to European hedgehogs.

Prevalence of Campylobacter and Salmonella in African food animals and meat: A systematic review and meta-analysis

BACKGROUND

Campylobacter and Salmonella, particularly non-typhoidal Salmonella, are important bacterial enteric pathogens of humans which are often carried asymptomatically in animal reservoirs. Bacterial foodborne infections, including those derived from meat, are associated with illness and death globally but the burden is disproportionately high in Africa. Commercial meat production is increasing and intensifying in many African countries, creating opportunities and threats for food safety.

METHODS

Following Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines, we searched six databases for English language studies published through June 2016, that reported Campylobacter or Salmonella carriage or infection prevalence in food animals and contamination prevalence in food animal products from African countries. A random effects meta-analysis and multivariable logistic regression were used to estimate the species-specific prevalence of Salmonella and Campylobacter and assess relationships between sample type and region and the detection or isolation of either pathogen.

RESULTS

Seventy-three studies reporting Campylobacter and 187 studies reporting Salmonella across 27 African countries were represented. Adjusted prevalence calculations estimate Campylobacter detection in 37.7% (95% CI 31.6-44.3) of 11,828 poultry samples; 24.6% (95% CI 18.0-32.7) of 1975 pig samples; 17.8% (95% CI 12.6-24.5) of 2907 goat samples; 12.6% (95% CI 8.4-18.5) of 2382 sheep samples; and 12.3% (95% CI 9.5-15.8) of 6545 cattle samples. Salmonella were detected in 13.9% (95% CI 11.7-16.4) of 25,430 poultry samples; 13.1% (95% CI 9.3-18.3) of 5467 pig samples; 9.3% (95% CI 7.2-12.1) of 2988 camel samples; 5.3% (95% CI 4.0-6.8) of 72,292 cattle samples; 4.8% (95% CI 3.6-6.3) of 11,335 sheep samples; and 3.4% (95% CI 2.2-5.2) of 4904 goat samples. 'External' samples (e.g. hide, feathers) were significantly more likely to be contaminated by both pathogens than 'gut' (e.g. faeces, cloaca) while meat and organs were significantly less likely to be contaminated than gut samples.

CONCLUSIONS

This study demonstrated widespread prevalence of Campylobacter species and Salmonella serovars in African food animals and meat, particularly in samples of poultry and pig origin. Source attribution studies could help ascertain which food animals are contributing to human campylobacteriosis and salmonellosis and direct potential food safety interventions.

Translating 'big data': better understanding of host-pathogen interactions to control bacterial foodborne pathogens in poultry

Recent technological advances has led to the generation, storage, and sharing of colossal sets of information ('big data'), and the expansion of 'omics' in science. To date, genomics/metagenomics, transcriptomics, proteomics, and metabolomics are arguably the most ground breaking approaches in food and public safety. Here we review some of the recent studies of foodborne pathogens (Campylobacter spp., Salmonella spp., and Escherichia coli) in poultry using big data. Genomic/metagenomic approaches have reveal the importance of the gut microbiota in health and disease. They have also been used to identify, monitor, and understand the epidemiology of antibiotic-resistance mechanisms and provide concrete evidence about the role of poultry in human infections. Transcriptomics studies have increased our understanding of the pathophysiology and immunopathology of foodborne pathogens in poultry and have led to the identification of host-resistance mechanisms. Proteomic/metabolomic approaches have aided in identifying biomarkers and the rapid detection of low levels of foodborne pathogens. Overall, 'omics' approaches complement each other and may provide, at least in part, a solution to our current food-safety issues by facilitating the development of new rapid diagnostics, therapeutic drugs, and vaccines to control foodborne pathogens in poultry. However, at this time most 'omics' approaches still remain underutilized due to their high cost and the high level of technical skills required.

Spatial relationships between small-holder farms coupled with livestock management practices are correlated with the distribution of antibiotic resistant bacteria in northern Tanzania

We examined the spatial distribution of antibiotic-resistant coliform bacteria amongst livestock from three distinct cultural groups, where group-level differences in practices (e.g., antibiotic use) may influence the magnitude of antibiotic resistance, while livestock interactions (e.g., mixing herds, shared markets) between these locations may reduce heterogeneity in the distribution of antibiotic resistant bacteria. Data was collected as part of a larger study of antibiotic-resistance in northern Tanzania. Simple regression and generalized linear regression were used to assess livestock management and care practices in relation to the prevalence of multidrug-resistant (MDR) coliform bacteria. Simple and multivariable logistic regression were then used to identify how different management practices affected the odds of households being found within MDR "hotspots." Households that had a higher median neighbourhood value within a 3000 m radius showed a significant positive correlation with livestock MDR prevalence (β = 4.33, 95% CI: 2.41-6.32). Households were more likely to be found within hotspots if they had taken measures to avoid disease (Adjusted Odds Ratio (AOR) 1.53, CI: 1.08-2.18), and if they reported traveling less than a day to reach the market (AOR 2.66, CI: 1.18-6.01). Hotspot membership was less likely when a greater number of livestock were kept at home (AOR 0.81, CI: 0.69-0.95), if livestock were vaccinated (AOR 0.32, CI: 0.21-0.51), or if distance to nearest village was greater (AOR 0.46, CI: 0.36-0.59). The probability of MDR increases when herds are mixed, consistent with evidence for passive transmission of resistant bacteria between animals. Reduced MDR with vaccination is consistent with many studies showing reduced antibiotic use with less disease burden. The neighbourhood effect has implications for design of intervention studies.

Occurrence, Genetic Diversities And Antibiotic Resistance Profiles Of Salmonella Serovars Isolated From Chickens

Purpose

Contamination with Salmonella on food products and poultry in particular has been linked to foodborne infections and/or death in humans. This study investigated the occurrence, genetic diversities and antibiotic resistance profiles of Salmonella strains isolated from chickens.

Patients and methods

Twenty each duplicate faecal swab samples were collected from five different poultry pens of broilers, layers and indigenous chickens in the North-West Province, South Africa. Isolates identities were confirmed through amplification and sequence analysis of 16S rRNA and the invA gene fragments after which phylogenetic tree was constructed. Salmonella enteritidis (ATCC:13076^TM), Salmonella Typhimurium (ATCC:14028^TM) and E. coli (ATCC:259622^TM) were used as positive and negative controls, respectively. The serotypes of Salmonella isolates were determined. Antibiotic-resistant profiles of the isolates against eleven antimicrobial agents were determined.

Results

Eighty-four (84%) of representative isolates possessed the invA genes. The percent occurrence and diversity of Salmonella subspecies in chickens were 1.81-30.9% and was highest in Salmonella enterica subsp. enterica. Notably, the following serotypes Salmonella bongori (10.09%), Salmonella Pullorum (1.81%), Salmonella Typhimurium (12.72%), Salmonella Weltevreden, Salmonella Chingola, Salmonella Houten and Salmonella Bareily (1.81%). Isolates (96.6%) displayed multidrug resistance profiles and the identification of isolates with more than nine antibiotic resistance was a cause for concern.

Conclusion

This study indicates that isolates had pre-exposure histories to the antibiotics tested and may pose severe threats to food security and public health.

Infection, colonization and shedding of Campylobacter and Salmonella in animals and their contribution to human disease: A review

Livestock meat and offal contribute significantly to human nutrition as sources of high-quality protein and micronutrients. Livestock products are increasingly in demand, particularly in low- and middle-income settings where economies are growing and meat is increasingly seen as an affordable and desirable food item. Demand is also driving intensification of livestock keeping and processing. An unintended consequence of intensification is increased exposure to zoonotic agents, and a contemporary emerging problem is infection with Campylobacter and Salmonella spp. from livestock (avian and mammalian), which can lead to disease, malabsorption and undernutrition through acute and chronic diarrhoea. This can occur at the farm, in households or through the food chain. Direct infection occurs when handling livestock and through bacteria shed into the environment, on food preparation surfaces or around the house and surroundings. This manuscript critically reviews Campylobacter and Salmonella infections in animals, examines the factors affecting colonization and faecal shedding of bacteria of these two genera as well as risk factors for human acquisition of the infection from infected animals or environment and analyses priority areas for preventive actions with a focus on resource-poor settings.

Antimicrobial resistance genes in Salmonella and Escherichia coli isolates from chicken droppings in Nairobi, Kenya

OBJECTIVE

Increase in antimicrobial resistance is a threat to health sector globally. Surveillance on the spread and emergence of antimicrobial resistance is therefore invertible. This study investigated prevalence of Salmonella and Escherichia coli, molecularly characterized their antimicrobial resistance patterns and spread among resistant isolates from chicken droppings.

RESULTS

A total of 150 chicken households were selected randomly within Nairobi and fresh chicken droppings collected. Salmonella and Escherichia coli were isolated and antimicrobial susceptibility test carried out. Beta-lactamase genes and class 1 integrons were determined among amoxicillin resistant isolates. Isolates carrying TEM gene were further subjected to (GTG)₅ PCR genotyping. Of the analysed samples, 57% and 12% contained Escherichia coli and Salmonella respectively. Most of the isolates were susceptible to the tested antibiotics with exemption of 53% of the isolates that were resistant to amoxicillin. The isolates were detected with TEM (46%), CTX-M (18%) resistance genes and class 1 integrons (25%). The study reveals presence of beta-lactamase genes and class 1 integrons across Salmonella and Escherichia coli isolates from droppings of reared chicken. Therefore, the wide distribution of chicken and their fecal waste is likely to increase development of antibiotic resistance.

Whole genome sequencing of Salmonella Chester reveals geographically distinct clusters, Norway, 2000 to 2016

IntroductionDuring summer 2016, Norway observed an increase in Salmonella enterica subsp. enterica serovar Chester cases among travellers to Greece.AimOur aim was to investigate genetic relatedness of S. Chester for surveillance and outbreak detection by core genome multilocus sequence typing (cgMLST) and compare the results to genome mapping.MethodsWe included S. Chester isolates from 51 cases of salmonellosis between 2000 and 2016. Paired-end sequencing (2 × 250 bp) was performed on Illumina MiSeq. Genetic relatedness by cgMLST for Salmonella enterica subsp. enterica, including 3,002 genes and seven housekeeping genes, was compared by reference genome mapping with CSI Phylogeny version 1.4 and conventional MLST.ResultsConfirmed travel history was available for 80% of included cases, to Europe (n = 13), Asia (n = 12) and Africa (n = 16). Isolates were distributed into four phylogenetic clusters corresponding to geographical regions. Sequence type (ST) ST411 and a single-locus variant ST5260 (n = 17) were primarily acquired in southern Europe, ST1954 (n = 15) in Africa, ST343 (n = 11) and ST2063 (n = 8) primarily in Asia. Part of the European cluster was further divided into a Greek (n = 10) and a Cypriot (n = 4) cluster. All isolates in the African cluster displayed resistance to ≥ 1 class of antimicrobials, while resistance was rare in the other clusters.ConclusionWhole genome sequencing of S. Chester in Norway showed four geographically distinct clusters, with a possible outbreak occurring during summer 2016 related to Greece. We recommend public health institutes to implement cgMLST-based real-time Salmonella enterica surveillance for early and accurate detection of future outbreaks and further development of cluster cut-offs.

Persistent Infection and Long-Term Carriage of Typhoidal and Nontyphoidal Salmonellae

The ability of pathogenic bacteria to affect higher organisms and cause disease is one of the most dramatic properties of microorganisms. Some pathogens can establish transient colonization only, but others are capable of infecting their host for many years or even for a lifetime. Long-term infection is called persistence, and this phenotype is fundamental for the biology of important human pathogens, including Helicobacter pylori, Mycobacterium tuberculosis, and Salmonella enterica Both typhoidal and nontyphoidal serovars of the species Salmonella enterica can cause persistent infection in humans; however, as these two Salmonella groups cause clinically distinct diseases, the characteristics of their persistent infections in humans differ significantly. Here, following a general summary of Salmonella pathogenicity, host specificity, epidemiology, and laboratory diagnosis, I review the current knowledge about Salmonella persistence and discuss the relevant epidemiology of persistence (including carrier rate, duration of shedding, and host and pathogen risk factors), the host response to Salmonella persistence, Salmonella genes involved in this lifestyle, as well as genetic and phenotypic changes acquired during prolonged infection within the host. Additionally, I highlight differences between the persistence of typhoidal and nontyphoidal Salmonella strains in humans and summarize the current gaps and limitations in our understanding, diagnosis, and curing of persistent Salmonella infections.

Antimicrobial resistance and genotypic profiles of Salmonella Saintpaul isolated along beef processing and distribution continuum

Salmonella Saintpaul (SSa) is increasingly reported from food and foodborne outbreak cases. Pulsed field gel electrophoresis (PFGE) is used for screening and tracking of Salmonella infections. Widespread use of antimicrobial agents in humans and food animals could result in antimicrobial resistant Salmonella serotypes. The aim of this study was to characterize S. Saintpaul (n = 28) isolated from various sampling locations at abattoir and meat processing plant lines in Ethiopia for phenotypic antimicrobial resistance and genotypic diversity, and to track its transfer routes. Sampling location, steps and occasions were considered for each isolate description. Antimicrobial sensitivity testing was performed against seven different antimicrobial agents using disc diffusion method. PFGE with XbaI^® enzymatic genomic digestion with BioNumerics^® analysis was used for genotypic diversity. Of all the isolates tested, only 17.9% were pan susceptible, and 82.1% were resistant to at least one and at most to three antimicrobials. All isolates were susceptible to gentamycin, trimethoprim-sulfamethoxazol and trimethoprim. Resistance to oxytetracycline (82.2%) was predominant followed by 3.6% resistance to each of chloramphenicol, neomycin and polymyxin B. PFGE analysis revealed three distinguishable clusters of pulsotypes but the majority of the isolates (25/28) belonged to cluster-I (SSaX1-4) pulsotype. Indistinguishable/similar cluster of (SSaX 1-4) isolates among and between sampling location, steps and occasions were observed. Majorities of S. Saintpaul (88%) in the cluster-I pulsotype were resistant to oxytetracycline. Our study indicated that oxytetracycline resistance is very common among the S. Saintpaul isolates studied; and the isolates were diverse with similar resistance profiles within the same genomic pulsotypes. Transfer of S. Saintpaul within, between and across sampling locations, during the same or different occasion were determined from SSaX 1-4 pulsotype while cluster-II (SSaX5) indicates transfer from abattoir to butchery. The unique isolate in cluster-III (SSaX6) shows the presence of other possible source of S. Saintpaul for the beef chain contamination.

Food Safety, Health Management, and Biosecurity Characteristics of Poultry Farms in Arusha City, Northern Tanzania, Along a Gradient of Intensification

BACKGROUND

With the growth, urbanisation, and changing consumption patterns of Tanzania's human population, new livestock production systems are emerging. Intensification of poultry production may result in opportunities and threats for food safety, such as improved awareness of biosecurity or increasing prevalence of foodborne pathogens including nontyphoidal Salmonella or Campylobacter spp. We conducted a semiquantitative analysis of poultry production systems in northern Tanzania, with emphasis on biosecurity, health management practices, and prevalence of foodborne pathogens, to gain insight into potential associations between intensification and food safety.

METHODS

Interviews were conducted with managers of 40 poultry farms, with equal representation of 4 production systems (extensive, semi-intensive, or intensive production with indigenous chickens, and broiler farming). Per farm, up to 10 birds (total, 386) were tested for cloacal shedding of nontyphoidal Salmonella, with a subset of farms tested for Campylobacter. Data were analysed using univariate statistics, and results were discussed during feedback workshops with participating farmers and extension officers.

RESULTS

Clear differences existed between farm types with regard to implementation of biosecurity and health management practices and use of extension services. By contrast, prevalence of foodborne pathogens (6 of 40 farms or 15% for nontyphoidal Salmonella and 13 of 26 farms or 50% for Campylobacter spp.) was not farm-type specific, indicating that it is driven by other factors. Across farming systems, knowledge and awareness of the presence of antimicrobials in poultry feed and the need to abide by post-treatment withdrawal times were limited, as was access to impartial professional advice regarding treatment.

CONCLUSION

Different control measures may be needed to protect poultry health compared to public health, and improvements in information provision may be needed for both.