Potential Sources and Transmission of Salmonella and Antimicrobial Resistance in Kampala, Uganda

Prevalence and Serotype of Poultry Salmonellosis in Africa: a Systemic Review and Meta-Analysis

Salmonellosis represents a significant economic and public health concern for the poultry industry in Africa, leading to substantial economic losses due to mortality, reduced productivity, and food safety problems. However, comprehensive information on the burden of poultry salmonellosis at the continental level are scarce. To address this gap, a systemic review and meta-analysis were conducted to consolidate information on the prevalence and circulating serotypes of poultry salmonellosis in African countries. This involved the selection and review of 130 articles published between 1984 and 2021. A detailed systematic review protocol was structured according to Cochrane STROBE and PRISMA statement guidelines. From the 130 selected articles from 23 different African countries, the overall pooled prevalence estimate (PPE) of poultry salmonellosis in Africa was found to be 14.4% (95% CI= 0.145-0.151). Cameroon reported the highest PPE at 71.9%, with the country also noting the highest specific prevalence of 93.3%. The PPE was notably high in meat and meat products at 23%, indicating significant contamination of Salmonella in African poultry meat and meat products. The number of research papers reporting poultry salmonellosis in Africa has been a threefold increase from 1984 to 2021. Salmonella Enteritidis and Typhimurium were the two most prevalent serotypes reported in 18 African countries. Besides, Salmonella Kentucky, Virchow, Gallinarum, and Pullorum were also widely reported. Western Africa had the highest diversity of reported Salmonella serotypes (141), in contrast to southern Africa, which reported only 27 different serotypes. In conclusion, poultry salmonellosis is highly prevalent across Africa, with a variety of known serotypes circulating throughout the continent. Consequently, it is crucial to implement strategic plans for the prevention and control of Salmonella in Africa.

Value chain hygiene practices and microbial contamination of street and market vended ready-to-eat grasshopper, Ruspolia differens in Uganda: Implications for food safety and public health

Food safety is a major public health issue particularly in developing countries. Ready-to-eat street-vended foods contribute significantly to dietary intake in urban and peri-urban areas, but with elevated public health risk. In this study, hygiene and food safety practices as well as the microbial contamination in Uganda's edible grasshopper value chain were evaluated."A total of 29 grasshopper-processing households participated, and grasshopper samples collected. Indicator pathogens were analyzed using standard microbiological methods. In Kampala 50% and in Masaka 12% households had earth floors. All households in Kampala were one or two-roomed dwellings with no separate room as a kitchen, and shared a toilet. In contrast, 59% of households in Masaka had three or more rooms, 35% had a separate room for a kitchen and 47% did not share a toilet. 83% households in Kampala and 56% in Masaka obtained drinking water from public taps. Handwashing was inadequate and none of the actors was observed to wash their hands after taking a break or handling waste. For vendors, wearing protective clothing was not common, with only 28.5% in Kampala and 30.8% in Masaka wearing an apron. Containers for vending grasshoppers were largely uncovered and the utensils for measuring the grasshoppers were left mainly uncovered. Indicator organisms, Escherichia coli and Salmonella typhimurium, were detected. E. coli was the most common contaminant, but with lower levels in Masaka compared to Kampala. S. typhimurium was mainly a burden in Kampala. Our findings demonstrate that there are enormous contributors to poor hygiene and sanitation along the edible grasshopper value chain. The existence of pathogenic bacteria such as E. coli in ready-to-eat foods imply that their consumption poses a health risk.

Prevalence and factors associated with malaria, typhoid, and co-infection among febrile children aged six months to twelve years at kampala international university teaching hospital in western Uganda

Background

Paediatric febrile illnesses pose diagnostic challenges in low-income countries. Western Uganda is endemic for both malaria and typhoid but the true prevalence of each individual disease, their co-infections and associated factors are poorly quantified.

Objective

To determine the prevalence of malaria, typhoid, their co-infection, and associated factors amongst febrile children attending the paediatrics and child health department of Kampala International University Teaching Hospital (KIU-TH) in Western Uganda.

Methods

Cross-sectional study used a survey questionnaire covering demographics, clinical and behavioural variables. We obtained blood for peripheral films for malaria and cultures for typhoid respectively; from 108 consecutively consented participants. Ethical approval was obtained from KIU-TH research and ethics committee (No. UG-REC-023/201,834). Multivariate regression analysis was performed using Stata 14.0 (StataCorp. 2015) at 95% confidence interval, regarding p < 0.05 as statistically significant.

Results

Majority of participants were males 62% (n = 67), cared for by their mothers 86.1% (n = 93). The prevalence of malaria was 25% (n = 27). The prevalence of typhoid was 3.7% (n = 4), whereas the prevalence of malaria-typhoid co-infection was 2.8% (n = 3). Using treated water from protected public taps was associated with low malaria-typhoid co-infection [p = 0.04; aOR = 0.05, 95%CI [0.003-0.87], whereas drinking unboiled water from open wells increased the risk for the co-infection [p = 0.037, cOR = 17, 95%CI (1.19-243.25)].

Conclusions

The prevalence of blood culture confirmed malaria-typhoid co-infection in children was lower than previously reported in serological studies. These findings emphasize the need to use gold standard diagnostic investigations in epidemiological studies. Educational campaigns should focus on the use of safe water, hygienic hand washing, and proper waste disposal; and should target mothers who mainly take care of these children.

Foodborne Pathogens at the Livestock-Wildlife-Human Interface in Rural Western Uganda

Foodborne pathogens are an important cause of morbidity and mortality worldwide. To assess the presence of Salmonella, Campylobacter and Arcobacter spp. in livestock, wildlife, and humans from different regions across western Uganda, 479 faecal samples were tested by PCR. Salmonella and Campylobacter spp. were more frequently detected in livestock (5.1% and 23.5%, respectively) compared to wildlife (1.9% and 16.8%, respectively). Wildlife from remote areas showed lower Salmonella and Campylobacter spp. occurrence than in areas where interactions with livestock are common, suggesting that spill-over may exist from livestock or humans. Further studies are needed to better understand the transmission dynamics of these pathogens at the wildlife-livestock-human interface in western Uganda.

Prevalence of multidrug-resistant and extended-spectrum β-lactamase-producing Escherichia coli from chicken farms in Egypt

Background and Aim

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli strains exhibit antibiotic resistance and are known to infect humans worldwide. This study assessed the phenotypic and genotypic prevalence of ESBL-resistant E. coli isolates recovered from the respiratory tracts of chickens in El-Sharkia Governorate, Egypt.

Materials and Methods

We obtained 250 lung samples (one lung/bird) from 50 chicken farms (5 chickens/farm) to isolate, identify, and serotype E. coli. Antimicrobial resistance susceptibility was determined using the disk diffusion method, while the ESBL phenotype was identified using double disk synergy. We detected the β-lactamase genes, blaTEM, and blaSHV, using a polymerase chain reaction.

Results

The results showed that 140/250 (56%) were infected with E. coli. All the serogroups of isolated E. coli exhibited high multi-antimicrobial resistance index values (>0.2), and 65.7% were confirmed to have ESBL. Among the isolates with the ESBL phenotypes, 55 (60%) and 32 (35%) contained the blaTEM and blaSHV genes, respectively.

Conclusion

The widespread distribution of multidrug-resistant and ESBL-producing E. coli among poultry farms is a significant human health hazard. These results will help the Egyptian authorities to implement a national one-health approach to combat the antimicrobial resistance problem.

The African Wastewater Resistome: Identifying Knowledge Gaps to Inform Future Research Directions

Antimicrobial resistance (AMR) is a growing global public health threat. Furthermore, wastewater is increasingly recognized as a significant environmental reservoir for AMR. Wastewater is a complex mixture of organic and inorganic compounds, including antibiotics and other antimicrobial agents, discharged from hospitals, pharmaceutical industries, and households. Therefore, wastewater treatment plants (WWTPs) are critical components of urban infrastructure that play a vital role in protecting public health and the environment. However, they can also be a source of AMR. WWTPs serve as a point of convergence for antibiotics and resistant bacteria from various sources, creating an environment that favours the selection and spread of AMR. The effluent from WWTPs can also contaminate surface freshwater and groundwater resources, which can subsequently spread resistant bacteria to the wider environment. In Africa, the prevalence of AMR in wastewater is of particular concern due to the inadequate sanitation and wastewater treatment facilities, coupled with the overuse and misuse of antibiotics in healthcare and agriculture. Therefore, the present review evaluated studies that reported on wastewater in Africa between 2012 and 2022 to identify knowledge gaps and propose future perspectives, informing the use of wastewater-based epidemiology as a proxy for determining the resistome circulating within the continent. The study found that although wastewater resistome studies have increased over time in Africa, this is not the case in every country, with most studies conducted in South Africa. Furthermore, the study identified, among others, methodology and reporting gaps, driven by a lack of skills. Finally, the review suggests solutions including standardisation of protocols in wastewater resistome works and an urgent need to build genomic skills within the continent to handle the big data generated from these studies.

Prevalence and distribution of antimicrobial resistance in effluent wastewater from animal slaughter facilities: A systematic review

The extensive use of antibiotics in food animal production and disposal of untreated wastewater from food animal slaughter facilities may create a shift in microbiomes of different ecosystems by generating reservoirs of antimicrobial resistance along the human-animal-environmental interface. This epidemiological problem has been studied, but its magnitude and impact on a global scale is poorly characterised. A systematic review was done to determine global prevalence and distribution patterns of antimicrobial resistance in effluent wastewater from animal slaughter facilities. Extracted data were stratified into rational groups for secondary analyses and presented as percentages. Culture and sensitivity testing was the predominant method; Escherichia spp., Enterococcus spp., and Staphylococcus aureus were the most targeted isolates. Variable incidences of resistance were detected against all major antimicrobial classes including reserved drugs such as ceftazidime, piperacillin, gentamicin, ciprofloxacin, and chloramphenicol; the median frequency and range in resistant Gram-negative isolates were: 11 (0-100), 62 (0-100), 8 (0-100), 14 (0-93) and 12 (0-62) respectively. Ciprofloxacin was the most tested drug with the highest incidences of resistance in livestock slaughterhouses in Iran (93%), Nigeria (50%) and China (20%), and poultry slaughterhouses in Germany (21-81%) and Spain (56%). Spatial global distribution patterns for antimicrobial resistance were associated with previously reported magnitude of antibiotic use in livestock or poultry farming and, the implicit existence of jurisdictional policies to regulate antibiotic use. These data indicate that anthropogenic activities in farming systems are a major contributor to the cause and dissemination of antimicrobial resistance into the environment via slaughterhouse effluents.

Revisiting the Biological Behavior of Salmonella enterica in Hydric Resources: A Meta-Analysis Study Addressing the Critical Role of Environmental Water on Food Safety and Public Health

The increasing number of studies reporting the presence of Salmonella in environmental water sources suggests that it is beyond incidental findings originated from sparse fecal contamination events. However, there is no consensus on the occurrence of Salmonella as its relative serovar representation across non-recycled water sources. We conducted a meta-analysis of proportions by fitting a random-effects model using the restricted maximum-likelihood estimator to obtain the weighted average proportion and between-study variance associated with the occurrence of Salmonella in water sources. Moreover, meta-regression and non-parametric supervised machine learning method were performed to predict the effect of moderators on the frequency of Salmonella in non-recycled water sources. Three sequential steps (identification of information sources, screening and eligibility) were performed to obtain a preliminary selection from identified abstracts and article titles. Questions related to the frequency of Salmonella in aquatic environments, as well as putative differences in the relative frequencies of the reported Salmonella serovars and the role of potential variable moderators (sample source, country, and sample volume) were formulated according to the population, intervention, comparison, and outcome method (PICO). The results were reported according to the Preferred Reporting Items for Systematic Review and Meta-Analyzes statement (PRISMA). A total of 26 eligible papers reporting 148 different Salmonella serovars were retrieved. According to our model, the Salmonella frequency in non-recycled water sources was 0.19 [CI: 0.14; 0.25]. The source of water was identified as the most import variable affecting the frequency of Salmonella, estimated as 0.31 and 0.17% for surface and groundwater, respectively. There was a higher frequency of Salmonella in countries with lower human development index (HDI). Small volume samples of surface water resulted in lower detectable Salmonella frequencies both in high and low HDI regions. Relative frequencies of the 148 serovars were significantly affected only by HDI and volume. Considering that serovars representation can also be affected by water sample volume, efforts toward the standardization of water samplings for monitoring purposes should be considered. Further approaches such as metagenomics could provide more comprehensive insights about the microbial ecology of fresh water and its importance for the quality and safety of agricultural 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.

Genomic diversity and antimicrobial resistance among non-typhoidal Salmonella associated with human disease in The Gambia

Non-typhoidal Salmonella associated with multidrug resistance cause invasive disease in sub-Saharan Africa. Specific lineages of serovars Typhimurium and Enteritidis have been implicated. Here we characterized the genomic diversity of 100 clinical non-typhoidal Salmonella collected from 93 patients in 2001 from the eastern, and in 2006-2018 from the western regions of The Gambia respectively. A total of 93 isolates (64 invasive, 23 gastroenteritis and six other sites) representing a single infection episode were phenotypically tested for antimicrobial susceptibility using the Kirby-Bauer disc diffusion technique. Whole genome sequencing of 100 isolates was performed using Illumina, and the reads were assembled and analysed using SPAdes. The Salmonella in Silico Typing Resource (SISTR) was used for serotyping. SNP differences among the 93 isolates were determined using Roary, and phylogenetic analysis was performed in the context of 495 African strains from the European Nucleotide Archive. Salmonella serovars Typhimurium (26/64; 30.6 %) and Enteritidis (13/64; 20.3 %) were associated with invasive disease, whilst other serovars were mainly responsible for gastroenteritis (17/23; 73.9 %). The presence of three major serovar Enteritidis clades was confirmed, including the invasive West African clade, which made up more than half (11/16; 68.8 %) of the genomes. Multidrug resistance was confined among the serovar Enteritidis West African clade. The presence of this epidemic virulent clade has potential for spread of resistance and thus important implications for systematic patient management. Surveillance and epidemiological investigations to inform control are warranted.

Occurrence of Extended Spectrum Beta Lactamase (ESBL) Producers, Quinolone and Carbapenem Resistant Enterobacteriaceae Isolated from Environmental Samples along Msimbazi River Basin Ecosystem in Tanzania

We conducted environmental surveillance of antimicrobial resistance (AMR) bacteria in the Msimbazi river basin in Tanzania to determine the occurrence of extended-spectrum β-lactamase (ESBL)-producing, carbapenem resistant Enterobacteriaceae (CRE) and quinolone resistant Escherichia coli and Klebsiella spp. A total of 213 Enterobacteriaceae isolates were recovered from 219 samples. Out of the recovered isolates, 45.5% (n = 97) were Klebsiella pneumoniae and 29.6% (n = 63) were Escherichia coli. K. pneumoniae isolates were more resistant in effluent (27.9%) compared to the E. coli (26.6%). The E. coli had a higher resistance in river water, sediment and crop soil than the K. pneumoniae (35 versus 25%), respectively. Higher resistance in K. pneumoniae was found in nalidixic acid (54.6%) and ciprofloxacin (33.3%) while the E. coli isolates were highly resistant to ciprofloxacin (39.7%) and trimethoprim/sulfamethoxazole (38%). Resistance increased from 28.3% in Kisarawe, where the river originates, to 59.9% in Jangwani (the middle section) and 66.7% in Upanga West, where the river enters the Indian Ocean. Out of 160 E. coli and K. pneumoniae isolates, 53.2% (n = 85) were resistant to more than three classes of the antibiotic tested, occurrence being higher among ESBL producers, quinolone resistant and carbapenem resistant strains. There is an urgent need to curb environmental contamination with antimicrobial agents in the Msimbazi Basin.

One hundred years of zoonoses research in the Horn of Africa: A scoping review

BACKGROUND

One Health is particularly relevant to the Horn of Africa where many people's livelihoods are highly dependent on livestock and their shared environment. In this context, zoonoses may have a dramatic impact on both human and animal health, but also on country economies. This scoping review aimed to characterise and evaluate the nature of zoonotic disease research in the Horn region. Specifically, it addressed the following questions: (i) what specific zoonotic diseases have been prioritised for research, (ii) what data have been reported (human, animal or environment), (iii) what methods have been applied, and (iv) who has been doing the research?

METHODOLOGY/PRINCIPAL FINDINGS

We used keyword combinations to search online databases for peer-reviewed papers and theses. Screening and data extraction (disease, country, domain and method) was performed using DistillerSR. A total of 2055 studies focusing on seven countries and over 60 zoonoses were included. Brucellosis attracted the highest attention in terms of research while anthrax, Q fever and leptospirosis have been comparatively under-studied. Research efforts did not always align with zoonoses priorities identified at national levels. Despite zoonoses being a clear target for 'One Health' research, a very limited proportion of studies report data on the three domains of human, animal and environment. Descriptive and observational epidemiological studies were dominant and only a low proportion of publications were multidisciplinary. Finally, we found that a minority of international collaborations were between Global South countries with a high proportion of authors having affiliations from outside the Horn of Africa.

CONCLUSIONS/SIGNIFICANCE

There is a growing interest in zoonoses research in the Horn of Africa. Recommendations arising from this scoping review include: (i) ensuring zoonoses research aligns with national and global research agendas; (ii) encouraging researchers to adopt a holistic, transdisciplinary One Health approach following high quality reporting standards (COHERE, PRISMA, etc.); and (iii) empowering local researchers supported by regional and international partnerships to engage in zoonoses research.

Prevalence of 16S rRNA Methylation Enzyme Gene armA in Salmonella From Outpatients and Food

Salmonella is the primary cause of community-acquired foodborne infections, so its resistance to antimicrobials, such as aminoglycosides, is a public health issue. Of concern, aminoglycoside resistance in Salmonella is increasing rapidly. Here, we performed a retrospective study evaluating the prevalence of Salmonella harboring armA-mediated aminoglycoside resistance in community-acquired infections and in food or environmental sources. The prevalence rates of armA-harboring Salmonella strains were 1.1/1,000 (13/12,095) and 8.7/1,000 (32/3,687) in outpatient and food/environmental isolates, respectively. All the armA-harboring Salmonella strains were resistant to multiple drugs, including fluoroquinolone and/or extended-spectrum cephalosporins, and most (34/45) belonged to serovar Indiana. The armA gene of these strains were all carried on plasmids, which spanned five replicon types with IncHI2 being the dominant plasmid type. All the armA-carrying plasmids were transferable into Escherichia coli and Acinetobacter baumannii recipients. The conjugation experiment results revealed that the armA-harboring S. Indiana strains had a relatively higher ability to acquire armA-carrying plasmids. The low similarity of their pulsed field gel electrophoresis patterns indicates that the armA-harboring Salmonella strains were unlikely to have originated from a single epidemic clone, suggesting broad armA spread. Furthermore, the genetic backgrounds of armA-harboring Salmonella strains isolated from outpatients exhibited higher similarity to those isolated from poultry than to those isolated from swine, suggesting that poultry consumption maybe an infection source. These findings highlight an urgent need to monitor the prevalence and transmission of armA-harboring Salmonella, especially S. Indiana, to better understand the potential public health threat and prevent the further spread of these strains.

Efforts to Identify and Combat Antimicrobial Resistance in Uganda: A Systematic Review

The global burden of antimicrobial resistance is on the rise, resulting in higher morbidity and mortality in our communities. The spread of antimicrobial resistance in the environment and development of resistant microbes is a challenge to the control of antimicrobial resistance. Approaches, such as antimicrobial stewardship programmes and enhanced surveillance, have been devised to curb its spread. However, particularly in lower- and middle-income countries, the overall extent of antimicrobial resistance and knowledge on ongoing surveillance, stewardship or investigation efforts, are often poorly understood. This study aimed to look at the efforts that have been undertaken to detect and combat antimicrobial resistance in Uganda as a means of establishing an overview of the situation, to help inform future decisions. We conducted a systematic literature review of the PubMed database to assess these efforts. A search combining keywords associated with antimicrobial resistance were used to find relevant studies between 1995 and 2020 on surveillance of antimicrobial resistance in Uganda, and susceptibility of microbes to different drugs. The search yielded 430 records, 163 of which met the inclusion criteria for analysis. The studies were categorized according to country and region, the type of antimicrobial resistance, context of the study, study design and outcome of the study. We observed that antibacterial resistance and antimalarial resistance had the most published studies while antiviral and antifungal resistance were represented by very few studies each. Most studies were conducted in humans and hospital settings, with few in veterinary and One Health contexts, and only one that included environmental sampling. The majority of studies have focused on surveillance, susceptibility testing or resistance genes; none of our included papers had a policy or stewardship focus. The results from our work can inform public health policy on antimicrobial stewardship as it contributes to understanding the status of antimicrobial resistance surveillance in Uganda, and can also help to guide future research efforts. Notably, a One Health approach needs to be followed with respect to surveillance of antimicrobial resistance to better understand the mechanisms of resistance transfer across the human-animal–environment interface, including additional investigation in antiviral and antifungal resistance.

Multidrug-Resistant, Including Extended-Spectrum Beta Lactamase-Producing and Quinolone-Resistant, Escherichia coli Isolated from Poultry and Domestic Pigs in Dar es Salaam, Tanzania

We determined the phenotypic profile of multidrug-resistant (MDR) Escherichia coli isolated from 698 samples (390 and 308 from poultry and domestic pigs, respectively). In total, 562 Enterobacteria were isolated. About 80.5% of the isolates were E. coli. Occurrence of E. coli was significantly higher among domestic pigs (73.1%) than in poultry (60.5%) (p = 0.000). In both poultry and domestic pigs, E. coli isolates were highly resistant to tetracycline (63.5%), nalidixic acid (53.7%), ampicillin (52.3%), and trimethoprim/sulfamethoxazole (50.9%). About 51.6%, 65.3%, and 53.7% of E. coli were MDR, extended-spectrum beta lactamase-producing enterobacteriaceae (ESBL-PE), and quinolone-resistant, respectively. A total of 68% of the extended-spectrum beta lactamase (ESBL) producers were also resistant to quinolones. For all tested antibiotics, resistance was significantly higher in ESBL-producing and quinolone-resistant isolates than the non-ESBL producers and non-quinolone-resistant E. coli. Eight isolates were resistant to eight classes of antimicrobials. We compared phenotypic with genotypic results of 20 MDR E. coli isolates, ESBL producers, and quinolone-resistant strains and found 80% harbored blaCTX-M, 15% aac(6)-lb-cr, 10% qnrB, and 5% qepA. None harbored TEM, SHV, qnrA, qnrS, qnrC, or qnrD. The observed pattern and level of resistance render this portfolio of antibiotics ineffective for their intended use.

The misuse of antiretrovirals to boost pig and poultry productivity in Uganda and potential implications for public health

Background and Aim: Since 2015, local newspapers reported that pig and poultry farmers in Uganda use antiretroviral drugs (ARVs) to promote growth in animals and control diseases. This study was conducted to assess farmers' knowledge, attitude and perceptions about the use of antiretroviral drugs as boosters in pigs and poultry and the possibility of detecting the antiretroviral drugs in meat using available laboratory methods. Materials and Methods: In 2019, a cross-sectional study was conducted in ten districts in Uganda. In 20 focus group discussions with 100 pig and poultry farmers and 70 animal health service providers, we assessed the use of ARV in livestock enterprises. Subsequently, samples of chicken, pigs, and animal feeds were collected from volunteer participants, and screened for residues of saquinavir, lopinavir, nevirapine, and efavirenz using liquid chromatography-tandem mass spectrophotometer. Results: Participants in all ten districts were predominantly smallholder farmers supplying the local markets. All groups reported the use of ARVs in pigs and broiler birds but not in layer hens. In the absence of good quality feeds, the motivation for feeding ARVs was rapid animal weight gain, as well as the control of animal diseases, for which farmers have no alternative solutions. ARVs were obtained within the community for free, against cash, or in-kind payment. Residues of lopinavir were detected in four, and saquinavir in seven districts, and all three sample matrices. Conclusion: Our study findings confirm anecdotal news reports on ARV use in livestock. While our findings are not generalizable to the whole country, they call for a representative follow-up. As the drugs were detected in tissues destined for human consumption, the potential risk to human health warrants further investigation.

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

Simple Summary

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

Abstract

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

Salmonella identified in pigs in Kenya and Malawi reveals the potential for zoonotic transmission in emerging pork markets

Salmonella is a major cause of foodborne disease globally. Pigs can carry and shed non-typhoidal Salmonella (NTS) asymptomatically, representing a significant reservoir for these pathogens. To investigate Salmonella carriage by African domestic pigs, faecal and mesenteric lymph node samples were taken at slaughter in Nairobi, Busia (Kenya) and Chikwawa (Malawi) between October 2016 and May 2017. Selective culture, antisera testing and whole genome sequencing were performed on samples from 647 pigs; the prevalence of NTS carriage was 12.7% in Busia, 9.1% in Nairobi and 24.6% in Chikwawa. Two isolates of S. Typhimurium ST313 were isolated, but were more closely related to ST313 isolates associated with gastroenteritis in the UK than bloodstream infection in Africa. The discovery of porcine NTS carriage in Kenya and Malawi reveals potential for zoonotic transmission of diarrhoeal strains to humans in these countries, but not for transmission of clades specifically associated with invasive NTS disease in Africa.

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.

Antimicrobial resistance genes in bacteria from animal-based foods

Antimicrobial resistance is a worldwide public health threat. Farm animals are important sources of bacteria containing antimicrobial resistance genes (ARGs). Although the use of antimicrobials in aquaculture and livestock has been reduced in several countries, these compounds are still routinely applied in animal production, and contribute to ARGs emergence and spread among bacteria. ARGs are transmitted to humans mainly through the consumption of products of animal origin (PAO). Bacteria can present intrinsic resistance, and once antimicrobials are administered, this resistance may be selected and multiply. The exchange of genetic material is another mechanism used by bacteria to acquire resistance. Some of the main ARGs found in bacteria present in PAO are the bla, mcr-1, cfr and tet genes, which are directly associated to antibiotic resistance in the human clinic.

Antimicrobial use and resistance in food-producing animals and the environment: an African perspective

BACKGROUND

The overuse of antimicrobials in food animals and the subsequent contamination of the environment have been associated with development and spread of antimicrobial resistance. This review presents information on antimicrobial use, resistance and status of surveillance systems in food animals and the environment in Africa.

METHODS

Information was searched through PubMed, Google Scholar, Web of Science, and African Journal Online databases. Full-length original research and review articles on antimicrobial use, prevalence of AMR from Africa covering a period from 2005 to 2018 were examined. The articles were scrutinized to extract information on the antimicrobial use, resistance and surveillance systems.

RESULTS

A total of 200 articles were recovered. Of these, 176 studies were included in the review while 24 articles were excluded because they were not relevant to antimicrobial use and/or resistance in food animals and the environment. The percentage of farms using antimicrobials in animal production ranged from 77.6% in Nigeria to 100% in Tanzania, Cameroon, Zambia, Ghana and Egypt. The most antibiotics used were tetracycline, aminoglycoside and penicillin groups. The percentage of multi drug resistant isolates ranged from 20% in Nigeria to 100% in South Africa, Zimbabwe and Tunisia. In the environment, percentage of multi drug resistant isolates ranged from 33.3% in South Africa to 100% in Algeria. None of the countries documented national antimicrobial use and resistance surveillance system in animals.

CONCLUSION

There is high level of antimicrobial use, especially tetracycline, aminoglycoside and penicillin in animal production systems in Africa. This is likely to escalate the already high prevalence of antimicrobial resistance and multi drug resistance in the continent. This, coupled with weak antimicrobial resistance surveillance systems in the region is a great concern to the animals, environment and humans as well.

International lineages of Salmonella enterica serovars isolated from chicken farms, Wakiso District, Uganda

The growing occurrence of multidrug-resistant (MDR) Salmonella enterica in poultry has been reported with public health concern worldwide. We reported, recently, the occurrence of Escherichia coli and Salmonella enterica serovars carrying clinically relevant resistance genes in dairy cattle farms in the Wakiso District, Uganda, highlighting an urgent need to monitor food-producing animal environments. Here, we present the prevalence, antimicrobial resistance, and sequence type of 51 Salmonella isolates recovered from 379 environmental samples from chicken farms in Uganda. Among the Salmonella isolates, 32/51 (62.7%) were resistant to at least one antimicrobial, and 10/51 (19.6%) displayed multiple drug resistance. Through PCR, five replicon plasmids were identified among chicken Salmonella isolates including IncFIIS 17/51 (33.3%), IncI1α 12/51 (23.5%), IncP 8/51 (15.7%), IncX1 8/51 (15.7%), and IncX2 1/51 (2.0%). In addition, we identified two additional replicons through WGS (Whole Genome Sequencing; ColpVC and IncFIB). A significant seasonal difference between chicken sampling periods was observed (p = 0.0017). We conclude that MDR Salmonella highlights the risks posed to animals and humans. Implementing a robust, integrated surveillance system will aid in monitoring MDR zoonotic threats.

Towards a bottom-up understanding of antimicrobial use and resistance on the farm: A knowledge, attitudes, and practices survey across livestock systems in five African countries

The nutritional and economic potentials of livestock systems are compromised by the emergence and spread of antimicrobial resistance. A major driver of resistance is the misuse and abuse of antimicrobial drugs. The likelihood of misuse may be elevated in low- and middle-income countries where limited professional veterinary services and inadequately controlled access to drugs are assumed to promote non-prudent practices (e.g., self-administration of drugs). The extent of these practices, as well as the knowledge and attitudes motivating them, are largely unknown within most agricultural communities in low- and middle-income countries. The main objective of this study was to document dimensions of knowledge, attitudes and practices related to antimicrobial use and antimicrobial resistance in livestock systems and identify the livelihood factors associated with these dimensions. A mixed-methods ethnographic approach was used to survey households keeping layers in Ghana (N = 110) and Kenya (N = 76), pastoralists keeping cattle, sheep, and goats in Tanzania (N = 195), and broiler farmers in Zambia (N = 198), and Zimbabwe (N = 298). Across countries, we find that it is individuals who live or work at the farm who draw upon their knowledge and experiences to make decisions regarding antimicrobial use and related practices. Input from animal health professionals is rare and antimicrobials are sourced at local, privately owned agrovet drug shops. We also find that knowledge, attitudes, and particularly practices significantly varied across countries, with poultry farmers holding more knowledge, desirable attitudes, and prudent practices compared to pastoralist households. Multivariate models showed that variation in knowledge, attitudes and practices is related to several factors, including gender, disease dynamics on the farm, and source of animal health information. Study results emphasize that interventions to limit antimicrobial resistance should be founded upon a bottom-up understanding of antimicrobial use at the farm-level given limited input from animal health professionals and under-resourced regulatory capacities within most low- and middle-income countries. Establishing this bottom-up understanding across cultures and production systems will inform the development and implementation of the behavioral change interventions to combat antimicrobial resistance globally.

Antimicrobial resistant enteric bacteria are widely distributed amongst people, animals and the environment in Tanzania

Antibiotic use and bacterial transmission are responsible for the emergence, spread and persistence of antimicrobial-resistant (AR) bacteria, but their relative contribution likely differs across varying socio-economic, cultural, and ecological contexts. To better understand this interaction in a multi-cultural and resource-limited context, we examine the distribution of antimicrobial-resistant enteric bacteria from three ethnic groups in Tanzania. Household-level data (n = 425) was collected and bacteria isolated from people, livestock, dogs, wildlife and water sources (n = 62,376 isolates). The relative prevalence of different resistance phenotypes is similar across all sources. Multi-locus tandem repeat analysis (n = 719) and whole-genome sequencing (n = 816) of Escherichia coli demonstrate no evidence for host-population subdivision. Multivariate models show no evidence that veterinary antibiotic use increased the odds of detecting AR bacteria, whereas there is a strong association with livelihood factors related to bacterial transmission, demonstrating that to be effective, interventions need to accommodate different cultural practices and resource limitations.

Translating pathogen knowledge to practice for sanitation decision-making

Sanitation planners make complex decisions in the delivery of sanitation services to achieve health outcomes. We present findings from a stakeholder engagement workshop held in Kampala, Uganda, to educate, interact with, and solicit feedback from participants on how the relevant scientific literature on pathogens can be made more accessible to practitioners to support decision-making. We targeted Water, Sanitation and Hygiene (WASH) practitioners involved in different levels of service delivery. Practitioners revealed that different sanitation planning tools are used to inform decision-making; however, most of these tools are not user-friendly or adapted to meet their needs. Most stakeholders (68%) expressed familiarity with pathogens, yet less than half (46%) understood that fecal coliforms were bacteria and used as indicators for fecal pollution. A number of stakeholders were unaware that fecal indicator bacteria do not behave and persist the same as helminths, protozoa, or viruses, making fecal indicator bacteria inadequate for assessing pathogen reductions for all pathogen groups. This suggests a need for awareness and capacity development around pathogens found in excreta. The findings underscore the importance to engage stakeholders in the development of support tools for sanitation planning and highlighted broader opportunities to bridge science with practice in the WASH sector.

Antimicrobial use policy change in pre-weaned dairy calves and its impact on antimicrobial resistance in commensal Escherichia coli: a cross sectional and ecological study

Background

This study is based on data collected to investigate the relation of peri-parturient events (colostrum quality, passive transfer of immunity, calving difficulty) on calf health and antimicrobial use. A component of the study was to provide feedback to farm management to identify calves at risk for disease and promote antimicrobial stewardship. At the start of the study (May 2016), a combination of enrofloxacin, penicillin, and sulfamethoxazole was the first treatment given to clinically abnormal calves. Based on feedback and interaction between study investigators, farm management and consulting veterinarians, a new policy was implemented to reduce antimicrobial use in calves. In August, the first treatment was changed to a combination of ampicillin and sulfamethoxazole. In September, the first treatment was reduced to only sulfamethoxazole. We investigated the effects of these policy changes in antimicrobial use on resistance in commensal Escherichia coli.

Results

We enrolled 4301 calves at birth and documented antimicrobial use until weaning. Most calves (99.4%) received antimicrobials and 70.4% received a total of 2–4 treatments. Antimicrobial use was more intense in younger calves (≤ 28 days) relative to older calves. We isolated 544 E. coli from fecal samples obtained from 132 calves. We determined resistance to 12 antimicrobials and 85% of the isolates were resistant to at least 3 antimicrobial classes. We performed latent class analysis to identify underlying unique classes where isolates shared resistance patterns and selected a solution with 4 classes. The least resistant class had isolates that were mainly resistant to only tetracycline and sulfisoxazole. The other 3 classes comprised isolates with resistance to ampicillin, chloramphenicol, aminoglycosides, sulfonamides, tetracycline, in addition to either ceftiofur; or nalidixic acid; or ciprofloxacin plus nalidixic acid and ceftiofur. Overall, E coli from younger calves and calves that received multiple treatments were more likely to have extensive resistance including resistance to fluoroquinolones and ceftiofur. In general, there was a declining trend in resistance to most antimicrobials during and after policy changes were implemented, except for ampicillin, ciprofloxacin, ceftiofur and gentamicin.

Conclusions

Information feedback to farms can influence farm managers to reduce antimicrobial use and this can change endemic farm resistance patterns.

Electronic supplementary material

The online version of this article (10.1186/s12866-019-1576-6) contains supplementary material, which is available to authorized users.

Cross-sectional study of IgG antibody levels to invasive nontyphoidal Salmonella LPS O-antigen with age in Uganda

Invasive nontyphoidal Salmonella (iNTS) disease is a major cause of deaths among children and HIV-infected individuals in sub-Saharan Africa. Acquisition of IgG to iNTS lipopolysaccharide (LPS) O-antigen in Malawi in early childhood corresponds with a fall in cases of iNTS disease suggesting that vaccines able to induce such antibodies could confer protection. To better understand the acquisition of IgG to iNTS in other African settings, we performed a cross-sectional seroepidemiological study using sera from 1090 Ugandan individuals aged from infancy to old age. Sera were analysed for IgG to LPS O-antigen of S. Typhimurium and S. Enteritidis using an in-house ELISA. Below 18 months of age, most children lacked IgG to both serovars. Thereafter, specific IgG levels increased with age, peaking in adulthood, and did not wane noticeably in old age. There was no clear difference in antibody levels between the sexes and the few HIV-infected individuals in the study did not have obviously different levels from uninfected subjects. While IgG to iNTS is acquired at a younger age in Malawian compared with Ugandan children, it is not clear whether this is due to differences in the populations themselves, their exposure to iNTS, or variations between assays used. In conclusion, there is a need to develop a harmonised method and standards for measuring antibodies to iNTS across studies and to investigate acquisition of such antibodies with age across different sites in sub-Saharan Africa.

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.

Phenotypic and genotypic analyses of antimicrobial resistant bacteria in livestock in Uganda

Antimicrobial resistant bacteria (ARB) in livestock are a global public health concern, not only because they prolong infectious diseases but also they can be transferred from animals to humans via the food chain. Here, we studied ARB in livestock at commercial and subsistence farms (n = 13) in Wakiso and Mpigi districts, Uganda. We enquired from the farmers about the type and the purpose of antimicrobial agents they have used to treat their livestock. After collecting faeces, we isolated antimicrobial resistant Escherichia coli from livestock faeces (n = 134) as an indicator bacterium. These strains showed resistance to ampicillin (44.8%), tetracycline (97.0%), and sulfamethoxazole-trimethoprim (56.7%). The frequency of ampicillin-resistance was significantly correlated with the usage of penicillins to livestock in the farms (p = 0.04). The metagenomics data detected 911 antimicrobial resistant genes that were classified into 16 categories. Genes for multidrug efflux pumps were the most prevalent category in all except in one sample. Interestingly, the genes encoding third-generation cephalosporins (bla_CTX-M ), carbapenems (bla_ACT ), and colistin (arnA) were detected by metagenomics analysis although these phenotypes were not detected in our E. coli strains. Our results suggest that the emergence and transmission of cephalosporin, carbapenem, and/or colistin-resistant bacteria among livestock can occur in future if these antimicrobial agents are used.

Diversity and Antimicrobial Resistance Genotypes in Non-Typhoidal Salmonella Isolates from Poultry Farms in Uganda

Non-typhoidal Salmonella (NTS) are foodborne pathogens of global public health significance. The aim of this study was to subtype a collection of 85 NTS originating from poultry farms in Uganda, and to evaluate a subgroup of phenotypically resistant isolates for common antimicrobial resistance genes and associated integrons. All isolates were subtyped by pulsed-field gel electrophoresis (PFGE). Phenotypically resistant isolates (n = 54) were screened by PCR for the most relevant AMR genes corresponding to their phenotypic resistance pattern, and all 54 isolates were screened by PCR for the presence of integron class 1 and 2 encoding genes. These genes are known to commonly encode resistance to ampicillin, tetracycline, ciprofloxacin, trimethoprim, sulfonamide and chloramphenicol. PFGE revealed 15 pulsotypes representing 11 serotypes from 75 isolates, as 10 were non-typable. Thirty one (57.4%) of the 54 resistant isolates carried at least one of the seven genes (blaTEM-1,cmlA, tetA, qnrS,sul1,dhfrI,dhfrVII) identified by PCR and six (11%) carried class 1 integrons. This study has shown that a diversity of NTS-clones are present in Ugandan poultry farm settings, while at the same time similar NTS-clones occur in different farms and areas. The presence of resistance genes to important antimicrobials used in human and veterinary medicine has been demonstrated, hence the need to strengthen strategies to combat antimicrobial resistance at all levels.

Characterization of Invasive Salmonella Serogroup C1 Infections in Mali

Nontyphoidal Salmonella (NTS) are the leading cause of foodborne infections worldwide and a major cause of bloodstream infections in infants and HIV-infected adults in sub-Saharan Africa (SSA). Salmonella Typhimurium (serogroup B) and Salmonella Enteritidis (serogroup D) are the most common serovars in this region. However, data describing rarer invasive NTS serovars, particularly those belonging to serogroups C1 and C2, circulating in SSA are lacking. We previously conducted systematic blood culture surveillance on pediatric patients in Bamako, Mali, from 2002 to 2014, and the results showed that serovars Typhimurium and Enteritidis accounted for 32% and 36% of isolates, respectively. Here, we present data on 27 Salmonella serogroup C1 strains that were isolated during this previous study. The strains were typed by serum agglutination and multilocus sequence typing (MLST). Sixteen strains were Salmonella Paratyphi C, four were Salmonella Colindale, and two were Salmonella Virchow. Interestingly, five strains were identified as the very rare Salmonella Brazzaville using a combination of serum agglutination and flagellin gene typing. Phenotypic characterization showed that Salmonella Brazzaville produced biofilm and exhibited catalase activity, which were not statistically different from the gastroenteritis-associated Salmonella Typhimurium sequence type (ST) 19. All tested Salmonella Paratyphi C strains were poor biofilm producers and showed significantly less catalase activity than Salmonella Typhimurium ST19. Overall, our study provides insight into the Salmonella serogroup C1 serovars that cause invasive disease in infants in Mali. In addition, we show that MLST and flagellin gene sequencing, in association with traditional serum agglutination, are invaluable tools to help identify rare Salmonella serovars.

Biosecurity aspects of cattle production in Western Uganda, and associations with seroprevalence of brucellosis, salmonellosis and bovine viral diarrhoea

BACKGROUND

Many low-income countries have a human population with a high number of cattle owners depending on their livestock for food and income. Infectious diseases threaten the health and production of cattle, affecting both the farmers and their families as well as other actors in often informal value chains. Many infectious diseases can be prevented by good biosecurity. The objectives of this study were to describe herd management and biosecurity routines with potential impact on the prevalence of infectious diseases, and to estimate the burden of infectious diseases in Ugandan cattle herds, using the seroprevalence of three model infections.

RESULTS

Farmer interviews (n = 144) showed that biosecurity measures are rarely practised. Visitors' hand-wash was used by 14%, cleaning of boots or feet by 4 and 79% put new cattle directly into the herd. During the 12 months preceding the interviews, 51% of farmers had cattle that died and 31% had noticed abortions among their cows. Interestingly, 72% were satisfied with the health status of their cattle during the same time period. The prevalence (95% CI) of farms with at least one seropositive animal was 16.7% (11.0;23.8), 23.6% (16.9;31.4), and 53.4% (45.0;61.8) for brucella, salmonella and BVD, respectively. A poisson regression model suggested that having employees looking after the cattle, sharing pasture with other herds, and a higher number of dead cattle were associated with a herd being positive to an increasing number of the diseases. An additive bayesian network model with biosecurity variables and a variable for the number of diseases the herd was positive to resulted in three separate directed acyclic graphs which illustrate how herd characteristics can be grouped together. This model associated the smallest herd size with herds positive to a decreasing number of diseases and having fewer employees.

CONCLUSION

There is potential for improvement of biosecurity practices in Ugandan cattle production. Salmonella, brucella and BVD were prevalent in cattle herds in the study area and these infections are, to some extent, associated with farm management practices.

Prevalence, antimicrobial susceptibility and risk factors associated with non-typhoidal Salmonella on Ugandan layer hen farms

BACKGROUND

Non-typhoidal Salmonella (NTS) are among the leading global foodborne pathogens and a significant public health threat. Their occurrence in animal reservoirs and their susceptibilities to commonly used antimicrobials are poorly understood in developing countries. The aim of this study was to estimate the prevalence, determine antimicrobial susceptibility and identify risk factors associated with NTS presence in laying hen farms in Uganda through a cross-sectional study.

RESULTS

Pooled faecal samples were collected from 237 laying hen farms and these were analysed for NTS following standard laboratory procedures. In total, 49 farms (20.7%; 95% Confidence interval (CI): 15.6-25.6%) were positive for NTS presence. Altogether, ten Salmonella serotypes were identified among the confirmed 78 isolates, and the predominant serotypes were Salmonella Newport (30.8%), S. Hadar (14.1%), S. Aberdeen (12.8%), S. Heidelberg (12.8%), and S. Bolton (12.8%). Phenotypic antimicrobial resistance was detected in 45(57.7%) of the isolates and the highest resistance was against ciprofloxacin (50.0%) followed by sulphonamides (26.9%) and sulphamethoxazole/trimethoprim (7.7%). Resistance was significantly associated with sampled districts (p = 0.034). Resistance to three or more drugs, multi-drug resistance (MDR) was detected in 12 (15.4%) of the isolates, 9 (75%) of these were from Wakiso district. A multivariable logistic model identified large farm size (OR = 7.0; 95% CI: 2.5-19.8) and the presence of other animal species on the farm (OR = 5.9; 95% CI: 2.1-16.1) as risk factors for NTS prevalence on farms. Having a separate house for birds newly brought to the farms was found to be protective (OR = 0,4; 95% CI: 0.2-0.8).

CONCLUSION

This study has highlighted a high prevalence and diversity of NTS species in laying hen farms in Uganda and identified associated risk factors. In addition, it has demonstrated high levels of antimicrobial resistance in isolates of NTS. This could be because of overuse or misuse of antimicrobials in poultry production. Also importantly, the insights provided in this study justifies a strong case for strengthening One Health practices and this will contribute to the development of NTS control strategies at local, national and international levels.

SEROTYPING AND ANTIMICROBIAL DRUG RESISTANCE OF SALMONELLA ISOLATED FROM LETTUCE AND HUMAN DIARRHEA SAMPLES IN BURKINA FASO

BACKGROUND

In Burkina Faso dirty water in particular those of the stoppings and the gutter ones are used for vegetables irrigation in the gardens. The aim of this study was to determine the prevalence and antibiotic susceptibility of Salmonella serotypes from humans and lettuce samples inBurkina Faso. Materials and Methods:Salmonella strains isolated from patients in 2009 to 2015 and lettuce samples in 2014 in Burkina Faso were serotyped using specific antisera. All strains were subjected to a set of 14 antibiotics to study their antibiogram by using Baeur-Kirby disk diffusion method.

RESULTS

Out of 154 Salmonella isolated, 60 were from human and 94 from lettuce samples. Serotyping revealed four different serotypes and 39% (60) untypeable strains from human and lettuce (14 and 46 strains). Salmonella serotypes from human and lettuce samples were: Paratyphi A (10% and 22%), Paratyphi B (34% and 8%), Paratyphi C (14% and 18%) and Typhi (21% and 1%). A high resistance of Salmonella Paratyphi B and Salmonella spp to tetracycline were 70% from human and 35 % from lettuce samples. Multiresistance was observed to tetracycline, chloramphenicol and amoxicillin/clavulanic-acid or ampicillin with Salmonella ParatyphiB 35% and Salmonella Typhi 33% from human samples and Salmonella spp 4% from lettuce samples.

CONCLUSION

This study showed the diversity of Salmonella serotypes from both clinical and environmental samples and emergence of multiresistant Salmonella to antibiotics in Burkina Faso. A lettuce is a potential source of transmission of Salmonella causing diarrhea among human in Burkina Faso. List of non-standard Abbreviations : HDB: Hôpital du District de Bogodogo, LNSP: Laboratoire National de Santé Publique, DSG : District Sanitaire de Gourcy, DSB : District Sanitaire de Boromo.

Molecular Characterization of Salmonella from Human and Animal Origins in Uganda

Sporadic Salmonella outbreaks with varying clinical presentations have been on the rise in various parts of Uganda. The sources of outbreaks and factors underlying the different clinical manifestation are curtailed by paucity of information on Salmonella genotypes and the associated virulence genes. This study reports molecular diversity of Salmonella enterica and their genetic virulence profiles among human and animal isolates. Characterization was done using Kauffman-White classification scheme and virulence genes analysis using multiplex PCR. Overall, 52% of the isolates belonged to serogroup D, 16% to serogroup E, 15% to poly F, H-S, and 12% to serogroup B. Serogroups A, C1, and C2 each consisted of only one isolate representing 5%. Virulence genes located on SPI-1 [spaN and sipB] and on SPI-2 [spiA] in addition to pagC and msgA were equally distributed in isolates obtained from all sources. Plasmid encoded virulence gene spvB was found in <5% of isolates from both human epidemic and animal origins whereas it occurred in 80% of clinical isolates. This study reveals that serogroup D is the predominant Salmonella serogroup in circulation and it is widely shared among animals and humans and calls for joint and coordinated surveillance for one health implementation in Uganda.

Complete Genome and Methylome Sequences of Salmonella enterica subsp. enterica Serovars Typhimurium, Saintpaul, and Stanleyville from the SARA/SARB Collection

In this announcement, we report the complete genome and methylome sequences of three Salmonella enterica strains from the SARA and SARB collection: S. enterica subsp. enterica serovar Typhimurium (SARA13), S. enterica subsp. enterica serovar Saintpaul (SARA26), and S. enterica subsp. enterica serovar Stanleyville (SARB61).

High occurrence and unusual serotype diversity of non-typhoidal Salmonella in non-clinical niches, Angola

Non-typhoidal Salmonella is an important burden, particularly in developing countries of the African region. We report for the first time in Angola, a sub-Saharan African country with commercial/travel relationships with Europe, an unexpectedly high occurrence of Salmonella (n = 12/63, 19%) from a high diversity of sources, particularly farm and wild animals. The detection of diverse serotypes (n = 12), involving putative new S. enterica subsp. salamae serotypes, is also of note, reinforcing the need for a comprehensive surveillance in Angola critical to identify animal/food/environmental sources of salmonellosis with impact on animal health, local people, tourists and exported products.

Salmonella in Swine: Microbiota Interactions

For the important foodborne pathogen Salmonella enterica to cause disease or persist in pigs, it has evolved an intricate set of interactions between itself, the host, and the indigenous microflora of the host. S. enterica must evade the host's immune system and must also overcome colonization resistance mediated by the pig's indigenous microflora. The inflammatory response against S. enterica provides the bacteria with unique metabolites and is thus exploited by S. enterica for competitive advantage. During infection, changes in the composition of the indigenous microflora occur that have been associated with a breakdown in colonization resistance. Healthy pigs that are low-level shedders of S. enterica also exhibit alterations in their indigenous microflora similar to those in ill animals. Here we review the literature on the interactions that occur between swine, S. enterica, and the indigenous microflora and discuss methods to reduce or prevent colonization of pigs with S. enterica.

Salmonella in Wild Birds Utilizing Protected and Human Impacted Habitats, Uganda

As human populations in Africa expand, humans encroach and modify wildlife habitats for farming, fishing, tourism, or settlement. Anthropogenic activities in shared environments may promote transmission of zoonotic pathogens between humans, domestic animals, and wildlife. Between July 2012 and February 2014, we evaluated Salmonella prevalence, serovars, genotypes, and antibiotic resistant phenotypes in resident and migratory birds utilizing human-impacted habitats in northwestern Lake Victoria and protected habitats in Queen Elisabeth National Park. Salmonella occurrence in the urban environment was assessed by sampling storm-water and wastewater from a channel that drains Kampala City into Lake Victoria. Salmonella was detected in 4.3% pooled bird fecal samples, and 57.1% of environmental samples. While birds in impacted and protected areas shared serovars, the genotypes were distinct. We found distinct strains in birds and the environment suggesting some strains in birds are host adapted, and strains circulating in the environment may not necessarily disseminate to birds. Conversely, birds in both impacted and protected areas shared strains with the urban environment, suggesting Salmonella disseminates between impacted environments and birds across sites. Overall, more strains were observed in the urban environment compared to birds, and poses risk of Salmonella reemergence in birds and transmission across species and space.