Yakhya Dieye

Background: Antimicrobial resistance (AMR) remains a global health threat, and the use of antibiotics in animal husbandry, particularly poultry production, is well documented. There is, therefore, a need to investigate the prevalence of priority bacterial pathogens as reservoirs of AMR genes in poultry. We aimed to ascertain the prevalence and resistant profiles of Extended-spectrum Beta-lactamase (ESBL)-producing and Carbapenem-resistant E. coli in retail poultry in Ghana. Methods: One hundred and sixty-five (165) poultry caecal content samples were collected from three vendors. After overnight culture and purity plating on MacConkey agar, strain identification was performed using the VITEK 2 Compact System. Antibiotic susceptibility testing and confirmation of ESBL-producing and carbapenem-resistant strains were conducted with the combination disc test. The laboratory data and antibiogram generation were managed using WHONET 2024 software. Prevalence and antibiotic resistance patterns were analyzed and presented using both Microsoft Excel 365 and the AMR package in R Studio. Results: Of the 165 poultry caecal content samples examined, an overall E. coli prevalence of 88.5% (n=146) was obtained. The prevalence of ESBL-producing and carbapenem-resistant E. coli was 90.4% (n = 132/146) and 1.4% (n = 2/146), respectively. All isolates demonstrated 100% resistance to amoxicillin/clavulanic acid and temocillin, and 99.0% resistance to ampicillin and cefpodoxime. Susceptibility to ceftazidime/avibactam, meropenem, and tigecycline was 100%. Monthly, between 80% and 100% of the isolates were resistant to amoxicillin-clavulanic acid, ampicillin, aztreonam, cefpodoxime, cefepime, and temocillin throughout the year. Conclusions: The prevalence of multidrug-resistant ESBL-producing E. coli in the caecal contents of retail poultry is high. Also, the resistance patterns of these isolates to all antibiotics except ceftazidime/avibactam and tigecycline throughout the year are of great concern. These observations raise questions about the use of antibiotics in poultry farming in Ghana. While veterinary officers are encouraged to intensify education and monitoring, poultry retailers are advised to adhere to good hygiene practices.

Background: Diarrhea is a leading cause of mortality in children under five, with rotavirus and enteric adenoviruses F40/F41 being significant contributors. In regions like Africa and Southeast Asia, the incidence is exacerbated by poor hygiene and sanitation, as well as the challenges around availability and affordability of healthcare and disease diagnostics. The objective of this systematic review was to identify and evaluate molecular assays for the detection of rotavirus and enteric adenoviruses F40/F41, with particular emphasis on diagnostic performance and suitability for point-of-care use. Methods: A systematic review of literature from 2001 to 2024 was conducted following PRISMA guidelines. Out of 659,613 records screened, a subset of primary studies reporting on molecular assays development or diagnostic performance met the inclusion criteria. Studies exclusively focused on epidemiology, vaccine impact, or narrative reviews were excluded from the analytical synthesis. Results: The review identified 26 PCR-based assays and 3 isothermal amplification assays. Reported clinical sensitivities ranged from approximately 85% to 100%, with specificities generally above 95% across studies. Several assays also demonstrated low limits of detection and turnaround times compatible with decentralized use. In particular, three LAMP assays and three PCR-based methods fulfilled key performance and operational criteria for point-of-care diagnostics. The review concluded that molecular diagnostics, especially LAMP assays, are effective for rapid detection of rotavirus and enteric adenoviruses F40/F41. Conclusion: While PCR assays are considered the gold standard, LAMP assays are more accessible and faster, making them better suited for use in resource-limited settings. These assays show promising performance and may support point-of-care diagnostics.

Salmonella is a major bacterial pathogen in low-income countries, where it circulates among humans, animals, and the environment. Children with sickle cell disease (SCD) are particularly vulnerable to severe Salmonella infections. This study aimed to characterize Salmonella isolates causing infections in Senegalese children with SCD. Using antimicrobial susceptibility testing, whole-genome sequencing, and bioinformatic analysis, we investigated antibiotic resistance, serovar diversity, and virulence factors on 23 isolates from SCD patients with diverse clinical infections. The isolates belonged to 12 serovars, with Enteritidis predominating (n = 7). Twenty-two isolates were fully susceptible to antibiotics, while one was multidrug-resistant. Eight isolates (Enteritidis and Typhimurium) carried a virulence plasmid harboring the spvRABCD gene cluster. Core Salmonella pathogenicity islands (SPIs-1 to -5, -11, and -13), as well as SPI-10 and SPI-23, were detected in all isolates, whereas other SPIs were variably present. These results show high serovar diversity and low antimicrobial resistance among Salmonella isolates in children with SCD in Dakar, Senegal. Our findings suggest that strains causing diarrhea in healthy individuals may also cause invasive disease in SCD patients, highlighting the need for dedicated surveillance in this vulnerable population.

Human enteric viruses are common pathogens that can cause acute gastroenteritis (AGE). The largest proportion of morbidity and mortality occurs in developi

Objectives: SCD is one of the most prevalent inherited hemoglobin disorders globally, affecting over 300 000 newborns annually, with the majority born in sub-Saharan Africa. Children with SCD are particularly vulnerable to severe bacterial infections, which are a major cause of morbidity and mortality. Among these, Salmonella species, especially non-typhoidal Salmonella, are frequently implicated and are notably associated with osteomyelitis, a serious bone infection. In this study, we performed whole genome sequencing and genomic analysis of 12 Salmonella isolates recovered from osteomyelitis cases in children with SCD in Dakar, Senegal. Methods: The isolates’ identity was confirmed using a MALDI-TOF biotyper and antimicrobial susceptibility testing carried out using the disc diffusion method. Whole-genome sequencing was conducted on an Illumina platform and bioinformatic analyses carried out using open-access and custom tools. Results: The isolates belonged to seven serovars, with Enteritidis and Typhimurium being the most frequent (three isolates each). Antibiotic susceptibility testing showed that 11 isolates were fully susceptible to all tested drugs, while one was an extensively drug-resistant strain previously linked to a nosocomial outbreak in a neonatal unit. Most of the isolates contained important Salmonella virulence factors including several Salmonella Pathogenicity Islands and plasmid-borne virulence genes. Conclusion: These findings highlight the clinical significance of Salmonella infections in children with SCD in low-income settings and underscore the urgent need for genomic surveillance and targeted public health interventions to protect this high-risk population.

Background: Despite the huge burden of deaths associated with or attributable to antimicrobial resistance, studies on sequencing based antimicrobial resistance (AMR) monitoring in Africa are scarce, specifically in the animal sector. Objective and Methods: With a view to deploy rapid AMR monitoring through leveraging advanced technologies, in the current study, nanopore sequencing was performed with 10 E. coli strains isolated from rectal swabs of pigs and poultry layers in Nigeria. Two sequence analysis methods including command line, where bacterial genomes were assembled, and subsequently antimicrobial resistance genes (ARGs) were detected through online databases, and EPI2ME, an integrated cloud-based data analysis platform with MinION, was used to detect ARGs. Results: A total of 95 ARGs were identified and most of the genes are known to be expressed in the chromosome. Interestingly, few genes including qnrS1, qnrS15, qnrS10, kdpE, cmlA1, MIR-14, sul3 and dfrA12 were identified which were previously reported as transferred through Mobile Genetic Elements (MGEs). The antibiotic susceptibility assay determined that the E. coli isolates were resistant to Penicillin (100%), Ciprofloxacin (70%), tetracycline (50%) and Ampicillin (40%). The accuracies of the command line and EPI2ME methods have been found to be 57.14% and 32.14%, respectively, in predicting AMR. Moreover, the analysis methods showed 62.5% agreement in predicting AMR for the E. coli isolates. Conclusions: Considering the multiple advantages of nanopore sequencing, the application of this rapid and field-feasible sequencing technique holds promise for rapid AMR monitoring in low- and middle-income countries (LMICs), including Nigeria. However, the development of a robust sequence analysis pipeline and the optimization of the existing analysis tools are crucial to streamline the deployment of nanopore sequencing in LMICs for AMR monitoring both in animal and human sectors.

Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) poses a significant public health concern due to its widespread prevalence and resistance to multiple antibiotics. This study aimed to assess the prevalence, resistance profile, and carriage of ESBL-encoding genes in ESBL-Ec isolates from broilers in two markets of Dakar, Senegal. Sampling over a one-year period revealed that 61.7% of broilers carried ESBL-Ec in their cecum. Antibiotic susceptibility testing of 186 ESBL-Ec isolates showed high resistance to β-lactam antibiotics, including ampicillin, ticarcillin, and third-generation cephalosporins. Notably, all isolates were susceptible to imipenem. Multidrug resistance was frequent, with 91.4% of the isolates displaying this phenotype. Comparison between the two markets revealed variations in resistance to quinolones. PCR analysis detected bla_CTX-M genes in all isolates, with bla_CTX-M-1 being the most prevalent subgroup. Additionally, bla_TEM and bla_OXA genes were found in 26.3% and 2.7% of isolates, respectively, while no bla_SHV genes were detected. Combinations of ESBL genes were common, with bla_CTX-M15-bla_TEM being the most frequent. These findings highlight the widespread prevalence of ESBL-Ec in broilers from Dakar markets, indicating a potential risk of transmission to humans through the food chain. Effective surveillance and intervention strategies are crucial to mitigate the spread of antimicrobial resistance in humans and animals.

Background: Although Helicobacter pylori infection (H. pylori) prevalence in Africa has declined in the last decade, it remains concerningly high. H. pylori is asymptomatic in the majority of patients but is associated with significant morbidity and mortality in 10%–20%.Materials and Methods: We conducted an online survey of 21 African countries, with the link distributed to members of the African Helicobacter Microbiota Study Group. The survey was completed by 562 respondents; the majority were from Nigeria (27.2%), South Africa (18.1%), Tanzania (17.6%), Egypt (16.9%), and Cameroon (14.2%).Results: The most common reason for H. pylori testing was dyspepsia in 83.9% of the cases. Abnormal findings at gastroscopy (62.3%) and heartburn (61.7%) were also common indications. Stool antigen testing and histological examination of gastric biopsies using Giemsa were the two most used methods for H. pylori testing at 62.3% and 50.3%, respectively. Most respondents reported the use of standard clarithromycin‐based triple therapy as first‐line treatment for H. pylori infection.Conclusion: This survey has demonstrated the diversity of practice and resource availability within the African continent. Several international guidelines exist on the management of H. pylori, but little data is available in Africa on how this condition is managed in every day clinical practice. There is an urgent need to formulate evidence‐based and locally relevant practice guidelines on the African continent. In this context, the African Helicobacter and Microbiota study group was formed to coordinate efforts across the continent on H. pylori research to provide guidance on its management. This paper, therefore, aimed to evaluate the practice of H. pylori diagnostics and management, as well as related resources in representative countries in Africa, to facilitate the development of such guidelines.

Antimicrobial resistance (AMR) is a global public health threat. Quality data are needed to address the rise of multidrug-resistant clones, particularly in sub-Saharan Africa. In this study, we analysed the prevalence, antimicrobial resistance profile, and presence of genes encoding extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) and Klebsiella pneumoniae (ESBL-Kp) in environmental samples from Ouagadougou, Burkina Faso. Of 264 samples collected, 95 (36%) and 74 (28%) contained ESBL-Kp and ESBL-Ec, respectively. ESBL-Kp was more prevalent in runoff water and in treated and untreated wastewater, while ESBL-Ec was more prevalent in manure. Interestingly, wastewater treatment did not significantly reduce the recovery of ESBL bacteria. As expected, resistance to third- and fourth-generation cephalosporins was predominant, and rare for second generation cefoxitin. Interestingly, all the isolates from treated wastewater were susceptible to ampicillin and piperacillin, while all the other clones were resistant to these antibiotics. Regarding the ESBL-encoding genes, the bla_CTX-M family was the most abundant, with the bla_CTX-M1 subfamily being the most prevalent. Carriage of combinations of ESBL genes was common, with the majority of the isolates harbouring 2–4 different genes. This study highlights the need for active surveillance to manage the risk of exposure to ESBL bacteria in Burkina Faso.

Malaria infection is a multifactorial disease partly modulated by host immuno-genetic factors. Recent evidence has demonstrated the importance of Interleukin-17 family proinflammatory cytokines and their genetic variants in host immunity. However, limited knowledge exists about their role in parasitic infections such as malaria. We aimed to investigate IL-17A serum levels in patients with severe and uncomplicated malaria, whether IL-17A gene polymorphisms are involved in severe malaria susceptibility and the polymorphism’s influence on the IL-17A serum levels. 125 malaria patients and 48 free malaria controls were enrolled in this research. Malaria patients were classified into severe malaria (SM) and uncomplicated malaria (UM). IL-17A serum levels were measured with ELISA. PCR and DNA sequencing were used to assess host genetic polymorphisms in IL-17A. We performed a multivariate regression to estimate the impact of human IL-17A variants on IL-17A serum level and malaria outcome. Elevated serum IL-17A levels accompanied by increased parasitemia were found in SM patients compared to UM and controls (P<0.0001). Also, the IL-17A levels were lower in SM patients who were deceased than in those who survived. In addition, the minor allele frequencies (MAF) of two IL-17A polymorphisms (rs3819024 and rs3748067) were more prevalent in SM patients than UM patients indicating an essential role in SM. Interestingly, the heterozygous rs8193038 AG genotype was significantly associated with higher levels of IL-17A than the homozygous wild type (GG). According to our results, it can be concluded that IL-17A may play a role in protection against fatal malaria outcomes.