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.

Carbapenem-resistant Acinetobacter baumannii (CRAB) is a critical antimicrobial resistance threat and a WHO-prioritized pathogen. With intrinsic resistance to multiple antibiotics and the emergence of pan-resistant isolates, CRAB infections are challenging to treat, often relying on polymyxins, tigecycline, aminoglycosides, or combinations, though co-resistance is rising globally. Phage therapy is considered as a potential treatment for multidrug-resistant A. baumannii. This study focused on isolating and characterizing phages active against CRAB strains from healthcare-associated infections in Dakar, Senegal. A lytic phage, Acinetobacter vAbaIN10, was isolated from wastewater collected at the Aristide Le Dantec Hospital in Dakar, Senegal. Isolation, host range, efficiency of plating, temperature and pH stability, lysis kinetics, one-step growth test, sequencing, and genomic analysis were performed. Phage vAbaIN10 belongs to the class Caudoviricetes and the genus Friunavirus. Its genome is 40,279 bp in size. Phage vAbaIN10 is stable across a wide pH range (3-9) and temperature range (25°C-60°C). The phage's lytic activity was evaluated at different multiplicities of infection (MOI): MOI 10, 1, and 10⁻¹. All MOIs significantly reduced the growth of host bacteria. The one-step growth curve showed that vAbaIN10 had a latency period of 25 min and a burst size of approximately 4.78 × 10³ phages per infected bacterial cell. No tRNA, mtRNA, clustered regularly interspaced short palindromic repeat, virulence factors, or antibiotic resistance genes were found in the genome. The biological and genomic characteristics of vAbaIN10 meet the requirements for its potential use in phage therapy.

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.

Two bacteriophages (phages) of Klebsiella pneumoniae were isolated from sewage water collected from Dakar, Senegal. Phage vKpIN17 belongs to the Przondovirus genus within the Autographiviridae family, with double-stranded DNA genomes, whereas vKpIN18 belongs to the Webervirus genus of the Drexlerviridae family.

Background and objectives Antimicrobial resistance (AMR) is a growing global threat, with carbapenemase-producing Enterobacterales (CPEs) representing a critical public health challenge. Rapid and accurate detection of CPEs is essential for controlling fatal bacterial AMR infections. This study evaluated the performance of MacConkey media supplemented with ertapenem (MacErt1 and MacErt2) for the detection of CPEs. Methods We formulated the media by supplementing MacConkey agar with ertapenem to final concentrations of 0.5 mg/L (MacErt1) and 1 mg/L (MacErt2). The media were assessed using a panel of 26 characterized Enterobacterales, including CPEs harboring oxacillinase (OXA)-48, OXA-181, New Delhi metallo-beta-lactamase (NDM)-5, and Klebsiella pneumoniae carbapenemase (KPC). All isolates were cultured on Mueller Hinton agar and incubated overnight at 36°C. Inocula were prepared and adjusted to a 0.5 McFarland standard. Ten microliter loops were used to streak MacErt1 and MacErt2 plates, which were then incubated overnight. After validation, MacErt1 was employed for the detection of CPEs in wastewater. A volume of 10 mL of wastewater was filtered, and the membrane was placed on MacErt agar, followed by overnight incubation. Grown colonies were identified using the Biotyper Sirius 2 MALDI-TOF (Bremen, Germany: Bruker), and the presence of carbapenem resistance genes was determined by lateral flow immunoassay (LFIA) tests and PCR. Results MacErt1 exhibited excellent sensitivity (100%) for all tested CPEs and a specificity of 77%. In contrast, MacErt2 demonstrated an overall sensitivity of 83%, primarily due to reduced sensitivity for OXA-181. However, it was 100% sensitive for detecting NDM, KPC, and OXA-48 producers. MacErt2 also maintained excellent specificity at 93%. The application of MacErt1 to wastewater samples resulted in 100% positivity and allowed the isolation of 124 CPEs among 150 examined isolates, predominantly NDM producers, followed by OXA-48-like and NDM+OXA-48-like strains. None of the isolates tested positive for blaKPC, blaVIM, or blaIMP. Conclusion This study demonstrated the efficacy of MacErt media for selectively detecting CPEs. MacErt1 exhibited 100% sensitivity for various CPEs and a specificity of 77%. MacErt2 showed 93% specificity and 100% sensitivity for NDM and KPC producers, making it suitable for targeted detection. These findings suggest that MacErt media provide an effective in-house solution for CPE surveillance, serving as a valuable tool in the ongoing battle against AMR.

The Presence of antimicrobial-resistant Salmonella in food remains a real threat. The aim of this study was to determine the antimicrobial resistance profiles of Salmonella strains isolated from the most consumed types of meat in Senegal. A total of 337 samples were collected including 247 samples of raw meat and 90 of meat-based ready-made meals. Salmonella strains were isolated according to the French standard EN-ISO-6579 and serotyped according to the KWLM scheme. Antimicrobial susceptibility tests were performed with 16 discs following the agar diffusion method. Our study showed that 37% of the samples carried Salmonella and allowed the isolation of 136 strains of Salmonella. We identified 47 different serotypes including S. Kentucky (11/136: 8%), S. Brancaster (10/136: 7%), S. Chester (10/136: 7%), S. Istanbul (5/136: 4 %), and S. Agona (5/136: 4%) which were respectively the most common. Of the 136 strains, 43 (31.6%) were resistant to at least one antibiotic, of which 15.4% (21/136) were multidrug-resistant. Interestingly, S. Kentucky that was the most common, exhibited also the highest level of resistance, being at least resistant to 8 antibiotics. In conclusion, The increasing resistance and spread of S. Kentucky in meat products demand special monitoring and to be further studied.