BackgroundAlthough rotavirus is the leading cause of severe diarrhea among children in sub-Saharan Africa, better knowledge of circulating enteric pathogenic bacteria and their antimicrobial resistance is crucial for prevention and treatment strategies.Methodology/Principal FindingsAs a part of rotavirus gastroenteritis surveillance in Maradi, Niger, we performed stool culture on a sub-population of children under 5 with moderate-to-severe diarrhea between April 2010 and March 2012. Campylobacter, Shigella and Salmonella were sought with conventional culture and biochemical methods. Shigella and Salmonella were serotyped by slide agglutination. Enteropathogenic Escherichia coli (EPEC) were screened by slide agglutination with EPEC O-typing antisera and confirmed by detection of virulence genes. Antimicrobial susceptibility was determined by disk diffusion. We enrolled 4020 children, including 230 with bloody diarrhea. At least one pathogenic bacterium was found in 28.0% of children with watery diarrhea and 42.2% with bloody diarrhea. Mixed infections were found in 10.3% of children. EPEC, Salmonella and Campylobacter spp. were similarly frequent in children with watery diarrhea (11.1%, 9.2% and 11.4% respectively) and Shigella spp. were the most frequent among children with bloody diarrhea (22.1%). The most frequent Shigella serogroup was S. flexneri (69/122, 56.5%). The most frequent Salmonella serotypes were Typhimurimum (71/355, 20.0%), Enteritidis (56/355, 15.8%) and Corvallis (46/355, 13.0%). The majority of putative EPEC isolates was confirmed to be EPEC (90/111, 81.1%). More than half of all Enterobacteriaceae were resistant to amoxicillin and co-trimoxazole. Around 13% (46/360) Salmonella exhibited an extended-spectrum beta-lactamase phenotype.ConclusionsThis study provides updated information on enteric bacteria diversity and antibiotic resistance in the Sahel region, where such data are scarce. Whether they are or not the causative agent of diarrhea, bacterial infections and their antibiotic resistance profiles should be closely monitored in countries like Niger where childhood malnutrition pre-disposes to severe and invasive infections.

ObjectiveWe conducted a parallel evaluation of the diagnostic accuracy of VIKIA® Rota-Adeno, a rapid diagnostic test (RDT) and Premier™ Rotaclone® an enzyme immunoassay (EIA) using reverse transcription polymerase chain reaction (RT-PCR) as the reference standard. The study was part of a rotavirus surveillance project in Niger.ResultsThe sensitivity of both tests was 80.7%. After exclusion of one indeterminate result by visual reading, the specificity of the Premier™ Rotaclone® was 100% by visual or optical density readings and that of VIKIA® Rota-Adeno test was 95.5%. Inter-reader agreement was excellent for both tests (kappa = 1). Our results showed almost similar performance of the EIA and RDT when compared to RT-PCR. Hence, the VIKIA® Rota-Adeno could be a good alternative for use in peripheral health centres where laboratory capacity is limited.

Background: Data on extended-spectrum β--lactamase-producing Escherichia coli (ESBL-E. coli) carriage in community settings, especially in developing countries, are scarce. Here, we describe the population structure and molecular characteristics of resistance of ESBL-E. coli faecal isolates in a rural African population. Methods and findings: Between April and May 2017, stools of 383 healthy participants were collected from 20 villages in rural Southern Niger during a clinical trial on ciprofloxacin prophylaxis carried out during a meningococcal meningitis outbreak. Of 383 individuals, 354 (92.4%) were carriers of ESBL-E. coli before any ciprofloxacin intake. A subset of 90 of these ESBL-E. coli containing stools were selected for further analysis, from which 109 different ESBL-E. coli were recovered and whole genome sequenced by short-(Illumina) and long-(Nanopore) reads. Most belonged to the commensal-adapted phylogroup A (91, 83.5%), with high clonal diversity (57 distinct clones). One-quarter harboured the high pathogenicity island previously associated with a longer duration of faecal carriage. The bla CTX-M-15 gene was the major ESBL determinant (107, 98.1%). It was chromosome-integrated in approximately half of the cases (48, 44.9%), at multiple integration sites in diverse chromosomal genetic backgrounds. When plasmid-borne, bla CTX-M-15 was found in a large diversity of incompatibility groups. A single genetic background was found for 20 distinct plasmids, whereas very closely related plasmids were found in different genetic backgrounds in six cases, suggesting plasmid spread among strains. No geographical or social links to resistance patterns were observed. Conclusions: Massive prevalence of community faecal carriage of CTX-M-15-producing E. coli was observed in a rural region of Niger without apparent antibiotic selective pressure. E. coli were highly diverse, well adapted commensal strains, with chromosomal integration of CTX-M-15 encoding gene in almost half of the cases. Evidence of clonal and plasmid spread suggest a risk of sustainable implementation in community faecal carriage.

No abstract

No abstract