Bacteremia Among Febrile Patients Attending Selected Healthcare Facilities in Ibadan, Nigeria.

BACKGROUND: The relative contribution of bacterial infections to febrile disease is poorly understood in many African countries due to diagnostic limitations. This study screened pediatric and adult patients attending 4 healthcare facilities in Ibadan, Nigeria, for bacteremia and malaria parasitemia. METHODS: Febrile patients underwent clinical diagnosis, malaria parasite testing, and blood culture. Bacteria from positive blood cultures were isolated and speciated using biochemical and serological methods, and Salmonella subtyping was performed by polymerase chain reaction. Antimicrobial susceptibility was tested by disk diffusion. RESULTS: A total of 682 patients were recruited between 16 June and 16 October 2017; 467 (68.5%) were <18 years of age. Bacterial pathogens were cultured from the blood of 117 (17.2%) patients, with Staphylococcus aureus (69 [59.0%]) and Salmonella enterica (34 [29.1%]) being the most common species recovered. Twenty-seven (79.4%) of the Salmonella isolates were serovar Typhi and the other 7 belonged to nontyphoidal Salmonella serovarieties. Thirty-four individuals were found to be coinfected with Plasmodium falciparum and bacteria. Five (14.7%) of these coinfections were with Salmonella, all in children aged <5 years. Antimicrobial susceptibility testing revealed that most of the Salmonella and Staphylococcus isolates were multidrug resistant. CONCLUSIONS: The study demonstrates that bacteria were commonly recovered from febrile patients with or without malaria in this location. Focused and extended epidemiological studies are needed for the introduction of typhoid conjugate vaccines that have the potential to prevent a major cause of severe community-acquired febrile diseases in our locality.

Evaluation of fecal occult blood testing for rapid diagnosis of invasive diarrhea in young children.

Antimicrobials are only indicated in acute childhood diarrhea if it is invasive or persistent. Rapid screening for invasive diarrhea can therefore inform treatment decisions but pathogen identification by culture is slow, expensive and cumbersome. This study aimed to assess the diagnostic utility of stool microscopy and immunochromatographic fecal occult blood test (FOBT) kits for identifying invasive or potentially invasive diarrhea in Ibadan, Nigeria. Fecal specimens from 46 children under 5 years old with diarrhea, collected as part of ongoing case-control studies, were subjected to stool microscopy for erythrocytes and leucocytes, and FOBT using the innovator's product and four locally procurable generic immunochromatographic kits, each according to manufacturers' instructions. Stool specimens were cultured for enteric bacterial pathogens using standard procedures. Presumptive pathogen isolates were identified biochemically and by PCR, and then confirmed by whole genome sequencing. Shigella, enteroinvasive Escherichia coli and Yersinia, pathogens that invariably cause invasive diarrhea, were detected in five of 46 specimens. Occult blood detection by microscopy was 55.6% sensitive and 78.4% specific, while the innovator's FOBT product was respectively 62.5% and 81.6% sensitive and specific compared to strict invasive pathogen recovery. Microscopy and FOBT testing were less sensitive in identifying specimens that contained pathogens that do not always elicit invasive diarrhea. Generic FOBT tests compared well with the innovator's product. Microscopy and FOBT testing have some value for delineating likely invasive diarrheas. They could inform treatment and serve as early warning indicators for dysentery outbreaks in resource limited settings. Inexpensive, generic FOBT kits that are locally procurable in Nigeria performed as well as the innovator's product.

PCR diagnostics are insufficient for the detection of Diarrhoeagenic Escherichia coli in Ibadan, Nigeria.

Understanding the contribution of different diarrhoeagenic Escherichia coli pathotypes to disease burden is critical to mapping risk and informing vaccine development. Targeting select virulence genes by PCR is the diagnostic approach of choice in high-burden, least-resourced African settings. We compared the performance of a commonly-used multiplex protocol to whole genome sequencing (WGS). PCR was applied to 3,815 E. coli isolates from 120 children with diarrhoea and 357 healthy controls. Three or more isolates per specimen were also Illumina-sequenced. Following quality assurance, ARIBA and Virulencefinder database were used to identify virulence targets. Root cause analysis of deviant PCR results was performed by examining target sensitivity using BLAST, Sanger sequencing false-positive amplicons, and identifying lineages prone to false-positivity using in-silico multilocus sequence typing and a Single Nucleotide Polymorphism phylogeny constructed using IQTree. The sensitivity and positive predictive value of PCR compared to WGS ranged from 0-77.8% while specificity ranged from 74.5-94.7% for different pathotypes. WGS identified more enteroaggregative E. coli (EAEC), fewer enterotoxigenic E. coli (ETEC) and none of the Shiga toxin-producing E. coli detected by PCR, painting a considerably different epidemiological picture. Use of the CVD432 target resulted in EAEC under-detection, and enteropathogenic E. coli eae primers mismatched more recently described intimin alleles common in our setting. False positive ETEC were over-represented among West Africa-predominant ST8746 complex strains. PCR precision varies with pathogen genome so primers optimized for use in one part of the world may have noticeably lower sensitivity and specificity in settings where different pathogen lineages predominate.

Epidemiology and Risk Factors for Diarrheagenic Escherichia coli Carriage among Children in Northern Ibadan, Nigeria.

Diarrhea is a leading cause of childhood morbidity in Africa, but few studies, focus on bacterial diarrheal etiology including multicountry studies that typically excluded Nigeria. We collected stool specimens from 477 children under 5 years of age, 120 with diarrhea, who were enrolled in our prospective case-control study between November 2015 and August 2019. All were attending primary health clinics on the northern outskirts of Ibadan. Up to 10 Escherichia coli isolates were obtained per specimen, and at least three of them were sequenced using Illumina whole-genome sequence technology. Genomes were assembled using SPAdes and evaluated for quality using QUAST. VirulenceFinder was used to identify virulence genes. The microbiological quality of water from 14 wells within the study area was assessed using total and coliform counts. Diarrheagenic E. coli (DEC) were isolated from 79 (65.8%) cases and 217 (60.8%) control children. A number of hybrid DEC pathotypes, Salmonella spp., Yersinia spp., and all DEC pathotypes except Shiga toxin-producing E. coli were detected, but no pathogen showed association with disease (P > 0.05). Enterotoxigenic E. coli were more commonly recovered from children without diarrhea aged below 6 months but exclusively detected in children with diarrhea aged over 9 months. Temporally linked, genetically similar enteroaggregative E. coli were isolated from children in different households in eight instances. No well water sample drawn in the study was potable. Children in northern Ibadan were commonly colonized with DEC. Access to water, proper sanitation, and vaccination against the prevailing pathogens may be critical for protecting children from the less overt consequences of enteric pathogen carriage.