Salmonella is an important human pathogen and poultry products constitute an important source of human infections. This study investigated prevalence; identified serotypes based on whole genome sequence, described spatial distribution of Salmonella serotypes and predicted risk factors that could influence the prevalence of Salmonella infection in commercial poultry farms in Nigeria. A cross sectional approach was employed to collect 558 pooled shoe socks and dust samples from 165 commercial poultry farms in North West Nigeria. On-farm visitation questionnaires were administered to obtain information on farm management practices in order to assess risk factors for Salmonella prevalence. Salmonella was identified by culture, biotyping, serology and polymerase chain reaction (PCR). PCR confirmed isolates were paired-end Illumina-sequenced. Following de novo genome assembly, draft genomes were used to obtain serotypes by SeqSero2 and SISTR pipeline and sequence types by SISTR and Enterobase. Risk factor analysis was performed using the logit model. A farm prevalence of 47.9% (CI 95 [40.3-55.5]) for Salmonella was observed, with a sample level prevalence of 15.9% (CI 95 [12.9-18.9]). Twenty-three different serotypes were identified, with S. Kentucky and S. Isangi as the most prevalent (32.9% and 11%). Serotypes showed some geographic variation. Salmonella detection was strongly associated with disposal of poultry waste and with presence of other livestock on the farm. Salmonella was commonly detected on commercial poultry farms in North West Nigeria and S. Kentucky was found to be ubiquitous in the farms.

BackgroundThe 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.MethodsFebrile 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.ResultsA 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.ConclusionsThe 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.

Diarrhea is a leading cause of childhood morbidity in Africa. Outside of multi-country sentinels, of which there are none in Nigeria, few studies focus on bacterial etiology. We performed a case-control study among children under five years of age. Stool specimens were collected from 120 children with, and 357 without, diarrhea attending primary health clinics on the northern outskirts of Ibadan between November 2015 and August 2019. Up to ten E. coli isolates were obtained per specimen and at least three were whole genome-sequenced using Illumina technology. Genomes were assembled using SPAdes, quality evaluated using QUAST, and 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. Diarrhoeagenic Escherichia coli (DEC) were isolated from 79 (65.8%) of cases and 217 (60.8%) control children. All DEC pathotypes except Shiga toxin-producing E. coli, a number of hybrid DEC pathotypes, Salmonella and Yersina spp. were detected but no pathogen showed association with disease (p>0.05). Enterotoxigenic E. coli were more commonly recovered from younger controls but exclusively detected in cases aged over nine months. Temporally-linked, highly similar enteroaggregative E. coli were isolated from children in different households in eight instances. No well water sample drawn in the study qualified as potable. Children in northern Ibadan are commonly colonized with DEC. Access to water and sanitation, and vaccines targeting the most abundant pathogens may be critical for protecting children from the less overt consequences of enteric pathogen carriage.

Background Bacterial resistance to commonly-used antibiotics has been on the increase especially in the clinical settings. This study focused on the detection of plasmid-mediated quinolone resistance (PMQR) determinants in ciprofloxacin-resistant bacteria recovered from Urinary Tract Infection (UTI) samples. Results Already characterized isolates from urine samples of UTI-diagnosed in- and out- patients were obtained from the culture pool of the Department of Medical Microbiology and Parasitology, University College Hospital (UCH), Ibadan, Nigeria. A total of seventy-three ciprofloxacin-resistant isolates were used in this study. Of the 73 UTI isolates, 43 carried at least one of the four PMQR genes targeted and they belonged to eight bacterial genera namely: Escherichia (25), Klebsiella (10), Pseudomonas (2), Proteus (2) and one isolate each belonging to Enterobacter, Acinetobacter, Citrobacter and Salmonella genera. qnrA was detected in 10.9% (8/73) of the isolates while the occurrence of qnrB and qnrS was 32.9% (24/73) and 20.5% (15/73), respectively. The quinolone efflux pump (qepA) was detected in 9/73 (12.3%) of the isolates. Thirty of the isolates carried only one PMQR gene, while thirteen carried two PMQR genes. There was no carriage of more than two PMQR genes in the forty-three isolates from which PMQR genes were detected. Conclusion This study reports the carriage of PMQR determinants by eight of the nine Gram-negative bacterial genera from urinary sources in patients attending the University College Hospital, Ibadan over the four-month period of study. This is quite worrisome as it suggests a high contribution of UTI cases to the burden of quinolone resistance. There is a need for more studies of this nature in other hospitals in Nigeria, to develop a database on the contribution of UTI cases to quinolone resistance.

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. colieae 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.