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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.

BackgroundScreening pregnant women for HIV and syphilis is recommended by WHO in order to reduce mother-to-child transmission. We evaluated the field performance, feasibility, and acceptability of a dual rapid diagnostic test (RDT) for HIV and syphilis test in antenatal clinic settings in Nigeria.Methods and findingsParticipants were recruited at 12 antenatal clinic sites in three states of Nigeria. All consenting individuals were tested according to the national HIV testing algorithm, as well as a dual RDT, the SD BIOLINE HIV/Syphilis Duo Test (Alere, USA), in the clinic. To determine sensitivity, specificity and concordance, whole blood samples were obtained for repeat RDT performance in the laboratory, as well as reference tests for HIV and syphilis. Dual test acceptability and operational characteristics were assessed among participants and clinic staff.The prevalence of HIV among the 4,551 enrollees was 3.0% (138/4551) using the national clinic-based HIV testing algorithm. Positive and negative percent agreement of the HIV component of the dual RDT were 100.0% (95% CI 99.7–100.0) and 99.9% (95% CI 99.7–100.0) respectively, when compared with the national rapid testing algorithm. The prevalence of syphilis, using TPHA as the reference test, was low at 0.09% (4/4550). The sensitivity of the syphilis component of the dual RDT could not be calculated as no positive results were observed for patients that were positive for syphilis by TPHA. Each of the only four TPHA-positive specimens had RPR titers of 1:1 (neat), indicative of non-active syphilis. The specificity of the syphilis component of the dual RDT was 99.9% (95% CI 99.8–100.0).The dual RDT received favorable feasibility ratings among antenatal care clinic staff. Acceptability among study participants was high with most women reporting preference for rapid dual HIV/syphilis testing.ConclusionsThe SD BIOLINE HIV/Syphilis Duo Test showed a high overall diagnostic accuracy for HIV and a high specificity for syphilis diagnosis in antenatal clinic settings. This study adds to a growing body of evidence that supports the clinic-based use of dual tests for HIV and syphilis among pregnant women.

Background Klebsiella pneumoniae is a World Health Organization high-priority antibiotic-resistant pathogen. However, little is known about Klebsiella lineages circulating in Nigeria. Methods We performed whole-genome sequencing (WGS) of 141 Klebsiella isolated between 2016 and 2018 from clinical specimens at 3 antimicrobial-resistance (AMR) sentinel surveillance tertiary hospitals in southwestern Nigeria. We conducted in silico multilocus sequence typing; AMR gene, virulence gene, plasmid, and K and O loci profiling; as well as phylogenetic analyses, using publicly available tools and Nextflow pipelines. Results Phylogenetic analysis revealed that the majority of the 134 K. pneumoniae and 5 K. quasipneumoniae isolates from Nigeria characterized are closely related to globally disseminated multidrug-resistant clones. Of the 39 K. pneumoniae sequence types (STs) identified, the most common were ST307 (15%), ST5241 (12%), ST15 (~9%), and ST25 (~6%). ST5241, 1 of 10 novel STs detected, is a single locus variant of ST636 carrying dfrA14, tetD, qnrS, and oqxAB resistance genes. The extended-spectrum β-lactamase (ESBL) gene blaCTX_M-15 was seen in 72% of K. pneumoniae genomes, while 8% encoded a carbapenemase. No isolate carried a combination of carbapenemase-producing genes. Four likely outbreak clusters from 1 facility, within STs 17, 25, 307, and 5241, were ESBL but not carbapenemase-bearing clones. Conclusions This study uncovered known and novel K. pneumoniae lineages circulating in 3 hospitals in Southwest Nigeria that include multidrug-resistant ESBL producers. Carbapenemase-producing isolates remain uncommon. WGS retrospectively identified outbreak clusters, pointing to the value of genomic approaches in AMR surveillance for improving infection prevention and control in Nigerian hospitals.