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Background: The human gut microbiome is implicated in health and disease. Yet, its functions in healthy adults from a divergent population like those seen in Africa are quite unclear. We set to reveal the roles of the gut microbiome of a healthy rural and urban Yoruba population of Lagos State. Methodology: Sociodemographic and clinical data, and fecal samples were obtained from rural (n = 10) and urban (n = 10) participants. fecal DNA extraction was done using ZR Fecal DNA MiniPrep™ D6010 and metagenomic next generation sequencing performed on Illumina Miseq platform. Functional roles prediction and antibiotics resistance genes (ARGs) were done using the Clusters of Orthologous Groups (COG) and Comprehensive Antibiotic Resistance Database (CARD) tools, respectively. The potential link between phenotypes and COG abundance were inferred using principal component analysis (PCA). Results: We found 12 (urban) and 11 (rural) COG classes of proteins from the gut microbes. Class E protein which denotes amino acid transport and metabolism was unique to urban respondents and was dominated by 5-enolpyruvylshikimate-3-phosphate synthase (45%) and asparagine synthase (30%), implying a high protein-based diet. Class S was found in both groups. COG families of proteins revealed the presence of exo-beta-1,3-glucanase (31%), pyruvate-decarboxylase, and thiamine pyrophosphate-requiring enzymes (22%) among the rural respondents’ indicative of carbohydrate-rich diets. In addition, uncharacterized protein linked to hypothetical functions was found in both. The COG proteins clustered with female sex, BMI (body mass index) and BP (blood pressure) for urban while for the rural populace, it clustered with height, BMI, and BP. CARD analysis showed ARGs in both groups (urban 90%; rural 10%) and all were Escherichia coli 16S rRNA (rrsB) mutation conferring resistance to streptomycin with gene variant model A523C n/a to aminoglycoside antibiotics. Conclusion: The study defined the classes of proteins from gut microbes of urban and rural respondents and highlighted the presence of uncharacterized proteins linked to hypothetical and unknown functions. Differences seen among the predicted roles appear to be driven by diet, clinical and sociodemographic factors. The higher abundance of ARGs observed in the urban population poses a serious public health concern with regards to the spread of antibiotic resistance.

Abstract Background The staphylococci are implicated in a variety of human infections; however, many clinical microbiology laboratories in Nigeria do not identify staphylococci (in particular coagulase negative staphylococci - CNS) to the species level. Moreover, data from multi-centre assessment on antibiotic resistance and epidemiology of the staphylococci are not available in Nigeria. This study investigated 91 non-duplicate staphylococcal isolates obtained from the microbiology laboratories of eight hospitals in Nigeria during the period January to April 2010. Methods Identification and antibiotic susceptibility testing was performed using the VITEK 2 system, detection of resistance genes by PCR, and molecular characterization was determined by SCCmec typing, spa and multilocus sequence typing (MLST). Results All the isolates were susceptible to mupirocin, tigecycline, vancomycin and linezolid, but 72.5% of CNS and 82.3% of Staphylococcus aureus were resistant to cotrimoxazole, while multiresistance was observed in 37 of the 40 CNS isolates. Untypeable SCCmec types (ccrC/Class A mec and ccr-negative/Class C2 mec gene complex) in two methicillin-resistant S. aureus (MRSA) were identified. Additionally, ccr-negative/Class A mec and ccr type 4/Class C2 mec gene complex was detected in one isolate each of S. sciuri and S. haemolyticus, respectively. The S. aureus isolates were classified into 21 spa types including two new types (t8987, t9008) among the methicillin-susceptible S. aureus (MSSA) isolates. Two (CC8-SCCmecnon-typeable and CC88-SCCmec IV) and four (CC8-SCCmec III/IV/V; CC30-SCCmec II/III; CC88-SCCmec IV; and ST152-SCCmecnon-typeable) MRSA clones were identified in Maiduguri (North-East Nigeria) and South-West Nigeria, respectively. The proportion of Panton-Valentine leukocidin (PVL)-positive MSSA was high (44.4%) and 56.3% of these strains were associated with sequence type (ST) 152. Conclusions The identification of multiresistant mecA positive S. haemolyticus and S. sciuri from clinical samples indicates that characterization of CNS is important in providing information on their diversity and importance in Nigeria. There is the need to develop new SCCmec classification methods for non-typeable methicillin-resistant staphylococci, and to curtail the spread and establishment of the S. aureus ST152 clone in Nigeria. The study presents the first report of a PVL-positive ST152-SCCmecnontypeable MRSA and SCCmec typing of methicillin-resistant CNS in Nigeria.

Abstract Background Lower-than-expected incidence of HIV undermines sample size calculations and compromises the power of a HIV prevention trial. We evaluated the effectiveness of interim monitoring of HIV infection rates and on-going modification of recruitment strategies to enroll women at higher risk of HIV in the Cellulose Sulfate Phase III study in Nigeria. Methods We analyzed prevalence and incidence of HIV and other sexually transmitted infections, demographic and sexual behavior characteristics aggregated over the treatment groups on a quarterly basis. The site investigators were advised on their recruitment strategies based on the findings of the interim analyses. Results A total of 3619 women were screened and 1644 enrolled at the Ikeja and Apapa clinics in Lagos, and at the Central and Peripheral clinics in Port Harcourt. Twelve months after study initiation, the overall incidence of HIV was less than one-third of the pre-study assumption, with rates of HIV that varied substantially between clinics. Due to the low prevalence and incidence rates of HIV, it was decided to close the Ikeja clinic in Lagos and to find new catchment areas in Port Harcourt. This strategy was associated with an almost two-fold increase in observed HIV incidence during the second year of the study. Conclusion Given the difficulties in estimating HIV incidence, a close monitoring of HIV prevalence and incidence rates during a trial is warranted. The on-going modification of recruitment strategies based on the regular analysis of HIV rates appeared to be an efficient method for targeting populations at greatest risk of HIV infection and increasing study power in the Nigeria trial. Trial Registration The trial was registered with the ClinicalTrials.gov registry under #NCT00120770 http://clinicaltrials.gov/ct2/show/NCT00120770