Pathogenomic profile and clonal diversity of potential zoonotic MRSA-CC7-ST789-t091-SCCmecV from human skin and soft tissue infections.

The whole genome sequence (WGS) of prevalent MRSA strains harboring mecA gene obtained from skin and soft tissue infections (SSTIs) in Nigerian hospitals were profiled for pathogenomic structure and evaluated for clonal diversity. The two MRSA strains identified among 66 isolated multi-drug resistant S. aureus from a collection of 256 clinical samples were phenotyped for antibiotic resistance and genotyped for mecA, SCCmec, and spa types. The mecA positive MRSA was analysed using whole-genome sequencing for resistomes, virulomes, phylogenomic profiles and clonal diversity. The identified MRSA-CC7-ST789-t091-SCCmecV strains from a female child (aged 1 year) with severe otorrhea and an adult male (aged 23) with purulent wound abscess showed high-level resistance to streptomycin, vancomycin, kanamycin, sulfamethoxazole and ciprofloxacin. Both strains harbored abundant resistomes, inherent plasmids, chromosomal replicons and typical seven housekeeping genes (arc3, aroE4, glpF1, gmk4, pta4, tpi6, yqiL3). The most abundant putative virulomes were pathogenesis-associated proteins (included hemolysin gamma, leucocidins, proteases, staphylococcal superantigen/enterotoxin-like genes (Set/Ssl), capsule- and biofilm-associated genes, and hyaluronate lyase). Comparative phylogenomic analysis revealed the relatedness of the two clonal strains with prevalent MRSA-CC7 pathotypes observed in Italy (2013 and 2014), Denmark (2014), Thailand (2015 and 2016), USA (2018), and Nigeria (2016 and 2020); and share high genetic similarities with livestock strains from cow milk and cattle. Identified MRSA-CC7-ST789-t091-SCCmecV pathotypes implicated in SSTIs from Nigeria harboring repertoires of antibiotic resistance and virulence genes, and genetic relatedness with livestock strains; show the possibility of gene transfer between animal and human. Adequate hospital MRSA infection control and geno-epidemiological surveillance for animal and human transfer is required.

Cluster analysis and geospatial mapping of antibiotic resistant Escherichia coli O157 in southwest Nigerian communities.

Geospatial spread and antibiotic-resistant relatedness of Escherichia coli O157, which are important virulent serotypes causing severe complications leading to high intestinal morbidity and occasional mortality in several communities in southwest Nigeria, were evaluated. Biotyped Escherichia coli strains (n = 508) from subjects with diarrhea and related intestinal infections, various domestic water sources and food animal products were evaluated for antibiotic resistance relatedness, conjugative activity, virulence factor and biofilm production. Antibiotic resistance of Escherichia coli O157 encoded with stx was mapped for geospatial spread. Detected stx-encoded Escherichia coli O157 (7.56%) of human strains were significantly higher compared to water and food animal strains (p = 0.001) with high conjugative and transformative activity (OR(95%CI) = 34.65(94.5); p = 0.023). Water- Escherichia coli O157 reveal significant median resistance to ciprofloxacin, gentamycin (p < 0.05) and human diarrheagenic strains showed >60% resistance to doxycycline (MIC50 8 µg/mL and MIC90 128 µg/mL; p = 0.018), tetracycline (MIC50 4 µg/mL and MIC90 64 µg/mL), ciprofloxacin (MIC50 2 µg/mL and MIC90 128 µg/mL) and gentamycin (MIC50 4 µg/mL and MIC90 256 µg/mL). Strains from human diarrhea, UTI, colitis, cattle, fish, sheep, ground waters, streams, and rivers characterized with biofilm, hemolysin, protease productions, R-plasmid (≈14.30kbp) and MARI (0.84) were highly related. Principal component analysis (score plot) revealed a significant association between resistant human diarrheic strains with cattle and poultry strains. A high population of heterogeneous stx-encoded diarrheagenic and colitis strains was predominant in urban settings spreading with food animal and water Escherichia coli O157 strains. Human diarrheagenic Escherichia coli O157 were highly related to antibiotic resistance and virulence pattern with water and animal products strains. Strategic interventions through the implementation of One Health approach and population-target antimicrobial stewardship are needed to mitigate the increasing intestinal morbidity and reduction of mortality impact. Regular application of spatial data on clonal dissemination is important for monitoring, surveillance of antimicrobial resistance and transmission of zoonotic food-borne Escherichia coli O157 pathogens.

Human rotavirus VP4 and VP7 genetic diversity and detection of GII norovirus in Ibadan as Nigeria introduces rotavirus vaccine.

OBJECTIVE: This cross-sectional study investigated the circulating strains of rotavirus and screened for noravirus in Ibadan, Nigeria as the country introduces the rotavirus vaccine into its national immunization program. METHODS: Sixty-five stool samples were collected from children younger than 5 years with clinically diagnosed diarrhea and screened for the presence of rotavirus and norovirus using RT-PCR. Rotavirus-positive samples were further analyzed to determine the G and P genotypes using semi-nested multiplex PCR. RESULTS: The rates of rotavirus and norovirus positivity were 30.8% and 10.8%, respectively, whereas the rate of rotavirus and norovirus mixed infection was 4.6%. G1 was the predominant VP7 genotype, followed by G2, G9, and G1G2G9, whereas the predominant VP4 genotype was P[4], followed by P[6], P[8], and P[9]. The mixed P types P[4]P[8] and P[4]P[6] were also detected. G1P[4] was the most common VP4 and VP7 combination, followed by G2P[4], G1[P6], G1P[8], G2P[6], G2P[9], G9P[6], G2G9P[4], G2P[4]P[6], G1P[4]P[8], G2G9P[8], G1G2G9P[8], and G1[non-typable] P[non-typable], which were detected in at least 5% of the samples. Four samples had a combination of non-typable G and P types. CONCLUSIONS: It is essential to monitor the circulation of virus strains prior to and during the implementation of the immunization program.

Molecular characterization and evolutionary dynamics of measles virus sequences isolated from children in Lagos and Ibadan, South Western, Nigeria.

Measles infection is endemic in Nigeria, with outbreaks occurring yearly. Genotype B3 is the dominant genotype and the only genotype characterized from Nigeria. The current study investigated the phylogenetic and Bayesian evolutionary dynamics of Nigerian measles virus Nucleoprotein (N) sequences isolated from Lagos and Ibadan, Nigeria. A total of 120 throat swab samples were analysed by RT-PCR and Sanger sequencing. Phylogenetic analysis and Bayesian demographic reconstructions were done using MEGA and BEAST software. Measles RNA positivity was 14.2% (17/120), age range 0-1 recorded the highest rate with 40.83%. Study sequences clustered within clade B3.1. The evolutionary rate of analysed B3 sequences was 1.108×10-3, higher posterior density HPD interval (1.462×10-3 - 7.886×10-4)subs/site/year. The time to most recent common ancestor (TMRC), was 1991. The Bayesian skyride analysis(BSP) of West African MV cladeB3.1, showed a stable, steady state population demography. This study has reemphasised the dominance of clade B3.1 in Nigeria. We have shown that clade B3.1 was recently introduced into circulation and has a slow population expansion. We advocate for the institution of molecular surveillance country wide in order to help monitor strain diversity and genetic evolution of Measles in Nigeria.

Phylogeography and evolutionary analysis of African Rotavirus a genotype G12 reveals district genetic diversification within lineage III.

Group A rotavirus (RVA) genotype G12 has spread globally and has become one of the most prevalent genotypes of rotavirus in Africa. To understand the drivers for its genetic diversity and rapid spread we investigated the Bayesian phylogeography, viral evolution and population demography of Rotavirus G12 in Africa. We downloaded and aligned VP7 gene sequences of Rotavirus genotype G12, from thirteen African countries (n = 96). Phylogenetic analysis, Evolutionary analysis and Bayesian Phylogeography was carried out, using MEGA Vs 6, BEAST, and SPREAD3. Phylogenetic analysis revealed that all the African sequences fell into lineage III diversifying into two major clades. The evolutionary rate of the African rotavirus G12 sequences was 1.678×10-3, (95% HPD, 1.201×10-3 - 2.198×10-3) substitutions/site/year, with TMRC of 16.8 years. The Maximum clade credibility (MCC) tree clustered into three lineages (II, III, IV), African strains fell within lineage III, and diversified into three clusters. Phylogeography suggested that South Africa seemed to be the epicentre of dispersal of the genotype. The demographic history of the G12 viruses revealed a steady increase between the years1998-2007, followed by a sharp decrease in effective population size between the years 2008-2011. We have shown the potential for genetic diversification of Rotavirus genotype G12 in Africa. We recommend the adoption of Molecular surveillance across Africa to further control spread and diversification of Rotavirus.

Epidemiology of Rotavirus A in Nigeria: Molecular Diversity and Current Insights.

Rotavirus induced acute gastroenteritis AGE has been a major disease burden in Nigeria, since it was first reported in 1985. Prevalence rates have increased with severe public health consequences particularly among children. The vaccine Rotarix® has been introduced and is commercially available in Nigeria. However routine rotavirus vaccination is yet to be introduced into the National Immunization Program. Molecular epidemiology of rotavirus in Nigeria has shown the presence of various genotypes, with genotype G12P[8] being the most recent introduction. There are however gaps in molecular data on rotavirus in Nigeria. We therefore reviewed molecular data on rotavirus isolated in Nigeria and also analyzed VP4 and VP7 genes of Nigerian rotavirus strains in Genbank. We have shown that there is a distinct trend in rotavirus molecular epidemiology in Nigeria, with new genotype introductions occurring after the year 2010. We also observed from our analysis the emergence of genotype G12 Lineage III as a dominant genotype. This information elucidates rotavirus molecular epidemiology in Nigeria and gives insight to the expanding landscape of rotavirus genotypes. We recommend the institution of molecular surveillance country wide, before considering the inclusion of rotavirus vaccination into the National Immunization Program in Nigeria, in other to monitor evolution of divergent or recombinant strains.

Species A Rotavirus (RVA) Isolated from Sewage in Nigeria, 2014: Close Genetic Relatedness of Partial G, P, and NSP4 Gene Sequences Encoding G1 with Cogent Genes of Other Asian and African Rotaviruses.

Rotavirus has been identified as a major cause of gastroenteritis in Nigeria. There is limited information on the intragenotype diversity of Nigerian rotavirus isolates. We therefore investigated the molecular characteristics of some rotavirus gene sequences detected in sewage from Nigeria. Seven sewage samples, out of a total of 68, tested positive for rotavirus RNA (10.3%). Genotype G1P[4] was the most common genotype (5 isolates) and one isolate for genotypes G1P[8] and G3P[6]. Phylogenetic analysis of the partial VP7 gene of 3 G1P[4] isolates analyzed identified them as genotype G1 Lineage 2 along with Chinese strains with 99.1% to 100% amino acid similarity. Amino acid substitutions D-97→E and S-147→D/N were observed within the 7-1a and 7-2 domains of VP7 gene among the study G1P4 isolates in reference to vaccine strain RotaTeq®. Phylogenetic analysis of the G3P[6] study isolate identified it as genotype G3 Lineage 3, forming a monophyletic cluster with 100% bootstrap value with other West African strains G3 isolates. Phylogenetic analysis of GIP[4] VP4 genes identified them as P4 Lineage 5, while 3 NSP4 gene sequences belonged to genotype E1, while 1 belonged to E2. The results from this study represent phylogenetic analysis of partial gene sequences of environmental group A rotavirus (RVA) isolates from Nigeria.

FIRST MOLECULAR DETECTION AND VP7 (G) GENOTYPING OF GROUP A ROTAVIRUS BY SEMI-NESTED RT-PCR FROM SEWAGE IN NIGERIA.

Rotavirus is the leading cause of viral gastroenteritis worldwide, and sewage is a major source of the virus dissemination in the environment. Our aim was to detect and genotype rotaviruses from sewages in Nigeria. One hundred and ninety sewage samples were collected between June 2014 and January 2015. The two phase concentration method using PEG 6000 and dextran was used to concentrate sewage samples following WHO protocols. Molecular detection was performed by RT-PCR, and VP7 genotyping by semi-nested multiplex PCR. A total of 14.2% (n = 27) samples tested positive. Monthly distribution showed that June to September had a lower rate (3.7% to 7.4%), while October to January recorded 11% to 26%. Genotype G1 predominated followed by G8, G9, G4 and lastly G2, 7.4% (n = 2) of isolates were nontypeable. This is the first report of rotavirus detection in sewages from Nigeria. Genotype G1 remains the most prevalent genotype. This observation calls for an effort by the governmental authorities to implement a molecular surveillance, both clinical and environmental, in order to provide vital information for the control and the vaccine efficacy not only in Nigeria, but globally.

CD4 Decay Rate as an Indicator of the Time Interval between Initial Infection and First Diagnosis among Drug-Naïve Human Immunodeficiency Virus Seropositive Individuals in Lagos, Nigeria.

OBJECTIVE: The aim of this study was to determine the time interval between human immunodeficiency virus (HIV) infection and the first diagnosis among drug-naïve individuals in Badagry, Nigeria. SUBJECTS AND METHODS: A sample of 213 subjects who tested HIV positive for the first time were enrolled in this study. The HIV diagnosis was performed using Startpak® and Determine® kits, and a CD4 count was carried out using a FACS Count® flow cytometer. The mean CD4 values were determined by gender and age groups. The time interval between initial HIV infection and first testing was calculated based on the average CD4 decay rate per calendar year, and data analysis was performed using SPSS software. RESULTS: At diagnosis, the mean CD4 values showed that females recorded 270 cells/µl and males 244 cells/µl. By age range, individuals <25 years recorded 437 cells/µl, those between 25 and 40 years of age had 237 cells/µl, and those aged ≥41 years had 192 cells/µl. There was a significant difference between CD4 cell categorization and age range (p < 0.001). Subjects aged between 25 and 40 years recorded the highest distribution of all CD4 cell counts. The time interval between infection and testing for females was 8.1 years and for males 6.7 years. Within the age group <25 years the interval was 5.1 years, whilst it was 8.1 years for those aged ≥41 years. CONCLUSION: Most of the population presented for testing during the advanced stages of infection. We suggest an upscaling of HIV voluntary counseling and testing to encourage early detection and better treatment outcomes.

Seasonal abundance and molecular identification of West Nile virus vectors, Culex pipens and Culex quinquefasciatus (diptera: culicidae) in Abeokuta, South-West, Nigeria.

BACKGROUND: West Nile virus (WNV) infection, is an arbovirus infection with high morbidity and mortality, the vector responsible for both human and animal transmission is Culex pipens complex. OBJECTIVE: To determine the species distribution and seasonal abundance of Culex pipens and Culex quinquefasciatus mosquitoes in Abeokuta, Nigeria. METHODS: Mosquitoes belonging to the Culex pipens complex were captured in three different locations located within Abeokuta Metropolis between March 2012 and January 2013. Individual species were identified using morphometric methods. Amplification of the Ace2 gene by PCR confirmed morphormetric identification of the mosquitoes. RESULTS: A total of 751 mosquitoes were captured. Culex quinquefaciatus recorded the highest distribution of vectors with 56.6% and Culex pipens 43.4% (P > 0.05). Idi aba community recorded the highest distribution of mosquito vectors with 42.9% (n=322) and Culex quinqueaciatus was more abundantly distributed with 183 mosquitoes. Aro community recorded 32% (n=240) of captured mosquitoes with Culex quinquefaciatus having a higher level of abundance and lastly Kemta with a distribution of 25.1% (n=189). CONCLUSION: Results from this study show that potential vectors of WNV abound within Abeokuta, putting residents at high risk of West Nile infection. We advocate for introduction of routine testing of WNV in Abeokuta and Nigeria.

Seroprevalence of transfusion transmissible infections (TTI), in first time blood donors in Abeokuta, Nigeria.

BACKGROUND: Transfusion transmissible infections, such as HIV, HBV, HCV and syphilis are on the rise and pose a threat to blood safety. OBJECTIVE: To determine prevalence and demographic profiles of TTI's among first time blood donors in Abeokuta, Nigeria. METHODS: The study was conducted between February to November 2013; 130 first time blood donors were tested for the presence of HIV, HBsAg, HCV antibodies and Treponema palidium antibodies using EIA based rapid immunochromatographic kits. Data analysis was done using SPSS with a level of significance of p<0.05. RESULTS: Prevalence rates to HIV, HBsAg, HCV antibody, were 6.2% (n=8), 10% (n=13) and 1.5% (n=2), there was 0% prevalence to Treponema palidium antibodies. Group specific prevalence rates revealed that educational status was associated with HBsAg positivity (p = 0.028), donors with a history of previous blood transfusion was also statistically associated with HIV sero-reactivity (p = 0.013). CONCLUSIONS: High levels of HBsAg and HIV were observed, there is need to revise the donor testing algorithm in Nigeria in line with the prevalence of TTI's. We also advocate that a National surveillance system for TTI's be established through our National blood transfusion service (NBTS) program, a second serological test is also suggested to reduce the risk of occult HBV infection in Nigeria.