Characterization of HIV-1 Integrase Gene and Resistance Associated Mutations Prior to Roll out of Integrase Inhibitors by Kenyan National HIV-Treatment Program in Kenya

BACKGROUND: Antiretroviral therapy containing an integrase strand transfer inhibitor plus two Nucleoside Reverse Transcriptase inhibitors has now been recommended for treatment of HIV-1-infected patients. This thus determined possible pre-existing integrase resistance associated mutations in the integrase gene prior to introduction of integrase inhibitors combination therapy in Kenya.METHODS: Drug experienced HIV patients were enrolled at Kisii Teaching and Referral in Kenya. Blood specimens from (33) patients were collected for direct sequencing of HIV-1 polintegrase genes. Drug resistance mutations were interpreted according to the Stanford algorithm and phylogenetically analysed using insilico tools.RESULTS: From pooled 188 Kenyan HIV integrase sequences that were analysed for drug resistance, no major mutations conferring resistance to integrase inhibitors were detected. However, polymorphic accessory mutations associated with reduced susceptibility of integrase inhibitors were observed in low frequency; M50I (12.2%), T97A (3.7%), S153YG, E92G (1.6%), G140S/A/C (1.1%) and E157Q (0.5%). Phylogenetic analysis (330 sequences revealed that HIV-1 subtype A1 accounted for majority of the infections, 26 (78.8%), followed by D, 5 (15.2%) and C, 2 (6%).CONCLUSION: The integrase inhibitors will be effective in Kenya where HIV-1 subtype A1 is still the most predominant. However, occurring polymorphisms may warrant further investigation among drug experienced individuals on dolutegravir combination or integrase inhibitor treatment.&nbsp

Characteristics and treatment outcomes of HIV infected elderly patients enrolled in Kisii Teaching and Referral Hospital, Kenya

Background: A better understanding of the baseline characteristics of elderly people living with HIV/AIDS (PLWHA) is relevant because the world\u2019s HIV population is ageing. Objectives: This study aimed to evaluate the baseline characteristics of PLWHA aged 65 50years at recruitment to HIV/AIDS clinic compared against the viral load (VL) and CD4 count among patients attending Kisii Teaching and Referral Hospital (KTRH), Kenya. Methods: We retrospectively evaluated temporal inclinations of CD4 levels, viral load change and baseline demographic characteristics in the electronic records at the hospital using a mixed error-component model for 1329 PLWHA attending clinic between January 2008 and December 2019. Results: Findings showed a significant difference in the comparison between baseline VL and WHO AIDS staging (p=0.026). Overall VL levels decreased over the period significantly by WHO AIDS staging (p<0.0001). Significant difference was observed by gender (p<0.0001), across age groups (p<0.0001) and baseline CD4 counts (p=0.003). There were significant differences in WHO staging by CD4 count >200cell/mm3 (p=0.048) and residence (p=0.001). Conclusion: Age, WHO AIDS staging, gender and residence are relevant parameters associated with viral load decline and CD4 count in elderly PLWHA. A noticeable VL suppression was attained confirming possible attainment of VL suppression among PLWHA under clinical care

Additional file 2: of Prevalence of Tinea capitis in school going children from Mathare, informal settlement in Nairobi, Kenya

Table S2. Prevalence of Tinea capitis infections among the study subjects in Mathare informal settlement

Prevalence and detection of drug resistant mutations in Mycobacterium tuberculosis among drug naïve patients in Nairobi, Kenya

Abstract Background Tuberculosis (TB), an ancient scourge of humanity known for several thousands of years, is still a significant public health challenge in many countries today even though some progress has been made in recent years in controlling the disease. The study’s aim was to determine the prevalence of mutations responsible for drug resistance in Mycobacterium tuberculosis among patients visiting selected health centers in Nairobi, Kenya. Methods The cross-sectional study involved 132 TB positive patients visiting Mbagathi and Chandaria hospitals between September 2015 and August 2016. Sputum samples were collected from the participants and handled in a biosafety level 3 laboratory at the Kenya Medical Research Institute (KEMRI). Samples were decontaminated using N-Acetyl-L-Cysteine (NALC) – Sodium Hydroxide (NALC-NaOH), stained using Zeihl–Neelsen (ZN), and cultured in Mycobacterium Growth Indicator Tube (MGIT). DNA extracted from cultured isolates using Genolyse™ technique was subjected to Multiplex PCR amplification and reverse hybridization for detection of drug resistance mutations on rpoB, katG, inhA, gyrA, gyrB, rrs and eis genes using Hain Genotype MTBDRplus and MTBDRsl. Results All 132 (100%) patients included in the study were culture positive for M. tuberculosis. Among them, 72 (54%) were male while the remaining 60 (46%) were female. The mean age of the patients was 26.4 ± 19.4 (SD) with a range of 18 to 60 years. Overall, the prevalence of the resistance to first and second-line TB drugs was 1.5% (2/132). Resistance to isoniazid (INH) was observed in 1 of 132 patients (0.8%), as was multi-drug resistant tuberculosis (MDR-TB), also at 0.8%. No resistance to fluoroquinolones (FQ) or kanamycin (KAN) was observed. The INH resistant strain had the katG mutations S315 T, while mutations detected for the MDR-TB were katG S513 T for INH, rpoB S531 L for rifampicin (RIF) and rrs G1484 T for cross-resistance to aminoglycosides/capreomycin (AG/CP). Conclusions Molecular analysis confirms transmission of the drug-resistant M. tuberculosis strains. The data suggested that there is homogeneity when it comes to the type of drug resistance and mutation that occurs in the region. This calls for intensified drug resistance surveillance and drug adherence among patients infected with TB

Antimicrobial resistance genes in Salmonella and Escherichia coli isolates from chicken droppings in Nairobi, Kenya

Abstract Objective Increase in antimicrobial resistance is a threat to health sector globally. Surveillance on the spread and emergence of antimicrobial resistance is therefore invertible. This study investigated prevalence of Salmonella and Escherichia coli, molecularly characterized their antimicrobial resistance patterns and spread among resistant isolates from chicken droppings. Results A total of 150 chicken households were selected randomly within Nairobi and fresh chicken droppings collected. Salmonella and Escherichia coli were isolated and antimicrobial susceptibility test carried out. Beta-lactamase genes and class 1 integrons were determined among amoxicillin resistant isolates. Isolates carrying TEM gene were further subjected to (GTG)5 PCR genotyping. Of the analysed samples, 57% and 12% contained Escherichia coli and Salmonella respectively. Most of the isolates were susceptible to the tested antibiotics with exemption of 53% of the isolates that were resistant to amoxicillin. The isolates were detected with TEM (46%), CTX-M (18%) resistance genes and class 1 integrons (25%). The study reveals presence of beta-lactamase genes and class 1 integrons across Salmonella and Escherichia coli isolates from droppings of reared chicken. Therefore, the wide distribution of chicken and their fecal waste is likely to increase development of antibiotic resistance

Data from: Hepatitis B virus sero-profiles and genotypes in HIV-1 infected and uninfected injection and non-injection drug users from coastal Kenya

Background: Information about HBV sero-markers, infection stages and genotypes in HIV-1 infected and uninfected injection and non-injection drug users (IDUs) in Kenya remains elusive. Methods: A cross-sectional study examining HBV sero-marker, infection stages and genotypes was conducted among HIV-1 infected and uninfected, respectively, IDUs (n = 157 and n = 214) and non-IDUs (n = 139 and n = 48), and HIV-1 uninfected non-drug using controls (n = 194) from coastal, Kenya. HBV sero-marker and infection stages were based on HBV 5-panel rapid test plasma sero-reactivity. DNA was extracted from acute and chronic plasma samples and genotypes established by nested-PCR and direct sequencing. Results: HBsAg positivity was higher in HIV-1 infected IDUs (9.6 %) relative to HIV-1 uninfected IDUs (2.3 %), HIV-1 infected non-IDUs (3.6 %), HIV-1 uninfected non-IDUs (0.0 %) and non-drug users (2.6 %; P = 0.002). Contrastingly, HBsAb positivity was higher in HIV-1 uninfected IDUs (14.6 %) and non-IDUs (16.8) in comparison to HIV-1 infected IDUs (8.3 %), and non-IDUs (8.6 %), and non-drug users (8.2 %; P = 0.023). HBcAb positivity was higher in HIV-1 infected IDUs (10.2 %) compared to HIV-1 uninfected IDUs (3.3 %), HIV-1 infected non-IDUs (6.5 %), HIV-1 uninfected non-IDUs (2.1 %) and non-drug users (4.6 %; P = 0.038). Acute (5.7 %, 1.4 %, 0.0 %, 0.0 % and 1.5 %) and chronic (5.1 %, 0.9 %, 3.6 %, 0.0 % and 1.5 %) stages were higher in HIV-1 infected IDUs, compared to HIV-1 uninfected IDUs, HIV-1 infected and uninfected non-IDUs and non-drug users, respectively. However, vaccine type response stage was higher in HIV-1 uninfected IDUs (15.4 %) relative to HIV-1 infected IDUs (6.4 %), and HIV-1 infected (6.5 %), and uninfected (10.4 %) non-IDUs, and non-drug users (5.7 %; P = 0.003). Higher resolved infection rates were also recorded in HIV-1 uninfected IDUs (11.2 %) compared to HIV-1 infected IDUs (8.3 %), and HIV-1 infected (7.2 %), uninfected (6.3 %) non-IDUs, and non-drug users (6.7 %; P = 0.479), respectively. Only A1 genotype showing minimal diversity was detected among the study participants. Conclusion: HBV sero-markers and infection staging are valuable in diagnosis and genotyping of HBV infections. Among IDUs, higher HBsAg and HBcAb positivity in HIV-1 infected and higher HBsAb positivity in HIV-1 negative IDUs suggests frequent exposure. Additionally, HBV genotype A is the dominant circulating genotype in both high and low risk populations of Kenya

Hepatitis B virus sero-profiles and genotypes in HIV-1 infected and uninfected injection and Non-injection drug users from coastal Kenya

AbstractBackground: Information about HBV sero-markers, infection stages and genotypes in HIV-1 infected and uninfectedinjection and non-injection drug users (IDUs) in Kenya remains elusive.Methods: A cross-sectional study examining HBV sero-marker, infection stages and genotypes was conductedamong HIV-1 infected and uninfected, respectively, IDUs (n = 157 and n = 214) and non-IDUs (n = 139 and n = 48),and HIV-1 uninfected non-drug using controls (n = 194) from coastal, Kenya. HBV sero-marker and infection stageswere based on HBV 5-panel rapid test plasma sero-reactivity. DNA was extracted from acute and chronic plasmasamples and genotypes established by nested-PCR and direct sequencing.Results: HBsAg positivity was higher in HIV-1 infected IDUs (9.6 %) relative to HIV-1 uninfected IDUs (2.3 %), HIV-1infected non-IDUs (3.6 %), HIV-1 uninfected non-IDUs (0.0 %) and non-drug users (2.6 %; P = 0.002). Contrastingly,HBsAb positivity was higher in HIV-1 uninfected IDUs (14.6 %) and non-IDUs (16.8) in comparison to HIV-1 infectedIDUs (8.3 %), and non-IDUs (8.6 %), and non-drug users (8.2 %; P = 0.023). HBcAb positivity was higher in HIV-1infected IDUs (10.2 %) compared to HIV-1 uninfected IDUs (3.3 %), HIV-1 infected non-IDUs (6.5 %), HIV-1 uninfectednon-IDUs (2.1 %) and non-drug users (4.6 %; P = 0.038). Acute (5.7 %, 1.4 %, 0.0 %, 0.0 % and 1.5 %) and chronic(5.1 %, 0.9 %, 3.6 %, 0.0 % and 1.5 %) stages were higher in HIV-1 infected IDUs, compared to HIV-1 uninfectedIDUs, HIV-1 infected and uninfected non-IDUs and non-drug users, respectively. However, vaccine type responsestage was higher in HIV-1 uninfected IDUs (15.4 %) relative to HIV-1 infected IDUs (6.4 %), and HIV-1 infected(6.5 %), and uninfected (10.4 %) non-IDUs, and non-drug users (5.7 %; P = 0.003). Higher resolved infection rateswere also recorded in HIV-1 uninfected IDUs (11.2 %) compared to HIV-1 infected IDUs (8.3 %), and HIV-1 infected(7.2 %), uninfected (6.3 %) non-IDUs, and non-drug users (6.7 %; P = 0.479), respectively. Only A1 genotype showingminimal diversity was detected among the study participants.Conclusion: HBV sero-markers and infection staging are valuable in diagnosis and genotyping of HBV infections.Among IDUs, higher HBsAg and HBcAb positivity in HIV-1 infected and higher HBsAb positivity in HIV-1 negativeIDUs suggests frequent exposure. Additionally, HBV genotype A is the dominant circulating genotype in both highand low risk populations of Kenya