Gideon Kikuvi

Molecular characterization of virulence factors in diarrhoeagenic Escherichia coli isolates from children in Nairobi, Kenya.

INTRODUCTION Among the bacterial causes, diarrheagenic Escherichia coli (DEC) is the most important etiologic agent of childhood diarrhoea and represents a major public health problem in developing countries. New evidence suggests that major differences in virulence among groups of DEC pathotypes may be related to the presence of specific pathogenicity islands (PAIs). METHODOLOGY Multiplex and conventional PCR assays were used to identify the DEC pathotypes and PAIs respectively from 207 E. coli isolates. RESULTS The predominant DEC pathotype isolated was EPEC 19.3% (40/207), followed by ETEC 7.25% (15/207), EAEC 3.86% (8/207), STEC 0.97% (2/207) and EIEC 0.48% (1/207). The PAIs detected were enteropathogenic secreted protein C (EspC) 12.2% (8/66), locus of enterocyte effacement (LEE) 62.1% (41/66), and high pathogenicity island (HPI) 57.6% (38/66). Six percent (4/66) expressed only fyuA gene, 12.2% (8/66) irp2 only, and 39.4% (26/66) expressed both fyuA and irp2 genes. SHI-2 39.4% (26/66), she 6% (4/66) and O island 33.3% (22/66), 19.8% (13/66) expressed only efa/lifA gene, 7.6% (5/66) pagC gene only and 6.1% (4/66) expressed both efa/lifA and pagC genes. Toxigenic invasion A (TIA) PAI was not detected. CONCLUSION This study revealed that in addition to eaeA, stx, aat, einv, st and lt virulence genes exhibited in the different DEC pathotypes there are numerous PAIs in the DEC pathotypes. The PAIs can increase gene mobility within various motile elements, which has implications for the spread of virulence factors from DEC to commensal E. coli.

High Prevalence of HIV Low Abundance Drug-Resistant Variants in a Treatment-Naive Population in North Rift Kenya.

The advent of antiretroviral treatment (ART) has resulted in a dramatic reduction in AIDS-related morbidity and mortality. However, the emergence and spread of antiretroviral drug resistance (DR) threaten to negatively impact treatment regimens and compromise efforts to control the epidemic. It is recommended that surveillance of drug resistance occur in conjunction with scale-up efforts to ensure that appropriate first-line therapy is offered relative to the resistance that exists. However, standard resistance testing methods used in Sub-Saharan Africa rely on techniques that do not include low abundance DR variants (LADRVs) that have been documented to contribute to treatment failure. The use of next generation sequencing (NGS) has been shown to be more sensitive to LADRVS. We have carried out a preliminary investigation using NGS to determine the prevalence of LDRVS among a drug-naive population in North Rift Kenya. Antiretroviral-naive patients attending a care clinic in North Rift Kenya were requested to provide and with consent provided blood samples for DR analysis. DNA was extracted and amplified and nested PCR was conducted on the pol RT region using primers tagged with multiplex identifiers (MID). Resulting PCR amplicons were purified, quantified, and pyrosequenced using a GS FLX Titanium PicoTiterPlate (Roche). Valid pyrosequencing reads were aligned with HXB-2 and the frequency and distribution of nucleotide and amino acid changes were determined using an in-house Perl script. DR mutations were identified using the IAS-USA HIV DR mutation database. Sixty samples were successfully sequenced of which 26 were subtype A, 9 were subtype D, 2 were subtype C, and the remaining were recombinants. Forty-six (76.6%) had at least one drug resistance mutation, with 25 (41.6%) indicated as major and the remaining 21 (35%) indicated as minor. The most prevalent mutation was NRTI position K219Q/R (11/46, 24%) followed by NRTI M184V (5/46, 11%) and NNRTI K103N (4/46, 9%). Our use of NGS technology revealed a high prevalence of LADRVs among drug-naive populations in Kenya, a region with predominantly non-B subtypes. The impact of these mutations on the clinical outcome of ART can be ascertained only through long-term follow-up.

Prevalence, aetiology and antibiotic sensitivity profile of asymptomatic bacteriuria isolates from pregnant women in selected antenatal clinic from Nairobi, Kenya

Introduction Asymptomatic bacteriuria (ASB) is the presence of bacteria in urine without apparent symptoms of urinary tract infections. The importance of asymptomatic bacteriuria lies in the insight it provides into symptomatic infections. To determine prevalence, bacterial isolates and Antibiotic Sensitivity Profile of asymptomatic bacterial urinary tract infection in pregnant women in selected clinics in Nairobi. Methods This was a cross-sectional study involving women attending antenatal clinic at selected clinics of Nairobi County. The women who met the inclusion criteria were included in the study. The midstream urine samples of these women were subjected to microscopy, culture and sensitivity. Results A total of 1020 of women on their first antenatal clinic visit participated in the study; 219 of them had ASB, giving a prevalence of 21.5 % at 95% confidence level. Escherichia coli were the common organism isolated at 38.8%. The majority of the organisms were sensitive to imipenem and gentamycin. Conclusion There is a high prevalence of ASB among pregnant women included in the study from the Nairobi county clinics. Therefore, routine ASB screening of pregnant women is recommended among the women attending antennal clinics in Nairobi county clinics.

Drug Resistance Testing in HIV Infected Individuals on Treatment and Naive: Implications on Treatment Outcome

Background: The Government of Kenya started offering ART in the public sector since 2003. Despite the dramatic reduction in AIDS related morbidity and mortality, the emergence and spread of drug resistance (DR) threatens to negatively impact on treatment regimens and compromise efforts to control the epidemic. Therefore, there is a need for information on the situation of DR Mutations (DRMS) and their implications on treatment.