HIV-1 Transmission Cluster in Injection Drug Users in Nairobi City, Kenya.

Background: While there is a striking increase in the prevalence of HIV in injection drug users, information on envelope-gene subtypes and transmission clusters in injection drug users is scarce. Method: In a cross-sectional study, 247 injection drug users were recruited via out-rich method. Deoxyribonucleic acid was extracted from dry blood spot samples, amplified by Polymerase Chain Reaction and sequenced. Subtyping was performed using COntext-based Modeling for Expeditious Typing (COMET) and Recombinant Identification Program (RIP) tools. Phylogenetic diversity and Transmission clusters were identified using MEGA version 6.0 and TreeLink, respectively. Results: Overall, 42 (17.0%) injection drug users were sero-positive for HIV-1. Of the 37 samples successfully sequenced, 29 (78.4%) sequences were identified as A1, 6 (16.2%) as AG while 1 (2.7%) as A1/G/AE and A1/C recombinants. The HIV subtypes formed clusters with little genetic diversity. Conclusion: The high HIV prevalence was associated with transmission clusters and diversity in subtypes indicating ongoing local transmission. Therefore, there is need for comprehensive HIV care tailored to this population.

Epidemiological patterns and antimicrobial resistance of bacterial diarrhea among children in Nairobi City, Kenya.

AIM: Determine the prevalence of enteric bacterial pathogens and their antimicrobial resistance among diarrheic children in Nairobi City, Kenya. BACKGROUND: Regardless of enteric bacterial pathogens being a major cause of gastroenteritis in children, their occurrence and antimicrobial resistance patterns reveals regional spatial and temporal variation. METHODS: In a cross-sectional study, a total of 374 children below five years presenting with diarrhea at Mbagathi County Hospital were recruited. Stool microbiology test was used to detect enteric bacterial infection. Antimicrobial resistance was determined using the disk diffusion method. RESULTS: Diarrheagenic E. coli (36.4%) was the leading species followed by Shigella (3.2%), Salmonella (2.4%), Campylobacter (1.6%), Yersinia (1.3%) and Aeromonas (1.1%) species. Escherichia coli pathotyping revealed that 20.9%, 4.0%, 10.2% and 0.5% of the study participants were infected with enteroaggregative E. coli (EAEC), enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC) and enteroinvasive E. coli (EIEC) pure isolates while the prevalence of mixed pathotype infections was 0.3% for EAEC/EPEC/ETEC and 0.5% for EAEC/ETEC. Shigella sero-grouping revealed that 0.5%, 0.3%, 1.9%, and 0.5% were infected with Shigella boydii, Shigella dysentriae, Shigella flexneri and Shigella sonnei pure isolates. Shigella species and E. coli co-infection was detected in 2.4% of the children, specifically, 1.1% for EAEC/Shigella boydii, 0.5% for EAEC/Shigella dysentriae and 0.3% in each case of EAEC/Shigella sonnei, EPEC/Shigella flexneri and ETEC/Shigella flexneri co-infections. Most of the isolates were resistant to commonly prescribed antibiotics. CONCLUSION: There was a high prevalence of enteric bacterial pathogens and co-infection alters epidemiological dynamics of bacterial diarrhea in children. Continuous antibiotic resistance surveillance is justified because the pathogens were highly resistant to commonly prescribed antimicrobials.

Pyrethroid resistance in Anopheles gambiae, in Bomi County, Liberia, compromises malaria vector control.

BACKGROUND: Long Lasting Insecticidal Nets (LLIN) and Indoor Residual Spraying (IRS) have both proven to be effective malaria vector control strategies in Africa and the new technology of insecticide treated durable wall lining (DL) is being evaluated. Sustaining these interventions at high coverage levels is logistically challenging and, furthermore, the increase in insecticide resistance in African malaria vectors may reduce the efficacy of these chemical based interventions. Monitoring of vector populations and evaluation of the efficacy of insecticide based control approaches should be integral components of malaria control programmes. This study reports on entomological survey conducted in 2011 in Bomi County, Liberia. METHODS: Anopheles gambiae larvae were collected from four sites in Bomi, Liberia, and reared in a field insectary. Two to five days old female adult An gambiae s.l. were tested using WHO tube (n=2027) and cone (n=580) bioassays in houses treated with DL or IRS. A sample of mosquitoes (n=169) were identified to species/molecular form and screened for the presence of knock down resistance (kdr) alleles associated with pyrethroid resistance. RESULTS: Anopheles gambiae s.l tested were resistant to deltamethrin but fully susceptible to bendiocarb and fenithrothion. The corrected mortality of local mosquitoes exposed to houses treated with deltamethrin either via IRS or DL was 12% and 59% respectively, suggesting that resistance may affect the efficacy of these interventions. The presence of pyrethroid resistance was associated with a high frequency of the 1014F kdr allele (90.5%) although this mutation alone cannot explain the resistance levels observed. CONCLUSION: High prevalence of resistance to deltamethrin in Bomi County may reduce the efficacy of malaria strategies relying on this class of insecticide. The findings highlight the urgent need to expand and sustain monitoring of insecticide resistance in Liberian malaria vectors, evaluate the effectiveness of existing interventions and develop appropriate resistance management strategies.

Evaluating genetic differentiation of Anopheles arabiensis in relation to larval habitats in Kenya.

Anopheles arabiensis, an important vector of malaria in sub-Saharan Africa shows great versatility in utilizing a broad range of larval habitats. Most studies on the population genetic structure of this species have focused on adult mosquitoes collected mainly indoors and have found populations within relatively short distances to be panmictic. Various authors suggested that the incipient speciation between the chromosomal forms of Anopheles gambiae s.s. in West Africa involved adaptation to different habitats of larvae. To investigate if similar process occurs in An. arabiensis, we analyzed samples from four different larval habitats alongside a sample of adult mosquitoes collected indoors at eight microsatellite loci. We tested the hypothesis that An. arabiensis is subdivided into populations that are adapted to exploit different larval habitats. Overall, the level of genetic differentiation among the larval subpopulations was low with the mean pairwise Fst estimate based on information from all the loci being 0.0232 (P=0.1691) although differentiation was only significant for comparisons between certain larval samples and the adult samples. In addition, there was strong evidence against subdivision among larvae when multilocus simultaneous assignment tests were used. These results do not provide sufficient support for the hypothesis that An. arabiensis is subdivided into subpopulations that specialize to exploit different larval habitats.

Population dynamics of malaria vectors in western Kenya highlands.

Studies were carried out at three sites in the highlands of western Kenya (Iguhu and Mbale in Kakamega and Vihiga districts, respectively, and Marani in Kisii district) and at one site in the western Kenya lowlands (Kombewa in Kisumu district) to determine the spatial-temporal dynamics of malaria vectors and intensity of malaria transmission from June 2003 to June 2004. At the highland sites, Anopheles gambiae Giles predominated, constituting >80% of the vector species, whereas An. funestus Giles made up <20%. In contrast, at the lowland site, An. funestus made up 68% of the vector species. The mean annual indoor resting densities of An. gambiae at Iguhu were 5.0 female mosquitoes per house per night, 14.2- and 26.3-fold greater than those at Mbale and Marani. During the main transmission season, the indoor resting densities of An. gambiae increased 4.1-, 10.1-, and 5.0-fold over the dry season period in Iguhu, Mbale, and Marani, respectively. The estimated annual entomological inoculation rate (EIR) at Iguhu was 16.6 infectious bites per person per year (ib/p/yr), 1.1 at Mbale, and 0.4 at Marani. This suggests high spatial variation in vector abundance and malaria transmission intensity. At the lowland site, Kombewa, the total annual EIR was 31.1 ib/p/yr and the indoor resting densities during the transmission season increased 7.1-fold in An. funestus and 18.5-fold in An. gambiae sensu lato over the dry season. The low level of transmission in the highlands suggests that it may be disrupted by vector control methods such as residual spraying.

A survey of the Anopheles funestus (Diptera: Culicidae) group of mosquitoes from 10 sites in Kenya with special emphasis on population genetic structure based on chromosomal inversion karyotypes.

We sampled Anopheles funestus Giles mosquitoes from 10 sites in Kenya to determine (1) the different members of this group present at these sites and (2) the population genetic structure of these species based on chromosomal inversion karyotypes with particular reference to the role of the Eastern arm of the Great Rift Valley and geographical distance as barriers to gene flow. Four members of this species group, namely An. funestus s.s., An. parensis, An. leesoni, and An. rivulorum, were found. An. funestus was found almost exclusively inside human dwellings while An. rivulorum was found almost exclusively outdoors. An. parensis was found both indoors and outdoors in comparable proportions. Earlier attempts to collect this group of mosquitoes from two of the sites yielded no mosquitoes, suggesting that numbers of mosquitoes change during the year, sometime reaching zero or very near zero. Significant levels of differentiation were observed among some An. funestus s.s. populations studied. Results suggest that the Rift Valley acts as a barrier to gene flow for An. funestus, but that levels of differentiation are not associated with the geographical distance between populations. The results are discussed in the light of the fact that inversions may have some adaptive significance to differences in environmental conditions.