Shifts in malaria vector species composition and transmission dynamics along the Kenyan coast over the past 20 years

Studies from 1990 to 2010 were conducted in 49 villages located in Malindi and Kilifi Districts on the Kenyan coast (Figure 1). The data collected during these periods was standardized to show mean indoor-resting mosquito densities over different periods. The study areas have been described in detail elsewhere [15, 19‐22, 24‐27, 29‐34]. Briefly, the coastal plain is made up of dense forest, savannah type vegetation, seasonal swamps, dry thorn bush, and a number of plantations interspersed with uncultivated land. Altitudes range from 0 to 400 m above sea level. Sisal, coconut, and cashew nut plantations are extensive along the coast, although subsistence farming is practiced throughout the coastal area. The houses in rural areas of coastal Kenya mainly consist of framed poles and branches from top to bottom covered with grass. Mud is often used to support the upper structure, while palm leaves often replace grass as roofing material. Many households keep goats, chickens, and cattle as domestic animals.

Coastal Kenya has two rainy seasons: the long rains occur between April and July and the short rains occur between October and November. Mean annual precipitation ranges from 750 to 1,200 mm [34]. Over the past 20 years, people living in near proximity to the Sabaki and Jaribuni rivers have started small-scale irrigated agriculture. The Kenyan Government, through the Economic Stimulus Programme and Vision 2030 Strategies has also continued to develop the Lango Baya Irrigation Scheme in Malindi. Horticultural crops grown under these irrigation activities include kale, hot pepper, okra, green maize, brinjals (aubergine) and tomatoes. The agronomic practices in the irrigation system use pesticides, mainly of the class organophosphates.

Several methods were used for entomological sampling, including Centers for Disease Control and prevention (CDC) light traps, pyrethrum spray collection (PSC), human landing catches, and manual aspiration for collecting day resting mosquitoes indoors (DRI) [15, 18, 20, 21, 25, 32]. The mosquitoes were expressed in densities (mean mosquitoes per house or trap) for the analyses. To overcome some of the limitation in data collections in which the relative use of each method was not the same during each year; the sampling was categorized according to the rainfall pattern along the Kenyan coast. This grouped each year in 4 categories namely long wet season (April to July), short wet season (October and November), long dry season (December to March) and short dry season (August and September).

Mosquitoes were identified to species based on morphological characteristics [35]. Females were further classified as unfed, blood-fed, semi-gravid or gravid [36]. Genomic DNA was extracted from the legs and wings of a proportion of females in the Anopheles gambiae complex using the methods of Collins et al[37, 38] and amplified using specific diagnostic primers for An. gambiae s.s., Anopheles arabiensis, Anopheles quadriannulatus and Anopheles merus according to previously described methods [39, 40]. Anopheles funestus, which is a complex of nine sibling species [41, 42], was not identified to sibling species level.

The mosquitoes were cut transversely between the thorax and abdomen. The heads and thoraces of anopheline mosquitoes were tested using a Plasmodium falciparum sporozoite enzyme linked immunosorbent assay (ELISA) [43‐45]. The fully blood-fed abdomens were tested for host sources of blood by ELISA [46]. Test samples were visually assessed for positivity [47].

The analyses were performed using STATA v10.1 (StataCorp, College Station, TX, USA). Both descriptive and inferential analyses were considered. To study the mosquito abundance over the 20-year period while adjusting for season and pre-post LLIN coverage scale-up, a negative binomial generalized estimating equations (GEE) model, assuming exchangeable working correlation, taking calendar year, pre-post scale-up (coded 1 if year is after 2003, and 0 otherwise) and season (wet or dry) as the covariates with household as the cluster was used [48, 49]. In this case, wet season comprised the months April, May, June, October, and November. Because of limiting software capability, a standard negative binomial model was used to initially obtain a maximum likelihood value for the ancillary parameter. The same model was fitted separately for An. gambiae and An. funestus. Mosquito collections were presented as densities in each sampling village. To study the sporozoite rate over the period while controlling for season, a multiple logistic regression model was fitted, but with season redefined into four categories: long wet season, short wet season, long dry season and short dry season. This is because field sampling was done in different months over the year. Odds ratios (OR) were computed for each season in comparison to the long wet season (April to July), which had the highest number of P. falciparum sporozoite positive mosquitoes.

Of 33,529 mosquitoes collected, 18,194 (54.3%: 96% CI 53.7–56.8) were An. gambiae and the rest An. funestus. This proportion was significantly greater in the wet season (63.6%) than in dry season (45.1%; X ²  = 1,158.3, df = 1, p < 0.001). Table 1 shows the distribution of the two species by year and season. Apart from recently in 2010, the densities of An. funestus s.l. only exceeded An. gambiae s.l. in 2001 and 2002 (Figure 2). Figure 2 and Table 1 show that the densities of both mosquito species increased between 1990 and 2001, thereafter the densities of both An. gambiae s.l. and An. funestus declined. After controlling for the other two factors, there was, on average, a significant 6% reduction the chance of observing an An. gambiae s.l. (IRR = 0.94, 95% CI 0.90–0.98), but a significant 32% increase in the chance of observing an An. funestus s.l. (IRR = 1.32, 95% CI 1.25–1.39) for a unit increase in time/year. Season was also significantly associated with the abundance of both An. gambiae and An. funestus s.l. The abundance of An. gambiae s.l. was significantly lower in dry season as compared to wet season (IRR = 0.51, 95% CI 0.49–0.53) after adjusting for year and LLIN scale-up. Anopheles funestus were, however, more abundant in dry season than wet season (IRR = 1.08, 95% CI 0.90–1.30), although not significantly so. A significant reduction of both species in the post LLIN distribution scale-up period was observed (An. gambiae s.l.: IRR = 0.08, 95% CI 0.04–0.17; An. funestus s.l.: IRR = 0.10, 95% CI 0.04–0.24). The ancillary parameter was 8.74 and 14.58 for An. gambiae and An. funestus models, respectively.

Of the four An. gambiae complex sibling species identified, An. gambiae s.s., which was the dominant indoor-resting mosquito species between 1997 and 1998 accounting for 78.89%, has been declining over the years significantly to very low levels and sometimes undetectable levels in the study sites, especially between 2007 and 2008. On the other hand, An. arabiensis has seen an upward trend from 14.84% between 1997 and 1998 to being the dominant An. gambiae complex sibling species in late 2000 (Table 2). Anopheles merus increased between 2002 and 2003 but declined after 2007. Anopheles quadriannulatus, a member of the An. gambiae complex, that was not known to occur along the Kenyan coast, was found in 2007, accounting for nearly 2% of the sample (Table 2).

A total of 33,383 mosquitoes (An. gambiae s.l. and An. funestus) were tested for P. falciparum sporozoites. Data for the years 1997 to 2008 was used. The overall sporozoite rate was 4.6%. High sporozoite rates were observed in 1997 (5.94%), 2000 (7.96%), 2001 (6.83%), and 2003 (8.65%), which had the highest rate. There was a significant association between P. falciparum sporozoite positivity and year. Compared to 1997 and after controlling for season, there was significantly lower sporozoite rate in 2002 (OR = 0.68, 95%CI 0.51–0.91), 2007 (OR = 0.03, 95% CI 0.01–0.10), and 2008 (OR = 0.06, 95%CI 0.03–0.11). The odds of a mosquito being positive were also lower in 1998, but not significantly so (OR = 0.65, 95% CI 0.35–1.19). After controlling for year, season was also found to be significantly associated with sporozoite positivity. Compared to long wet season, the odds of being positive were significantly high during the long dry (OR = 1.23, 95% CI 1.02–1.49) and short dry seasons (OR = 1.14, 95% CI 1.00–1.29) (Table 3).

Further analyses indicated that although P. falciparum infectiousness by Anopheles mosquitoes as indicated by positive sporozoite rates was found to be taking place throughout the four seasons, there was seasonal variability in sporozoite rates during each year (Table 4). The highest sporozoite rate observed during this period was 23.81% during the short dry season in 1998.

Table 5 presents a summary of the feeding patterns over time. There has been a significant reduction in human blood index (HBI) from 99% and 100% to 16% and 3% for An. gambiae s.l. and An. funestus, respectively, between 1997 and 2008. These mosquitoes have switched to primarily feeding on bovines. Other meal sources included, bovine, goat, donkey, human-bovine, and chicken – although only An. gambiae was noted to feed on chicken but, again, this was only in 1997.