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Background Molecular diagnostic tools have been incorporated in insecticide resistance monitoring programmes to identify underlying genetic basis of resistance and develop early warning systems of vector control failure. Identifying genetic markers of insecticide resistance is crucial in enhancing the ability to mitigate potential effects of resistance. The knockdown resistance ( kdr ) mutation associated with resistance to DDT and pyrethroids, the acetylcholinesterase-1 ( ace -1  R  ) mutation associated with resistance to organophosphates and carbamates and 2La chromosomal inversion associated with indoor resting behaviour, were investigated in the present study. Methods Anopheles  mosquitoes sampled from different sites in Kenya and collected within the context of malaria vector surveillance were analysed. Mosquitoes were collected indoors using light traps, pyrethrum spray and hand catches between August 2016 and November 2017. Mosquitoes were identified using morphological keys and  Anopheles gambiae  sensu lato ( s.l .) mosquitoes further identified into sibling species by the polymerase chain reaction method following DNA extraction by alcohol precipitation.  Anopheles gambiae  and  Anopheles arabiensis  were analysed for the presence of the  kdr  and  ace-1   R   mutations, while 2La inversion was only screened for in  An. gambiae  where it is polymorphic. Chi-square statistics were used to determine correlation between the 2La inversion karyotype and  kdr -east mutation. Results The  kdr -east mutation occurred at frequencies ranging from 0.5 to 65.6% between sites. The  kdr- west mutation was only found in Migori at a total frequency of 5.3% (n = 124). No  kdr  mutants were detected in Tana River. The  ace-1   R   mutation was absent in all populations. The 2La chromosomal inversion screened in  An. gambiae  occurred at frequencies of 87% (n = 30), 80% (n = 10) and 52% (n = 50) in Baringo, Tana River and Migori, respectively. A significant association between the 2La chromosomal inversion and the  kdr -east mutation was found. Conclusion The significant association between the 2La inversion karyotype and  kdr -east mutation suggests that pyrethroid resistant  An. gambiae  continue to rest indoors regardless of the presence of treated bed nets and residual sprays, a persistence further substantiated by studies documenting continued mosquito abundance indoors. Behavioural resistance by which  Anopheles  vectors prefer not to rest indoors may, therefore, not be a factor of concern in this study’s malaria vector populations.

Genetic markers associated with insecticide resistance and resting behaviour in Anopheles gambiae mosquitoes in selected sites in Kenya