The vector biology and microbiome of parasitic mites and other ectoparasites of rodents

Abstract

Background: Rodents have become increasingly recognised as hosts of ectoparasites and reservoirs of numerous vector-borne bacterial zoonoses including scrub typhus (Orientia spp.), bartonellosis (Bartonella spp.), Lyme disease (Borrelia burgdorferi complex), and plague (Yersinia pestis). While these diseases are emerging or re-emerging worldwide, the epidemiology and ecology is often poorly described outside Europe and North America, adversely affecting timely surveillance. Objectives: This study aimed to define the taxonomic diversity and bacterial microbiome of ectoparasites collected from wild rodents in the Asir Region of southwestern Saudi Arabia, with a main focus on chigger mites (family Trombiculidae), the vectors of scrub typhus. The distribution of non-pathogenic bacterial symbionts in ectoparasites that might impact disease transmission was also explored, including in a preliminary study on a laboratory colony of the tropical rat mite, Ornithonyssus bacoti. Methods: Wild rodents were trapped in scrubland across one site on the slopes of the Asir Mountains in 2016 (Alous village) and three sites in 2017 (Alous, Alogl and Wosanib). Rodents were euthanized prior to examination and all ectoparasites were collected and stored in absolute ethanol. A 10% subsample of ectoparasites was selected from each rodent for mounting in Berlese fluid and morphometric examination. Following DNA extraction, the v4 region of the bacterial 16S rRNA gene was amplified by PCR, and amplicons were sequenced using Illumina technology. Specific PCRs were used to confirm the presence and strain of selected bacterial pathogens and symbionts. For the O. bacoti colony, the mite microbiome was profiled using Illumina and Oxford Nanopore sequencing technologies alongside conventional culture on solid media. Results: A total of 8,270 ectoparasites were obtained from 74 rodent specimens belonging to five species (Acomys dimidiatus, Myomyscus yemeni, Mus musculus, Rattus rattus and Meriones rex), comprising 6,774 chigger mites and 1,496 other ectoparasites. Based on the morphology of the scutum, chiggers were assigned to subgenera and provisionally into 19 species, including four newly described species: Schoutedenichia asirensis sp. nov., Schoutedenichia saudi sp. nov., Microtrombicula microscuta sp. nov., and Microtrombicula muhaylensis sp. nov. Fifteen species were for the first time recorded in Saudi Arabia and ii on new host species. The site with the highest mean chigger infestation (97.05%) was Alous, and the host species with the greatest mean infestation rate (60.81%) was the Eastern spiny mouse (A. dimidiatus). Three flea species, two louse species and two gamasid mite species were identified with high confidence; whereas immature ticks of the genera Rhipicephalus and Haemaphysalis were allocated to three and two molecular clades, respectively. Potentially pathogenic bacteria detected in ectoparasites included Orientia chuto and a Coxiella burnetii-like organism in chiggers, Bartonella acomydis in fleas, and organisms related to Ehrlichia ewingii and Anaplasma spp. in ticks. Symbiotic bacteria with putative mutualistic or parasitic phenotypes were present in fleas (Wolbachia clade B, Candidatus Cardinium and Spiroplasma ixodetis), lice (Candidatus Legionella polyplacis), ticks (Coxiella- and Francisella-like endosymbionts), and chiggers (Wolbachia and Candidatus Cardinium) as first records for Saudi Arabia. In the O. bacoti colony, the mite microbiome included Staphylococcus, Proteus and Bacillus, while Alcaligenes faecalis was isolated from mites infected with filarial worms. Conclusions: This is the first survey of rodent ectoparasite diversity and zoonotic bacterial pathogens performed in the Asir region of Saudi Arabia. The chigger diversity in the region is especially high, and the presence of Orientia and Coxiella spp. in these mit