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Background  Conventional gold standard characterization of chigger mites involves chemical preparation procedures (i.e. specimen clearing) for visualization of morphological features, which however contributes to destruction of the arthropod host DNA and any endosymbiont or pathogen DNA harbored within the specimen.    Methodology/Principal findings  In this study, a novel work flow based on autofluorescence microscopy was developed to enable identification of trombiculid mites to the species level on the basis of morphological traits without any special preparation, while preserving the mite DNA for subsequent genotyping. A panel of 16 specifically selected fluorescence microscopy images of mite features from available identification keys served for complete chigger morphological identification to the species level, and was paired with corresponding genotype data. We evaluated and validated this method for paired chigger morphological and genotypic ID using the mitochondrial cytochrome c oxidase subunit I gene ( coi ) in 113 chigger specimens representing 12 species and 7 genera ( Leptotrombidium ,  Ascoschoengastia ,  Gahrliepia ,  Walchia ,  Blankaartia ,  Schoengastia  and  Schoutedenichia ) from the Lao People’s Democratic Republic (Lao PDR) to the species level (complete characterization), and 153 chiggers from 5 genera ( Leptotrombidium ,  Ascoschoengastia ,  Helenicula ,  Schoengastiella  and  Walchia)  from Thailand, Cambodia and Lao PDR to the genus level.  A phylogenetic tree constructed from 77  coi  gene sequences (approximately 640 bp length, n = 52 new  coi  sequences and n = 25 downloaded from GenBank), demonstrated clear grouping of assigned morphotypes at the genus levels, although evidence of both genetic polymorphism and morphological plasticity was found.    Conclusions/Significance  With this new methodology, we provided the largest collection of characterized  coi  gene sequences for trombiculid mites to date, and almost doubled the number of available characterized  coi  gene sequences with a single study. The ability to provide paired phenotypic-genotypic data is of central importance for future characterization of mites and dissecting the molecular epidemiology of mites transmitting diseases like scrub typhus.

plos one

Autofluorescence microscopy for paired-matched morphological and molecular identification of individual chigger mites (Acari: Trombiculidae), the vectors of scrub typhus