Microbiome of Dipteran vectors associated with integron and antibiotic resistance genes in South Korea.

The spread of antibiotic resistance genes (ARGs) across the environment and the role that organisms that interact with humans play as reservoirs of resistant bacteria pose important threats to public health. Flies are two-winged insects composing the order Diptera, which includes synanthropic species with significant ecological roles as pollinators, vectors, and decomposers. Here, we used iSeq100 metabarcoding to characterize the microbiome of six dipteran species in South Korea: Lucilia sericata, Lucilia illustris, Culex pipiens, Aedes vexans, Psychoda alternata and Clogmia albipunctata. We profiled a panel of common ARGs and performed correlation network analysis of the microbiome and resistome to identify co-occurrence patterns of bacterial amplicon sequence variants (ASVs) and resistance genes. We detected blaTEM, ermB, tetB, tetC, aac(6')-Ib-cr, cat2, sul1, qepA, int1 and int2, but no blaSHV, mecA, tetA or cat1. Notably, co-occurrence analysis showed highly mobile genes such as qepA, ermB and sul1 were associated with integron of class 1 integrase presence. These, along with aac(6')-Ib-cr were detected at higher rates across multiple species. Microbiome composition was distinct across species. Amplicon sequence variants (ASVs) of Pseudomonas, Corynebacterium, Clostridium, Ignatzschineria, Bacteroides, Streptococcus, Treponema and Dietzia showed strong co-occurrence with multiple ARGs. This study contributes to the understanding of the role of dipterans as reservoirs of antibiotic resistance.