Characterization of Airborne Metagenomics across Major United States Metropolitan Areas

VIVIAN TAT, Kostiantyn Botnar, Sean Kinahan, Shanna A. Ratnesar-Shumate, Madison Farnsworth, Sarah Alnemrat, Justin Nguyen, David Kimmel, Hema Narra, Christine Tomlinson, George Golovko, Kamil Khanipov, The University of Texas Medical Branch

     Abstract Number: 692
     Working Group: Aerosol Exposure

Abstract
Despite public health and biosurveillance advances, emerging and endemic infectious disease outbreaks continue to impact regional and global health systems, and the systems remain largely reactionary to symptomatic cases. Pre-symptomatic surveillance of bioaerosols and pathogens is crucial to understanding, preventing, and controlling future outbreaks transmitted through the air and in detecting novel pathogens.

We have collected more than 600 high-volume air filters from over 140 indoor and outdoor locations across the United States. These teflon (PTFE) air filters collectors are located in major metropolitan areas and are collected at over 100 liters per minute during different seasons, beginning in January 2024. Our team evaluated and cross-compared nucleic acid extraction kits, including the DNeasy PowerSoil Pro, DNeasy PowerWater, ZymoBiomics DNA/RNA Miniprep, and MagMax Viral Ultra. Additionally, six cDNA synthesis approaches were evaluated using, including SuperScript kits, Maxima H Minus, iScript, and Oxford Nanopore Technologies cDNA conversion, as well as a variety of second strand conversions. The sample preparation approaches were evaluated using Qubit, BioAnalyzer 2100, Nanodrop 2000, and through results of DNA/RNA sequencing.

We determined that there were differences in the microbial composition of indoor and outdoor environments, depending on time point collected, and we are working on establishing the background air microbiome. The resulting raw sequencing data, basecalls, sample metadata, and bioinformatic pipelines for environmental aerosol collector are being shared to a public repository. The development of systems capable of discriminating between background aerosols and biological incidents such as novel pathogens, especially at low incidence rates, has been a substantial challenge for deployment of bioaerosol detection systems. Understanding unique and evolving outdoor and indoor microbiome environments will allow us to better identify hazardous anomalies and changes affecting human health.