High throughput genomic sequencing of bioaerosols in broiler chicken production facilities

Abstract

SummaryChronic inhalation exposure to agricultural dust promotes the development of chronic respiratory diseases among poultry workers. Poultry dust is composed of dander, chicken feed, litter bedding and microbes. However, the microbial composition and abundance has not been fully elucidated. Genomic DNA was extracted from settled dust and personal inhalable dust collected while performing litter sampling or mortality collection tasks. DNA libraries were sequenced using a paired‐end sequencing‐by‐synthesis approach on an Illumina HiSeq 2500. Sequencing data showed that poultry dust is predominantly composed of bacteria (64–67%) with a small quantity of avian, human and feed DNA (< 2% of total reads). Staphylococcus sp. AL1, Salinicoccus carnicancri and Lactobacillus crispatus were the most abundant bacterial species in personal exposure samples of inhalable dust. Settled dust had a moderate relative abundance of these species as well as Staphylococcus lentus and Lactobacillus salivarius. There was a statistical difference between the microbial composition of aerosolized and settled dust. Unlike settled dust composition, aerosolized dust composition had little variance between samples. These data provide an extensive analysis of the microbial composition and relative abundance in personal inhalable poultry dust and settled poultry dust.

Bioaerosols in agriculture

“…Bioaerosols measured could be composed of many types' of microorganisms ranging from bacteria, viruses, fungi, and other living components at varying concentrations. We expected that the majority of the bioaerosols would be of bacteria origin based on previous studies that have found bacterial species to be the most abundant in airborne agricultural dust (Karwowska, 2005;O'Brien et al, 2016;Oppliger et al, 2018 4.1.6.2 Press * to navigate to the flashing screen display of "---". Then press the "up" arrow 4.1.7 The pumps should start and the "black ball" on the rotameter should be floating at 4.0 L/Min.…”

“…Livestock workers are exposed to inorganic and organic dusts, gases, microorganisms, and biological constitutes. For example, poultry dust is composed of chicken feed, animal dander, urine, feces, and microbes (O'Brien et al, 2016).…”

Measuring bioaerosol concentrations generated from toilet flushes during hospital-based patient care

“…Metagenomics sequencing is a novel technique that has been shown to quantify and characterize bioaerosols in various settings (King et al, 2016;Nonnenmann et al, 2010;O'Brien et al, 2016). However with time restraints for our study, culture based analysis was the quickest way to estimate concentrations of airborne organisms.…”

“…Molecular based analysis occurs when bioaerosols are collected or extracted into liquid solution where the DNA or RNA are analyzed, however viability of the microorganism may not be determined (ACGIH, 1999). Molecular analysis can include techniques such as polymerase chain reaction (PCR) or metagenomic techniques (e.g., shotgun sequencing) (King et al, 2016;Mukoda, Todd, & Sobsey, 1994;Nonnenmann, Bextine, Dowd, Gilmore, & Levin, 2010;O'Brien et al, 2016;Stetzenbach, Buttner, & Cruz, 2004). PCR is the oldest molecular method that quantifies microorganisms obtained in a sample and is limited for use in microorganisms which have a fully or partially sequenced genome (Mukoda et al, 1994).…”

“…However, some microorganisms do not conserve either of the 16S or 18S genes or have multiple copies in their genome which leads to error in estimates of quantification (Stetzenbach et al, 2004). Metagenomics has emerged as a new molecular method to characterize diverse bioaerosols, which first quantified and identified bioaerosols in agriculture and has most recently been used for healthcare aerosols (King et al, 2016;Nonnenmann et al, 2010;O'Brien et al, 2016). Within the healthcare setting, several of the microorganisms cultured from previous studies were identified to exist as well as other microorganisms that have not yet been cultured (King et al, 2016).…”