Host tracheal and intestinal microbiomes inhibitCoccidioidesgrowthin vitro

Abstract

AbstractCoccidioidomycosis, also known as Valley fever, is a disease caused by the fungal pathogenCoccidioides. Unfortunately, patients are often misdiagnosed with bacterial pneumonia leading to inappropriate antibiotic treatment. Soil bacteriaB. subtilis-like species exhibits antagonistic properties againstCoccidioides in vitro; however, the antagonistic capabilities of host microbiota againstCoccidioidesare unexplored. We sought to examine the potential of the tracheal and intestinal microbiomes to inhibit the growth ofCoccidioides in vitro. We hypothesized that an uninterrupted lawn of microbiota obtained from antibiotic-free mice would inhibit the growth ofCoccidioideswhile partialin vitrodepletion through antibiotic disk diffusion assays would allow a niche for fungal growth. We observed that the microbiota grown on 2xGYE (GYE) and CNA w/ 5% sheep’s blood agar (5%SB-CNA) inhibited the growth ofCoccidioides, but that grown on chocolate agar does not. Partial depletion of the microbiota through antibiotic disk diffusion revealed that microbiota depletion leads to diminished inhibition and comparable growth ofCoccidioidesgrowth to controls. To characterize the bacteria grown and narrow down potential candidates contributing to the inhibition ofCoccidioides, 16s rRNA sequencing of tracheal and intestinal agar cultures and murine lung extracts was performed. The identity of host bacteria that may be responsible for this inhibition was revealed. The results of this study demonstrate the potential of the host microbiota to inhibit the growth ofCoccidioides in vitroand suggest that an altered microbiome through antibiotic treatment could negatively impact effective fungal clearance and allow a niche for fungal growthin vivo.ImportanceCoccidioidomycosis is caused by a fungal pathogen that invades host lungs, causing respiratory distress. In 2019, 20,003 cases of Valley fever were reported to the CDC. However, this number likely vastly underrepresents the true number of Valley fever cases as many go undetected due to poor testing strategies and lack of diagnostic models. Valley fever is also often misdiagnosed as bacterial pneumonia, resulting in 60-80% of patients being treated with antibiotics prior to accurate diagnosis. Misdiagnosis contributes to a growing problem of antibiotic resistance and antibiotic induced microbiome dysbiosis, and the implications on disease outcome are currently unknown. 5%-10% of symptomatic Valley fever patients develop disseminated and/or chronic disease. Valley fever causes a significant financial burden and reduced quality of life. Little is known regarding what factors contribute to the development of chronic infection and treatments for disease are limited.