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Updated: Aug 9, 2026
On-Site Molecular Detection of Soil-Borne Phytopathogens Using a Portable Real-Time PCR System
Published on: February 23, 2018
Direct detection of Histoplasma capsulatum in soil suspensions by two-stage PCR
1Divisions of Biomedical and Behavioral Sciences, National Institute for Occupational Safety and Health, 4676 Columbia Parkway, Cincinnati, Ohio, 45226, USA. tar9@cdc.gov
Abstract:
Histoplasmosis is the most common pulmonary mycosis in the United States. The responsible fungal pathogen, Histoplasma capsulatum, grows in soils contaminated with bird or bat droppings. Inhalation of dust from contaminated areas containing H. capsulatum spores is a primary route of infection. The ability to detect H. capsulatum in soil samples has been limited by the lack of fast, reliable and inexpensive methods. A polymerase chain reaction (PCR) method was developed that allows the direct detection of H. capsulatum in soil. A two-stage PCR protocol was followed employing both fungal-specific primers and nested primers specific for the internal transcribed spacer (ITS) region of the 5.8S rRNA gene of H. capsulatum. The estimated limit of detection of this method is 10 spores. In contrast to the more expensive and indirect mouse inoculum assay, which requires 6-8 weeks for sample analysis, PCR analysis of soil contaminated with H. capsulatum can be completed in less than 2 days.
Insights
A new polymerase chain reaction (PCR) method enables rapid and reliable detection of Histoplasma capsulatum spores in soil. This advancement offers a faster, more cost-effective alternative to traditional methods for identifying this common fungal pathogen.
Area of Science:
- Mycology
- Environmental Microbiology
- Infectious Diseases
Background:
- Histoplasmosis, a common pulmonary mycosis in the US, is caused by Histoplasma capsulatum.
- Histoplasma capsulatum thrives in soil contaminated with bird or bat guano.
- Infection occurs through inhalation of airborne spores from contaminated soil.
Purpose of the Study:
- To develop a fast, reliable, and inexpensive method for detecting Histoplasma capsulatum in soil samples.
- To improve upon existing diagnostic limitations for environmental detection of the fungus.
Main Methods:
- A two-stage polymerase chain reaction (PCR) protocol was designed.
- The PCR employed fungal-specific primers and nested primers targeting the ITS region of the 5.8S rRNA gene of Histoplasma capsulatum.
- The method allows direct detection of the pathogen in soil.
Main Results:
- The developed PCR method demonstrated a limit of detection as low as 10 spores.
- PCR analysis of soil samples was completed in under 2 days.
- This contrasts with the mouse inoculum assay, which takes 6-8 weeks and is more expensive.
Conclusions:
- The novel PCR technique provides a rapid, sensitive, and cost-effective means for detecting Histoplasma capsulatum in environmental soil samples.
- This method significantly improves upon the time and cost associated with traditional diagnostic assays.
- Facilitates quicker identification and potentially earlier intervention strategies for histoplasmosis outbreaks.
