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Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons
Published on: August 29, 2014
Added Value of Next-Generation Sequencing for Multilocus Sequence Typing Analysis of a Pneumocystis jirovecii
Abstract:
Pneumocystis jirovecii is a major threat for immunocompromised patients, and clusters of pneumocystis pneumonia (PCP) have been increasingly described in transplant units during the past decade. Exploring an outbreak transmission network requires complementary spatiotemporal and strain-typing approaches. We analyzed a PCP outbreak and demonstrated the added value of next-generation sequencing (NGS) for the multilocus sequence typing (MLST) study of P. jirovecii strains. Thirty-two PCP patients were included. Among the 12 solid organ transplant patients, 5 shared a major and unique genotype that was also found as a minor strain in a sixth patient. A transmission map analysis strengthened the suspicion of nosocomial acquisition of this strain for the 6 patients. NGS-MLST enables accurate determination of subpopulation, which allowed excluding other patients from the transmission network. NGS-MLST genotyping approach was essential to deciphering this outbreak. This innovative approach brings new insights for future epidemiologic studies on this uncultivable opportunistic fungus.
Insights
Next-generation sequencing multilocus sequence typing (NGS-MLST) identified a unique Pneumocystis jirovecii genotype in a transplant unit outbreak. This method was crucial for tracking transmission and understanding this opportunistic fungus in immunocompromised patients.
Area of Science:
- Medical Mycology
- Infectious Diseases
- Genomics
Background:
- Pneumocystis jirovecii pneumonia (PCP) poses a significant risk to immunocompromised individuals.
- Increasing clusters of PCP in transplant units necessitate advanced outbreak investigation methods.
Purpose of the Study:
- To analyze a Pneumocystis jirovecii pneumonia outbreak in a transplant unit.
- To evaluate the utility of next-generation sequencing multilocus sequence typing (NGS-MLST) for strain-typing P. jirovecii.
Main Methods:
- Analysis of 32 PCP patients, including 12 solid organ transplant recipients.
- Application of next-generation sequencing for multilocus sequence typing (NGS-MLST).
- Transmission map analysis to assess potential nosocomial acquisition.
Main Results:
- A unique P. jirovecii genotype was identified in 5 out of 12 solid organ transplant patients, and as a minor strain in a sixth patient.
- Transmission mapping supported nosocomial acquisition of this specific strain for 6 patients.
- NGS-MLST accurately determined subpopulations, enabling the exclusion of other patients from the identified transmission network.
Conclusions:
- NGS-MLST is an effective tool for deciphering P. jirovecii outbreaks by accurately identifying transmission networks.
- This innovative genotyping approach provides crucial insights for future epidemiological studies of this uncultivable fungus.
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