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Rapid Diagnosis of Pneumocystis jirovecii Pneumonia and Respiratory Tract Colonization by Next-Generation Sequencing
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Rapid Diagnosis of Pneumocystis jirovecii Pneumonia and Respiratory Tract Colonization by Next-Generation Sequencing
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Journal Article
Rapid Diagnosis of Pneumocystis jirovecii Pneumonia and Respiratory Tract Colonization by Next-Generation Sequencing
2024
Overview
Objectives
To describe the epidemiology of
Pneumocystis jirovecii
pneumonia and colonization diagnosed by next-generation sequencing (NGS) and explore the usefulness of the number of
P. jirovecii
sequence reads for the diagnosis of
P. jirovecii
pneumonia.
Methods
We examined the NGS results for
P. jirovecii
in respiratory samples collected from patients and analysed their clinical, radiological and microbiological characteristics.
Results
Among 285 respiratory samples collected over a 12-month period (January to December 2022),
P. jirovecii
sequences were detected in 56 samples from 53 patients. Fifty (94.3%) of the 53 patients were HIV-negative. Following our case definitions, 37 (69.8%) and 16 (30.2%) of the 53 patients had
P. jirovecii
infection and colonization respectively.
P. jirovecii
infection was associated with presence of underlying disease with immunosuppression (94.6% vs 18.8%,
P
< 0.05), positive serum 1,3-β-D-glucan (41.2% vs 0%,
P
< 0.01) and higher number of
P. jirovecii
sequence reads (
P
< 0.005). In contrast,
P. jirovecii
colonization was associated with the male sex (93.8% vs 54.1%,
P
< 0.01), another definitive infectious disease diagnosis of the respiratory tract (43.8% vs 2.7%,
P
< 0.001) and higher survival (100% vs 67.6%,
P
< 0.01). Although
P. jirovecii
pneumonia was associated with higher number of
P. jirovecii
reads in respiratory samples, only a sensitivity of 82.14% and a specificity of 68.75% could be achieved.
Conclusion
Detection of
P. jirovecii
sequences in respiratory samples has to be interpreted discreetly. A combination of clinical, radiological and laboratory findings is still the most crucial in determining whether a particular case is genuine
P. jirovecii
pneumonia.
Publisher
Springer Netherlands,Springer,Springer Nature B.V
Subject
/ Aged
/ Biomedical and Life Sciences
/ Female
/ High-Throughput Nucleotide Sequencing
/ HIV
/ Human immunodeficiency virus
/ Humans
/ Male
/ Molecular Diagnostic Techniques - methods
/ Original
/ Pneumocystis carinii - genetics
/ Pneumocystis carinii - isolation & purification
/ Pneumonia, Pneumocystis - diagnosis
/ Pneumonia, Pneumocystis - microbiology
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