Comparative evaluation of probe-capture and conventional metagenomic sequencing across multiple clinical…

Cohort studyMicrobiology spectrum· Aug 2026

Comparative evaluation of probe-capture and conventional metagenomic sequencing across multiple clinical sample types, with analysis of paired bronchoalveolar lavage fluid and blood samples.

Xiao Liu, Xiaoai Fan, Wanting Wu … Wenjuan Li

Infectious DiseaseCohort studyQ1IF 4.0

Probe-capture sequencing found more pathogens in blood than conventional metagenomic sequencing

Comparative evaluation of probe-capture and conventional metagenomic sequencing across multiple clinical sample types, with analysis of paired bronchoalveolar lavage fluid and blood samples.

Xiao Liu … Wenjuan Li

Microbiology spectrum · Aug 2026

Background

Conventional metagenomic next-generation sequencing (mNGS) suffers from host nucleic acid interference and poor performance in low-biomass samples.

Purpose

This study compared PC-mNGS and mNGS across diverse clinical specimens (bronchoalveolar lavage fluid [BALF], blood, cerebrospinal fluid [CSF]) and assessed the clinical utility of pathogen co-detection in paired BALF-blood samples from sepsis patients.

66.67%

Results

66.67%

vs 47.52%

PC-mNGS found pathogens in blood far more often than conventional mNGS

n = 282 samples

More results

PC-mNGS detected more bacteria (19 species exclusive) and fungi (11 species exclusive) than mNGS.

BALF and CSF exhibited high overall agreement (OPA: 96.30% and 88%, respectively), while blood had lower concordance (NPA: 54.05%, OPA: 70.92%).

A total of 60.55% of BALF-positive samples (PC-mNGS) had co-detected pathogens in blood.

More results

Gram-negative bacteria (e.g., Klebsiella pneumoniae ) and fungi (e.g., Candida albicans ) showed higher blood co-detection rates than viruses.

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Conclusion

These findings support the use of PC-mNGS as a more sensitive diagnostic tool, which could lead to faster, more targeted therapies and better outcomes for patients with complex infections.

Comparative evaluation of probe-capture and conventional metagenomic sequencing across multiple clinical sample types, with analysis of paired bronchoalveolar lavage fluid and blood samples.

Comparative evaluation of probe-capture and conventional metagenomic sequencing across multiple clinical sample types, with analysis of paired bronchoalveolar lavage fluid and blood samples.

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