A cluster of cases of pneumocystis pneumonia identified by shotgun metagenomics approach.

•Metagenomics sequencing performed well in diagnosing PCP compared to conventional methods.•Metagenomics exhibited the ability to detect co-infections in PCP patients.•Blood samples metagenomics might suit patients who couldn't tolerate invasive procedures.•Pathogen reads ranking and proportion rate may be the promising cutoff value.