Identification of the first case of Penicillium marneffei infection in Shaanxi province by nanopore sequencing

Abstract

Introduction: Penicillium marneffei is one of the most common opportunistic infectious fungi associated with AIDS (Acquired Immunodeficiency Syndrome). It is prevalent in Southeast Asia and southern China (such as Guangdong), but rare in inland provinces of China. Penicillium marneffei infections are often misdiagnosed.

Case Report: Here, we report a patient with Penicillium marneffei infection from Shaanxi Province, China, who was previously repeatedly diagnosed as Kala-azar in two hospitals. The patient received medical treatment due to fever and multiple papules, worked as a tour guide, and had travel history in Southeast Asian countries. We performed nanopore genome sequencing on blood samples of the patient and obtained 84,000 reads in 3.5 hours. The average length of the sequences was 7088.7 bases and the longest sequence was 87471 bases. Through comparison with the pathogenic bacteria database, 13 homologous Penicillium marneffei sequences were identified. Furthermore, by using specific quantitative real time-polymerase chain reaction of Penicillium marneffei, fungal ITS (Internal Transcribed Spacer) sequencing, and fungal biphasic culture, we further confirmed the pathogen as Penicillium marneffei. Meanwhile, the patient was confirmed to be HIV (Human Immunodeficiency Virus) positive. Thus, the patient was diagnosed with AIDS combined with Penicillium marneffei infection, which, to the best of our knowledge, is the first report of Penicillium marneffei infection in Shaanxi Province, China.

Conclusions: Metagenomic analysis based on nanopore sequencing provides an important reference for the diagnosis of Penicillium marneffei infection in this case.