Rapid diagnosis of fatal Nocardia kroppenstedtii bacteremic pneumonia and empyema thoracis by next-generation sequencing: a case report

Fanfan Xing; Yao Xia; Qianyun Lu; Simon K F Lo; Susanna K P Lau; Patrick C Y Woo

doi:10.3389/fmed.2023.1226126

Rapid diagnosis of fatal Nocardia kroppenstedtii bacteremic pneumonia and empyema thoracis by next-generation sequencing: a case report

Front Med (Lausanne). 2023 Jul 18:10:1226126. doi: 10.3389/fmed.2023.1226126. eCollection 2023.

Authors

Fanfan Xing¹, Yao Xia², Qianyun Lu¹, Simon K F Lo¹, Susanna K P Lau², Patrick C Y Woo^{2

3

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Affiliations

¹ Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China.
² Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
³ Doctoral Program in Translational Medicine and Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan.
⁴ The iEGG and Animal Biotechnology Research Center, National Chung Hsing University, Taichung, Taiwan.

Abstract

Nocardia species do not replicate as rapidly as other pyogenic bacteria and nocardial infections can be highly fatal, particularly in immunocompromised patients. Here, we present the first report of fatal Nocardia kroppenstedtii bacteremic pneumonia and empyema thoracis diagnosed by next-generation sequencing (NGS) using the Oxford Nanopore Technologies' MinION device. The bacterium was not identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Due to its low equipment cost, short turn-around-time, and portable size, the Oxford Nanopore Technologies' MinION device is a useful platform for NGS in routine clinical microbiology laboratories.

Keywords: MinION; Nocardia kroppenstedtii; Oxford Nanopore; immunocompromised patients; next-generation sequencing.

Publication types

Case Reports

Grants and funding

This work was partly supported by the Sanming Project of Medicine in Shenzhen (SZSM201911014) and the framework of the Higher Education Sprout Project by the Ministry of Education (MOE-112-S-023-A) in Taiwan.