Pneumonia Caused by Chlamydia psittaci and SARS-CoV-2 Coinfection Diagnosed Using Metagenomic Next-Generation Sequencing: A Case Report

Abstract

We report a case of pneumonia caused by coinfection with Chlamydia psittaci and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron XBB.1 variant, confirmed using metagenomic next-generation sequencing (mNGS) and quantitative polymerase chain reaction (qPCR). C. psittaci and SARS-CoV-2 were detected in bronchoalveolar lavage fluid using mNGS. Additionally, mNGS detected C. psittaci in blood and nasopharyngeal specimens and was more sensitive than qPCR. The patient recovered after treatment with moxifloxacin. This report highlights the use of coinfections of C. psittaci and SARS-CoV-2, as mNGS has already been recognized to be a diagnostic tool for identifying coinfections.

Keywords: bronchoalveolar lavage fluid; coinfection; quantitative reverse-transcription polymerase chain reaction; zoonoses.

Figure 1

Chest computed tomography. (A–C) Chest computed tomography (CT) on admission showing massive consolidation in the left lower lung field and left-sided pleural effusion. (D–F) Chest CT after 1 week of treatment with moxifloxacin, showing a reduction in the consolidation, lung lesions, and pleural infusion. (G–I) Chest CT after 2 weeks of treatment with moxifloxacin.

Figure 2

Detection depths and coverage of SARS-CoV-2 Omicron XBB.1 and Chlamydia psittaci in different sample types. (A and B) Detection depths and coverage of SARS-CoV-2 Omicron XBB.1 in (A) BALF and (B) nasopharyngeal swab specimens. (C and D) Detection depths and coverage of C. psittaci in (C) BALF and (D) nasopharyngeal swab specimens.

Figure 3

The patient’s clinical course and treatment. Body temperature alterations and antibacterial therapy, (i) 4.5 g piperacillin-tazobactam administered as an intravenous bolus every 8 hours on days 1–3 and (ii) 0.4 g of moxifloxacin administered as an intravenous bolus once daily on days 4–11.