Metagenomic Analysis Identified Stenotrophomonas maltophilia Pneumonia in an Infant Suffering From Unexplained Very Severe Pneumonia

Abstract

Pneumonia poses a significant global morbidity and mortality burden on children. Etiological diagnosis and matched anti-microbial therapy are particularly important for very severe pneumonia. Although great advances have been achieved in diagnostic approaches, it remains challenging to identify pathogens in unexplained pneumonia (UP) cases. In this study, we applied next-generation sequencing (NGS) technology and a metagenomic approach to detect and characterize respiratory bactiera in an UP case in infant. Stenotrophomonas maltophilia was the only bacterial pathogen detected in blood. Metagenomic sequencing also provided bacteria genomic sequences, which could be used to evaluate the role of this pathogen in the disease. This NGS method has the potential to improve the identification of causative organisms in patients with pneumonia and the delivery of appropriate, pathogen-directed antibiotic therapy.

Keywords: Stenotrophomonas maltophilia; infant; metagenomics; next-generation sequencing; severe pneumonia.

Figure 1

Timeline of the patient's clinical course and outcome. MEM, Meropenem; VA, Vancomycin; VOR, Voriconazole; TZP, Tazobactam and Piperacillin; TMP-SMX, Trimethoprim/Sulfamethoxazole.

Figure 2

Computer tomography imaging showing lung lesion. (A) CT of the chest obtained around the time of clinical presentation most severely, showing bilateral alveolar multiple patchy shadows and local consolidation, more prominent on the left lung than right. (B) CT of the chest obtained after treatment 14 days with TMP-SMX, showing absorption multiple patchy and local consolidation. (C) CT of the chest obtained around the time of 2 weeks after discharge from NICU, showing that dual markings slightly increased, the lung parenchyma was no significant consolidation.

Figure 3

Next-generation sequencing and a metagenomic analysis. (A) Stenotrophomonas maltophilia specific reads and its nucleotide position along Stenotrophomonas maltophilia genome. (B) Penicillium chrysogenum specific reads and its nucleotide position along Penicillium chrysogenum genome. (C) Pichia anomala specific reads and its nucleotide position along Pichia anomala genome. (D) Candida parapsilosis specific reads and its nucleotide position along Candida parapsilosis genome.