Clinical utility of universal 16S rRNA PCR using sterile body fluids: lung abscess caused by Nocardia farcinica

Abstract

Nocardiosis is an infectious disease caused by Gram-positive rod-shaped bacteria and presents as a suppurative granulomatous disease in patients with compromised immune systems. Few studies have investigated the clinical utility of the universal 16S rRNA polymerase chain reaction (PCR) method using sterile body fluids for diagnosing nocardiosis. A 64-year-old female patient was admitted to Chosun University Hospital with the complaint of fever. Computed tomography scans of her chest revealed the presence of empyema and an abscess in the right lung. Pus samples were collected using closed chest thoracostomy and were cultured. The results revealed the presence of Gram-positive bacilli, but the culture tests were unable to identify the causative microorganism. Despite antibiotic treatment, the patient died of the suspected empyema and abscess. Universal 16S PCR of her sterile body fluids in combination with sequencing was performed, which led to the diagnosis of Nocardia farcinica infection. Postmortem, the remainder of the pus samples cultured for 8 days confirmed the presence of N. farcinica. This study illustrates the importance of using routine universal 16S rRNA PCR with sterile body fluids to help diagnose atypical bacterial infections such as nocardiosis.

Lung abscess: an update on the current knowledge and call for future investigations

“…Numerous case reports have been published, for instance cases describing the clinical course of patients with Lemierre's syndrome [19 ▪ ] or granulomatosis with polyangiitis [23 ▪ ,24 ▪ ,25 ▪ ] highlighting the many differential diagnoses to consider. A few case reports also described new diagnostic tools including radiomics and metagenomic NGS [29 ▪ ,35 ▪ ,36 ▪ ,37 ▪ ] which could inspire future studies. Regarding treatment, a few case reports have described new intervention techniques and treatment options [41 ▪ ,42 ▪ ].…”

“…However, identifying the pathogens is often difficult, with positive sputum cultures in only around 50% [17,34]. Metagenomic NGS offers the possibility of identifying pathogens in cases with false-negative cultures [35 ▪ ,36 ▪ ]. In addition, this method is able to distinguish infection from colonization which could support clinical management and antimicrobial stewardship [37 ▪ ].…”