Prevalence of Fungal and Bacterial Co-Infection in Pulmonary Fungal Infections: A Metagenomic Next Generation Sequencing-Based Study

Abstract

With the widespread use of antibacterial drugs and increasing number of immunocompromised patients, pulmonary fungal infections are becoming more common. However, the incidence of pulmonary fungal and bacterial co-infection is rarely reported. In this study, 119 patients definitively diagnosed with pulmonary fungal infections between July 2018 and March 2020 were assessed using metagenomic next-generation sequencing (mNGS) as well as traditional pathogen detection to gauge the incidence of fungal and bacterial co-infection and evaluate the associated risk factors. We found that of the 119 patients with fungal infections, 48 (40.3%) had pulmonary fungal and bacterial co-infection. We identified immunocompromised status and the presence of one or more pulmonary cavities as risk factors associated with fungal and bacterial co-infection. The most commonly isolated fungi species were Aspergillus, Pneumocystis, and Rhizopus. The most commonly isolated bacterial species were Pseudomonas aeruginosa, Acinetobacter baumannii, and Stenotrophomonas maltophilia. Seventy-nine (66.4%) patients had received empirical antibiotic treatment before their pathogenic test results became available, and 41.7% (fungal infection group) and 38.7% (fungal and bacterial co-infection group) of the patients had their antibacterial drug dosage changed accordingly. This mNGS-based study showed that the incidence of fungal and bacterial co-infection is significant. Our research outcomes can, thus, guide the use of antibacterial drugs in the treatment of clinical fungal infections.

Next-Generation Metagenome Sequencing Shows Superior Diagnostic Performance in Acid-Fast Staining Sputum Smear-Negative Pulmonary Tuberculosis and Non-tuberculous Mycobacterial Pulmonary Disease

“…In our study, 46% of the patients with co-infection were infected with more than two types of microorganisms. Our findings also indicated that the analysis of BALF samples using mNGS can lead to the simultaneous detection of mixed infections by bacteria, fungi, viruses, and mycobacteria, which is consistent with other reports (Pan et al, 2019;Xie et al, 2019;Zhao et al, 2021). The results of our study suggested that mNGS is a good diagnostic method for patients with pulmonary infections who have poor responses to empirical antibiotics and are AFS sputum smear-negative.…”

“…During bronchoscopy, the surgeon recorded complications such as bleeding, fatal hemoptysis, arrhythmia, and death. Within 2 h after collection, lung biopsy specimens were sent to the histopathology laboratory and then processed according to standard procedures (Zhao et al, 2021). The remaining lung biopsy specimens were stored at −80 • C for mNGS.…”

Sanger Sequencing Implementation in Clinically Ill Patients for Bacterial and Fungal Pathogens Identification

“…It is worth noting that it was possible to determine the bacterial and fungal co-infection in four patients; those co-infections were among Staphylococcus This finding is in accordance with the rise of co-infection case reports in several unrelated illnesses patients since the next-generation sequencing (NGS) approach implementation has allowed the accurate bacterial and fungal co-infection characterization, such as immunocompromised patients and COVID-19 patients [13] [14] [15].…”

Application of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in patients with lower respiratory tract infections

“…The low observed prevalence of Candida pneumonia is consistent with that reported in previous studies. 19 , 20 Therefore, it is important to rationally and objectively utilize mNGS results, and to note that they currently cannot fully replace conventional detection methods. Future diagnoses and treatments of infectious diseases should combine multiple disciplines in diagnosis, thereby enabling precise treatments to be carried out.…”