Feasibility of Metatranscriptomics for Pneumonia Surveillance in Adults With HIV

Positive HIV (human immunodeficiency virus) blood test results, computer illustration.
Researchers evaluated the use of metatranscriptomic RNA sequencing for the epidemiologic surveillance of pneumonia pathogens in patients with HIV infection.

Metatranscriptomic RNA sequencing, a culture-independent method to detect respiratory pathogens, was effective in the epidemiologic surveillance of pneumonia pathogens in adults with HIV infection, according to results of a study published in The Lancet Microbe.

A retrospective observational study was performed at a single hospital in Uganda between October 2009 and December 2011 to assess the feasibility of metatranscriptomics to identify pathogenic causes of pneumonia in hospitalized adults with HIV infection. Within 72 hours of hospital admission, bronchoalveolar lavage fluid was collected for RNA sequencing and Mycobacterium tuberculosis culture analysis plus polymerase chain reaction testing. The primary outcome was the detection of an established or possible respiratory pathogen.

Overall, 217 patients were consecutively enrolled and a potential microbial cause of pneumonia was identified in 211 (97%). The mean patient age was 36 years, 60% were women, 22% were on antiretroviral therapy, 56% were receiving prophylaxis against Pneumocystis jirovecci, and 7% were previously diagnosed with tuberculosis infection.

Among the 211 patients in whom a potential microbial cause of pneumonia was identified, 113 (52%) had at least 1 established respiratory pathogen identified, and a possible pathogenic cause was identified in 98 (45%). The most commonly identified established pathogen was M tuberculosis in 35 (16%) patients, and the most commonly identified bacterial organism was Streptococcus mitis in 37 (17%), an organism not previously reported as a cause of pneumonia in HIV-positive patients. The most commonly identified established bacterial pathogen was Haemophilus influenzae in 20 (9%) patients, and P jirovecii was identified only among those with CD4 counts of less than 200 cells/mL (7%; n=166).

In 113 patients with established lower respiratory tract pathogens, 28 (25%) were found to have pathogens from 1 or more groups, including bacterial, viral, mycobacterial, or fungal. In addition, 26 (33%), 30 (27%), 22 (19%), and 7 (6%) patients had only viral, nonmycobacterial, mycobacterial, and fungal pathogens detected via metatranscriptomics. Of note, 70-day survival outcomes were significantly more likely among patients with baseline CD4 counts of 200 cells/mL or greater.

The researchers also assessed metatranscriptomic sequencing data to identify patients with antimicrobial resistant bacterial pathogens. Bacterial genes resistant to tetracycline and aminoglycoside, and β-lactam resistance were found in 75 (35%) of patients, and extended-spectrum β-lactamase resistance was found in 11 (5%).

This study was limited as enrollment occurred prior to the COVID-19 pandemic and subsequent public health measures such as masking may have lasting effects on the prevalence of pathogens. The researchers also noted an inability to assess the effect of RNA sequencing on mortality outcomes due to limited outcome data and the cross-sectional study design.

The researchers concluded, “this study provides a proof-of-concept for culture independent metatranscriptomics for respiratory pathogen surveillance in a vulnerable population [residing in] a region with a high burden of pneumonia.”

Disclosure: Some authors declared affiliations with biotech, pharmaceutical, and/or device companies. Please see the original reference for a full list of disclosures. 


Spottiswoode N, Bloomstein JD, Caldera S, et al. Pneumonia surveillance with culture-independent metatranscriptomics in HIV-positive adults in Uganda: a cross-sectional study. Lancet Microbe. Published online March 25, 2022. doi:10.1016/S2666-5247(21)00357-8