Characterization of bacterial and viral pathogens in the respiratory tract of children with HIV-associated chronic lung disease: a case–control study
Authors: Mushunje Prince K. , Dube Felix S. , Olwagen Courtney , Madhi Shabir , Odland Jon Ø , Ferrand Rashida A. , Nicol Mark P. , Abotsi Regina E. ,   The BREATHE study team, Bandason Tsitsi , Dauya Ethel , Madanhire Tafadzwa , Corbett Elizabeth L. , Kranzer Katharina , Majonga Edith D. , Simms Victoria , Rehman Andrea M. , A.Weiss Helen , Mujuru Hilda , Bowen Dan , Yindom Louis-Marie , Rowland-Jones Sarah L. , Flaegstad Trond , Gutteberg Tore J. , Cavanagh Jorunn Pauline , Flygel Trym Thune , Sovarashaeva Evegeniya , Chikwana Jessica , Mapurisa Gugulethu Newton , Gonzalez-Martinez Carmen , Semphere Robina , Moyo Brewster Wisdom , Ngwira Lucky Gift , Mbhele Slindile 
Published: June 2024

Introduction

Chronic lung disease is a major cause of morbidity in African children with HIV infection; however, the microbial determinants of HIV-associated chronic lung disease (HCLD) remain poorly understood. We conducted a case–control study to investigate the prevalence and densities of respiratory microbes among pneumococcal conjugate vaccine (PCV)-naive children with (HCLD +) and without HCLD (HCLD-) established on antiretroviral treatment (ART).

Methods

Nasopharyngeal swabs collected from HCLD + (defined as forced-expiratory-volume/second < -1.0 without reversibility postbronchodilation) and age-, site-, and duration-of-ART-matched HCLD- participants aged between 6–19 years enrolled in Zimbabwe and Malawi (BREATHE trial-NCT02426112) were tested for 94 pneumococcal serotypes together with twelve bacteria, includingStreptococcus pneumoniae(SP),Staphylococcus aureus(SA),Haemophilus influenzae(HI),Moraxella catarrhalis(MC), and eight viruses, including human rhinovirus (HRV), respiratory syncytial virus A or B, and human metapneumovirus, using nanofluidic qPCR (Standard BioTools formerly known as Fluidigm). Fisher's exact test and logistic regression analysis were used for between-group comparisons and risk factors associated with common respiratory microbes, respectively.

Results

A total of 345 participants (287 HCLD + , 58 HCLD-; median age, 15.5 years [IQR = 12.8–18], females, 52%) were included in the final analysis. The prevalence of SP (40%[116/287]vs.21%[12/58],p = 0.005) and HRV (7%[21/287]vs.0%[0/58],p = 0.032) were higher in HCLD + participants compared to HCLD- participants. Of the participants positive for SP (116 HCLD + & 12 HCLD-), 66% [85/128] had non-PCV-13 serotypes detected. Overall, PCV-13 serotypes (4, 19A, 19F: 16% [7/43] each) and NVT 13 and 21 (9% [8/85] each) predominated. The densities of HI (2 × 104genomic equivalents [GE/ml]vs.3 × 102GE/ml,p = 0.006) and MC (1 × 104GE/mlvs.1 × 103GE/ml, p = 0.031) were higher in HCLD + compared to HCLD-. Bacterial codetection (≥ any 2 bacteria) was higher in the HCLD + group (36% [114/287]vs.(19% [11/58]), (p = 0.014), with SP and HI codetection (HCLD + : 30% [86/287]vs.HCLD-: 12% [7/58],p = 0.005) predominating. Viruses (predominantly HRV) were detected only in HCLD + participants. Lastly, participants with a history of previous tuberculosis treatment were more likely to carry SP (adjusted odds ratio (aOR): 1.9 [1.1 -3.2],p = 0.021) or HI (aOR: 2.0 [1.2 – 3.3],p = 0.011), while those who used ART for ≥ 2 years were less likely to carry HI (aOR: 0.3 [0.1 – 0.8],p = 0.005) and MC (aOR: 0.4 [0.1 – 0.9],p = 0.039).

Conclusion

Children with HCLD + were more likely to be colonized by SP and HRV and had higher HI and MC bacterial loads in their nasopharynx. The role of SP, HI, and HRV in the pathogenesis of CLD, including how they influence the risk of acute exacerbations, should be studied further.

Trial registration

The BREATHE trial (ClinicalTrials.gov Identifier:NCT02426112, registered date: 24 April 2015).