Pneumonia surveillance with culture-independent metatranscriptomics in HIV-positive adults in Uganda: a cross-sectional study

Association between respiratory pathogens and severe clinical outcomes in people living with HIV-1 and pulmonary infections: A 180-day longitudinal cohort study

BACKGROUND

Many respiratory pathogens have been identified in people living with HIV-1 and pulmonary infection, but their impact on clinical outcomes remains largely unclear.

METHODS

Metagenomic sequencing and traditional laboratory diagnostics were applied to identify bacterial, viral, and fungal respiratory pathogens. Clinical outcomes were assessed by (i) mortality or ICU transfer during hospitalization, and (ii) 30-day re-hospitalization and 180-day mortality after hospital discharge.

RESULTS

Microbiological analyses of bacterial, viral and fungal pathogens in 237 in-patients with HIV-1 and pulmonary infections revealed Pneumocystis jirovecii (58 %) as the most prevalent respiratory pathogen, followed by Cytomegalovirus (39 %), Mycobacterium tuberculosis (22 %), Talaromyces marneffei (17 %), and Epstein-Barr virus (16 %). Fifty-six patients (24 %) were coinfected with bacterial, viral and fungal pathogens, referred to as bacterial+fungal+viral coinfections. Risk factors for bacterial+fungal+viral coinfections (RR=8.41, 95 %CI: 4.2-14.3), severe pneumonia (RR=13.6, 95 %CI: 8.14-19.3), and elevated C-reactive protein levels (RR=6.42, 95 %CI: 1.58-10.13) were significantly associated with mortality or ICU transfer during hospitalization. After hospital discharge, 38 patients (16 %) were rehospitalized within 30 days. Antiretroviral therapy reduced the risk of 30-day rehospitalization (HR=0.21, p = 0.01). During the 180-day follow-up, 13 patients (5.5 %) died. Survival analyses identified severe pneumonia and age ≥ 60 years as risk factors for 180-day mortality.

CONCLUSIONS

Multiple pulmonary coinfections are associated with severe outcomes in in-patients with HIV-1 infection. Effective management of both HIV-1 and pulmonary infections is crucial to reduce hospitalization rates and mortality risk.

Bacterial Profile, Susceptibility Patterns, and Factors Associated with Culture-Positive Sputum Among HIV Patients Presenting with a Cough in Northern Uganda

Aim

Sub-Saharan Africa bears the highest burden of HIV/AIDS infections and constitutes 72% and 69% of AIDS-related deaths and people living with HIV worldwide, respectively. Due to the relationship between pulmonary infections and HIV/AIDS, it is biologically plausible that the surge in morbidity and mortality among HIV/AIDS patients could be attributed to an increase in pulmonary infections among this cohort of patients. This study determined the bacterial profile, susceptibility patterns, and factors associated with culture-positive sputum among HIV patients presenting with cough at the Lira Infectious Disease Centre in Northern Uganda.

Material and Methods

This prospective cross-sectional study recruited 180 participants. Culture and sensitivity of the sputum samples were done to determine the causative organism and its susceptibility. Blood agar, MacConkey's agar, and Chocolate agar were deployed for the culture media. Antimicrobial susceptibility testing was done using the Kirby-Bauer disc diffusion test. Data were analyzed using SPSS version 26.

Results

Out of the 180 enrolled patients, 113 were females with a mean age of 45. Bacterial growth was seen in 56 of the 180 samples. The most common isolate was Staphylococcus aureus at 35.7% of the 56 growths. The minority that accounted for 1.8% each were Citrobacter freundii, Salmonella species and Acinetobacter baumanii, respectively. A combination of ceftriaxone and gentamicin was effective against most organisms isolated in this study. At the multivariate level of analysis, an unsuppressed viral load and low peripheral oxygen saturation were independently associated with a sputum culture-positive cough.

Conclusion

HIV patients at LIDC who present with productive cough with low oxygen saturation and an unsuppressed viral load may be screened for Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pneumonia, Klebsiella pneumonia, and Enterobacter species infection. A combination of ceftriaxone and gentamicin may be used as empiric therapy before the culture and sensitivity results are available.

Monthly Sulfadoxine-Pyrimethamine During Pregnancy Prevents Febrile Respiratory Illnesses: A Secondary Analysis of a Malaria Chemoprevention Trial in Uganda

Background

Trials evaluating antimalarials for intermittent preventive treatment in pregnancy (IPTp) have shown that dihydroartemisinin-piperaquine (DP) is a more efficacious antimalarial than sulfadoxine-pyrimethamine (SP); however, SP is associated with higher birthweight, suggesting that SP demonstrates "nonmalarial" effects. Chemoprevention of nonmalarial febrile illnesses (NMFIs) was explored as a possible mechanism.

Methods

In this secondary analysis, we leveraged data from 654 pregnant Ugandan women without HIV infection who participated in a randomized controlled trial comparing monthly IPTp-SP with IPTp-DP. Women were enrolled between 12 and 20 gestational weeks and followed through delivery. NMFIs were measured by active and passive surveillance and defined by the absence of malaria parasitemia. We quantified associations among IPTp regimens, incident NMFIs, antibiotic prescriptions, and birthweight.

Results

Mean "birthweight for gestational age" Z scores were 0.189 points (95% CI, .045-.333) higher in women randomized to IPTp-SP vs IPTp-DP. Women randomized to IPTp-SP had fewer incident NMFIs (incidence rate ratio, 0.74; 95% CI, .58-.95), mainly respiratory NMFIs (incidence rate ratio, 0.69; 95% CI, .48-1.00), vs IPTp-DP. Counterintuitively, respiratory NMFI incidence was positively correlated with birthweight in multigravidae. In total 75% of respiratory NMFIs were treated with antibiotics. Although overall antibiotic prescriptions were similar between arms, for each antibiotic prescribed, "birthweight for gestational age" Z scores increased by 0.038 points (95% CI, .001-.074).

Conclusions

Monthly IPTp-SP was associated with reduced respiratory NMFI incidence, revealing a potential nonmalarial mechanism of SP and supporting current World Health Organization recommendations for IPTp-SP, even in areas with high-grade SP resistance. While maternal respiratory NMFIs are known risk factors of lower birthweight, most women in our study were presumptively treated with antibiotics, masking the potential benefit of SP on birthweight mediated through preventing respiratory NMFIs.

Global prevalence, mortality, and main characteristics of HIV-associated pneumocystosis: A systematic review and meta-analysis

The epidemiology of Human Immunodeficiency Virus (HIV)-associated pneumocystosis (HAP) is poorly described on a worldwide scale. We searched related databases between January 2000 and December 2022 for studies reporting HAP. Meta-analysis was performed using StatsDirect (version 2.7.9) and STATA (version 17) according to the random-effects model for DerSimonian and Laird method and metan and metaprop commands, respectively. Twenty-nine studies with 38554 HIV-positive, 79893 HIV-negative, and 4044 HAP populations were included. The pooled prevalence of HAP was 35.4% (95% CI 23.8 to 47.9). In contrast, the pooled prevalence of PCP among HIV-negative patients was 10.16% (95% CI 2 to 25.3). HIV-positive patients are almost 12 times more susceptible to PCP than the HIV-negative population (OR: 11.710; 95% CI: 5.420 to 25.297). The mortality among HAP patients was 52% higher than non-PCP patients (OR 1.522; 95% CI 0.959 to 2.416). HIV-positive men had a 7% higher chance rate for PCP than women (OR 1.073; 95% CI 0.674 to 1.706). Prophylactic (OR: 6.191; 95% CI: 0.945 to 40.545) and antiretroviral therapy (OR 3.356; 95% CI 0.785 to 14.349) were used in HAP patients six and three times more than HIV-positive PCP-negatives, respectively. The control and management strategies should revise and updated by health policy-makers on a worldwide scale. Finally, for better management and understanding of the epidemiology and characteristics of this coinfection, designing further studies is recommended.

The antibiotic resistance reservoir of the lung microbiome expands with age in a population of critically ill patients

Antimicrobial resistant lower respiratory tract infections are an increasing public health threat and an important cause of global mortality. The lung microbiome can influence susceptibility of respiratory tract infections and represents an important reservoir for exchange of antimicrobial resistance genes. Studies of the gut microbiome have found an association between age and increasing antimicrobial resistance gene burden, however, corollary studies in the lung microbiome remain absent. We performed an observational study of children and adults with acute respiratory failure admitted to the intensive care unit. From tracheal aspirate RNA sequencing data, we evaluated age-related differences in detectable antimicrobial resistance gene expression in the lung microbiome. Using a multivariable logistic regression model, we find that detection of antimicrobial resistance gene expression was significantly higher in adults compared with children after adjusting for demographic and clinical characteristics. This association remained significant after additionally adjusting for lung bacterial microbiome characteristics, and when modeling age as a continuous variable. The proportion of adults expressing beta-lactam, aminoglycoside, and tetracycline antimicrobial resistance genes was higher compared to children. Together, these findings shape our understanding of the lung resistome in critically ill patients across the lifespan, which may have implications for clinical management and global public health.

Effect of seven anti-tuberculosis treatment regimens on sputum microbiome: a retrospective analysis of the HIGHRIF study 2 and PanACEA MAMS-TB clinical trials

BACKGROUND

Respiratory tract microbiota has been described as the gatekeeper for respiratory health. We aimed to assess the impact of standard-of-care and experimental anti-tuberculosis treatment regimens on the respiratory microbiome and implications for treatment outcomes.

METHODS

In this retrospective study, we analysed the sputum microbiome of participants with tuberculosis treated with six experimental regimens versus standard-of-care who were part of the HIGHRIF study 2 (NCT00760149) and PanACEA MAMS-TB (NCT01785186) clinical trials across a 3-month treatment follow-up period. Samples were from participants in Mbeya, Kilimanjaro, Bagamoyo, and Dar es Salaam, Tanzania. Experimental regimens were composed of different combinations of rifampicin (R), isoniazid (H), pyrazinamide (Z), ethambutol (E), moxifloxacin (M), and a new drug, SQ109 (Q). Reverse transcription was used to create complementary DNA for each participant's total sputum RNA and the V3-V4 region of the 16S rRNA gene was sequenced using the Illumina metagenomic technique. Qiime was used to analyse the amplicon sequence variants and estimate alpha diversity. Descriptive statistics were applied to assess differences in alpha diversity pre-treatment and post-treatment initiation and the effect of each treatment regimen.

FINDINGS

Sequence data were obtained from 397 pre-treatment and post-treatment samples taken between Sept 26, 2008, and June 30, 2015, across seven treatment regimens. Pre-treatment microbiome (206 genera) was dominated by Firmicutes (2860 [44%] of 6500 amplicon sequence variants [ASVs]) at the phylum level and Streptococcus (2340 [36%] ASVs) at the genus level. Two regimens had a significant depressing effect on the microbiome after 2 weeks of treatment, HR20mg/kgZM (Shannon diversity index p=0·0041) and HR35mg/kgZE (p=0·027). Gram-negative bacteria were the most sensitive to bactericidal activity of treatment with the highest number of species suppressed being under the moxifloxacin regimen. By week 12 after treatment initiation, microbiomes had recovered to pre-treatment level except for the HR35mg/kgZE regimen and for genus Mycobacterium, which did not show recovery across all regimens. Tuberculosis culture conversion to negative by week 8 of treatment was associated with clearance of genus Neisseria, with a 98% reduction of the pre-treatment level.

INTERPRETATION

HR20mg/kgZM was effective against tuberculosis without limiting microbiome recovery, which implies a shorter efficacious anti-tuberculosis regimen with improved treatment outcomes might be achieved without harming the commensal microbiota.

FUNDING

European and Developing Countries Clinical Trials Partnership and German Ministry of Education and Research.

Understanding human health through metatranscriptomics

Metatranscriptomics has revolutionized our ability to explore and understand transcriptional programs in microbial communities. Moreover, it has enabled us to gain deeper and more specific insight into the microbial activities in human gut, respiratory, oral, and vaginal communities. Perhaps the most important contribution of metatranscriptomics arises, however, from the analyses of disease-associated communities. We review the advantages and disadvantages of metatranscriptomics analyses in understanding human health and disease. We focus on human tissues low in microbial biomass and conditions associated with dysbiotic microbiota. We conclude that a more widespread use of metatranscriptomics and increased knowledge on microbe activities will uncover critical interactions between microbes and host in human health and provide diagnostic basis for culturing-independent, direct functional pathogen identification.