ArticleClinical infectious diseases : an official publication of the Infectious Diseases Society of America2020
Cotrimoxazole Prophylaxis Increases Resistance Gene Prevalence and α-Diversity but Decreases β-Diversity in the Gut Microbiome of Human Immunodeficiency Virus-Exposed, Uninfected Infants.
Article in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 5 of them syntheses that pooled it.
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Who cites it
40 citing papers in PubMed, 5 syntheses or guidelines pooled it, 70 citations in OpenAlex.
- Determinants of pneumococcal carriage by age in Africa (2000-2021): a systematic analysis.Frontiers in medicine · 2025Pooled it
- The effect of antibiotics on the intestinal microbiota in children - a systematic review.Frontiers in allergy · 2024Pooled it
- Impact of antibiotics on gut microbiome composition and resistome in the first years of life in low- to middle-income countries: A systematic review.PLoS medicine · 2023Pooled it
- Co-trimoxazole prophylaxis for children who are HIV-exposed and uninfected: a systematic review.Journal of the International AIDS Society · 2023Pooled it
- Pooled it
- Randomized Controlled Trial of Oral Vancomycin Treatment in Clostridioides difficile-Colonized Patients.mSphere · 2021Trial
- Brief Report: Cessation of Long-Term Cotrimoxazole Prophylaxis in HIV-Infected Children Does Not Alter the Carriage of Antimicrobial Resistance Genes.Journal of acquired immune deficiency syndromes (1999) · 2020Trial
- Early-life colonization withScience (New York, N.Y.) · 2026Article
- Prevalence of antimicrobial resistance in acute community-acquired urinary tract infections in Sub-Saharan Africa: a systematic review.JAC-antimicrobial resistance · 2026Review
- Decoding the functional landscape and resistome profile of the gut microbiome in the Pangwala tribal community of India.BMC microbiology · 2026Article
- Review
- Mapping 25 years of research on gut microbiota and antibiotic resistance: bibliometric insights and future directions.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Review
- Effects of commonly used antibiotics on children's developing gut microbiomes and resistomes in peri-urban Lima, Peru.The Journal of antimicrobial chemotherapy · 2025Article
- Effects of commonly used antibiotics on children's developing gut microbiomes and resistomes in peri-urban Lima, Peru.medRxiv : the preprint server for health sciences · 2024Article
- Early changes in the gut microbiome among HIV-infected Individuals in Uganda initiating daily TMP/SMX.medRxiv : the preprint server for health sciences · 2024Article
- Review
- Longitudinal dynamics of farmer and livestock nasal and faecal microbiomes and resistomes.Nature microbiology · 2024Article
- A Mixture of Formic Acid, Benzoic Acid, and Essential Oils Enhanced Growth Performance via Modulating Nutrient Uptake, Mitochondrion Metabolism, and Immunomodulation in Weaned Piglets.Antioxidants (Basel, Switzerland) · 2024Article
- Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe.Microbiome · 2024Article
- Antibiotic perturbations to the gut microbiome.Nature reviews. Microbiology · 2023Review
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundProphylactic cotrimoxazole treatment is recommended in human immunodeficiency virus (HIV)-exposed, uninfected (HEU) infants, but the effects of this treatment on developing HEU infant gut microbiotas and resistomes are largely undefined.
methodsWe analyzed whole-metagenome sequencing data from 163 longitudinally collected stool samples from 63 HEU infants randomized to receive (n = 34; CTX-T) or to not receive (n = 29; CTX-N) prophylactic cotrimoxazole treatment. We generated taxonomic, functional pathway, and resistance gene profiles for each sample and compared microbiome signatures between the CTX-T and CTX-N infants.
resultsMetagenomic analysis did not reveal significant differences in taxonomic or functional pathway α-diversity between CTX-T and CTX-N infants. In contrast, resistance gene prevalence (P = .00719) and α-diversity (P = .0045) increased in CTX-T infants. These differences increased over time for both resistance gene prevalence measured by log-normalized abundance (4-month mean, 0.71 [95% confidence interval {CI}, .2-1.2] and 6-month mean, 0.85 [95% CI, .1-1.7]) and α-diversity (P = .0045). Unlike α-diversity, interindividual gut microbiome taxonomic (mean, -0.11 [95% CI, -.15 to -.077]), functional taxonomic (mean, -0.050 [95% CI, -.084 to -.017]), and resistance gene (mean, -0.13 [95% CI, -.17 to -.099]) β-diversity decreased in CTX-T infants compared with CTX-N infants. These results are consistent with persistent antibiotic selection pressure.
conclusionsCotrimoxazole prophylaxis in HEU infants decreased gut microbiome β-diversity and increased antibiotic resistance gene α-diversity and prevalence. Antibiotic resistance is a growing threat, especially in low- and middle-income countries where the higher perinatal HIV exposure rates result in cotrimoxazole prophylaxis. Understanding effects from current HEU infant antibiotic prophylaxis guidelines will inform guideline revisions and efforts to reduce increasing antibiotic resistance.
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