Strain-level analysis of gut-resident pro-inflammatory viridans group Streptococci suppressed by long-term cotrimoxazole prophylaxis among HIV-positive children in Zimbabwe

Abstract

Antimicrobials have become a mainstay of healthcare in the past century due to their activity against pathogens. More recently, it has become clear that they can also affect health via their impact on the microbiota and inflammation. This may explain some of their clinical benefits despite global increases in antimicrobial resistance (AMR) and reduced antimicrobial effectiveness. We showed in a randomized controlled trial of stopping versus continuing cotrimoxazole prophylaxis among HIV-positive Zimbabwean children taking antiretroviral therapy (ART), that continuation of cotrimoxazole persistently suppressed gut-resident viridans group streptococcal species (VGS) that were associated with intestinal inflammation. In this addendum, we provide a broader overview of how antibiotics can shape the microbiota and use high read-depth whole metagenome sequencing data from our published study to investigate whether (i) the impact of cotrimoxazole on gut VGS and (ii) VGS associated inflammation, is attributable to strain-level variability. We focus on S. salivarius, the VGS species that was most prevalent in the cohort and for which there was sufficient genome coverage to differentiate strains. We demonstrate that suppression of S. salivarius by cotrimoxazole is not strain specific, nor did stool concentration of the pro-inflammatory mediator myeloperoxidase vary by S. salivarius strain. We also show that gut-resident S. salivarius strains present in this study population are distinct from common oral strains. This is the first analysis of how cotrimoxazole prophylaxis used according to international treatment guidelines for children living with HIV influences the gut microbiome at the strain-level. We also provide a detailed review of the literature on the mechanisms by which suppression of VGS may act synergistically with cotrimoxazole's anti-inflammatory effects to reduce gut inflammation. A greater understanding of the sub-clinical effects of antibiotics offers new insights into their responsible clinical use.

Keywords: HIV; antimicrobial resistance; cotrimoxazole; gut health; immune modulation; inflammation; microbiota; septra; septrin.

Figure 1.

Cotrimoxazole has multiple anti-inflammatory effects in people living with HIV. Graphical summary of the anti-inflammatory effects of cotrimoxazole identified using samples from the ARROW trial and complimentary in vitro models. Effects of cotrimoxazole include (a) reduced circulating inflammatory mediators (CRP and IL-6), (b) suppression of viridans group streptococci (VGS), a type of bacteria that lives in the gut and promotes intestinal inflammation, which can be measured by stool levels of myeloperoxidase (MPO; a neutrophil-derived reactive oxygen species involved in antimicrobial immune responses). Stool MPO is an indicator of neutrophil accumulation and activity in the gut mucosa, (c) inhibition of pro-inflammatory mediator production (TNFα and IL-6) by immune cells activated by being experimentally exposed to bacteria, and 4) suppression of neutrophil chemoattractant protein production (IL-8) by gut epithelial cells. IL-8 is one of the signals that attracts neutrophils to the gut mucosa and perpetuates intestinal inflammation. IL-8 production is also stimulated by mevalonate pathway metabolites.

Figure 2.

Comparison of gene profiles from S. salivarius strains in stool samples from ART-treated HIV-positive children randomized to continue versus stop cotrimoxazole prophylaxis. (a) Nonmetric multidimensional scaling ordination plot of S. salivarius gene presence/absence profiles in ARROW strains identified in ART-treated HIV-positive Zimbabwean children randomized to stop cotrimoxazole (orange) or continue cotrimoxazole (green), and the PanPhlAn reference strain genomes (black). The blue circle represents the minimal area occupied by ARROW strains. (b) Nonmetric multidimensional scaling ordination plot of S. salivarius gene presence/absence in ARROW strains colored from lowest stool myeloperoxidase concertation (light blue) to highest stool myeloperoxidase concentration (dark blue). (c) Boxplots showing the distance of ARROW S. salivarius strains (blue) and PanPhlAn reference strains (white) from their respective group centroids.