Impact of integrase inhibitors on gut and oral microbiome stars

Resum

Human immunodeficiency virus (HIV) infection is now considered a chronic disease thanks to the extended use of antiretroviral treatment (ART). However, chronic immune activation, inflammation, and increased bacterial translocation (BT) could persist in these patients despite ART. These facts have been described as predictors for clinical events and mortality in these patients. Gut microbiota (GM) changes induced by HIV infection and ART seem to be related to such inflammatory state. The role of integrase strand transfer inhibitors (INSTIs), the preferred choice for the treatment of naive patients, on GM (bacteriome) has not been deeply investigated. There are also no studies focused on the effects of HIV infection and/or ART on gut virome, despite the fact that viruses are the most abundant components of human GM. The main objective of this Doctoral Thesis was to deeply characterize GM composition (both bacteriome and virome) and oral bacteriome of HIV-infected patients in comparison with non-HIV-infected subjects, and to analyse the impact of INSTIs-based treatments. To accomplish this objective, 26 non-HIV-infected volunteers and 30 HIV-infected patients (15 naive and 15 under INSTI-regimen) were recruited. Blood samples were extracted to analyse biochemical parameters and markers of BT, inflammation, cardiovascular risk, gut permeability, and bacterial metabolism. Gut bacteriome composition and oral bacteriome composition was analysed using 16S rRNA gene sequencing and gut virome composition was studied using shotgun sequencing. Our results showed that HIV-infection increased BT, inflammation, cardiovascular risk, and gut permeability, whereas INSTIs counteracted these effects. Regarding gut bacteriome, the reduction in bacterial richness induced by HIV infection was restored by INSTIs (p<0.05 naive vs. control Observed features and Chao1 estimator indexes). β-diversity revealed that HIV-infected people were separated from the control group independently of treatment (p<0.05 naive vs. control and p<0,05 INSTIs vs. control). Considering gut virome, the results showed that bacteriophages are the most abundant and diverse viruses in the gut independent from the HIV status and the use of treatment. Neither HIV infection nor INSTIs-based treatment had an effect on eukaryotic viruses composition. On the other hand, HIV infection was accompanied by a decrease in phage richness which was reverted after INSTIs-based treatment (p<0.01 naive vs. control Observed features index and p<0.05 naive vs. control Fisher’s alpha index). β-diversity of phages revealed that samples from HIV-infected patients clustered separately from those belonging to the control group (padj<0.01 naive vs. control and padj<0.05 INSTIs vs. control). However, it is worth mentioning that samples coming from INSTIs-treated patients grouped more closely together compared to naive patients. Differential abundant analysis showed an increase in phages belonging to the Caudoviricetes class in the naive group compared to the control group (padj<0.05) and a decrease of Malgrandaviricetes class phages in the INSTIs-treated group compared to the control group (padj<0.001). Besides, it was observed that INSTIs-based treatment was not able to reverse the increase of lysogenic phages associated with HIV infection (p<0.05 vs. control) or to modify the decrease observed on the relative abundance of Proteobacteria-infecting phages (p<0.05 vs. control). Finally, with respect to oral bacteriome, our study was unable to detect differences neither in α-diversity nor in β-diversity between the three groups analysed, although some taxa were revealed to be increased in the naive group and in the INSTIs-treated group compared to controls. In conclusion, this Doctoral Thesis shows that current antiretroviral regimens based on INSTIs are able to reverse the impact of HIV infection on BT, systemic inflammation, gut permeability, and gut bacterial diversity/richness reaching similar levels than those observed in an uninfected/control population. Besides, our study describes for the first time the impact of HIV and INSTIs on the gut virome and demonstrates that INSTIs-based treatments are able to partially restore gut dysbiosis, not only at the bacterial, but also at the viral level. These results suggest a protective role of INSTIs in disease progression, in subsequent immune activation, and in the development of future age-related complications such as cardiovascular events and opens several opportunities for new studies focused on microbiota-based therapies.