The role of microbial translocation and gut microbiota in HIV-1 infection

HIV-1 infection is characterized by persistent systemic inflammation and immune activation, even in patients receiving effective antiretroviral therapy (ART). Translocation of microbial compounds from a leaky gut to systemic circulation, so called microbial translocation (MT), is a major driver of the immune activation. Additionally, gut microbiota dysbiosis in HIV-1 infected patients further facilitate and fuel MT. The objectives of this thesis were to study: * how different ART regimens and usage of antibiotics affect markers of MT (I, II), * the alternations of gut microbiota during HIV-1 infection and the effect of ART (III,IV).

In a clinical randomized trial, HIV-1 infected subjects started ART based on efavirenz (n=37) or ritonavir-boosted lopinavir (n=34). Levels of MT markers and of enterocyte death were elevated at baseline (BL), and MT markers declined until follow up after 72 weeks, but the reduction of anti-flagellin IgG antibodies was significant only in lopinavir treated patients. Levels of Intestinal Fatty Acid Binding Protein (I-FABP) remained unchanged at 72 weeks, but were temporarily increased after one month in efavirenz treated patients. 29 subjects with concomitant use of antibiotics had superior reduction of soluble CD14 (sCD14) levels. These data show that choice of ART and antibiotics usage could affect the kinetics of some MT markers.

To further explore the impact of antibiotics usage on MT, we performed a longitudinal study on HIV-1 patients initiating ART without (n=13) or with (n=13) co-trimoxazole (TMP-SMX) as prophylaxis against Pneumocystis jirovecii. Following ART, levels of LPS-binding protein (LBP) were reduced only in the TMP-SMX group, whilst levels of sCD14 declined in both groups after one year. The LBP decrease remained significant in a multivariate analysis model adjusting for co-variates including BL CD4+ T-cell count. This study confirmed that concomitant use of antibiotics and ART in severely immune deteriorated individuals may beneficially influence the kinetics of MT markers.

In the third study, the composition of gut microbiota was determined by 16S rRNA sequencing in 28 HIV-1 progressors, 3 Elite controllers (EC) and 9 uninfected controls at BL, and additionally after ten months of ART in 16 subjects. Gut microbiome α-diversity was reduced in HIV-1 infected individuals as compared to controls, and further declined after introduction of ART. At BL, α-diversity was positively correlated with CD4+ T-cell counts, but in contrary several markers of MT/immune activation were inversely correlated. Microbiome of EC had the lowest interindividual variation (ß-diversity), clustering together in PCoA analysis. The bacterial composition at genus level was altered in HIV-1 progressors with higher abundance of Lactobacillus, and depletion of Lachnobacterium, Faecalibacterium and Hemophilus. Thus, this study showed that the alternations of gut microbiota during HIV-1 infection are associated with the level of immune dysfunction, and that almost one year of ART does not restore the shifts in the gut microbiome.

In the last work, we studied the gut microbiome of 16 EC in relation to 32 matched ART naive HIV-1 positive individuals and 16 uninfected controls. The number of observed genera and richness indices Chao-1 and ACE were significantly higher in EC as compared to naive patients. The gut microbiota in EC was enriched in genera Succinivibrio, Sutterella, Rhizobium, Delftia, Anaerofilum and Oscillospira, whilst Blautia and Anaerostipes were reduced. Determination of inferred bacterial functionality by PICRUSt analysis revealed that carbohydrate metabolism related genes were depleted in EC. In contrary, pathways related to fatty acid metabolism, PPAR-signaling and lipid biosynthesis proteins were more abundant in EC vs naive. The kynurenine pathway of tryptophan metabolism was altered only during progressive HIV-1 infection, and kynurenine tryptophan (K/T) ratio was inversely associated with gut microbiota richness. This study shows that EC have richer gut microbiota than untreated HIV-1 patients with progressive infection, with a unique bacterial composition and a distinct metabolic profile which may be involved in the control of HIV-1.

In summary, data from the studies in my thesis reveal that MT in HIV-1 infection is reduced by ART but also that the choice of ART influences this decline. Additionally, the antibiotics usage may affect the levels of MT. The complexity, composition and functionality of gut microbiota are disturbed in HIV-1 infected individuals with progressive disease, whilst EC have a unique gut microbiota profile that eventually contributes to their control of HIV-1.

List of scientific papers

I. Vesterbacka Jan, Nowak Piotr, Barqasho Babilonia, Abdurahman Samir, Nyström Jessica, Nilsson Staffan, Funaoka Hiroyuki, Kanda Tatsuo, Andersson Lars-Magnus, Gisslèn Magnus, Sönnerborg Anders. Kinetics of microbial translocation markers in patients on efavirenz or lopinavir/r based antiretroviral therapy. PLoS One. 2013;8(1):e55038.
https://doi.org/10.1371/journal.pone.0055038

II. Vesterbacka Jan, Barqasho Babilonia, Häggblom Amanda, Nowak Piotr. Effects of Co-Trimoxazole on Microbial Translocation in HIV-1-Infected Patients Initiating Antiretroviral Therapy. AIDS Res Hum Retroviruses. 2015 Aug;31(8):830-6.
https://doi.org/10.1089/AID.2014.0366

III. Nowak Piotr, Troseid Marius, Avershina Ekatarina, Barqasho Babilonia, Neogi Ujjwal, Holm Kristian, Hov Johannes R, Noyan Kajsa, Vesterbacka Jan, Svärd Jenny, Rudi Knut, Sönnerborg Anders. Gut microbiota diversity predicts immune status in HIV-1 infection. AIDS. 2015 Nov;29(18):2409-18.
https://doi.org/10.1097/QAD.0000000000000869

IV. Vesterbacka Jan, Rivera Javier, Noyan Kajsa, Parera Mariona, Neogi Ujjwal, Calle Malu, Paredes Roger, Sönnerborg Anders, Noguera-Julian Marc, Nowak Piotr. Richer gut microbiota with distinct metabolic profile in HIV infected Elite Controllers. Sci Rep. 2017 Jul 24;7(1):6269.
https://doi.org/10.1038/s41598-017-06675-1