Plasma Levels of Bacterial DNA in HIV Infection: The Limits of Quantitative Polymerase Chain Reaction

Ferri, Emanuele; Novati, Stefano; Casiraghi, Maurizio; Sambri, Vittorio; Genco, Francesca; Gulminetti, Roberto; Bandi, Claudio

doi:10.1086/653215

Cited by 20 publications

(17 citation statements)

References 10 publications

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“…The majority of 16S rRNA gene PCR assays are designed for the qualitative detection of amplicons, which allows for the identification of different bacterial species (39,40,50). Novel and highly sensitive real-time PCRs have recently been developed, focusing on the accurate quantification of 16S rRNA gene sequences (45,46,51,52). However, exogenous DNA contamination during workflow or the presence of DNA traces in PCR reagents, including Taq DNA polymerase from the production strain, may account for false-positive results (53,54).…”

Section: Measurement Of Microbial Translocationmentioning

confidence: 99%

Microbial Translocation in the Pathogenesis of HIV Infection and AIDS

2013

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SUMMARYIn pathogenic simian immunodeficiency virus (SIV) and human immunodeficiency virus (HIV) infections, the translocation of microbial products from the gastrointestinal (GI) tract to portal and systemic circulation has been proposed as a major driver of the chronic immune activation that is associated with disease progression. Consistently, microbial translocation is not present in nonpathogenic SIV infections of natural host species.In vivostudies demonstrated that HIV/SIV-associated microbial translocation results from a series of immunopathological events occurring at the GI mucosa: (i) early and severe mucosal CD4+depletion, (ii) mucosal immune hyperactivation/persistent inflammation; (iii) damage to the integrity of the intestinal epithelium with enterocyte apoptosis and tight junction disruption; and (iv) subverted the gut microbiome, with a predominance of opportunistic bacteria. Directin situevidence of microbial translocation has been provided for SIV-infected rhesus macaques showing translocated microbial products in the intestinal lamina propria and distant sites. While the mechanisms by which microbial translocation causes immune activation remain controversial, a key pathogenic event appears to be innate immunity activation via Toll-like receptors and other pathogen recognition receptors. Accumulating clinical observations suggest that microbial translocation might affect HIV disease progression, response to therapy, and non-AIDS comorbidities. Given its detrimental effect on overall immunity, several interventions to prevent/block microbial translocation are currently under investigation as novel therapeutic agents for HIV/AIDS.

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Section: Measurement Of Microbial Translocationmentioning

confidence: 99%

Microbial Translocation in the Pathogenesis of HIV Infection and AIDS

2013

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“…Thus, a substantial breach of the anatomo-functional GI barrier occurs, with progressive failure of mucosal immunity and leakage into the systemic circulation of bacterial by-products, such as lipopolysaccharide (LPS) and bacterial DNA fragments, which contribute to systemic immune activation [1] [4], [5], [6].…”

Section: Introductionmentioning

confidence: 99%

Evidence for Polymicrobic Flora Translocating in Peripheral Blood of HIV-Infected Patients with Poor Immune Response to Antiretroviral Therapy

et al. 2011

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In advanced HIV infection, the homeostatic balance between gastrointestinal indigenous bacteria and gut immunity fails and microbes are able to overcome the intestinal barrier and gain the systemic circulation. Because microbial translocation is not fully controlled by antiviral therapy and is associated with inefficient CD4+ reconstitution, we investigated the profile of translocating bacteria in peripheral blood of 44 HIV-infected patients starting therapy with advanced CD4+ T-lymphopenia and displaying poor CD4+ recovery on virologically suppressive HAART. According to CD4+ reconstitution at 12-months HAART, patients were considered Partial Immunological Responders, PIRs (CD4+≥250/µl, n = 29) and Immunological non Responders, INRs (CD4+<200/µl, n = 15)). We show that PIRs and INRs present similarly elevated plasma levels of lipopolysaccharide (LPS) and its ligand sCD14 that were not lowered by virologically suppressive therapy. Bacterial 16S rRNA gene amplification and sequencing resulted in a highly polymicrobic peripheral blood microbiota both prior and after 12-month HAART. Several differences in bacterial composition were shown between patients' groups, mainly the lack of probiotic Lactobacillaceae both prior and after therapy in INRs. Failure to control microbial translocation on HAART is associated with a polymicrobic flora circulating in peripheral blood that is not substantially modified by therapy.

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“…However 16S rDNA-PCR is vulnerable to contamination from exogenous and endogenous bacterial DNA. [26][27][28][29] Without sequencing the amplicons, these results are therefore potentially artifactual and indeed thus far sequencing has largely yielded results compatible with environmental contaminants and not recognized gut commensals. 17,30,31 …”

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confidence: 99%

“…17,31 Previous work in this field has largely relied on the detection of LPS or surrogate markers of MT such as sCD14 (a coreceptor for LPS produced by monocytes) and LPS-binding protein (LBP). 9,22,40,41 In view of ongoing debate about optimal methods to detect MT in HIV-infected people, 29,42,43 there is an urgent need for further assay development and optimization. This need is compounded by the conflicting data generated in pediatric populations in particular, but also in adult populations.…”

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confidence: 99%

Short Communication: Evidence That Microbial Translocation Occurs in HIV-Infected Children in the United Kingdom

Fitzgerald

Harris

Doyle

et al. 2013

AIDS Research and Human Retroviruses

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Microbial translocation (MT) from the gut is implicated in driving immune activation, increasing morbidity and mortality in HIV. We used bacterial 16S rDNA PCR, Sanger sequencing, and high-throughput sequencing to identify microbial DNA in the bloodstream of HIV-infected children in London, United Kingdom. Blood samples were collected from sequential children attending the HIV clinic at Great Ormond Street Hospital, London. DNA extraction, broad range 16S rDNA PCR, and standard Sanger sequencing were carried out. A subset of positive samples was analyzed by high-throughput sequencing (Roche 454 platform). Of 105 samples collected from sequential children, nine were positive using broad range 16S rDNA PCR (8.6%; 95% CI 4.4-16%). From three amplicons, 16S rDNA sequences were identified as Streptococcus, Propionibacterium acnes, and coagulase-negative Staphylococcus. Four positive samples were analyzed by high-throughput sequencing. In the three samples in which organisms were identified by Sanger sequencing, the same species were identified. Further species, in differing proportions, were identified in all four samples. The identified organisms included known gut orders Bifidobacteriaceae, Lactobacillaceae, Bacteroidales, and Clostridiales. In immunocompetent children of equivalent age, no bacterial DNA was detected in blood using this approach. This is the first study to our knowledge using molecular techniques to identify MT in children in the developed world. Our data indicate that 16S rDNA is detectable in 8.6% of HIV-infected children. Levels of DNA were low and from multiple bacterial species. Further studies are needed to ascertain the importance of MT in HIV-infected children.

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Plasma Levels of Bacterial DNA in HIV Infection: The Limits of Quantitative Polymerase Chain Reaction

Cited by 20 publications

References 10 publications

Microbial Translocation in the Pathogenesis of HIV Infection and AIDS

Microbial Translocation in the Pathogenesis of HIV Infection and AIDS

Evidence for Polymicrobic Flora Translocating in Peripheral Blood of HIV-Infected Patients with Poor Immune Response to Antiretroviral Therapy

Short Communication: Evidence That Microbial Translocation Occurs in HIV-Infected Children in the United Kingdom

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