Use of next-generation sequencing on HIV-1 DNA to assess archived resistance in highly treatment-experienced people with multidrug-resistant HIV under virological control: data from the PRESTIGIO Registry.

BACKGROUND: To clarify whether next-generation sequencing (NGS) can be useful for resistance assessment in virologically suppressed highly treatment-experienced (HTE) individuals with MDR HIV. METHODS: Ninety-one participants from the PRESTIGIO Registry were included. NGS was performed on HIV-DNA at 1%, 5% and 20% cut-offs; major drug resistance mutations (DRMs) were evaluated and compared with those detected in historical plasma genotypic resistance testing (h-GRT). APOBEC editing was also characterized. RESULTS: Participants had a complex and long treatment history [median 23 (IQR 21-25) years of ART exposure) and had been virologically suppressed since a median of 3 (IQR 2-5) years. Among all major DRMs detected by HIV-DNA NGS and/or h-GRT, 30% were exclusively found through NGS. The highest detection rate of historical major DRMs was reached with NGS set at 1%, but unusual substitutions and extensive APOBEC hypermutations suggest technical issues and poor clinical relevance in the 1%-5% interval. At NGS set at 5%, 67.2% of historical major DRMs were detected. The number of major DRMs detected exclusively by DNA-NGS as minority variants (frequency 5%-20%) was significantly higher in individuals who later experienced virological rebound compared with those who maintained virological control [median 2 (IQR 1-3) versus 1 (0-2), P = 0.030] and positively correlated with viraemia levels at rebound (rho = 0.474, P = 0.030). CONCLUSIONS: In non-viraemic people with an MDR virus, HIV-1 DNA NGS set at 5% is an acceptable technical cut-off that might help to reveal mutations with a potential clinical relevance. Moreover, the number of minority resistance mutations additionally detected by NGS might be associated with loss of virological control.

The real-time analysis of gastric juice (Endofaster) for detection of Helicobacter Pylori: a reliable tool in substitution of histology.

BACKGROUND: EndoFaster perform gastric juice analysis providing real-time Helicobacter pylori (HP) diagnosis during esophagogastroduodenoscopy (EGD), based on ammonium level. We aimed to assess its accuracy in detecting HP infection compared to the paired histology and to establish the optimum ammonium concentration cut-off point (COP). METHODS: Consecutive adult outpatients referred for EGD were prospectively enrolled between December 2021 and March 2022. In-patients, those with surgically altered anatomy, suspected neoplasia, and bleeding were excluded. EndoFaster and histology were performed in all patients, with additional stool antigen test (SAT) reserved for discordant cases. EndoFaster diagnostic measures were calculated, and ammonium level COP established using AUROC curve analysis. RESULTS: 101 patients (64 female, mean age 56.7±16.1 years) were included. HP infection was diagnosed in 35 (34.6%) and 15 (14.8%) patients by EndoFaster and histology, respectively. Diagnostic accuracy in comparison with histology was 77.8% (95%CI 68.3% - 85.5%). After implementing SAT for gold standard assessment, EndoFaster accuracy increased to 81.6% (95%CI 72.5%-88.7%). AUROC curve (0.93±0.03, 95%CI 0.86-0.99) identified an ammonium COP of ≥67.5ppm. Using the new COP, EndoFaster accuracy further increased to 88.8% (95%CI 80.8%-94.2%). CONCLUSIONS: Endofaster showed high accuracy for HP detection, with moderate agreement to histology. An ammonium COP of 67.5 ppm seems to be the threshold with the highest accuracy for HP detection.