CROI 2024 Abstract eBook

Abstract eBook

Poster Abstracts

time to culture positivity in bone marrow and blood was: 10.5 (IQR, 7 – 16.5) days and 17 (IQR, 11.5 – 19) days, P=0.160, Wilcoxon. 7/28 (25%) patients died by month 6 despite antifungal therapy. Conclusion: Our study demonstrates an excellent diagnostic performance of the HAg EIA and unveils a substantial burden of histoplasmosis in AHD in Vietnam. The mortality remains high (25%) despite antifungal therapy, highlighting the need to screen for Histoplasma antigen, preferably before patients become symptomatic.

897

Tuberculosis Drug Resistance Profiling by Targeted Next-Generation Sequencing in Sub-Saharan Africa Tiana C Schwab 1 , Lavania Joseph 2 , Andrew Moono 3 , Pauline Göller 1 , Guy Muula 3 , Denise Evans 4 , Carolyn Bolton 3 , Alban N. Ramette 1 , Matthias Egger 1 , Shaheed Omar 2 , Lukas Fenner 1 , for IeDEA Southern Africa (IeDEA-SA) 1 University of Bern, Bern, Switzerland, 2 National Institute for Communicable Diseases, Johannesburg, South Africa, 3 Centre for Infectious Disease Research in Zambia, Lusaka, Zambia, 4 Health Economics and Epidemiology Research Office, Johannesburg, South Africa Background: Drug-resistant tuberculosis (DR-TB) remains a global health threat. Drug susceptibility testing (DST) is essential for diagnosing and treating DR-TB effectively, but culture-based methods are time and resource-intensive. Culture-free targeted next-generation sequencing (tNGS) can comprehensively detect drug resistance mutations but its practicality in routine settings requires further exploration. We tested Oxford Nanopore Technologies' tNGS assay for TB in two laboratories in sub-Saharan Africa. Methods: The study was conducted at two sites, Johannesburg/South Africa and Lusaka/Zambia, as part of an ongoing prospective cohort study. On-site lab procedures included automated DNA extraction, amplification of 25 gene regions linked to drug resistance across 18 TB drugs, and real-time Nanopore sequencing and analysis with compact MinION sequencers. Native sputa and decontaminated sediments of 70 TB-positive patients with a GeneXpert MTB/ RIF Ultra result of "low" to "high", were sequenced. Sequencing results were compared to local routine DST (phenotypic MGIT DST to first-line drugs and GeneXpert MTB/XDR). Results: Predicted DR results were available 24 hours after initiating DNA extraction. We obtained sequencing results for 51/82 (62%) native sputum and 59/82 (72%) sediment samples (p=0.25, Fig. A). Complete sequencing results, covering all 25 targets, were obtained for 25/51 (49%) sputum and 46/59 (78%) sediment samples (p<0.01, Fig. B). For incomplete samples the median number of targets missed in sputum and sediment samples was similar (9 vs. 11). Among five samples with rifampicin resistance detected by GeneXpert MTB/RIF Ultra and confirmed by phenotypic DST, sequencing predicted resistance in 3 of these samples, was indeterminate in one sample, and missed resistance in one. Sequencing also predicted resistance to isoniazid and ethionamide in four and one samples, respectively, all confirmed by local DST. Xpert MTB/XDR results were available for a subset of 40 samples, for which predicted DR profiles were all concordant. Recruitment, sequencing, and reference testing, using local routine DST are ongoing. Conclusion: Nanopore tNGS was implemented successfully at both sites. Sequencing from sputum and sediment samples was comparable and detected TB and DR-associated mutations. Nanopore tNGS promises a feasible and rapid sequencing approach for comprehensive genotypic DR profiling in TB high burden countries but technical and logistic challenges complicate its routine implementation.

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Ultra Xpert in Blood and Urine and Myco/F Lytic Blood Culture in Patients With Advanced HIV Disease Dieu Q. Nguyen 1 , Hao T. Nguyen 1 , Thu D. Do 1 , Quang L. Nguyen 1 , Vu Quoc Dat 2 , Phuong L. Trinh 1 , Khanh H. Dang 1 , Thach N. Pham 3 , Nguyen Thanh Dung 4 , Nguyen Phu Huong Lan 4 , Vo Trieu Ly 4 , Nguyen Thuy Thuong Thuong 1 , H. Rogier van Doorn 1 , Thuy Le 5 , for the Talaromycosis Study Group 1 Oxford University Clinical Research Unit in Vietnam, Ho Chi Minh City, Vietnam, 2 Hanoi Medical University, Hanoi, Vietnam, 3 National Hospital for Tropical Diseases, Hanoi, Vietnam, 4 Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam, 5 Duke University School of Medicine, Durham, NC, USA Background: TB is a leading cause of death in patients with advanced HIV disease (AHD). Current TB screening in AHD relies mainly on Xpert in sputum and urine LAM; both have low yield. We report results of an ongoing multi-center prospective study testing an intensified screening approach using Ultra Xpert (UXpert) directly from blood and urine and Myco/F lytic (MFL) blood culture compared to a conventional symptom-based diagnostic approach for detecting mycobacterial infections in AHD in Vietnam. Methods: This sub-study was part of a triple fungal screening program in AHD (N=900 patients). Eligible patients included all hospitalized adults aged ≥18 with CD4 count ≤ 100 cells/µL or WHO stage 3 or 4 disease, not on ART or were on ART for ≤ 3 months or >12 months from two major hospitals for tropical diseases in Hanoi and Ho Chi Minh City. Intensified screening approach included blood UXpert and MFL blood culture in all patients. Urine UXpert was an add on for the last 174 patients. Conventional approach included acid-fast stain, UXpert and MGIT culture of sputum and other specimens as clinically indicated. Patients were followed up monthly over 6 months. Diagnostic yield was compared between two approaches. Results: The 900 patients were recruited between February 2021 and July 2023. 82.9% were men. Median age was 36 (IQR: 29-44) years. A total of 301 (33.4%) patients had microbiological-confirmed mycobacterial infections: 243 (80.7%) had TB; 30 (10.0%) had non-TB mycobacteria (NTM) - 27/30 (90.9%) were due to M. avium complex. The number of cases diagnosed by conventional, intensified, and both approaches were 83, 106, and 112 respectively. The intensified screening approach increased the number of mycobacterial diagnoses from 195 to 301 (54.4% increase) compared to conventional approach alone. In the 106 cases diagnosed by intensified approach only, 55 (52%) were diagnosed from blood and/or urine UXpert, enabling TB therapy earlier than would otherwise. 75 of 301 (24.9%) mycobacteria-infected patients died before completing TB/NTM treatment by month 6 of follow up. Conclusion: The intensified screening approach using UXpert in blood and urine and MFL blood culture increases the number of mycobacterial diagnoses by 54% compared to conventional method alone in hospitalized patients with AHD. Implementation of UXpert in blood and urine in routine care is feasible, reduces time to diagnosis and treatment, and has the potential to reduce HIV mortality.

Poster Abstracts

CROI 2024 280