Authors (including presenting author) :
Cheng CK(1), Lok TM(1)(2), Chau KY(1), Yau CY(3), Wong CW(4), Ho YM(5), Yip KT(6), Siu KH(2)
Affiliation :
(1) Department of Pathology, United Christian Hospital (2) Department of Health Technology and Informatics, The Hong Kong Polytechnic University (3) Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital (4) Department of Microbiology, Prince of Wales Hospital (5) Department of Pathology, Princess Margaret Hospital (6) Department of Clinical Pathology, Tuen Mun Hospital
Introduction :
Respiratory infections are a significant cause of morbidity and mortality worldwide. Target capture sequencing (TCS) provides rapid and accurate identification of respiratory pathogens even in the presence of high levels of host and commensal background, offering substantial benefits to patients and aiding in epidemic prevention. The Illumina Respiratory Pathogen ID/AMR Enrichment Panel (RPIP) is one of the TCS assays. It can detect over 280 respiratory pathogens and more than 2000 antimicrobial resistance genes (ARGs).
Objectives :
(1) To evaluate diagnostic performance of TCS; (2) To evaluate feasibility of application of a TCS assay in clinical microbiology laboratories.
Methodology :
This multi-center study involved five hospitals. Different hospitals used various platforms for nucleic acid extraction. Respiratory specimens, including bronchial aspirates (BA)/ bronchoalveolar lavage (BAL), sputum, nasopharyngeal swab (NPS), and tracheal aspirates, were collected to evaluate RPIP's diagnostic performance. This study compared pathogen identification, antimicrobial susceptibility testing, and strain typing accuracy with conventional methods.
Result & Outcome :
A total of 128 specimens were tested. RPIP demonstrated an overall agreement of 79%. Among different specimen types, BA/BAL and sputum showed the highest accuracy at 85.7% and 84.0%, respectively. Different extraction platforms showed similar performance, with overall agreement ranging from 71.7% to 90.5%. The concordance rate of antimicrobial resistance genes (ARGs) is 85.7% compared to the culture method. Phylogenetic analysis of SARS-CoV-2 showed a 100% match in strain typing results compared to Pangolin amplicon sequencing results. Conclusions: The consistent performance of different extraction systems indicated that they can be well-suited into clinical microbiology laboratory setups. Detecting a comprehensive pathogen profile, including bacteria, viruses, fungi, and resistance markers in a single assay, reduces the need for multiple patient samples and enables targeted antibiotic therapy. This study offers evidence-based recommendations for hospitals considering the adoption of TCS facilitated by using the RPIP assay, potentially advancing diagnostic capabilities and treatment modalities in clinical practice.
