{"doi":"10.1101/2022.09.09.22279790","title":"Noninvasive diagnosis of secondary infections in COVID-19 by sequencing of plasma microbial cell-free DNA","abstract":"Abstract Background Secondary infection (SI) diagnosis in COVID-19 is challenging, due to overlapping clinical presentations, practical limitations in obtaining samples from the lower respiratory tract (LRT), and low sensitivity of microbiologic cultures. Research Question Can metagenomic sequencing of plasma microbial cell-free DNA (mcfDNA-Seq) help diagnose SIs complicating COVID-19? Study Design and Methods We enrolled 42 inpatients with COVID-19 classified as microbiologically-confirmed SI (Micro-SI, n=8), clinically-diagnosed SI (Clinical-SI, n=13, i.e. empiric antimicrobials), or no clinical suspicion for SI (No-Suspected-SI, n=21) at time of enrollment. From baseline and follow-up plasma samples (days 5 and 10 post-enrollment), we quantified mcfDNA for all detected microbes by mcfDNA sequencing and measured nine host-response biomarkers. From LRT samples among intubated subjects, we quantified bacterial burden with 16S rRNA gene quantitative PCR. Results We performed mcfDNA-Seq in 82 plasma samples. Sequencing was successful in 60/82 (73.2%) samples, which had significantly lower levels of human cfDNA than failed samples (p<0.0001). McfDNA detection was significantly higher in Micro-SI (15/16 [94%]) compared to Clinical-SI samples (8/14 [57%], p=0.03), and unexpectedly common in No-Suspected-SI samples (25/30 [83%]), similar to detection rate in Micro-SI. We detected culture-concordant mcfDNA species in 13/16 Micro-SI samples (81%) and mcfDNA levels tracked with SI outcome (resolution or persistence) under antibiotic therapy. McfDNA levels correlated significantly with LRT bacterial burden (r=0.74, p=0.02) as well as plasma biomarkers of host response (white blood cell count, IL-6, IL-8, and SPD, all p<0.05). Baseline mcfDNA levels were predictive of worse 90-day survival (hazard ratio 1.30 [1.02-1.64] for each log 10 mcfDNA, p=0.03). Interpretation High circulating levels of mcfDNA in a substantial proportion of patients with COVID-19 without clinical suspicion for SI suggest that SIs may often remain undiagnosed. McfDNA-Seq, when clinically available, can offer a non-invasive diagnostic tool for pathogen identification, with prognostic value on host inflammatory response and clinical outcomes.","journal":"medRxiv","year":2022,"id":311345,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9566,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":11747,"name":"Radha Duttagupta","orcid":null,"position":1,"is_corresponding":false},{"id":633527,"name":"Asim Ahmed","orcid":null,"position":2,"is_corresponding":false},{"id":629744,"name":"Matthew K. Hensley","orcid":"0000-0001-9859-6700","position":3,"is_corresponding":false},{"id":717973,"name":"Nameer Al‐Yousif","orcid":"0000-0002-2657-2360","position":4,"is_corresponding":false},{"id":913513,"name":"Michael Lu","orcid":"0000-0001-7878-4675","position":5,"is_corresponding":false},{"id":313759,"name":"William Bain","orcid":"0000-0001-8506-0552","position":6,"is_corresponding":false},{"id":313761,"name":"Faraaz Shah","orcid":"0000-0002-2847-7738","position":7,"is_corresponding":false},{"id":375424,"name":"Caitlin Schaefer","orcid":null,"position":8,"is_corresponding":false},{"id":360798,"name":"Shulin Qin","orcid":"0000-0003-2496-3007","position":9,"is_corresponding":false},{"id":395182,"name":"Xiaohong Wang","orcid":"0000-0002-2346-4882","position":10,"is_corresponding":false},{"id":288811,"name":"Yingze Zhang","orcid":"0000-0001-6947-2901","position":11,"is_corresponding":false},{"id":988067,"name":"Kevin J. Mitchell","orcid":"0000-0002-1870-5522","position":12,"is_corresponding":false},{"id":988069,"name":"Ellen K. Hughes","orcid":"0000-0001-7253-4552","position":13,"is_corresponding":false},{"id":258958,"name":"Jana L. Jacobs","orcid":"0000-0002-0322-585X","position":14,"is_corresponding":false},{"id":631228,"name":"Asma Naqvi","orcid":null,"position":15,"is_corresponding":false},{"id":536897,"name":"Ghady Haidar","orcid":"0000-0003-0634-8211","position":16,"is_corresponding":false},{"id":258969,"name":"John W. Mellors","orcid":"0000-0002-3737-9742","position":17,"is_corresponding":false},{"id":19811,"name":"Barbara A. Methé","orcid":"0000-0001-8711-1448","position":18,"is_corresponding":false},{"id":3878,"name":"Bryan J. McVerry","orcid":"0000-0002-1175-4874","position":19,"is_corresponding":false},{"id":313765,"name":"Alison Morris","orcid":"0000-0002-7290-6536","position":20,"is_corresponding":false},{"id":16243,"name":"Georgios D. Kitsios","orcid":"0000-0002-1018-948X","position":21,"is_corresponding":false},{"id":1007938,"name":"Grace Lisius","orcid":null,"position":0,"is_corresponding":true}],"reference_count":20,"raw_metadata":null,"created_at":"2026-07-19T00:33:28.480200Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}