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Rapid nanopore sequencing and predictive susceptibility testing of positive blood cultures from intensive care patients with sepsis

Authors :
Papp-Wallace, Krisztina M
Papp-Wallace, K M ( Krisztina M )
Harris, Patrick N A; https://orcid.org/0000-0002-2895-0345
Bauer, Michelle J
Lüftinger, Lukas
Beisken, Stephan
Forde, Brian M; https://orcid.org/0000-0002-2264-4785
Balch, Ross
Cotta, Menino; https://orcid.org/0000-0002-2058-2314
Schlapbach, Luregn J; https://orcid.org/0000-0003-2281-2598
Raman, Sainath; https://orcid.org/0000-0002-0152-9980
Shekar, Kiran
Krüger, Peter; https://orcid.org/0000-0002-1247-9886
Lipman, Jeff
Bialasiewicz, Seweryn; https://orcid.org/0000-0001-9474-6943
Coin, Lachlan
Roberts, Jason A; https://orcid.org/0000-0001-6218-435X
Paterson, David L
Irwin, Adam D
Papp-Wallace, Krisztina M
Papp-Wallace, K M ( Krisztina M )
Harris, Patrick N A; https://orcid.org/0000-0002-2895-0345
Bauer, Michelle J
Lüftinger, Lukas
Beisken, Stephan
Forde, Brian M; https://orcid.org/0000-0002-2264-4785
Balch, Ross
Cotta, Menino; https://orcid.org/0000-0002-2058-2314
Schlapbach, Luregn J; https://orcid.org/0000-0003-2281-2598
Raman, Sainath; https://orcid.org/0000-0002-0152-9980
Shekar, Kiran
Krüger, Peter; https://orcid.org/0000-0002-1247-9886
Lipman, Jeff
Bialasiewicz, Seweryn; https://orcid.org/0000-0001-9474-6943
Coin, Lachlan
Roberts, Jason A; https://orcid.org/0000-0001-6218-435X
Paterson, David L
Irwin, Adam D
Source :
Harris, Patrick N A; Bauer, Michelle J; Lüftinger, Lukas; Beisken, Stephan; Forde, Brian M; Balch, Ross; Cotta, Menino; Schlapbach, Luregn J; Raman, Sainath; Shekar, Kiran; Krüger, Peter; Lipman, Jeff; Bialasiewicz, Seweryn; Coin, Lachlan; Roberts, Jason A; Paterson, David L; Irwin, Adam D (2024). Rapid nanopore sequencing and predictive susceptibility testing of positive blood cultures from intensive care patients with sepsis. Microbiology Spectrum, 12(2):e0306523.
Publication Year :
2024

Abstract

We aimed to evaluate the performance of Oxford Nanopore Technologies (ONT) sequencing from positive blood culture (BC) broths for bacterial identification and antimicrobial susceptibility prediction. Patients with suspected sepsis in four intensive care units were prospectively enrolled. Human-depleted DNA was extracted from positive BC broths and sequenced using ONT (MinION). Species abundance was estimated using Kraken2, and a cloud-based system (AREScloud) provided in silico predictive antimicrobial susceptibility testing (AST) from assembled contigs. Results were compared to conventional identification and phenotypic AST. Species-level agreement between conventional methods and AST predicted from sequencing was 94.2% (49/52), increasing to 100% in monomicrobial infections. In 262 high-quality AREScloud AST predictions across 24 samples, categorical agreement (CA) was 89.3%, with major error (ME) and very major error (VME) rates of 10.5% and 12.1%, respectively. Over 90% CA was achieved for some taxa (e.g.,Staphylococcus aureus) but was suboptimal for Pseudomonas aeruginosa. In 470 AST predictions across 42 samples, with both high quality and exploratory-only predictions, overall CA, ME, and VME rates were 87.7%, 8.3%, and 28.4%. VME rates were inflated by false susceptibility calls in a small number of species/antibiotic combinations with few representative resistant isolates. Time to reporting from sequencing could be achieved within 8–16 h from BC positivity. Direct sequencing from positive BC broths is feasible and can provide accurate predictive AST for some species. ONT-based approaches may be faster but significant improvements in accuracy are required before it can be considered for clinical use. IMPORTANCE Sepsis and bloodstream infections carry a high risk of morbidity and mortality. Rapid identification and susceptibility prediction of causative pathogens, using Nanopore sequencing direct from blood cultures, may offer clinical benefit. We ass

Details

Database :
OAIster
Journal :
Harris, Patrick N A; Bauer, Michelle J; Lüftinger, Lukas; Beisken, Stephan; Forde, Brian M; Balch, Ross; Cotta, Menino; Schlapbach, Luregn J; Raman, Sainath; Shekar, Kiran; Krüger, Peter; Lipman, Jeff; Bialasiewicz, Seweryn; Coin, Lachlan; Roberts, Jason A; Paterson, David L; Irwin, Adam D (2024). Rapid nanopore sequencing and predictive susceptibility testing of positive blood cultures from intensive care patients with sepsis. Microbiology Spectrum, 12(2):e0306523.
Notes :
application/pdf, info:doi/10.5167/uzh-253578, English, English
Publication Type :
Electronic Resource
Accession number :
edsoai.on1443056055
Document Type :
Electronic Resource