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- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 classification A1.
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 date "2024".
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 language "eng".
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 type journalArticle.
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 hasPart 01JJ1ZRQVVWHPH1B7HB7ZGM8K0.pdf.
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 subject "Medicine and Health Sciences".
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 doi "10.3390/diagnostics14161800".
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 issn "2075-4418".
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 issue "16".
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 volume "14".
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 abstract "Whole-genome sequencing (WGS) is revolutionizing clinical bacteriology. However, bacterial typing remains investigated by reference techniques with inherent limitations. This stresses the need for alternative methods providing robust and accurate sequence type (ST) classification. This study optimized and evaluated a GridION nanopore sequencing protocol, adapted for the PromethION platform. Forty-eight Escherichia coli clinical isolates with diverse STs were sequenced to assess two alternative typing methods and resistance profiling applications. Multi-locus sequence typing (MLST) was used as the reference typing method. Genomic relatedness was assessed using Average Nucleotide Identity (ANI) and digital DNA-DNA Hybridization (DDH), and cut-offs for discriminative strain resolution were evaluated. WGS-based antibiotic resistance prediction was compared to reference Minimum Inhibitory Concentration (MIC) assays. We found ANI and DDH cut-offs of 99.3% and 94.1%, respectively, which correlated well with MLST classifications and demonstrated potentially higher discriminative resolution than MLST. WGS-based antibiotic resistance prediction showed categorical agreements of >= 93% with MIC assays for amoxicillin, ceftazidime, amikacin, tobramycin, and trimethoprim-sulfamethoxazole. Performance was suboptimal (68.8-81.3%) for amoxicillin-clavulanic acid, cefepime, aztreonam, and ciprofloxacin. A minimal sequencing coverage of 12x was required to maintain essential genomic features and typing accuracy. Our protocol allows the integration of PromethION technology in clinical laboratories, with ANI and DDH proving to be accurate and robust alternative typing methods, potentially offering superior resolution. WGS-based antibiotic resistance prediction holds promise for specific antibiotic classes.".
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 author 00EBF70E-F0EE-11E1-A9DE-61C894A0A6B4.
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 author 0160F766-F0EE-11E1-A9DE-61C894A0A6B4.
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 author 0D4B3CC6-F0EE-11E1-A9DE-61C894A0A6B4.
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 author C69913BA-02FD-11E4-89C9-5E074B2F559A.
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 author F465E2B0-F0ED-11E1-A9DE-61C894A0A6B4.
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 author F5BB79FE-F0ED-11E1-A9DE-61C894A0A6B4.
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 author F5BC58D8-F0ED-11E1-A9DE-61C894A0A6B4.
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 author urn:uuid:54b4a56c-35d4-47db-8334-36a1e51cad6d.
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 author urn:uuid:e9ddaafe-2c1e-43fb-8fba-e3d437837fa8.
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 author urn:uuid:f1283d1b-ef81-4da3-a8b3-54cafbc2ea8f.
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 dateCreated "2025-01-20T13:41:16Z".
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 dateModified "2025-01-21T11:20:02Z".
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 name "Average nucleotide identity and digital DNA-DNA hybridization analysis following PromethION nanopore-based whole genome sequencing allows for accurate prokaryotic typing".
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 pagination urn:uuid:d4422d0a-d99e-4342-8ae4-024edaa3d9c5.
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 sameAs LU-01JJ1Z4DYMVYE0CCB9ZRFBQBM2.
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 sourceOrganization urn:uuid:51d95bab-18b8-461c-9817-f3dfcbc4ced5.
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 sourceOrganization urn:uuid:a0bff5f5-cd4f-43f2-ab89-8d3b58262fbb.
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 sourceOrganization urn:uuid:c82fa2e9-f550-4f07-8c00-b6c6b0afc03f.
- 01JJ1Z4DYMVYE0CCB9ZRFBQBM2 type A1.