Isolates with MICs higher than 4, 8 and 4 mg/L to metronidazole, meropenem and imipenem, respectively, or carrying the cfiA gene, as determined by MALDI-TOF MS, were subjected to WGS. DNA extraction was performed using the DNeasy Ultraclean Microbial kit (MO BIO Laboratories, Carlsbad, CA, USA). Library preparation was performed using the Nextera XT v2 kit (Illumina, San Diego, CA, USA), followed by short-read sequencing on an Illumina MiSeq (Illumina) generating 250–300 bp paired-end reads using the MiSeq reagent kit v2 or v3, respectively.17 (link) Using CLC Genomics workbench v12 (QIAGEN, Hilden, Germany), de novo assembly was performed.17 (link) Analysis of WGS data, including detection of ARGs and MGEs, was performed as described previously.12 (link) The identity of the isolates was confirmed by comparing the 16S rRNA gene with the NCBI database using BLASTn (https://blast.ncbi.nlm.nih.gov/ ).
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Whole Genome Sequencing of Resistant Isolates
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Corresponding Organization :
Other organizations : University Medical Center Groningen, University of Groningen, National Institute for Public Health and the Environment, Academic Medical Center, University Medical Center Utrecht, Leiden University Medical Center, Erasmus MC, Radboud University Nijmegen, Radboud University Medical Center, Maastricht University, PAMM, Certe, Isala, University of Utah
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Variable analysis
independent variables
- Isolates with MICs higher than 4, 8 and 4 mg/L to metronidazole, meropenem and imipenem, respectively
- Isolates carrying the cfiA gene, as determined by MALDI-TOF MS
- Whole-genome sequencing (WGS) data
- DNA extraction using the DNeasy Ultraclean Microbial kit (MO BIO Laboratories, Carlsbad, CA, USA)
- Library preparation using the Nextera XT v2 kit (Illumina, San Diego, CA, USA)
- Short-read sequencing on an Illumina MiSeq (Illumina) generating 250–300 bp paired-end reads using the MiSeq reagent kit v2 or v3
- De novo assembly using CLC Genomics workbench v12 (QIAGEN, Hilden, Germany)
- Analysis of WGS data, including detection of ARGs and MGEs, as described previously
- None specified
- None specified
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