Comprehensive Genomics-based Bacterial Profiling

An individual sequencing library was prepared for each isolate using the NexteraXT DNA sample preparation kit (Illumina, San Diego, CA, USA). Then, isolates were pooled and multiplexed for paired-end sequencing on a single MiSeq instrument, using the MiSeq reagent kit v3 150 bp (Illumina). Libraries were assembled by SeqSphere+ software version 4.1.9 (Ridom GmbH, Muenster, Germany) for automated quality trimming and assembly. The resulting FASTA files were uploaded to the KmerFinder 3.1 on the Center for Genomic Epidemiology and the top Kmer result for each isolate was recorded (18 (link)– (link)20 (link)). Each isolate was also analyzed by the Comprehensive Antibiotic Resistance Database (CARD) and the presence of mecA, mecC, and vanA was determined (17 (link), 21 (link)– (link)23 (link)).

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Garner C.D., Brazelton de Cardenas J., Suganda S, & Hayden R.T. (2021). Accuracy of Broad-Panel PCR-Based Bacterial Identification for Blood Cultures in a Pediatric Oncology Population. Microbiology Spectrum, 9(1), 10.1128/spectrum.00221-21.

Publication 2021

NexteraXT DNA sample preparation kit MiSeq reagent kit v3 150 bp SeqSphere+ software version 4.1.9

Antibiotic resistance Genomic Library Meca Mecc

Corresponding Organization : St. Jude Children's Research Hospital

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Variable analysis

independent variables

None explicitly mentioned

dependent variables

Presence/absence of mecA, mecC, and vanA genes

control variables

None explicitly mentioned

controls

Positive control: Not mentioned
Negative control: Not mentioned

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