Genomic Analysis of E. coli Isolates

We extracted purified DNA from the isolates using Wizard® Genomic DNA Purification (Promega) kits and QIAGEN© DNEasy Blood & Tissue Kits according to the manufacturer’s instructions. Whole-genome sequencing of E. coli isolates was carried out at the University of Minnesota using Illumina MiSeq with Nextera XT libraries. Raw reads were quality-trimmed and adapter-trimmed using trimmomatic^{40 (link)} and assembled using SPAdes (Bankevich et al. 2012). Antibiotic resistance genes (ARGs) were detected using ABRicate (version 0.813) and a curated version of the ResFinder database (Zankari et al. 2012). We also performed in silico multilocus sequence typing (MLST) based on seven housekeeping genes (adk, fumC, gyrB, icd, mdh, purA, and recA), an additional eight housekeeping genes (dinB, icdA, pabB, polB, putP, trpA, trpB, and uidA), and core genome (cgMLST) using MLST 2.0^{41 (link)} and cgMLSTFinder 1.1^{42 (link)}. Detailed methods are previously described^{43 (link)}.

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Amato H.K., Loayza F., Salinas L., Paredes D., García D., Sarzosa S., Saraiva-Garcia C., Johnson T.J., Pickering A.J., Riley L.W., Trueba G, & Graham J.P. (2023). Leveraging the COVID-19 pandemic as a natural experiment to assess changes in antibiotic use and antibiotic-resistant E. coli carriage in semi-rural Ecuador. Scientific Reports, 13, 14854.

Publication 2023

Wizard® Genomic DNA Purification DNEasy Blood & Tissue Kits

Antibiotic resistance Blood E coli Genes Genome Housekeeping genes Polb Promega Pura Tissue

Corresponding Organization :

Other organizations : University of California, Berkeley, Universidad San Francisco de Quito, University of Minnesota

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Variable analysis

independent variables

DNA extraction method (Wizard® Genomic DNA Purification (Promega) kits and QIAGEN© DNEasy Blood & Tissue Kits)
Whole-genome sequencing method (Illumina MiSeq with Nextera XT libraries)

dependent variables

Antibiotic resistance genes (ARGs) detected
Multilocus sequence typing (MLST) based on seven housekeeping genes, additional eight housekeeping genes, and core genome (cgMLST)

control variables

Manufacturer's instructions for DNA extraction kits
Trimmomatic and SPAdes for read quality-trimming, adapter-trimming, and assembly

positive controls

Not explicitly mentioned

negative controls

Not explicitly mentioned

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