Multilocus Sequence Typing and PFGE Analysis

The sequences of seven loci (adk, fumC, gyrB, icd, mdh, purA, and recA) were amplified using PCR, and STs were determined by sequence alignment using the Achtman scheme available at https://pubmlst.org/escherichia/. Genetic relatedness among identified isolates were analyzed using the PFGE method as described previously (31 (link)). The similarity index was calculated with the Dice coefficient and dendrogram constructed by the UPGMA (unweighted pair group method using average linkages) algorithm using GelCompar II software (Applied Maths, Belgium).

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Wang C.H., Siu L.K., Chang F.Y., Chiu S.K, & Lin J.C. (2021). A Resistance Mechanism in Non-mcr Colistin-Resistant Escherichia coli in Taiwan: R81H Substitution in PmrA Is an Independent Factor Contributing to Colistin Resistance. Microbiology Spectrum, 9(1), 10.1128/spectrum.00022-21.

Publication 2021

GelCompar II software

Escherichia Pfge Pura Sequence alignment

Corresponding Organization : Tri-Service General Hospital

Other organizations : National Health Research Institutes

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Variable analysis

independent variables

PCR amplification of sequences of seven loci (adk, fumC, gyrB, icd, mdh, purA, and recA)

dependent variables

Sequence typing (ST) determined by sequence alignment using the Achtman scheme
Genetic relatedness among identified isolates analyzed using the PFGE method
Similarity index calculated with the Dice coefficient
Dendrogram constructed by the UPGMA (unweighted pair group method using average linkages) algorithm

control variables

Achtman scheme available at https://pubmlst.org/escherichia/
PFGE method as described previously (31 (link))
GelCompar II software (Applied Maths, Belgium)

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