Molecular Epidemiological Analysis of Bacterial Isolates

All isolates were subjected to molecular epidemiological analysis by PFGE after SmaI digestion using the CHEF Genomic DNA Plug kit (Bio-Rad) according to a standardized protocol [21 (link)]. PFGE was run using a CHEF DRIII system (Bio-Rad). The InfoQuest FP (v5) software (Bio-Rad Laboratories) was used to analyze PFGE profiles, according to interpretation criteria described by Tenover et al. [22 (link)]. Clustering analysis was achieved using Dice similarity coefficients and the unweighted pair group method with averages (UPGMA) at 1.5% optimization and 1.5% position tolerance. Additionally, isolates were typed based on sequencing of the hypervariable region of the S. aureus protein A gene (spa); spa types were assigned MLST sequence types (ST) inferred on the Ridom spaServer (http://spaserver.ridom.de) curated by the SeqNet.org initiative [23 (link)].

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Asiimwe B.B., Baldan R., Trovato A, & Cirillo D.M. (2017). Prevalence and molecular characteristics of Staphylococcus aureus, including methicillin resistant strains, isolated from bulk can milk and raw milk products in pastoral communities of South-West Uganda. BMC Infectious Diseases, 17, 422.

Publication 2017

CHEF Genomic DNA Plug kit CHEF DRIII system

Digestion Gene Genomic Pfge Protein gene Protein region S aureus protein a Smai Tolerance

Corresponding Organization : Istituti di Ricovero e Cura a Carattere Scientifico

Other organizations : Vita-Salute San Raffaele University

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Variable analysis

independent variables

Molecular epidemiological analysis by PFGE after SmaI digestion using the CHEF Genomic DNA Plug kit (Bio-Rad)

dependent variables

PFGE profiles
Spa types
MLST sequence types (ST)

control variables

Standardized protocol for PFGE [21]
Interpretation criteria for PFGE profiles described by Tenover et al. [22]
Ridom spa Server and SeqNet.org initiative for spa typing [23]

controls

Positive control: Not explicitly mentioned.
Negative control: Not explicitly mentioned.

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