Computational protocol: Antimicrobial resistance acquisition after international travel in U.S. travelers

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Protocol publication

[…] At the time of enrollment and within 6 weeks of return from travel, patients had culture swabs obtained from the anterior nares, oropharynx, groin, and perirectal area to determine bacterial colonization. BD CultureSwab™ MaxV(+) (Becton, Dickinson and Company, Franklin Lakes, NJ) was used to sample all sites for detection of bacteria. Swabs were plated onto sheep blood, MacConkey agar, and CHROMagar™ Staph aureus in order to isolate all gram-negative bacterial colonies and S. aureus. Colonies demonstrating morphology consistent with gram-negative or S. aureus were subcultured onto sheep blood agar in order to assure culture purity. All isolates were frozen at −80 °C in Trypticase Soy Broth with 15 % glycerol. Individual colonies underwent further automated testing (BD Phoenix™ Automated Microbiology System-Becton Dickinson, Franklin Lakes, NJ) for identification and antimicrobial susceptibility testing.Non-ESBL pre- and ESBL-producing post-travel E. coli within a subject were compared by pulsed-field gel electrophoresis (PFGE) to determine genetic relatedness. The U.S. Food and Drug Administration protocol for gram-negative rods and Xba I endonuclease were utilized to evaluate genotypic patterns among the isolates and subsequently group them into pulsed-field types (PFTs). Clonality was assessed using the commercial software BioNumerics (Applied Maths, Inc., Austin, TX) and defined by 85 % similarity. Multiplex PCRs were performed to determine their phylogenetic groups (A, B1, B2, C, D, E, F, Clade I) per the revised Clermont method []. [...] The McNemar test was used to compare overall rates of pre- and post-travel ESBL and resistant gram-negative bacteria, S. aureus, and resistance to select antibacterial agents. Risk factor analysis was evaluated with χ 2 and Fisher’s exact test (when expected cell counts were less than 5) for categorical variables and Mann–Whitney U for continuous variables. A p value of <0.05 was used as a significant cutoff. Statistical analyses were performed using SPSS software (IBM® SPSS® Statistics Version 19, Chicago, Illinois). […]

Pipeline specifications

Software tools BioNumerics, SPSS
Applications Miscellaneous, Phylogenetics
Organisms Escherichia coli, Epipremnum aureum, Staphylococcus aureus, Homo sapiens
Diseases Malaria
Chemicals Ampicillin, Proguanil, Methicillin, Sulbactam, Tetracycline, Trimethaphan, Atovaquone