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Epidemiology and Surveillance

Whole-Genome Sequencing for Detecting Antimicrobial Resistance in Nontyphoidal Salmonella

Patrick F. McDermott, Gregory H. Tyson, Claudine Kabera, Yuansha Chen, Cong Li, Jason P. Folster, Sherry L. Ayers, Claudia Lam, Heather P. Tate, Shaohua Zhao
Patrick F. McDermott
aDivision of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
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Gregory H. Tyson
aDivision of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
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Claudine Kabera
aDivision of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
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Yuansha Chen
aDivision of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
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Cong Li
aDivision of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
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Jason P. Folster
bDivision of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Sherry L. Ayers
aDivision of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
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Claudia Lam
aDivision of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
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Heather P. Tate
aDivision of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
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Shaohua Zhao
aDivision of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
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DOI: 10.1128/AAC.01030-16
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  • TABLE 1

    Genotype and phenotype comparison of Salmonella isolates from humans and retail meat, 2011 to 2013a

    AntibioticNo. of test resultsSensitivity (%)Specificity (%)PPV (%)NPV (%)
    Phenotype: resistantPhenotype: susceptible
    Genotype: resistantGenotype: susceptibleGenotype: resistantGenotype: susceptible
    Aminoglycosides
        GEN996553094.399.195.298.9
        STR25733534598.890.888.099.1
    Beta-lactam/beta-lactam inhibitor
        AMC1142052498.3100.010099.6
    Cephems
        FOX9322152497.996.181.699.6
        TIO11304523100.099.296.6100
        CRO11601523100.099.899.1100
    Penicillin
        AMP2411139799.699.799.699.7
    Folate pathway inhibitors
        FIS2441039599.6100.010099.7
        SXT193061886.4100.010099.5
    Macrolide
        AZM100639100.0100.0100100
    Phenicol
        CHL4401595100.099.897.8100
    Quinolones
        CIP400636100.0100.0100100
        NAL132062586.7100.010099.7
    Tetracycline
        TET34900291100.0100.0100100
    Total1,70720687,16498.899.196.299.7
    • ↵a Abbreviations: GEN, gentamicin; STR, streptomycin; AMC, amoxicillin-clavulanic acid; FOX, cefoxitin; TIO, ceftiofur; CRO, ceftriaxone; AMP, ampicillin; FIS, sulfisoxazole; SXT, trimethoprim-sulfamethoxazole; AZM, azithromycin; CHL, chloramphenicol; CIP, ciprofloxacin; NAL, nalidixic acid; TET, tetracycline; PPV, positive predictive value; NPV, negative predictive value.

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      Table S1

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      Table S2

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    • Supplemental file 3 -

      Table S3

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    • Supplemental file 4 -

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Whole-Genome Sequencing for Detecting Antimicrobial Resistance in Nontyphoidal Salmonella
Patrick F. McDermott, Gregory H. Tyson, Claudine Kabera, Yuansha Chen, Cong Li, Jason P. Folster, Sherry L. Ayers, Claudia Lam, Heather P. Tate, Shaohua Zhao
Antimicrobial Agents and Chemotherapy Aug 2016, 60 (9) 5515-5520; DOI: 10.1128/AAC.01030-16

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Whole-Genome Sequencing for Detecting Antimicrobial Resistance in Nontyphoidal Salmonella
Patrick F. McDermott, Gregory H. Tyson, Claudine Kabera, Yuansha Chen, Cong Li, Jason P. Folster, Sherry L. Ayers, Claudia Lam, Heather P. Tate, Shaohua Zhao
Antimicrobial Agents and Chemotherapy Aug 2016, 60 (9) 5515-5520; DOI: 10.1128/AAC.01030-16
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