Variable,Label,Data Role,Data Type,Units,Level Codes,Prevalence,Ecoli REP-PCR,Antibiotic Resistance,Comments
SampleN,Sample number,Pseudo-Identifier,Count,,,X,X,X,Variable included for ease of sample sorting (Sample ID sorts oddly b/c alphanumeric starting with a number)
Sample ID,Sample identification,Identifier,Nominal,,,X,X,X,
Site,Sampling site,Grouping,Nominal,,Control=Residential neighborhood south of Dairy; Dairy=University Dairy Farm; BeefB=Beef facility south of Dairy Facility; BeefA=Beef facility nearest Dairy,X,X,X,
Source,Sample source,Grouping,Nominal,,"Bird=bird fecal sample or cloacal swab, Env=cow manure or environmental sample",X,X,X,
SourceLong,Source long description,Grouping,Nominal,,Free text description of the sample source for environmental samples and bird age and sex when known,X,,,
BirdSpp,Bird species code,Grouping,Nominal,,"AMGO=American goldfinch, AMRO=American robin, BASW=Barn swallow, BHCB=Brown-headed cowbird, COGR=Common grackle, EAME=Eastern meadowlark, EUST=European starling, GRCB=Grey catbird, GRSP=Grasshopper sparrow, HOSP=House sparrow, MODO=mourning dove, NA=not applicable (environmental sample), RWBB=Red-winged blackbird, SOSP=Song sparrow",X,X,X,
EcoliPA,Presence/absence of Ecoli,Observation,Binomial,,"Positive=isolate from sample confirmed as E. coli, Negative=E. coli was not detected on culture",X,,,
EntPA,Presence/absence of Enterococcus,Observation,Binomial,,"Positive=isolate from sample confirmed as Enterococcus genus, Negative=Enterococcus was not detected on culture",X,,,
EntSpp,Enterococcus species,Observation,Nominal,,"Identification of Enterococcus species from multiplex PCR/sequencing: vium, Casseliflaves, Durans, Faecalis, Faecium, Gallinarum, Haemoperoxidus, Hirae, NA=Not applicable for Enterococcus negative samples",X,,,
SalmPA,Presence/absence of Salmonella,Observation,Binomial,,"Positive=isolate from sample confirmed as Salmonella, Negative=Salmonella was not detected on culture",X,,,
SalmSerovar,Salmonella serovar,Observation,Nominal,,"Identification of Salmonella serovar by serologic testing at NVSL: Havana, Montevideo",X,,,
Band#,REP-PCR band number,Observation,Binomial,,1=Present; 0=Absent,,X,,REP-PCR results are columns labeled Band1-Band58 from genomic fingerprints
BactGenus,Bacterial genus,Grouping,Nominal,,"Escherichia, Enterococcus",,,,
BactSpp,Bacterial species,Grouping,Nominal,,"Ecoli=Escherichia coli, remaining codes for Enterococcus genus are the same as in EntSpp",,,X,
1plusR,Resistant to one or more antibiotic (excluding rifampin),Derived,Binomial,,"1=at least one antibiotic was R, 0=no antibiotics tested R",,,X,"Derived from NR, where 1 was assigned if the value was 2 or greater (excluding Rifamicin, which was resistant for all E. coli isolates)"
1plusRI,Resistant or intermediate to one or more antibiotic (excluding rifampin),Derived,Binomial,,"1=at least one antibiotic was R or I, 0=no antibiotics tested R or I",,,X,"Derived from NRI, where 1 was assigned if the value was 2 or greater (excluding Rifamicin, which was resistant for all E. coli isolates)."
NR,Number of antibiotics in resistant category,Derived,Count,Number of antibiotics,,,,X,Derived by counting the number of R codes in each row
NRI,Number of antibiotics in resistant or intermediate category,Derived,Count,Number of antibiotics,,,,X,Derived by counting the number of R or I codes in each row
NTested,Number of antibiotics tested,Derived,Count,Number of antibiotics,,,,,Derived by counting the number of antibiotics tested for each isolate
Gentamicin (CN120),Gentamicin: diameter of zone of inhibition (mm),Observation,Continuous,mm,,,,X,Measured zone of inhibition from disc diffusion assay
Sulfamethoxazole (SXT1.25/23.75),Sulfamethoxazole: diameter of zone of inhibition (mm),Observation,Continuous,mm,,,,X,Measured zone of inhibition from disc diffusion assay
Tetracycline (TE30),Tetracycline: diameter of zone of inhibition (mm),Observation,Continuous,mm,,,,X,Measured zone of inhibition from disc diffusion assay
Erythromycin (E15),Erythromycin: diameter of zone of inhibition (mm),Observation,Continuous,mm,,,,X,Measured zone of inhibition from disc diffusion assay
Pen G (P10),Penicillin G: diameter of zone of inhibition (mm),Observation,Continuous,mm,,,,X,Measured zone of inhibition from disc diffusion assay
Vancomycin (VA30),Vancomycin: diameter of zone of inhibition (mm),Observation,Continuous,mm,,,,X,Measured zone of inhibition from disc diffusion assay
Cephalothin (KF30),Cephalothin: diameter of zone of inhibition (mm),Observation,Continuous,mm,,,,X,Measured zone of inhibition from disc diffusion assay
Ceftiofur (EFT30),Ceftiofur: diameter of zone of inhibition (mm),Observation,Continuous,mm,,,,X,Measured zone of inhibition from disc diffusion assay
Ampicillin (AM10),Ampicillin: diameter of zone of inhibition (mm),Observation,Continuous,mm,,,,X,Measured zone of inhibition from disc diffusion assay
Tetracycline (TE30),Tetracycline: diameter of zone of inhibition (mm),Observation,Continuous,mm,,,,X,Measured zone of inhibition from disc diffusion assay
Rifampicin (RD5),Rifampicin: diameter of zone of inhibition (mm),Observation,Continuous,mm,,,,X,Measured zone of inhibition from disc diffusion assay
Azithromycin (AZM15),Azithromycin: diameter of zone of inhibition (mm),Observation,Continuous,mm,,,,X,Measured zone of inhibition from disc diffusion assay
AmoxicillinC (AMC30),AmoxicillinC: diameter of zone of inhibition (mm),Observation,Continuous,mm,,,,X,Measured zone of inhibition from disc diffusion assay
Chloramphenicol (C30),Chloramphenicol: diameter of zone of inhibition (mm),Observation,Continuous,mm,,,,X,Measured zone of inhibition from disc diffusion assay
Gentamicin (CN120)-RIS,Susceptibility categorization for Gentamicin,Derived,Ordinal,,"R=Resistance, I=Intermediate, S=Susceptible",,,X,"Ecoli: 6, 7-9, 10; Ent: 6, 7-9, 10; references=CLSI and produce insert from Oxoid/Remel and Difco"
Sulfamethoxazole (SXT1.25/23.75)-RIS,Susceptibility categorization for Sulfamethoxazole,Derived,Ordinal,,"R=Resistance, I=Intermediate, S=Susceptible",,,X,"Ecoli: 10, 11-15, 16; Ent: 10, 11-15, 16; references=CLSI and produce insert from Oxoid/Remel and Difco"
Tetracycline (TE30)-RIS,Susceptibility categorization for Tetracycline,Derived,Ordinal,,"R=Resistance, I=Intermediate, S=Susceptible",,,X,"Ecoli: 14, 15-18, 19; Ent: 14, 15-18, 19;references=CLSI and produce insert from Oxoid/Remel and Difco"
Erythromycin (E15)-RIS,Susceptibility categorization for Erythromycin,Derived,Ordinal,,"R=Resistance, I=Intermediate, S=Susceptible",,,X,"Ecoli: Ecoli are all R; Ent: 13, 14-22, 23; references=CLSI and produce insert from Oxoid/Remel and Difco"
Pen G (P10)-RIS,Susceptibility categorization for Penicillin G,Derived,Ordinal,,"R=Resistance, I=Intermediate, S=Susceptible",,,X,"Ecoli: None for Ecoli; Ent: 14, -, 15; references=CLSI and produce insert from Oxoid/Remel and Difco"
Vancomycin (VA30)-RIS,Susceptibility categorization for Vancomycin,Derived,Ordinal,,"R=Resistance, I=Intermediate, S=Susceptible",,,X,"Ecoli: None for Ecoli; Ent: 14, 15-16, 17; references=CLSI and produce insert from Oxoid/Remel and Difco"
Cephalothin (KF30)-RIS,Susceptibility categorization for Cephalothin,Derived,Ordinal,,"R=Resistance, I=Intermediate, S=Susceptible",,,X,"Ecoli: 14, 15-17, 18; Ent: None for Ent; references=CLSI and produce insert from Oxoid/Remel and Difco"
Ceftiofur (EFT30)-RIS,Susceptibility categorization for Ceftiofur,Derived,Ordinal,,"R=Resistance, I=Intermediate, S=Susceptible",,,X,"Ecoli: 17, 18-20, 21; Ent: None for Ent; references=CLSI and produce insert from Oxoid/Remel and Difco"
Ampicillin (AM10)-RIS,Susceptibility categorization for Ampicillin,Derived,Ordinal,,"R=Resistance, I=Intermediate, S=Susceptible",,,X,"Ecoli: 13, 14-16,17; Ent: 16, -, 17; references=CLSI and produce insert from Oxoid/Remel and Difco"
Rifampicin (RD5)-RIS,Susceptibility categorization for Rifampicin,Derived,Ordinal,,"R=Resistance, I=Intermediate, S=Susceptible",,,X,"Ecoli: <8, >10 (ref?); Ent: 16, 17-19, 20; references=CLSI and produce insert from Oxoid/Remel and Difco"
Azithromycin (AZM15)-RIS,Susceptibility categorization for Azithromycin,Derived,Ordinal,,"R=Resistance, I=Intermediate, S=Susceptible",,,X,"Ecoli: -,-,18; Ent: 13, 14-17, 18; references=CLSI and produce insert from Oxoid/Remel and Difco"
AmoxicillinC (AMC30)-RIS,Susceptibility categorization for AmoxicillinC,Derived,Ordinal,,"R=Resistance, I=Intermediate, S=Susceptible",,,X,"Ecoli: 13, 14-17, 18; Ent: none listed for ent.; references=CLSI and produce insert from Oxoid/Remel and Difco"
Chloramphenicol (C30)-RIS,Susceptibility categorization for Chloramphenicol,Derived,Ordinal,,"R=Resistance, I=Intermediate, S=Susceptible",,,X,"Ecoli: 12, 13-17, 18; Ent: non listed for ent.; references=CLSI and produce insert from Oxoid/Remel and Difco"