Evaluation of the InTray and Compact Dry culture systems for the diagnosis of urinary tract infections - ARGUS study dataset

Persistent Identifier:

https://doi.org/10.17037/DATA.00001997

Description:

Antimicrobial resistance surveillance data is lacking from many resource-limited settings mainly due to limited laboratory testing. Novel culture systems may address some of the limitations of conventional culture media and expand the availability of microbiology services. This data was collected for an evaluation of the performance of two novel culture media: InTray COLOREX Screen/ESBL and Compact Dry for the detection of uropathogens and of extended-spectrum beta-lactamase (ESBL) producing organisms from urine samples.

Description of data capture:

Basic demographic data was collected during interviews with study participants who provided written informed consent prior to enrollment into the study. The dataset focuses on the results of laboratory testing. Urine cultures were performed using a reference media and the performance of two novel culture media was evaluated and compared to the reference. Culture result data was captured using case report forms.

Intray Dataset Codebook

CFU: colony forming units

Variable name Variable description Variable type Answer code Answer label
Number Non-linked participant ID number integer 1 to 431  
Age_group Age bands of 5 years (excepting 18-24 years) categorical    
      18-24  
      25-29  
      30-34  
      35-39  
      40-44  
      45-49  
      50-54  
      55-59  
      60-64  
      65-69  
      70-74  
      75-79  
      80-84  
      85-89  
      90-95  
sex Sex categorical    
      1 Male
      2 Female
HIV status Reported HIV status categorical    
      0 Negative
      1 Positive
      9 unknown/ not answered
Culture result Culture result on the reference media categorical    
      No growth  
      Contamination  
      103-104 CFU/ml  
      104-105 CFU/ml  
      105 CFU/ml  
Organism Organism isolated from culture (positive cultures only: culture result =1) categorical      
      E. coli  
      Coliforms  
      Morganella group  
      Enterococcus spp  
      S. aureus  
      Missing not applicable if culture negative/ contaminated
cefpodoxime Antibiotic susceptibility test for cefpodoxime (for Enterobacteriaceae only = E. coli, Coliforms or Proteus, Providencia and Morganella group) Categorical      
      0 sensitive
      1 resistant
      Missing not done if culture negative/ contaminated/ organism Enterococcus spp or Staphylococcus spp
ESBL Presence of extended-spectrum beta-lactamases IF organism is Enterobacteriaceae (E. coli, Coliforms or Proteus, Providencia and Morganella group) AND cefpodoxime =1 (resistant) Categorical      
      Present  
      Absent  
      Missing not done if organism is not Enterobacteriaceae and cefpodoxime is sensitive
Intray taken out Number of times the InTray was taken out of the refrigerator to be sent to the field Integer    
      Number  
      Missing missing value
Intray result Culture result using the InTray screen categorical    
      0 No growth
      1 Positive culture with a pathogen
      2 Some growth of non-pathogenic bacteria or insignificant growth of a pathogen (<5 CFU)
      3 Growth of a non-pathogenic bacteria (more than at #2)
Intray organism Organism identified using the InTray (only for positive cultures with pathogenic bacteria: InTray result = “1”) categorical          
      E. coli  
      Coliforms  
      Proteus (includes Proteus, Providencia, Morganella)  
      Enterococcus spp.  
      S. aureus  
      Missing culture negative on InTray/ contamination/ growth of non-pathogenic organisms
Intray growth (enterobacteria) Growth on InTray (classification applicable to enterobacteria) categorical    
      0 negative/ insignificant growth
      1 5-49 CFU/ plate
      2 50-100 CFU/ plate
      3 confluent growth (CFUs cannot be counted)
      Missing Culture is contaminated on Brilliance UTI agar
CD 103 Number of colonies on Compact Dry at 1: 103 dilution integer    
      Numeric value Number of colonies on Compact Dry at 1: 103 dilution
      999 semi-confluent growth
      9999 confluent growth
CD 106 Number of colonies on Compact Dry at 1: 106 dilution integer    
      Numeric value Number of colonies on Compact Dry at 1: 106 dilution
      999 semi-confluent growth
      9999 confluent growth
CD category 103 Growth on Compact Dry at dilution 103 (this is a variable derived from CD 103) categorical    
      0 Negative/ insignificant growth
      5 5-49 CFU/ml
      50 50-250 CFU/ml
      250 >250 colonies/ semi-confluent growth
      9998  Confluent growth
CD category 106 Growth on Compact Dry at dilution 106 (this is a variable derived from CD 106) categorical    
      0 Negative/ insignificant growth
      5   5-49 CFU/ml
      50 50-250 CFU/ml
      250 >250 colonies/ semi-confluent growth
      9998 Confluent growth
CD positive Growth on Compact Dry categorical    
      0 No growth  
      1 Growth (significant)