Data
element Name
|
Data
element Definition
|
Program_or_pathogen
|
ARLN program
|
Reported_to_submitter_date
|
Date reported to
the submitter (clinical lab or healthcare facility of origin) by
the jurisdictional PHL
Granularity = day
|
Clinical_sample_or_isolate
|
Indicates
whether the specimen received for testing was a clinical sample or
an isolate
|
Reporting_month
|
This is the year
and month this report is counted for CDC reporting; it is based on
the date of collection.
|
Patient_ID
|
1.Unique patient
ID assigned by the public health department,
2. Unique
patient ID assigned by the ARLN testing lab. This could be the
Accession number of the isolate tested by PHLab (Also known as the
ARLN specimen ID), or
3. Other unique patient ID
|
Patient_age
|
Age at specimen
collection date
|
Patient_age_unit
|
Could be years,
months, days
|
Patient_sex
|
This is the
administrative sex (PID-8)
|
PHL
|
The coded
representation of any state PHL plus PR and some city labs
|
ARLN_PHL
|
The coded
representation of the ARLN regional lab
|
Healthcare_facility_of_origin_ID
|
All: ID of the
Healthcare facility of origin (ad-289) Where patient is located
when testing was initiated. Preferred ID type is either the NPI
or the Medicare ID (collected by NHSN program, so helpful for
linking)
|
Healthcare_facility_of_origin_name
|
All: Where the
patient was located when testing was initiated.
For
CPO Colonization this may be the same “submitter”
(duplicate of data contained in Submitter_facility_name).
Example: Fairview Hospital
|
Healthcare_facility_of_origin_state
|
State of the
healthcare facility of origin (ad-289)
|
Healthcare_facility_of_origin_zipcode
|
Zip code of the
healthcare facility of origin (ad-289)
|
Processing_Laboratory_ID
|
CRE/CRPA/CRAB/CPO
col This is the ID for the Processing laboratory (ad-192). The
preferred identifier type to use is CLIA number, NPI is also
allowed.
|
Submitter_facility_ID
|
ID of the
submitting facility (ad-124)
|
Submitter_facility_name
|
The name of the
facility or clinical laboratory that collected and processed the
specimen and sent it (and a request for testing) to the ARLN lab,
and to which the testing public health lab is reporting the
results back to.
|
Submitter_facility_state
|
State of the
submitting facility (ad-124)
|
Submitter_facility_zipcode
|
Zip code of the
submitting facility (ad-124)
|
Specimen_collection_date
|
Date or
Date/Time specimen collected
|
Specimen_received_date
|
Date or
Date/Time specimen received for ARLN testing
|
Submitter_Specimen_ID
|
This is the
Specimen ID assigned by the submitting entity (facility,
laboratory, etc). This is the placer specimen ID and is populated
in SPM-2.1.
|
ARLN_Specimen_ID
|
The
ARLN_Specimen_ID is the testing lab's specimen ID, this is also
the filler specimen ID, which is populated in SPM 2.2.
|
Specimen_type
|
Specimen
type
This is describing the clinical specimen.
|
Isolate_forwarded_to_RegLab
|
Identifies that
the PHL has forwarded an isolate to an ARLN regional lab for
additional testing.
|
Date_forwarded_to_RegLab
|
The date a PHL
has forwarded an isolate to an ARLN regional lab (ad-159) for
additional testing. Granularity = day
|
Organism_tested
|
Identifies the
organism that testing was performed on
|
Confirmed_carbapenem_resistant
|
Was the
phenotypic test result confirmed by AST testing (Yes/No)
|
AST_method_used
|
Identifies which
method of susceptibility testing was used; e.g. Etest, broth micro
dilution, disk diffusion
|
Amikacin_AST_MIC
|
Amikacin MIC
|
Amikacin_AST_zone_diameter
|
Amikacin zone
diameter
|
Ciprofloxacin_AST_MIC
|
Ciprofloxacin
MIC
|
Ciprofloxacin_AST_zone_diameter
|
Ciprofloxacin
zone diameter
|
Doxycycline_AST_MIC
|
Doxycycline MIC
|
Doxycycline_AST_zone_diameter
|
Doxycycline zone
diameter
|
Gentamicin_AST_MIC
|
Gentamicin MIC
|
Gentamicin_AST_zone_diameter
|
Gentamicin zone
diameter
|
HP_Aztreonam_MIC
|
Aztreonam MIC by
HP printer method
|
HP_Aztreonam_Avibactam_MIC
|
Aztreonam
Avibactam MIC by HP printer method
|
HP_Ceftazidime_Avibactam_MIC
|
Ceftazidime
Avibactam MIC by HP printer method
|
HP_Ceftazidime_Aztreonam_Avibactam_MIC
|
Ceftazidime
Aztreonam Avibactam MIC by HP printer method
|
HP_new_drug_mic
|
New drug MIC
tested using HP Printer method
|
Aztreonam_AST_MIC
|
Numeric value
(SN data type)
|
Aztreonam_AST_zone_diameter
|
Numeric value
(SN data type)
|
Cefepime_AST_MIC
|
Numeric value
(SN data type)
|
Cefepime_AST_zone_diameter
|
Numeric value
(SN data type)
|
Cefotaxime_AST_MIC
|
Numeric value
(SN data type)
|
Cefotaxime_AST_zone_diameter
|
Numeric value
(SN data type)
|
Cefotaxime_clavulanate_AST_MIC
|
Numeric value
(SN data type)
|
Cefotaxime_clavulanate_AST_zone_diameter
|
Numeric value
(SN data type)
|
Ceftazidime_AST_MIC
|
Numeric value
(SN data type)
|
Ceftazidime_AST_zone_diameter
|
Numeric value
(SN data type)
|
Ceftazidime_clavulanate_AST_MIC
|
Numeric value
(SN data type)
|
Ceftazidime_clavulanate_AST_zone_diameter
|
Numeric value
(SN data type)
|
Ceftriaxone_AST_MIC
|
Numeric value
(SN data type)
|
Ceftriaxone_AST_zone_diameter
|
Numeric value
(SN data type)
|
Colistin_AST_MIC
|
Numeric value
(SN data type)
|
Doripenem_AST_MIC
|
Numeric value
(SN data type)
|
Doripenem_AST_zone_diameter
|
Numeric value
(SN data type)
|
Ertapenem_AST_MIC
|
Numeric value
(SN data type)
|
Ertapenem_AST_zone_diameter
|
Numeric value
(SN data type)
|
Imipenem_AST_MIC
|
Numeric value
(SN data type)
|
Imipenem_AST_zone_diameter
|
Numeric value
(SN data type)
|
Meropenem_AST_MIC
|
Numeric value
(SN data type)
|
Meropenem_AST_zone_diameter
|
Numeric value
(SN data type)
|
Piperacillin_tazobactam_AST_MIC
|
Numeric value
(SN data type)
|
Piperacillin_tazobactam_AST_zone_diameter
|
Numeric value
(SN data type)
|
Other_3rdGen_cephalosporin_name
|
If another 3rd
generation cephalosporin was tested, specify its name
|
Other_3rdGen_cephalosporin_AST_MIC
|
Numeric value
(SN data type)
|
Other_3rdGen_cephalosporin_AST_zone_diameter
|
Susceptibility
result for other 3rd generation cephalosporin. Method is disk
diffusion
|
Other_new_drug
|
New drug name
|
Other_new_drug_result
|
New drug
MIC/Zone diameter results
|
PCR_method_used
|
Identifies which
PCR test method was used; e.g. Cepheid Xpert Carba-R assay, CDC
assay, Other assay.
|
IMP_gene
|
Result of PCR
for IMP carbapenemase gene
|
KPC_gene
|
Result of PCR
for KPC carbapenemase gene
|
mcr_1_gene
|
Result of PCR
for mcr-1 mobile colistin resistance gene
|
mcr_2_gene
|
Result of PCR
for mcr-2 mobile colistin resistance gene
|
mcr_3_gene
|
Result of PCR
for mcr-3 mobile colistin resistance gene
|
mcr_4_gene
|
Result of PCR
for mcr-4 mobile colistin resistance gene
|
NDM_gene
|
Result of PCR
for NDM carbapenemase gene
|
OXA_48_like_gene
|
Result of PCR
for OXA-48-like carbapenemase gene
|
OXA_24_40_gene
|
Result of PCR
for OXA-24/40-like carbapenemase gene
|
OXA_58_gene
|
Result of PCR
for OXA-58-like carbapenemase gene
|
OXA_235_gene
|
Result of PCR
for OXA-235-like carbapenemase gene
|
OXA_23_gene
|
Provisional
definition: Result of PCR for OXA-23-like carbapenemase gene
|
VIM_gene
|
Result of PCR
for VIM carbapenemase gene
|
Other_gene_name
|
Free text entry
to name the carbapenemase gene that was tested for, that is not
pre-defined.
|
Other_gene_result
|
Result of PCR
for other carbapenemase gene
|
WGS_SRA
|
NCBI SRA
Accession number (SRX#), is one of the IDs generated by NCBI when
public health labs upload whole genome sequence data to NCBI. This
provides access to both the sequence data and metadata connected
with the isolate and serves as the link between sequencing data
and phenotypic data generated for each isolate.
|
WGS_MetaData
|
any data
associated with the WGS isolates
|
Outbreak_ID
|
ID assigned to
isolates for outbreak purposes
|
RegLab_comment
|
Any comment from
the ARLN Regional Lab
|
Index_case_information
|
Elements
associated with index case that initiates screening in a facility
(may include organism, resistance mechanisms, public health ID, or
facility ID).
|