Monthly Data Report Form for Carbapenemase-producing Org

Form Approved

OMB Control No.: 0920-1310

Expiration date: XX/XX/XXXX

Monthly Data Report Form for Carbapenemase-producing Organisms

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).
phenotypic_test_result	Result of the mCIM or Carba NP carbapenemase test.
Plazomicin_MIC	Plazomicin [Susceptibility] by Minimum inhibitory concentration (MIC)
Plazomicin_zd	Plazomicin [Susceptibility] by Disk Diffusion (KB)
Polymixin_B_MIC	Polymyxin B [Susceptibility] by Minimum inhibitory concentration (MIC)
Polymixin_B_zd	Polymyxin B [Susceptibility] by Disk diffusion (KB)
processing_laboratory_id_assigner	The organization or system that assigned the Laboratory Identifier
protein_test_method	Identifies what protein detection method was used - e.g. Carba 5. This element has been replaced by Test_method.
reason_for_study	Reason for testing by the AR lab
reglab_comment_obr	Any comment from the testing Lab
reglab_comment_obx	Any comment from the testing Lab
reglab_comment_pid	Any comment from the testing Lab
reglab_comment_pid reglab_comment_obr reglab_comment_obx	Any comment from the testing Lab
sending_facility	The coded representation of any state PHL plus PR and some city labs that are performing ARLN testing (includes the ARLN Regional Labs (previously the ARLN_PHL data element))
sim_gene	Result of PCR for SIM carbapenemase gene
specimen_type_free_text	Specimen type This is describing the clinical specimen.
spm_gene	Result of PCR for SPM carbapenemase gene
srr_number	Sequence Read Run (SRR) Number uniquely identifies an individual sequence obtained during one rune of the experiment (linked to SRX).
submitter_facility_name	For CPO Colonization: The name of the facility that collected and processed the specimen and sent it (and a request for testing) to the ARLN regional lab; e.g. the organization who enters the order into the portal for CPO Colonization. This can be either the Healthcare Facility of origin (ad-289), or the Public Health Department (ad-295) For CRE/CRPA/Act2: The name of the clinical laboratory (ad-NEW), defined as a hospital or external reference laboratory that the testing lab is reporting the results back to. For MDB: The name of the Public Health laboratory (ad-285), that the testing lab is reporting the results back to. For GC: The coded representation of the Jurisdiction_PHL (ad-187) or the GC_facility name (ad-302), that the testing lab is reporting the results back to.
submitter_specimen_id_assigner1	The organization or system that assigned the specimen identifier
submitter_specimen_id_assigner2	The organization or system that assigned the specimen identifier
test_method	CPO Col/CRE/CRPA/Act2: Identifies which method was used for testing For susceptibility testing e.g. Etest, broth micro dilution, disk diffusion, for PCR e.g. Cepheid Xpert Carba-R assay, CDC assay, Other assay or for phenotypic testing e.g. mCIM, CIM or Carba NP
test_performed	This describes the data element to be collected. It can be used as a generic for NEW tests
Tetracycline_MIC	Tetracycline [Susceptibility] by Minimum inhibitory concentration (MIC)
Tetracycline_zd	Tetracycline [Susceptibility] by Disk diffusion (KB)
Ticarcillin_Clavulanate_Constant2_MIC	Ticarcillin+Clavulanate [Susceptibility] by Minimum inhibitory concentration (MIC)
Ticarcillin_Clavulanate_Constant2_zd	Ticarcillin+Clavulanate [Susceptibility] by Disk diffusion (KB)
Tigecycline_MIC	Tigecycline [Susceptibility] by Minimum inhibitory concentration (MIC)
Tigecycline_zd	Tigecycline [Susceptibility] by Disk diffusion (KB)
Tobramycin_MIC	Tobramycin [Susceptibility] by Minimum inhibitory concentration (MIC)
Tobramycin_zd	Tobramycin [Susceptibility] by Disk diffusion (KB)
Trimethoprim_Sulfamethoxazole_MIC	Trimethoprim+Sulfamethoxazole [Susceptibility] by Minimum inhibitory concentration (MIC)
Trimethoprim_Sulfamethoxazole_zd	Trimethoprim+Sulfamethoxazole [Susceptibility] by Disk diffusion (KB)
vim_protein	Result of Rapid Immunoassay for VIM
wgs_date_id_created	Date the WGS ID was created
wgs_date_put_on_sequencer	Date the sample was placed on the sequencing instrument
wgs_date_sent_to_seqfac	Date the sample was sent to the core sequencing facility within the PHL
wgs_id	Lab assigned Sequence ID: this is the ID used by the lab to upload the sequencing data to the national repositories (e.g., GISAID, NCBI Gene Bank) and will be useful in retrieving more data about the variant from those repositories as it will be incorporated into the virus name for the sequence.

Public reporting burden of this collection of information is estimated to average 20 minutes per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing the collection of information.  An agency may not conduct or sponsor, and a person is not required to respond to a collection of information unless it displays a currently valid OMB Control Number.  Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing this burden to CDC/ATSDR Reports Clearance Officer, 1600 Clifton Road NE, MS H21-8, Atlanta, Georgia 30333; ATTN: PRA 0920-1310