CAROS Data Dictionary_ Feb24 {24DS}

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Overview

LAB TABLE
CLINIC TABLE
ALERT REPORT

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Sheet 1: LAB TABLE

Variable Name	Variable Definition/Description	Value Definition	Var Type	Var Length	Null Allowed?	Acceptable Null Value
CARGOS_SPEC_ID	Unique Specimen ID consisting of sentinel site code + YYYYMM (month isolate collected) + isolate number (001 through 999) generated at the clinic/lab. If a patient has more than one specimen on the same date, the CARGOS_SPEC_ID will be the unique identifier for each specimen. Note: This CARGOS_SPEC_ID must be included on the specimen sent to the ARLN and will be used to link laboratory, clinic, and epi investigation data.	Character ID. Ex: ABC-202301-001 ABC-202301-199	char	14	No
SITE	3 character sentinel site code.	DEN=Denver (CO)	char	3	No
PATIENTID	Unique patient/person identification number; 18 character limit. ID must be unique per person and cannot include any personally identifiable information (PII). CARGOS grantees may elect to have this ID match the unique patient ID generated from their NEDDS Surveillance system for GC-positive patients or other unique patient ID. Note: This patient ID must be the same as the patient ID attached to CARGOS isolates sent to the ARLN and will be used to link all laboratory, clinical, and epi investigation data.		char	18	No
EVENTID	Case ID/Event ID of case. Event identifier distinguishes each GC diagnosis, or for GC-negative contacts, each clinic testing visit event. This ID stays the same for the entire GC event, which could include testing, treatment, and TOC visits. This ID is up to 18 characters in length.		char	18	No
LAB_GENDER	Gender	1=Male 2=Female 3=Female-to-male transgender (FTM) 4=Male-to-female transgender (MTF) 5=Other gender identity (including: non-binary, transgender unspecified, etc.) 8=Refused to Answer 9=Unknown	char	1	No
JURIS_PHL	Local public health laboratory where specimen was processed	DEL=Denver PHL (CO)	char	3	No
FACILITY	Submitter facility ID from where specimen was collected.	Facility codes (See Appendix for more details)	char	6	No
SPEC_COLLECT_DATE	Specimen collection date	YYYY/MM/DD; YYMMDDs10.	date	10	No
SPEC_SOURCE	Source of specimen collection	B=Blood C=Conjunctival E=Endocervical O=Other P=Pharyngeal R=Rectal U=Urethral UR=Urine V=Vaginal NC=Not captured	char	2	No
TESTTYPE	Type of specimen test	1=Culture 2=Nucleic acid amplification test (NAAT) 3=Molecular probe/AMR assay 8=Other 9=Unknown	char	1	No	9=unknown
NMENING	Isolate presumed to be N. meningitidis. Isolates are suggestive of N. meningitidis when they have “discordant results” demonstrated by bacterial growth on culture consistent with N. gonorrhoeae (positive culture) and have a negative gonorrhea NAAT result. In the case of urethral specimens, the isolate should demonstrate Gram-negative intracellular diplococci by microscopy but have a negative gonorrhea NAAT result. Please note: Variable used to identify isolates presumed to be N. meningitidis. For all isolates presumed to be N. meningitidis, select response option "1" and leave DATESENTARLN blank. For all N. gonorrhoeae isolates, leave null.	1= Presumed N. meningitidis isolate	char	1	Yes	null
OTH_TEST	Other test		char	50	Yes	null
OTH_RESULT	Other test result		char	50	Yes	null
DATESENTARLN	Date isolate sent to ARLN laboratory	YYYY/MM/DD; YYMMDDs10.	date	10	Yes	null
PENA311	Molecular testing result for penA 311 genetic marker. Note: For N. gonorrhoeae isolates only	0=Mutation absent 1=Mutation present 2=Test failed 3=Indeterminate 9=Test not performed	char	1	Yes	null
PENA311_DATE	Date of molecular test for penA 311 genetic mutation.	YYYY/MM/DD; YYMMDDs10.	date	10	Yes	null
PENA515	Molecular testing result for penA 515 genetic mutation. Note: For N. gonorrhoeae isolates only	0=Mutation absent 1=Mutation present 2=Test failed 3=Indeterminate 9=Test not performed	char	1	Yes	null
PENA515_DATE	Date of molecular test for penA 515 genetic mutation.	YYYY/MM/DD; YYMMDDs10.	date	10	Yes	null
PENA545	Molecular testing result for penA 545 genetic mutation. Note: For N. gonorrhoeae isolates only	0=Mutation absent 1=Mutation present 2=Test failed 3=Indeterminate 9=Test not performed	char	1	Yes	null
PENA545_DATE	Date of molecular test for penA 545 genetic mutation	YYYY/MM/DD; YYMMDDs10.	date	10	Yes	null
GYRA91	Molecular testing result for gyrA 91 genetic mutation. Note: For N. gonorrhoeae isolates only	0=Mutation absent 1=Mutation present 2=Test failed 3=Indeterminate 9=Test not performed	char	1	Yes	null
GYRA91_DATE	Date of molecular test for gyrA 91 genetic mutation.	YYYY/MM/DD; YYMMDDs10.	date	10	Yes	null
_23S2611	Molecular testing result for 23S 2611 genetic mutation. Note: For N. gonorrhoeae isolates only	0=Mutation absent 1=Mutation present 2=Test failed 3=Indeterminate 9=Test not performed	char	1	Yes	null
_23S2611_DATE	Date of molecular test for 23S 2611 genetic mutation.	YYYY/MM/DD; YYMMDDs10.	date	10	Yes	null
_23S2059	Molecular testing result for 23S 2059 genetic mutation. Note: For N. gonorrhoeae isolates only	0=Mutation absent 1=Mutation present 2=Test failed 3=Indeterminate 9=Test not performed	char	1	Yes	null
_23S2059_DATE	Date of molecular test for 23S 2059 genetic mutation.	YYYY/MM/DD; YYMMDDs10.	date	10	Yes	null
PORA	Molecular testing result for por A genetic mutation. Note: For N. gonorrhoeae isolates only	0=Mutation absent 1=Mutation present 2=Test failed 3=Indeterminate 9=Test not performed	char	1	Yes	null
PORA_DATE	Date of molecular test for por A genetic mutation.	YYYY/MM/DD; YYMMDDs10.	date	10	Yes	null
PENA501	Molecular testing result for penA 501 genetic mutation. Note: For N. gonorrhoeae isolates only	0=Mutation absent 1=Mutation present 2=Test failed 3=Indeterminate 9=Test not performed	char	1	Yes	null
PENA501_DATE	Date of molecular test for penA 501 genetic mutation.	YYYY/MM/DD; YYMMDDs10.	date	10	Yes	null

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Sheet 2: CLINIC TABLE

Variable Name	Variable Definition/Description	Value Definition	Var Type	Var Length	Null Allowed?	Acceptable Null Value
PATIENTID	Unique patient/person identification number; 18 character limit. ID must be unique per person and cannot include any personally identifiable information (PII). CARGOS grantees may elect to have this ID match the unique patient ID generated from their NNDSS Surveillance system for GC-positive patients or other unique patient ID. Note: This patient ID must be the same as the patient ID attached to CARGOS isolates sent to the ARLN and will be used to link all laboratory, clinical, and investigation data.		char	18	No
EVENTID	Case ID/Event ID of case. Event identifier distinguishes each GC diagnosis, or for GC-negative contacts, each clinic testing visit event. This ID stays the same for the entire GC event, which could include testing, treatment, and TOC visits. This ID is up to 18 characters in length.		char	18	No
STATE	Patient's state of residence	2-digit FIPS STATE code	char	2	No
VISDATE	Date of clinic visit	YYYY/MM/DD; YYMMDDs10.	date	10	No
CL_FACILITY	Submitter clinic ID where specimen was collected	Facility codes assigned by CDC	char	6	No
GENDER	Patient’s gender. How do you describe your gender identity?	1=Male 2=Female 3=Female-to-male transgender (FTM) 4=Male-to-female transgender (MTF) 5=Other gender identity (including: non-binary, transgender unspecified, etc.) 8=Refused to Answer 9=Unknown	char	1	No	9=unknown
SEXBIRTH	Sex assigned at birth. What sex were you assigned at birth?	1=Male 2=Female 8=Refused to Answer 9=Unknown	char	1	No	9=unknown
AGE	Patient age	999=Unknown	num	3	No	12<PT_AGE<=99 or PT_AGE=999
HISP_ETH	Ethnicity: Hispanic or Latino Is the patient of Hispanic ethnicity?	0=No, not Hispanic/Latino 1=Yes, Hispanic/Latino 8=Refused to Answer 9=Unknown	char	1	No	9=unknown
AIAN	Race: AI/AN-American Indian or Alaskan Native Does the patient identify as American Indian or Alaska Native?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No	9=unknown
ASIAN	Race: Asian Does the patient identify as Asian?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No	9=unknown
NHOPI	Race: NH/PI-Native Hawaiian or Other Pacific Islander Does the patient identify as Native Hawaiian or Pacific Islander?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No	9=unknown
BLACK	Race: Black or African American Does the patient identify as black or African-American?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No	9=unknown
WHITE	Race: White Does the patient identify as White?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No	9=unknown
MULTIRACE	Race: Multirace Does the patient identify as Multirace?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No	9=unknown
OTHRACE	Race: Other Does the patient identify as Other race?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No	9=unknown
GENDER_SP	Gender of sex partners Provider documented gender of patient’s sex partners. For example, sex with partners who are males and/or F-to-M transgender only should be recorded as 1 (Males only). Sex with a questioning/nonbinary/intersex partner should be recorded as 9 (Unknown/Gender not listed). Sex partners who include male and female partners or questioning/intersex partner(s) AND male and/or female partners should be recorded as 3 (more than 1 gender).	1=Males only (includes F-to-M transgender) 2=Females only (includes M-to-F transgender) 3=More than 1 gender 8=Refused to answer 9=Unknown/Gender not listed	char	1	No	9=unknown/gender not listed
HIV_STATUS	Patient- or provider-reported current HIV status	0=HIV-negative 1=HIV-positive 8=Refused to answer 9=Unknown	char	1	No	9=unknown
TRMT1	What is the patient's treatment for gonorrhea?	00=none 03=spectinomycin (Trobicin) 2 gm 04=ceftriaxone (Rocephin) 250 mg 05=ceftriaxone (Rocephin) 125 mg 06=ciprofloxacin (Cipro) 500 mg 07=cefoxitin (Mefoxin) 2 gm 12=cefixime (Suprax) 400 mg 14=cefpodoxime proxetil (Vantin) 200 mg 15=ofloxacin (Floxin) 400 mg 17=ceftizoxime (Cefizox) 500 mg 18=cefotaxime (Claforan) 500 mg 21=azithromycin (Zithromax) 2 gm 22=levofloxacin (Levaquin) 250 mg 23=cefpodoxime proxetil (Vantin) 400 mg 24=ceftibuten (Cedax) 400 mg 25=cefdinir (Omnicef ) 300 mg 26=cefdinir (Omnicef ) 600 mg 27= gemifloxacin 320 mg 28= gentamicin 240 mg (or weight-based dosage) 29=ceftriaxone (Rocephin) 500 mg 30=ceftriaxone (Rocephin) 1g 31=cefixime (Suprax) 800 mg 77=other (please indicate in Other medication prescribed) 99=unknown	char	2	No
MEDICATION1_OTH	If TRMT1 was coded as 77 for ‘other’, please provide the name of the other medication.	Free text field	char	50	Yes	Null
TRMT2	If a second antimicrobial was given specifically for the patient’s gonorrhea treatment, what was it? Note: Please only complete TRMT2 for patients who received two antimicrobials for gonorrhea treatment.	11=azithromycin (Zithromax) 1 gm 21=azithromycin (Zithromax) 2 gm 28= gentamicin 240 mg (or weight-based dosage) 31=cefixime (Suprax) 800 mg 77=other (please indicate in Other medication prescribed)	char	2	Yes	Null
MEDICATION2_OTH	If TRMT2 was coded as 77 for ‘other’, please provide the name of the other medication.	Free text field	char	50	Yes	Null
DATETX	Date patient received treatment for gonococcal infection	YYYY/MM/DD; YYMMDDs10.	date	10	No	Null
HIV_PREP	Current patient HIV PrEP use	0=No 1=Yes 7=Not applicable 8=Refused to Answer 9=Unknown	char	1	No	7=not applicable if patient self-reports being HIV-positive
DOXY_PEP	Has patient taken doxycycline for STI post-exposure prophylaxis within 60 days of clinic visit?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	Yes	Null
MENING_VAX	Prior history of meningococcal vaccination	1= MenACWY vaccine only 2= MenB vaccine only 3= Men ACWY + MenB vaccine 4= Meningococcal/meningitis vaccine, but unknown 5= No meningitis vaccine 9= Unknown	char	1	Yes	null

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Sheet 3: ALERT REPORT

Variable Name	Variable Definition/Description	Value Definition	Var Type	Var Length	Null Allowed?	Acceptable Null Value
PATIENTID	Unique patient/person identification number; 18 character limit. ID must be unique per person and cannot include any personally identifiable information (PII). CARGOS grantees may elect to have this ID match the unique patient ID generated from their NNDSS Surveillance system for GC-positive patients or other unique patient ID. Note: This patient ID must be the same as the patient ID attached to CARGOS isolates sent to the ARLN and will be used to link all laboratory, clinical, and investigation data.		char	18	No
EVENTID	Case ID/Event ID of case. Event identifier distinguishes each GC diagnosis, or for GC-negative contacts, each clinic testing visit event. This ID stays the same for the entire GC event, which could include testing, treatment, and TOC visits. This ID up to 18 characters in length.		char	18
CARGOS_SPEC_ID	Unique Specimen ID consisting of sentinel site code + YYYYMM (month isolate collected) + isolate number (001 through 999) generated at the clinic/lab. If a patient has more than one specimen on the same date, the CARGOS_SPEC_ID will be the unique identifier for each specimen. Note: This CARGOS_SPEC_ID must be included on the specimen sent to the ARLN and will be used to link laboratory, clinic, and epi investigation data.	Character ID. Ex: ABC-202301-001 ABC-202301-199	char	14	No
FACILITY	Submitter facility ID from where specimen was collected.	Facility codes (See Appendix for more details)	char	6	No
STATE	Patient's state of residence	State FIPS	char	2	No
SPEC_COLLECT_DATE	Specimen collection date	YYYY/MM/DD; YYMMDDs10.	date	8	No
SPEC_SOURCE	Source of specimen collection **To be reported for each isolate collected at initial evaluation	B=Blood C=Conjunctival E=Endocervical O=Other P=Pharyngeal R=Rectal U=Urethral UR=Urine V=Vaginal NC=Not captured	char	2	No
GENDER	Patient’s gender. How does the patient describe their current gender identity?	1=Male 2=Female 3=Female-to-male transgender (FTM) 4=Male-to-female transgender (MTF) 5=Other gender identity 8=Refused to Answer 9=Unknown	char	1	No	9=unknown
SEXBIRTH	Sex assigned at birth. What sex was the patient assigned at birth?	1=Male 2=Female 8=Refused to Answer 9=Unknown	char	1	No	9=unknown
AGE	Patient age	999=Unknown	num	3	No	999=unknown
HISP_ETH	Ethnicity: Hispanic or Latino Is the patient of Hispanic ethnicity?	0=No, not Hispanic/Latino 1=Yes, Hispanic/Latino 8=Refused to Answer 9=Unknown	char	1	No	9=unknown
AIAN	Race: AI/AN-American Indian or Alaskan Native Does the patient identify as American Indian or Alaska Native?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No	9=unknown
ASIAN	Race: Asian Does the patient identify as Asian?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No	9=unknown
NHOPI	Race: NH/PI-Native Hawaiian or Other Pacific Islander Does the patient identify as Native Hawaiian or Pacific Islander?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No	9=unknown
BLACK	Race: Black or African American Does the patient identify as black or African-American?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No	9=unknown
WHITE	Race: White Does the patient identify as White?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No	9=unknown
MULTIRACE	Race: Multirace Does the patient identify as Multirace?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No	9=unknown
OTHRACE	Race: Other Does the patient identify as Other race?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No	9=unknown
GENDER_SP	Gender of sex partners Provider documented gender of patient’s sex partners. For example, sex with partners who are males and/or F-to-M transgender only should be recorded as 1 (Males only). Sex with a questioning/nonbinary/intersex partner should be recorded as 9 (Unknown/Gender not listed). Sex partners who include male and female partners or questioning/intersex partner(s) AND male and/or female partners should be recorded as 3 (more than 1 gender).	1=Males only (includes F-to-M transgender) 2=Females only (includes M-to-F transgender) 3=More than 1 gender 8=Refused to answer 9=Unknown/Gender not listed	char	1	No	9=unknown/gender not listed
ETEST_DATE	Date of completion of Etest (final result)	YYYY/MM/DD; YYMMDDs10.	date	10	No
CFX_MIC_DD	Etest Cefixime MIC reported in doubling dilutions Record the MIC number only (ignore greater than (>) or less than (<) symbols), >256 recorded as 256 999=insufficient growth Blank if Etest not performed **To be reported for each isolate collected at initial evaluation with Etest performed	0.016, 0.032, 0.064, 0.125, 0.25, 0.50, 1, 2, 4, 8, 16, 32, 64, 128, 256, 999	num	8	No
CRO_MIC_DD	Etest Ceftriaxone MIC reported in doubling dilutions Record the MIC number only (ignore greater than (>) or less than (<) symbols), >256 recorded as 256 999=insufficient growth Blank if Etest not performed **To be reported for each isolate collected at initial evaluation with Etest performed	0.002, 0.004, 0.008, 0.016, 0.032, 0.064, 0.125, 0.25, 0.50, 1, 2, 4, 8, 16, 32, 999	num	8	No
TRMT1	What is the patient's treatment for gonorrhea?	00=none 03=spectinomycin (Trobicin) 2 gm 04=ceftriaxone (Rocephin) 250 mg 05=ceftriaxone (Rocephin) 125 mg 06=ciprofloxacin (Cipro) 500 mg 07=cefoxitin (Mefoxin) 2 gm 12=cefixime (Suprax) 400 mg 14=cefpodoxime proxetil (Vantin) 200 mg 15=ofloxacin (Floxin) 400 mg 17=ceftizoxime (Cefizox) 500 mg 18=cefotaxime (Claforan) 500 mg 21=azithromycin (Zithromax) 2 gm 22=levofloxacin (Levaquin) 250 mg 23=cefpodoxime proxetil (Vantin) 400 mg 24=ceftibuten (Cedax) 400 mg 25=cefdinir (Omnicef ) 300 mg 26=cefdinir (Omnicef ) 600 mg 27= gemifloxacin 320 mg 28= gentamicin 240 mg (or weight-based dosage) 29=ceftriaxone (Rocephin) 500 mg 30=ceftriaxone (Rocephin) 1g 31=cefixime (Suprax) 800 mg 77=other (please indicate in Other medication prescribed) 99=unknown	char	2	No
MEDICATION1_OTH	If TRMT1 was coded as 77 for ‘other’, please provide the name of the other medication.	Free text field	char	50	Yes	Null
TRMT2	If a second antimicrobial was given specifically for the patient’s gonorrhea treatment, what was it? Note: Please only complete TRMT2 for patients who received two antimicrobials for gonorrhea treatment.	11=azithromycin (Zithromax) 1 gm 21=azithromycin (Zithromax) 2 gm 28= gentamicin 240 mg (or weight-based dosage) 31=cefixime (Suprax) 800 mg 77=other (please indicate in Other medication prescribed)	char	2	Yes	Null
MEDICATION2_OTH	If TRMT2 was coded as 77 for ‘other’, please provide the name of the other medication.	Free text field	char	50	Yes	Null
DATETX	Date patient received gonorrhea treatment	YYYY/MM/DD; YYMMDDs10.	date	10	No
TRAVEL	Has the patient traveled outside of US in the past 3 months?	0=No 1=Yes 9=Unknown	char	1	No
TRAVEL_FOLLOW1	If TRAVEL="Yes", please specify location(s) (if known).	Free text field	char	50
TRAVEL_FOLLOW2	If TRAVEL="Yes", did the patient report having sex while outside of the US?	0=No 1=Yes 9=Unknown	char	1
CONTACT_TRAVEL	In the past 3 months, did the patient have sex with someone who traveled from outside the US within the 6 months prior to sexual encounter?	0=No 1=Yes 9=Unknown	char	1
SEXWORK	Does patient have a history of giving or receiving drugs/money/food/lodging for sex in the previous 12 months (prior to the initial evaluation)?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No
SXPHARYNGEAL	At initial evaluation: Does the patient report any pharyngeal/throat symptoms (e.g., pain, discomfort)?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No
SXDYSURIA	At initial evaluation: Does the patient report dysuria?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No
SXDISCHARGE	At initial evaluation: Does the patient report genital discharge?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No
SXRECTAL	At initial evaluation: Does the patient report rectal symptoms (e.g. pain or tenesmus)?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No
SXABDOMEN	At initial evaluation: Does the patient report abdominal pain?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No
DOXY_PEP	At initial evaluation: Has patient taken doxycycline for STI post-exposure prophylaxis within 60 days of clinic visit?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	Yes	9=unknown or null
TOC	Did the patient return for a test-of-cure visit?	0=No 1=Yes 9=Unknown	char	1	No
TOC_DATE	Date of patient's test-of-cure visit	YYYY/MM/DD; YYMMDDs10.	date	10	No
TOC_SEXACT	Has the patient been sexually active between treatment and test-of-cure visit?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No
TOC_SXSTATUS	Did the patient present with new, persistent, or worsening symptoms at the test-of-cure visit? If yes, please specify symptom(s) using variables TOC_SXPHARYNGEAL, TOC_SXDYSURIA, TOC_SXDISCHARGE, TOC_SXRECTAL, TOC_SXABDOMEN	0=No 1=Yes 8=Refused to answer 9=Unknown
TOC_SXPHARYNGEAL	At test-of-cure evaluation: Does the patient report any pharyngeal/throat symptoms (e.g., pain, discomfort)?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No
TOC_SXDYSURIA	At test-of-cure evaluation: Does the patient report dysuria?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No
TOC_SXDISCHARGE	At test-of-cure evaluation: Does the patient report genital discharge?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No
TOC_SXRECTAL	At test-of-cure evaluation: Does the patient report rectal symptoms (e.g. pain or tenesmus)?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No
TOC_SXABDOMEN	At test-of-cure evaluation: Does the patient report abdominal pain?	0=No 1=Yes 8=Refused to answer 9=Unknown	char	1	No