National Health and Nutrition Examination Survey

2017-2018 Data Documentation, Codebook, and Frequencies

Mycoplasma genitalium Resistance – Urine (Surplus) (SSMR_J_R)

RDC Only Data File: SSMR_J_R.xpt

First Published: August 2025

Last Revised: NA

At this time, this dataset is not available publicly. Access may be obtained through the NCHS Research Data Center (https://www.cdc.gov/rdc).

Component Description

Mycoplasma genitalium is a sexually transmitted bacterium that causes male urethritis and is associated with cervicitis, pelvic inflammatory disease, infertility, and preterm delivery (Taylor-Robinson, et. al., 2011; Lis, et. al., 2014). Nucleic acid amplification testing (NAAT) for M. genitalium was previously performed on urine samples in the 2017-2018 NHANES cycle (URXMYGE).

Resistance to the two main antibiotics used to treat M. genitalium in the U.S. (azithromycin-a macrolide antibiotic and moxifloxacin-a fluoroquinolone antibiotic) emerged rapidly just prior to 2010 and has expanded rapidly (Chua, et. al., 2024). The prevalence of macrolide and quinolone resistance has not been measured in a nationally representative sample of people in the U.S.

Eligible Sample

Participants aged 14-59 testing positive for Mycoplasma genitalium in urine (URXMYGE = 1) were eligible (see: MGEA_J_R and MGEN_J_R).

Description of Laboratory Methodology

Mutations in M. genitalium that are characteristic of antibiotic resistance were sought in the Jensen Laboratory at the Statens Serum Institut in Copenhagen, Denmark using pristine urine specimens received from the National Center for Health Statistics.

DNA was extracted from 1 mL of the transport medium and eluted in 0.1 mL on a Roche MagNaPure 96 instrument. Macrolide resistance mutations (MRMs) were detected using a modification of the published method(Salado-Rasmussen, et. al., 2014) by using a reverse transcriptase PCR (rt-PCR) followed by PyroMark24 sequencing to detect mutations in the 23S rRNA gene. Quinolone resistance-associated mutations (QRAMs) were detected using conventional PCR assays detecting the parC gene (Fernandez-Huerta, et. al., 2019) and the gyrA gene(Shimada, et. al., 2010) followed by Sanger sequencing.

All results were quality-checked.

Laboratory Quality Assurance and Monitoring

Urine specimens stored in Aptima transport medium were received and accessioned by the Jensen Laboratory at the Statens Serum Institut. After being accessioned, the specimens were stored in a secure −80°C freezer until assaying.

Before analyzing the specimens, the rt-PCR MRM detection method was optimized using previously tested M. genitalium-positive and -negative urine specimens in Aptima transport medium received for diagnostic testing for MRM in an accredited laboratory (ISO 17025). After optimization, the 2017-2018 NHANES urine specimens previously testing positive for M. genitalium by nucleic acid amplification testing (NAAT) were analyzed for MRM and parC and gyrA resistance mutations in an accredited laboratory environment.

Specimens not amplified initially were re-analyzed using the double amount of extracted DNA template. All entries were double-checked by experienced staff. Finalized sequencing results were tabulated and variables denoting presence vs. absence of MRM and QRAM were created; both individual sequencing results and presence vs. absence data were provided to NCHS.

Data Processing and Editing

The data were reviewed. Incomplete data or improbable values were sent to the performing laboratory for confirmation.

Analytic Notes

Only those participants aged 14-59 testing positive for Mycoplasma genitalium in urine (URXMYGE = 1) were eligible for inclusion in this file (see: MGEA_J_R and MGEN_J_R). This file is intended to be used in conjunction with the MGEA_J_R and MGEN_J_R files. Participants who were part of the eligible population but who did not have sufficient volume of biospecimens or who did not give consent for their specimens to be used for future research are included in the file, but have results listed as missing. Participants who were outside of the eligible population were not included in the file.

Refer to the 2017–2018 Laboratory Data Overview for general information on NHANES laboratory data.

There are over 800 laboratory tests performed on NHANES participants. However, not all participants provided biospecimens or enough volume for all the tests to be performed. Additionally, availability of specimens for surplus projects is lower than for other laboratory tests performed on NHANES participants. The specimen availability can also vary by age or other population characteristics. Analysts should evaluate the extent of missing data in the dataset related to the outcome of interest as well as any predictor variables used in the analyses to determine whether additional re-weighting for item non-response is necessary.

Please refer to the NHANES Analytic Guidelines and the on-line NHANES Tutorial for further details on the use of sample weights and other analytic issues.

Demographic and Other Related Variables

The analysis of NHANES laboratory data must be conducted using the appropriate survey design and demographic variables. The NHANES 2017-2018 Demographics File contains demographic data, health indicators, and other related information collected during household interviews as well as the sample weight and design variables. The recommended procedure for variance estimation requires use of stratum and PSU variables (SDMVSTRA and SDMVPSU, respectively) in the demographic data file.

This laboratory data file can be linked to the other NHANES data files using the unique survey participant identifier (i.e., SEQN).

References

Chua T.P., Vodstrcil L.A., Murray G.L, et al. Evolving patterns of macrolide and fluoroquinolone resistance in Mycoplasma genitalium: an updated global systematic review and meta-analysis. Lancet Microbe. (2025): 101047.
Fernandez-Huerta M., Bodiyabadu K., Esperalba J, et al. Multicenter clinical evaluation of a novel multiplex real-time PCR (qPCR) assay for detection of fluoroquinolone resistance in Mycoplasma genitalium. J Clin Microbiol. (2019) 57(11):e00886-19.
Lis R., Rowhani-Rahbar A., Manhart L.E. Mycoplasma genitalium infection and female reproductive tract disease: A meta-analysis. Clin Infect Dis. (2015) 61(3): 418-26.
Salado-Rasmussen K., Jensen J.S. Mycoplasma genitalium testing pattern and macrolide resistance: a Danish nationwide retrospective survey. Clin Infect Dis. (2014) 59(1): 24-30.
Shimada Y., Deguchi T., Nakane K., et al. Emergence of clinical strains of Mycoplasma genitalium harbouring alterations in ParC associated with fluoroquinolone resistance. Int J Antimicrob Agents. (2010) 36(3):255-8.
Taylor-Robinson D., Jensen J.S. Mycoplasma genitalium: from Chrysalis to multicolored butterfly. Clin Microbiol Rev. (2011) 24(3):498-514.

Codebook and Frequencies

SEQN - Respondent sequence number

Variable Name:: SEQN
SAS Label:: Respondent sequence number
English Text:: Respondent sequence number.
Target:: Both males and females 14 YEARS - 59 YEARS

SSMRMMUT - MG 23S rRNA mutation name

Variable Name:: SSMRMMUT
SAS Label:: MG 23S rRNA mutation name
English Text:: Mutations detected in M. genitalium (MG) 23S rRNA by rt-PCR and sequencing (E. coli numbering)
Target:: Both males and females 14 YEARS - 59 YEARS

Code or Value	Value Description	Count	Cumulative
0	Wild type	25	25
1	A2058C	2	27
2	A2058G	14	41
3	A2058T	2	43
4	A2059C	0	43
5	A2059G	6	49
6	A2059T	0	49
8	Other (specify)	0	49
9	Not done (did not amplify)	9	58
.	Missing	9	67

SSMRM - MG 23S rRNA MRM mutation detected

Variable Name:: SSMRM
SAS Label:: MG 23S rRNA MRM mutation detected
English Text:: Detections of any macrolide resistance mutations (MRM) in in M. genitalium (MG) 23S rRNA by rt-PCR and sequencing (E. coli numbering)
Target:: Both males and females 14 YEARS - 59 YEARS

Code or Value	Value Description	Count	Cumulative
0	No MRM detected	25	25
1	MRM detected (A2058C, A2058G, A2058T, A2059C, A2059G, A2059T)	24	49
.	Missing	18	67

SSPARMUT - MG parC gene mutation name

Variable Name:: SSPARMUT
SAS Label:: MG parC gene mutation name
English Text:: Mutations detected in M. genitalium (MG) parC gene by rt-PCR and sequencing (MG numbering)
Target:: Both males and females 14 YEARS - 59 YEARS

Code or Value	Value Description	Count	Cumulative
0	Wild type	35	35
1	D87H	0	35
2	D87N	0	35
3	D87Y	0	35
4	S83I	0	35
5	S83N	0	35
6	S83R	0	35
7	Mutations in the quinolone resistance determining region of unknown significance (D82N, G81C, G81T, S95N)	0	35
8	Other (specify)	6	41
9	Not done (did not amplify)	17	58
.	Missing	9	67

SSPARSPE - MG parC gene other mutation,specify name

Variable Name:: SSPARSPE
SAS Label:: MG parC gene other mutation,specify name
English Text:: Detection of other specific mutations in M. genitalium (MG) parC gene by rt-PCR and sequencing (MG numbering), specify:
Target:: Both males and females 14 YEARS - 59 YEARS

Code or Value	Value Description	Count	Cumulative
1	c234t (Silent)	5	5
2	P62S	1	6
.	Missing	61	67

SSPARQR - MG parC QRAM mutation detected

Variable Name:: SSPARQR
SAS Label:: MG parC QRAM mutation detected
English Text:: Detections of any quinolone associated resistance mutations (QRAM) in the parC gene in M. genitalium (MG) by rt-PCR and sequencing (MG numbering)
Target:: Both males and females 14 YEARS - 59 YEARS

Code or Value	Value Description	Count	Cumulative
0	No QRAM detected	41	41
1	QRAM detected (D87H, D87N, D87Y, S83I, S83N, or S83R)	0	41
.	Missing	26	67

SSGYRMUT - MG gyrA gene mutation name

Variable Name:: SSGYRMUT
SAS Label:: MG gyrA gene mutation name
English Text:: Mutations detected in M. genitalium (MG) gyrA gene by rt-PCR and sequencing (MG numbering)
Target:: Both males and females 14 YEARS - 59 YEARS

Code or Value	Value Description	Count	Cumulative
0	Wild type	40	40
1	M95I	0	40
2	D99N	0	40
3	D99Y	0	40
4	D99G	0	40
8	Other (specify)	2	42
9	Not done (did not amplify)	16	58
.	Missing	9	67

SSGYRSPE - MG gyrA gene other mutation,specify name

Variable Name:: SSGYRSPE
SAS Label:: MG gyrA gene other mutation,specify name
English Text:: Detection of other specific mutations in M. genitalium (MG) gyrA gene by rt-PCR and sequencing (MG numbering), specify:
Target:: Both males and females 14 YEARS - 59 YEARS

Code or Value	Value Description	Count	Cumulative
1	c217t (R73C)	1	1
2	t345c (Silent)	1	2
.	Missing	65	67

SSGYRQR - MG gyrA QRAM mutation detected

Variable Name:: SSGYRQR
SAS Label:: MG gyrA QRAM mutation detected
English Text:: Detections of any quinolone associated resistance mutations (QRAM) in the gyrA gene in M. genitalium (MG) by rt-PCR and sequencing (MG numbering)
Target:: Both males and females 14 YEARS - 59 YEARS

Code or Value	Value Description	Count	Cumulative
0	No QRAM detected	42	42
1	QRAM detected (M95I, D99N, D99Y, D99G)	0	42
.	Missing	25	67

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