National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention 

Division of Tuberculosis Elimination

JUNE 13, 2011

Tuberculosis Laboratory

Aggregate Report

INTRODUCTION

The Laboratory Capacity Team (LCT) in the Laboratory 

Branch (LB) in the Division of Tuberculosis Elimination 

(DTBE) at Centers for Disease Control and Prevention 

(CDC) is pleased to present the “Tuberculosis Laboratory 

Aggregate Report.” The information contained in the 

report is a compilation of the aggregate calendar year 2009 

workload and turnaround time (TAT) data self-reported 

in progress reports by public health laboratories (PHL) 

supported in part by the TB Elimination Cooperative 

Agreement. In addition, current PHL methods and 

practices are included. These data serve as a tool to 

assess benchmarks and make peer comparisons. These 

may be useful guides for identifying testing practices and 

algorithms that are successful or need examination.

The past year has been an eventful time in the LB. First, the 

name of the branch changed from the Mycobacteriology 

Laboratory Branch to the “Laboratory Branch.” This name 

change is consistent with the titles of other laboratory 

branches within the National Center for HIV/AIDS, 

Viral Hepatitis, STD, and TB Prevention (NCHHSTP). In 

addition, LB has a new team. The Laboratory Capacity 

Activity is now the Laboratory Capacity Team (LCT) and 

joins the Applied Research and Reference Laboratory 

Teams. Expanded functions of LCT include oversight for 

the laboratory component of cooperative agreements, site 

visits, technical assistance, development of educational 

products, training, and operational research studies aimed 

at identifying model practices for laboratory diagnosis 

of tuberculosis. In collaboration with the Association 

of Public Health Laboratories (APHL), LCT recently 

conducted the National TB Laboratory Services Survey 

and will work with APHL to use the data to develop 

recommendations for strengthening laboratory capacity 

and the development of regional training opportunities. 

Since late 2009, members of LCT have developed two 

Web conferences for PHL, participated in 22 site visits, 

presented data at national and regional conferences, and 

in collaboration with the Reference Laboratory Team, 

developed the user’s guide for the Molecular Detection of 

Drug Resistance (MDDR) service. Recently, LCT completed 

data collection for their first operational research project 

aimed at assessing the currently recommended practice 

of holding mycobacterial cultures for six to eight weeks 

before declaring as negative. In the coming year, LCT 

plans to conduct an operational research project for the 

potential revision of national TAT indicators in light of 

current methodologies and testing practices. 

Recently, DTBE awarded APHL a one-time supplement 

for increasing patient access to molecular diagnostics 

in PHL. As a result, there is an anticipated shift in the 

methodologies used by jurisdictions providing nucleic 

acid amplification testing (NAAT) to include assays for 

the molecular detection of mutations associated with 

drug resistance. Through collaboration with APHL, a 

shipping contract has been developed for use by PHL 

until December 31, 2011 for submission of material to 

CDC’s MDDR service based on criteria for potential drug 

resistance. In addition, LB can provide a library of 15 DNA 

samples that includes both wild-type and mutated alleles 

associated with first-line and second-line antituberculosis 

drug resistance. PHL interested in obtaining samples for 

validation studies may contact their LCT consultant for 

additional information.

Members of LCT have learned a great deal through site 

visits and want to take this opportunity to thank PHL 

colleagues for taking time to participate. LCT members 

encourage you to consider participation in an upcoming 

LCT operational research project and look forward to 

another year of collaboration with PHL colleagues.

Suggested Citation: CDC. TUBERCULOSIS LABORATORY 

AGGREGATE REPORT. Atlanta, GA: U.S. Department of Health and 

Human Services, CDC; 2011.
2

INSIDE THIS REPORT

Comparison of 2008 and 2009 

National Workload Data 3

Criteria for Direct Detection of 

MTBC in Clinical Specimens 4

NAAT Workload and TAT 

Indicators, 2009 4

First-line DST Methods 5

Second-line DST Methods 5

Second-line DST in U.S. PHL 5

Changes in TAT, 2008 to 2009 6

Percent ID Reported Within 

21 Days of Specimen Receipt 

Stratified by Testing Volume 7

Percent DST Reported Within 

28 Days of Specimen Receipt 

Stratified by Testing Volume 7

References 8

TB Resources 8

Other Publications of Interest 8

CS223689-A

HOW TO GET THE MOST FROM THIS REPORT

Workload and TAT indicators are an integral part of an overall quality assurance 

program. As detailed in the TB cooperative agreement guidance document, it is 

important for each laboratory to set their own goals for each of the TAT indicators, 

to periodically analyze their laboratory data, and determine where improvements 

might be made. For example, a laboratory may, after carefully examining specimen 

delivery TAT data, notice that one particular provider is far slower at sending in 

specimens than others and may be batching specimens. This assessment aids in 

identifying an opportunity for educating the submitter on the importance of rapid 

transport and the potential negative clinical and public health consequences of 

delay on downstream testing and TAT. 

In using this report, PHL can compare their TAT indicators to those of their peers 

with similar testing volume. With each TAT indicator, the national average has 

been included in the figure as indicated by the horizontal red line. Stratified TAT 

indicators and the corresponding national averages provide reference points from 

which PHL might assess their performance. For example, if your PHL performs 

100 drug susceptibility tests (DST) per year, you would examine the percent of 

DSTs completed within 28 days of specimen receipt within the stratum of 51–100 

DSTs, which is 57%, and compare the percentage calculated for your laboratory. 

In addition, you would compare the TAT in your laboratory to the overall national 

average of 49%. If your laboratory completes a higher percentage of DSTs than 

the stratum specific and national averages, then you know you are on target 

and should strive for continued improvement in TAT for this national indicator. 

However, if your laboratory has a lower percentage, you should investigate 

factors contributing to delays in TAT. Potential factors may include change or 

reduction in staff, change in methodologies, quality control issues, problematic 

isolates, or workflow impediments. Some of these factors are outside the control 

of the laboratory. However, others within the analytical and post-analytical 

phases could be identified and quality improvements implemented. A final step 

would be periodic reevaluation of the indicator to measure the effect of quality 

improvements. 

This report can also serve as a quality data-checking tool; if your calculations are 

far above or below the averages for any of the indicators, a data re-check may be 

in order. Lastly, data provided in this document can and should be used to tout 

the accomplishments of your laboratory, or provide evidence that your laboratory 

may benefit from additional personnel or changes in testing algorithms, workflow, 

or procedures. 

Any suggestions for improvements for future aggregate reports are welcomed 

and encouraged. For any questions regarding the data requirements for the TB 

cooperative agreement or your laboratory specific data provided to you with this 

report, please contact your LCT consultant.

LCT CONTACT DETAILS

Angela Starks, PhD—astarks@cdc.gov, (404) 639-3205

Tracy Dalton, PhD—tldalton@cdc.gov, (404) 639–3904

Frances Tyrrell, MPH, MT (ASCP), SM—ftyrrell@cdc.gov, (404) 639-5451

Mitchell Yakrus, MPH—myakrus@cdc.gov, (404) 639-1288
3

Table 1. Comparison of 2008 and 2009 National Workload Data 

Variable

2008 2009

% change 

(p value b)

Total number 

(No. PHL 

reporting)

Median 

(Range)

Total number 

(No. PHL 

reporting)

Median 

(Range)

Clinical specimens receiveda 295,416

(58)

3,228.5 

(306–23,500)

272,152 

(58)

3,050.5 

(288–23,951)

−7.9

(≤0.05)

Patients for whom a specimen 

was submitted c

118,914

(58)

1,428.0 

(124–10,934)

112,061

(57)

1,404.0 

(88–10,282)

−5.8

(≤0.05)

Patients culture positive for 

MTBCd

5,745

(58)

56.0 

(1–792)

5,005

(58)

40.5 

(1–834)

−12.9

(≤0.05)

Patients for whom a reference 

isolate was submitted e

21,250

(58)

228.5 

(0–2,575)

20,331

(58)

188.5 

(0–2,739)

−4.3

(0.09)

Patients with a reference 

isolate identified as MTBC

3,327

(55)

28.0

(0–276)

3,871

(57)

28.0 

(0–342)

14.1

(0.61)

Patients for whom DST f

 was 

performed

8,255

(58)

81.5 

(2–895)

7,549 

(58)

76.0 

(2–883)

−8.6

(≤0.05)

Patients for whom a clinical 

specimen was tested by either 

NAATg or other rapid test

13,745

(58)

51.5 

(0–5,855)

15,827

(58)

98.5 

(0–6,901)

13.2

(≤0.05)

Patients NAAT positive for 

MTBC

2,533

(52)

24.0 

(0–567)

2,357

(56)

21.0 

(0–459)

−7.0

(0.30)

a Processed and cultured, not including isolates referred from other laboratories, b Wilcoxon signed-rank test, c Processed and a TB culture inoculated, dMycobacterium tuberculosis complex, e Received to either rule out or confirm the identification (ID) of MTBC, f Drug susceptibility testing, g Nucleic acid 

amplification test 

For 2009 as compared to 2008, PHL reported statistically significant (p value ≤ 0.05) decreases in the number of clinical 

specimens received, patients for whom a specimen was submitted, patients culture positive for MTBC, and patients for whom 

DST was performed. The decreases in key workload categories correlate with a 10.5% decrease in reported tuberculosis 

cases in the United States from 2008 (12,906 cases) to 2009 (11,545 cases) reported to CDC (1). There was a significant 

increase of 13.2% in direct testing for MTBC from 2008 to 2009 as measured by the number of patients for whom a clinical 

specimen was tested by either NAAT or other rapid test. 
4

Figure 1. Criteria for Direct Detection of MTBC in Clinical Specimens Number of Public Health Laboratories

Referred

In-house

30

25

20

15

10

5

0

All smear

positive (smear

negative on

request)

25

8

8

4 5

1

1 1

1

2

All smear

positive

On request

only

At least one

specimen per

patient

(Universal)

2009 CDC

guidelines*

Unknown

Data presented above were taken from multiple sources including TB cooperative agreement narratives, APHL NAAT 

expansion grant proposals, and LB site visits. Direct detection of MTBC in diagnostic clinical specimens was performed 

in-house by 44 PHL and through referral by 12 PHL. Two PHL reported no access to direct detection. Of these criteria, the 

most utilized was testing a diagnostic specimen from all patients with a smear positive result and on request, for patients 

with a smear negative result. 

*Performed NAAT based on updated CDC MMWR guidelines, which state that NAAT should be performed on at least one respiratory specimen from each 

patient with signs and symptoms of pulmonary TB for whom a diagnosis of TB is being considered but has not yet been established, and for whom the 

test result would alter case management or TB control activities (2).

Table 2. NAAT Workload and TAT Indicators, 2009

Number patients 

NAAT performed 

(2009)

Number of 

PHL

Percent of patient 

specimens 

processed at PHL 

that also had NAAT 

performed

Percent of 

patients with 

NAAT performed 

that were NAAT 

positive for MTBC

Percent of patients 

with culture 

confirmed MTBC 

with a NAAT 

positive result 

reported within 48 

hours (HP 2020)

Percent of patients 

with positive NAAT 

result reported 

within 48 hours of 

specimen receipt

≤25 11 1% 19% 5% 35%

26–100 10 3% 30% 24% 77%

101–200 13 5% 34% 38% 72%

201–500 6 9% 23% 30% 73%

>500 5 34% 18% 54% 84%

All PHL reporting 45 8% 24% 36% 76%

Overall, 8% of patient specimens processed were tested by NAAT in 2009. Current national progress towards meeting the 

Healthy People 2020 goal (TB diagnosis within 2 days from receipt of clinical specimen for 75% of cases that are later culture 

confirmed) is 36%. It is important to note that when patient specimens do receive a NAAT, 76% of NAAT positive results 

are reported within 48 hours of specimen receipt. In general, all indicators improve as the volume of NAA testing in the 

laboratory increases with the exception of the proportion of specimens tested by NAAT that are NAAT positive, which is 

lowest in the highest volume category. One limitation to the data above is the potential for laboratories to include referred 

sediments that are not processed for culture in their NAAT counts. 
5

Figure 2. First-line DST Methods 

Referred: 6

Versa Trek: 3

Direct Agar 

Proportion: 1

Bactec 460: 11

Bactec MGIT960: 37

Figure 3. Second-line DST Methods

 

Unknown: 10

Referred: 30

Indirect AP: 10

Bactec 460: 5

Disk Elution: 1

Bactec MGIT960: 2

Methods used by 58 PHL for first-line and second-line DST of MTBC from culture. The proportion of laboratories using 

the Bactec 460 for DST will change as reagents for this platform are being discontinued in 2011. Of the 52 laboratories 

performing drug susceptibility in-house, 38 included pyrazinamide as part of the first-line DST panel. Five laboratories did 

not test for susceptibility to pyrazinamide and nine laboratories did not describe their panel for DST. Currently, 18 PHL 

reported performing second-line DST in-house.

Table 3. Second–line DST in U.S. PHL

No. PHL performing SL-DST 18

No. PHL that reported SL-DST panel 16

Mean no. of SLD included in SL-DST panels 5.1

Median no. of SLD included in SL-DST panels 4.5

Range no. of SLD included in SL-DST panels 3–10

No. PHL testing at least 1 SL-INJ and 1 FQ 16

No. PHL testing >1 FQ 4

No. PHL testing all 3 SL-INJ 4

No. PHL testing 2 SL-INJ 6

KAN, CAP 4

AMK, CAP 2

No. PHL testing 1 SL-INJ 6

KAN 3

AMK 1

CAP 2

No., number; KAN, kanamycin; AMK, amikacin; CAP, capreomycin; FQ, fluoroquinolone; SL-INJ, second-line injectables

Current second-line DST (SL-DST) panels tested in-house by 16 PHL were reported. Four laboratories test all three SL-INJ 

(KAN, AMK, and CAP). Twelve laboratories reported testing either one or two SL-INJ. Current CLSI guidelines state that 

testing both AMK and KAN in addition to CAP may be desirable (3). The availability of DST for all three SL-INJ is beneficial 

due to incomplete cross-resistance between these drugs that could result in a missed opportunity to identify XDR-TB and 

potentially compromise treatment regimens (4). 
6

Figure 4. Changes in TAT, 2008 to 2009

Percent difference of aggregate means within recommended times, 

2009 compared to 2008

Specimen receipt in 1 day

Specimen receipt in 2 days

Specimen receipt in 3 days

Smear results in 1 day

ID of MTBC in 21 days

DST in 28 days

-20%

2%

2%

All labs

City labs

State labs

0%

 0.2%

 4%

3%

-2%

-3%

-6%

-15% -10% -5% 0% 5% 10% 15% 20%

Measure

Mean %, 2008 

(No. PHL 

reporting) 

Mean %, 2009

 (No. PHL 

reporting) Range, 2009

Receipt of specimens within 1 day

City Laboratories 83 (5) 85 (6) 72–100

State Laboratories 37 (47) 39 (49) 0–89

Receipt of specimens within 2 days

City Laboratories 87 (5) 91 (6) 86–100

State Laboratories 56 (41) 59 (46) 0–94

Receipt of specimens within 3 days

City Laboratories 98 (5) 98 (6) 96–100

State Laboratories 74 (41) 74 (42) 12–100

Smear results within 1 day 91 (51) 89 (57) 54–100

ID of MTBC within 21 days of specimen 

receipt 75 (49) 72 (57) 0–100

DST results within 28 days of specimen 

receipt 55 (51) 49 (56) 0–100

TAT for specimen receipt decreased slightly in 2009 compared to 2008. Other TAT for smear result, ID, and DST increased 

during this period resulting in a decreased percentage of results reported within the recommended TATs. The differences in 

TAT between 2008 and 2009 were not statistically significant and it is unknown if the increases truly represent slower time 

to reporting or whether other factors have influenced the TAT data. TATs will be periodically monitored to look for trends. 
7

Figure 5. Percent ID Reported Within 21 Days of Specimen Receipt, Stratified by Testing Volume

Number of patients with specimen received by laboratory

Percent ID within 21 days

100%

90%

80%

70%

60%

50%

40%

30%

20%

10%

0%

0–1000 1001–2000 2001–3000 3001–4000 >4000

72%

72% 69% 74% 76% 66%

Percent ID reported within 21 days of specimen receipt National Average

The percent of isolates identified as MTBC within 21 days of specimen receipt dropped for each category in 2009 relative to 

2008. As a result, the national average for turnaround time dropped from 75% in 2008 to 72% in 2009. The reasons for this 

decline are unknown but might include reductions in staff and batching due to economic circumstances. Laboratories should 

monitor this indicator and identify potential solutions to ensure continued progress in meeting national recommendations.

Figure 6. Percent DST Reported Within 28 Days of Specimen Receipt, Stratified by Testing Volume

Number of patients for whom DST performed

Percent DST within 28 days

100%

90%

80%

70%

60%

50%

40%

30%

20%

10%

0%

0–25 26–50 51–100 101–200 >200

49%

37% 48% 57% 48% 64%

Percent DST reported within 28 days of specimen receipt National Average

The percentage of isolates with DST results reported within 28 days of specimen receipt increased for laboratories 

performing 51–100 and >200 DST per year in 2009 relative to 2008. However, slower DST TATs were reported for the other 

three categories and as a result, the national average for turnaround time dropped from 55% in 2008 to 49% in 2009. The 

reasons for this decline are unknown but are likely similar to those affecting earlier analytical processes (i.e., smear and 

ID). Laboratories should monitor this indicator and identify potential solutions to ensure continued progress in meeting 

national recommendations.
8

REFERENCES

1. Reported Tuberculosis in the United States, 2009: CDC TB Surveillance Report: 

http://www.cdc.gov/tb/statistics/reports/2009/default.htm

2. Updated Guidelines for the Use of Nucleic Acid Amplification Tests in the Diagnosis of Tuberculosis: 

http://www.cdc.gov/mmwr/preview/mmwrhtml/mm5801a3.htm?s_cid=mm5801a3_e

3. “Susceptibility Testing of Mycobacteria, Nocardiae, and Other Aerobic Actinomycetes; Approved Standard—Second 

Edition,” CLSI. March 2011 M24-A2, Vol. 31 No. 5.

4. “Molecular analysis of cross-resistance to capreomycin, kanamycin, amikacin, and viomycin in Mycobacterium 

tuberculosis,” CE Maus et al., Antimicrob Agents Chemother. 2005 Aug;49(8):3192-7.

TB RESOURCES

CDC TB Website: http://www.cdc.gov/tb/

APHL TB Website: http://www.aphl.org/aphlprograms/infectious/tuberculosis/pages/default.aspx

CDC Molecular Detection of Drug Resistance (MDDR) Service: http://www.cdc.gov/tb/topic/laboratory/guide.htm

CDC Model Performance Evaluation Program: http://wwwn.cdc.gov/mpep/default.aspx

APHL TB Laboratory Self-Assessment tool: http://www.aphl.org/aphlprograms/infectious/tuberculosis/Pages/tbtool.aspx

TB Education and Training Resources: http://www.findtbresources.org/scripts/index.cfm

Evidence-Based Tuberculosis Diagnostics: http://www.tbevidence.org/

Regional Training and Medical Consultation Centers: http://www.cdc.gov/tb/education/rtmc/default.htm

Report of Expert Consultations on Rapid Molecular Testing to Detect Drug-Resistant Tuberculosis in the United States: 

http://www.cdc.gov/tb/topic/laboratory/rapidmoleculartesting/default.htm

Updated Guidelines for Using Interferon Gamma Release Assays to Detect Mycobacterium tuberculosis Infection—United 

States, 2010: http://www.cdc.gov/mmwr/preview/mmwrhtml/rr5905a1.htm?s_cid=rr5905a1_w

Guide to the Application of Genotyping to Tuberculosis Prevention and Control: 

http://www.cdc.gov/tb/programs/genotyping/manual.htm

Core TB Laboratory Services for Public Health Laboratories, by the APHL TB Steering Committee: 

http://www.aphl.org/aphlprograms/infectious/tuberculosis/Documents/Core_TB_Services.pdf

OTHER PUBLICATIONS OF INTEREST

“Molecular detection of mutations associated with first and second-line drug resistance compared with conventional drug 

susceptibility testing in M. tuberculosis,” PJ Campbell et al., Antimicrob Agents Chemother. 2011 Feb 7. [Epub ahead of print]

“Monitoring the performance of mycobacteriology laboratories: a proposal for standardized indicators,” KD McCarthy et al., 

INT J TUBERC LUNG DIS 12(9):1015–1020. 

“Mycobacterium tuberculosis Strains with Highly Discordant Rifampin Susceptibility Test Results,” A Van Deun et al., J Clin 

Microbiol. 2009 November; 47(11): 3501–3506.

“Validation of laboratory-developed molecular assays for infectious diseases,” EM Burd, Clin Microbiol Rev. 2010 Jul;23(3):

550-76.

“Evaluation of the Cepheid Xpert MTB/RIF Assay for Direct Detection of Mycobacterium tuberculosis Complex in Respiratory 

Specimens,” EM Marlowe et al., J Clin Microbiol. 2011 Apr;49(4):1621-3. Epub 2011 Feb 2.