THIRD EDITION

Tuberculosis Laboratory 

Aggregate Report
Suggested Citation: CDC. Tuberculosis Laboratory Aggregate Report, Atlanta, Georgia: 

U.S. Department of Health and Human Services, CDC; 2013

Use of trade names and commercial sources is for identification only and does not imply endorsement by 

Centers for Disease Control and Prevention or U.S. Department of Health and Human Services
1

Inside This Report

Introduction ......................................... 1

How to Get the Most 

from this Report .................................. 1

Workload ............................................ 2

Culture Positivity ................................. 3

NAAT .................................................. 4

Turnaround Time ................................ 5

Comparisons to Surveillance Data ..... 6

Methods .............................................. 7

Technical Notes .................................. 8

Glossary ............................................. 8

References ......................................... 9

Resources .......................................... 9

Journal Articles of Interest ................ 10

LCT Contact Details

Angela Starks, PhD

astarks@cdc.gov

(404) 639-3205

Tracy Dalton, PhD 

tldalton@cdc.gov

(404) 639-3904

Cortney Stafford, MPH 

cstafford@cdc.gov

(404) 639-3420

Frances Tyrrell, MPH 

ftyrrell@cdc.gov

(404) 639-5451

Mitchell Yakrus, MPH 

myakrus@cdc.gov

(404) 639-1288

Introduction 

The Laboratory Capacity Team (LCT) in the Laboratory Branch 

(LB) of the Division of Tuberculosis Elimination (DTBE) at 

U.S. Centers for Disease Control and Prevention (CDC) is 

pleased to present the “Tuberculosis Laboratory Aggregate 

Report.” This report, the third edition, includes a comparison 

of the aggregate workload data for calendar years 2010 and 

2011, select 2011 data, and four year trends (2008–2011) for 

turnaround time (TAT) and other data. See Technical Note 

#1. Data are self-reported by public health laboratories (PHL) 

supported in part by the CDC TB Elimination Cooperative 

Agreement. Current PHL methods and practices (2010 

compared to 2012) are also included in this report. These 

data serve as a tool to assess benchmarks and make peer 

comparisons. Providing the self-reported data back to grantees 

in a meaningful format is an important mission of LCT.

How to Get the Most from this Report

An important aspect of a quality assurance program for 

laboratories is to monitor workload and TAT indicators. By 

assessing these indicators over time internally, as well as 

externally against peer data, laboratories can track progress and 

set realistic yet ambitious interim goals. The aggregate report 

provides the nationally aggregated data for comparison and acts 

as a guide to define your laboratory’s TAT goals using national 

averages and trends. The aggregate report also contains data 

that is stratified by laboratory volume for a more applicable 

comparison across laboratories. For details regarding data 

sources and abbreviations and terms used in this report, please 

see the Technical Notes section and Glossary.

Use the data in this report to your advantage. This report can 

serve as evidence to substantiate change within specific activities 

in your laboratory, possibly in methodology, protocols, or staffing. 

Use this report to document your laboratory’s accomplishments 

and to increase awareness of your program’s impact.

Please contact your LCT consultant with any questions regarding 

the data requirements for the CDC TB Cooperative Agreement 

or your laboratory’s specific data. Also any recommendations 

concerning the aggregate report and its content are welcomed.
2

Laboratory Workload 

Table 1. Comparison of 2010 and 2011 National Workload Data

2010 2011

Variable Total 

number

Sites 

reporting

Median

(Range)

Total 

number

Sites 

reporting

Median

(Range)

% change p 

valuea

Clinical 

specimensb

received

257,005 58 2,643.5

(251–23,250)

239,982 58 2,515 

(283–21,943)

−6.6 ≤0.05

Patients for 

whom a specimen 

was submittedc

114,700 58 1,249.5

 (126–10,404)

107,144 58 1,182.0 

(94–10,057)

−6.6 ≤0.05

Patients culture 

positive for MTBC 

4,285 58 43.0 

(0–599)

4,399 58 40.5 

(2–586)

2.6 0.33

Patients for 

whom a reference 

isolate was 

submittedd

18,905 58 195.0 

(0–2,619)

17,944 58 200.5 

(0–2,496)

−5.1 0.19

Patients with a 

reference isolate 

identified as 

MTBC

3,343 58 27.0

 (0–406)

3,331 58 26.0 

(0–368)

−0.4 0.105

Patients for 

whom DST was 

performed

7,217 58 71.0 

(0–758)

6,822 58 66.5 

(1–705)

−5.5 ≤0.05

Patients tested 

by NAAT or other 

rapid test

14,081 58 78.5 

(0–6,253)

15,077 58 100.5

 (0–6,450)

6.6 ≤0.05

Patients NAAT 

positive for MTBC

2,507 58 16.0 

(0–408)

2,430 57 18.0

 (0–361)

−3.1 0.33

a

Wilcoxon signed-rank test, bProcessed and cultured, not including isolates referred from other laboratories, cProcessed and a TB culture 

inoculated, dReceived to either rule out or confirm the identification of MTBC

From 2010 to 2011, PHLs reported statistically significant (p value ≤ 0.05) decreases in the number of clinical 

specimens received, patients for whom a specimen was submitted, and patients for whom a DST was 

performed. However, there was no significant change in the number of patients that were culture positive for 

MTBC. There was a significant increase in the number of patients for whom a clinical specimen was tested by 

either NAAT or other direct detection assay. 

Figure 1. Ratio of Specimens to Patients Tested, 2011

Figure 1 represents the number of total specimens 

received in relation to the number of patients from 

whom the specimens were collected. In 2011, 

the median ratio of specimens to patients across 

laboratories was 2.2, and this median has been 

consistent over the last four years (see Technical 

Note #2). A ratio less than 2 indicates that only 

a single specimen per patient was submitted 

for many patients. A high ratio indicates excess 

specimens are received per patient. Laboratories 

should work with TB control programs and 

clinicians to develop guidelines for accepting 

diagnostic and repeat specimens from patients 

that ensure effective patient management while 

reducing unnecessary testing. 
3

Positivity of Cultures and Isolates for MTBC

Figure 2. Trends in Positivity of Cultures and Isolates, 2008–2011

Positivity of patient specimens and reference isolates has remained fairly stable from 2008–2011.

Figure 3. Positivity of Cultures Stratified by Volume of Patient Specimens Tested, 2011

In 2011, culture positivity increased 

as volume decreased (except for the 

highest volume laboratories). This 

indicates that although low-volume 

laboratories may see relatively few 

MTBC-positive patients, they are 

finding a higher proportion of positive 

results among patient-specimens 

received. For all public health 

laboratories, 4.1% culture positivity 

was seen for MTBC in 2011, and 

is similar to previous years (see 

Technical Notes #2 and #3). 
4

Trends in Nucleic Acid Amplification Testing (NAAT)

Table 2. NAAT volumes 2009–2011

Year 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 TB

Percent of 

patients 

with culture 

confirmed MTBC 

with a NAAT 

positive result 

reported within 

48 hours (HP 

2020)

Percent 

positive 

NAAT results 

reported 

within 

48 hours of 

specimen 

receipt

2009 45 8% 24% 36% 76%

2010 36 16% 13% 40% 72%

2011 43 16% 13% 42% 81%

The percent of patients that had NAAT performed did not change in 2011 when compared to 2010; however, 

the percent of patients did increase significantly in 2010 compared to 2009. Increasing access to this type of 

testing in PHL may be due in part to the Association of Public Health Laboratories one-time grant funding for the 

expansion of NAAT in 2010. Please see Technical Note #4 for explanation of how Number of PHL was derived. 

Table 3. NAAT numbers stratified by NAA testing volume, 2010-2011

Number 

patients 

NAAT 

performed

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 TB

Percent of 

patients 

with culture 

confirmed 

MTBC with 

a NAAT 

positive result 

reported 

within 48 

hours (HP 

2020)

Percent 

positive 

NAAT 

results 

reported 

within 48 

hours of 

specimen 

receipt

2010 2011 2010 2011 2010 2011 2010 2011 2010 2011

 25 6 8 0.7% 2% 32% 26% 8% 21% 65% 75%

26-100 13 13 4% 6% 28% 19% 32% 37% 67% 86%

101-200 6 9 4% 5% 29% 31% 27% 34% 68% 71%

201-500 7 9 11% 12% 21% 23% 25% 36% 51% 80%

>500 4 4 58%* 64%* 9% 7% 70% 63%* 88% 87%

*

For the highest volume laboratories, data are likely skewed because of inclusion of data from 2 laboratories receiving 

referred sediments for NAAT only without culture.

In general, as NAAT volume increased, positivity decreased. Prompt reporting of NAAT results has increased for 

all laboratories in 2011 compared to 2010. Please see Technical Notes #3 and #4 for explanation of years used 

for comparison and how Number of PHL was derived. 
5

Turnaround Times

Figure 4. Timea to Specimen Receipt, 2011

a

 Times represent days from collection of specimen to receipt in laboratory. 

State PHLs continue to face challenges in receipt of 

specimens within one calendar day, while city and 

county PHLs remain at high levels for this indicator, 

as seen in previous editions of this report1. Please see 

Technical Note #2. 

Figure 5. National Trends in Meeting TAT 

Recommendations, 2008–2011 

Laboratories saw improvements in meeting TAT 

recommendations for ID of MTBC within 21 days but, 

although progressing, still face challenges for DST 

within 28 days from 2008 to 2011. Providing smear 

results within one day continued at high levels.

Figure 6. Association of ID TAT with DST TAT for MTBC in 2011

Delays in DST TAT are often a result 

of delays in obtaining upstream 

testing results. For example, none 

of the laboratories reporting ≤79% 

of their ID results within 21 days are 

able to report at least 80% of their 

DST results within 28 days, while 

64% of laboratories reporting ≥90% 

ID results within 21 days were able 

to report at least 80% of their DST 

results within 28 days. Upstream 

delays could occur because of low 

bacterial load in initial specimen, slow 

growth of extrapulmonary specimens, 

or contamination issues. Please see 

Technical Note #2. 
6

Testing Performed in PHL when Compared 

to National Surveillance Data 

Table 4. Proportion of TB testing done in PHLs

Year Total 

culture 

confirmed 

TB casesa

MTBC-culture 

positive 

patients in 

PHLb

Proportion 

of culture 

confirmed 

cases tested 

by PHL

Total 

culture 

confirmed 

cases 

with DST 

reporteda

Patient DST 

performed 

by PHLb 

Proportion 

of DST 

performed

 by PHL

2008 10,030 5,745 57% 9,365 8,255 88%

2009 8,876 5,005 56% 8,495 7,531 89%

2010 8,413 4,285 51% 8,063 7,213 89%

2011 8,070 4,399 55% 7,727 6,822 88%

a

Surveillance data, Reported Tuberculosis in the United States2, 2008–2011. bTB Laboratory Aggregate Report Data, 

2008–2011

PHL performed a significant proportion of culture and DST for TB cases reported in the United States. 

The proportions shown include self-reported data. Duplication of testing may have occurred possibly 

resulting in an overestimate. 

Table 5. NAAT positivity among culture confirmed TB cases reported through national surveillance

Year Total culture 

confirmed TB casesa

 

NAAT positive patients 

for MTBC in PHLb

Proportion of culture 

confirmed TB cases 

detected by NAAT in PHL

2008 10,030 2,533 25%

2009 8,876 2,355 27%

2010 8,413 2,506 30%

2011 8,070 2,430 30%

a

Surveillance data, Reported Tuberculosis in the United States2, 2008–2011. bTB Laboratory Aggregate Report Data, 

2008–2011 

The proportion of culture confirmed TB cases in the United States detected by NAAT in a PHL appears to 

be increasing. The proportion shown includes self-reported data. Duplication of testing may have occurred 

possibly resulting in an overestimate. One barrier to continued progress in rapidly detecting cases is that many 

laboratories do not routinely perform NAAT on smear-negative specimens. Laboratories should collaborate with 

TB control programs to provide NAA testing for all TB suspects and devise algorithms that are not dependent on 

smear status, but rather focus on clinical suspicion of TB.3
7

Trends in Laboratory Methods

Figure 7. NAAT Methods, 2010 and 2012 

NAAT technology methods 

changed, with a decrease in the 

use of the MTDTM test and an 

increase in use of the GeneXpertTM 

MTB/RIF assay and laboratory 

developed real-time PCR. 

Please see Technical Note #5 for 

description of source of data. 

Figure 8. First-Line DST Systems, 2010 and 2012

As the BacTec 460TM media 

became commercially unavailable, 

laboratories shifted to use of the 

BacTec MGITTM for their culture 

system and first-line DST method. 

Please see Technical Note #5 for 

description of source of data.
8

Technical Notes

1.Unless otherwise specified, the source of all data 

and information for the tables and figures in this 

report comes from the Interim and Final Progress 

Reports of the TB Elimination and Laboratory 

Cooperative Agreement submitted to CDC by 

U.S. Public Health Laboratories. 

2.Figures 1, 3, 4, and 6 show data for 2011 only 

because data were not notably different from 2010. 

3.Data were not aggregated for years 2010 and 

2011 because of a shift between categorical 

levels (i.e., testing volume) by some laboratories 

between years.

4.For Tables 2 and 3, laboratories had to report data 

for all categories described for inclusion in analysis.

5.Figures 7 and 8 compare laboratory methods 

between 2010 and 2012. The data from 2012 were 

used to indicate changes in methodology that 

occurred in 2011, when many laboratories were in 

a transition period evaluating newer techniques.

Glossary

BacTec 460TM: Becton Dickinson and Co. A 

commercial radiometric broth-based mycobacterial 

culture system

CDC: U.S. Centers for Disease Control 

and Prevention

DST: Drug susceptibility testing 

DTBE: Division of Tuberculosis Elimination

GeneXpertTM MTB/RIF, Cepheid, Inc. A 

commercial molecular assay for the direct 

detection of MTBC and mutations associated with 

rifampin resistance in clinical specimens

HP 2020: Healthy People 2020 TB Goal is to 

increase the percent of TB cases detected within 

48 hours to 77% of those later culture-confirmed. 

ID: Bacterial species identification of MTBC 

LB: Laboratory Branch, DTBE

LCT: Laboratory Capacity Team, LB, DTBE

MGITTM, BacTec MGIT TM: Mycobacterium 

Growth Indicator Tube, Becton Dickinson and 

Co. A commercial non-radiometric broth-based 

mycobacterial culture system

MTBC: Mycobacterium tuberculosis complex

MTDTM: Mycobacterium Direct Test, Gen Probe, 

Inc. A commercial molecular assay for the direct 

detection of MTBC in clinical specimens

NAAT: Nucleic Acid Amplification Test. Generic 

terminology for molecular method used for the 

direct detection of MTBC in clinical specimens

PCR: Polymerase Chain Reaction

PHL: Public Health Laboratory

Positivity (in reference to culture, isolate, or NAAT): 

Percent positive for MTBC of all specimens or 

isolates assayed, determined on a per-patient basis

Reference isolate: A growing culture of 

mycobacteria, for example, a positive MGITTM tube 

or growth on a Lowenstein-Jensen slant

TAT: Turnaround time

TB: Tuberculosis (disease)
9

References 

1. CDC. Tuberculosis Laboratory Aggregate 

Report. Atlanta, GA: U.S. Department of Health 

and Human Services, CDC; 2010 and 2011. 

http://www.cdc.gov/tb/publications/reportsarticles/

labreports.htm

2.Reported Tuberculosis in the United States, 2008 

to 2011, CDC. Atlanta, GA http://www.cdc.gov/tb/

statistics/default.htm

3.Updated Guidelines for the Use of Nucleic 

Acid Amplification Tests in the Diagnosis of 

Tuberculosis http://www.ncbi.nlm.nih.gov/

pubmed/19145221

Resources

APHL Resources

APHL TB page http://www.aphl.org/aphlprograms/

infectious/tuberculosis/pages/default.aspx

APHL TB Core Services http://www.aphl.org/

aphlprograms/infectious/tuberculosis/Documents/

ID_2009Dec_Core-TB-Services.pdf

APHL Self-assessment tool http://www.aphl.org/

aphlprograms/infectious/tuberculosis/Pages/TBSelf-Assessment-Tool.aspx

Essentials for the Mycobacteriology Laboratory: 

Promoting Quality Practices http://www.aphl.

org/aphlprograms/infectious/tuberculosis/

tb-core-curriculum/Pages/default.aspx

APHL Fact Sheet for Cepheid Xpert MTB/RIF 

Assay http://images.magnetmail.net/images/clients/

APHL/attach/CepheidXpert_FactSheet_090913.pdf

CDC Resources

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

CDC Molecular Detection of Drug Resistance 

(MDDR) Service http://www.cdc.gov/tb/topic/

laboratory/guide.htm

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

TB Notes Newsletter http://www.cdc.gov/tb/

publications/newsletters/notes/default.htm 

CDC Model Performance Evaluation Program 

http://www.cdc.gov/tb/topic/laboratory/mpep/

MMWR on use of GeneXpert http://www.cdc.

gov/mmwr/preview/mmwrhtml/mm6241a1.

htm?s_cid=mm6241a1_e

Other Resources

TB Education and Training Resources http://www.

findtbresources.org/

Evidence-based TB Diagnosis http://tbevidence.org/
10

Journal Articles of Interest

Angra, P. K., T. H. Taylor, et al. (2012). 

“Performance of tuberculosis drug susceptibility 

testing in U.S. laboratories from 1994 to 2008.” J 

Clin Microbiol 50(4): 1233-1239. http://www.ncbi.

nlm.nih.gov/pubmed/22301024

Dalton, T., P. Cegielski, et al. (2012). “Prevalence 

of and risk factors for resistance to second-line 

drugs in people with multidrug-resistant 

tuberculosis in eight countries: a prospective cohort 

study.” Lancet 380(9851): 1406-1417. http://www.

ncbi.nlm.nih.gov/pubmed/22938757

Espasa, M., M. Salvado, et al. (2012). “Evaluation 

of the VersaTREK system compared to the Bactec 

MGIT 960 system for first-line drug susceptibility 

testing of Mycobacterium tuberculosis.” J Clin 

Microbiol 50(2): 488-491. http://www.ncbi.nlm.nih.

gov/pubmed/22135258

Hall, L., K. P. Jude, et al. (2012). “Evaluation of the 

Sensititre MycoTB plate for susceptibility testing of 

the Mycobacterium tuberculosis complex against 

first- and second-line agents.” J Clin Microbiol 

50(11): 3732-3734. http://www.ncbi.nlm.nih.gov/

pubmed/22895034

Han, L. L., P. Elvin, et al. (2012). “Nonclinical 

selection criteria for maximizing yield of nucleic 

acid amplification tests in tuberculosis diagnosis.” 

J Clin Microbiol 50(8): 2592-2595. http://jcm.asm.

org/content/50/8/2592.long

Hanif, S. N., H. S. Eldeen, et al. (2011). 

“GeneXpert(R) MTB/RIF for rapid detection of 

Mycobacterium tuberculosis in pulmonary and 

extra-pulmonary samples.” Int J Tuberc Lung Dis 

15(9): 1274-1275. http://www.ncbi.nlm.nih.gov/

pubmed/21943862

Heysell, S. K. and E. R. Houpt (2012). “The 

future of molecular diagnostics for drug-resistant 

tuberculosis.” Expert Rev Mol Diagn 12(4): 

395-405. http://www.ncbi.nlm.nih.gov/

pubmed/22616704

Peña, J, Mary Jane Ferraro, M., et al. (2012) 

“Growth Detection Failures by the Nonradiometric 

Bactec MGIT 960 Mycobacterial Culture System” 

Clin. Microbiol. 2012, 50(6):2092. DOI: 10.1128/

JCM.00108-12.J.

Kalokhe, A. S., M. Shafiq, et al. (2012). 

“Discordance in Mycobacterium tuberculosis 

rifampin susceptibility.” Emerg Infect Dis 

18(3): 537-539. http://www.ncbi.nlm.nih.gov/

pubmed/22377132

Perez-Osorio, A. C., D. S. Boyle, et al. (2012). 

“Rapid identification of mycobacteria and 

drug-resistant Mycobacterium tuberculosis by use 

of a single multiplex PCR and DNA sequencing.” J 

Clin Microbiol 50(2): 326-336. http://www.ncbi.nlm.

nih.gov/pubmed/22162548

Piersimoni, C., A. Mustazzolu, et al. (2013). 

“Prevention of False Resistance Results Obtained 

in Testing the Susceptibility of Mycobacterium 

tuberculosis to Pyrazinamide with the Bactec MGIT 

960 System Using a Reduced Inoculum.” J Clin 

Microbiol 51(1): 291-294. http://www.ncbi.nlm.nih.

gov/pubmed/23100351

Tyrrell, F. C., G. E. Budnick, et al. (2012). 

“Probability of negative mycobacterium 

tuberculosis complex cultures based on time 

to detection of positive cultures: a multicenter 

evaluation of commercial-broth-based culture 

systems.” J Clin Microbiol 50(10): 3275-3282. 

http://www.ncbi.nlm.nih.gov/pubmed/22837326
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