Tuberculosis Laboratory 

Cooperative Agreement: 

Annual Aggregate Report, 2008 

Inaugural Report 

The Laboratory Capacity Activity in the Mycobacteriology Laboratory Branch (MLB) in the 

Division of Tuberculosis Elimination (DTBE) is pleased to introduce the first edition of the 

“Tuberculosis Laboratory Cooperative Agreement: Annual Aggregate Report”. The data 

contained herein are a compilation of the workload and turnaround time for calendar 

year 2008 taken from TB Elimination Cooperative Agreement narratives by public health 

laboratories (PHLs) receiving support via this mechanism. These data provide an opportunity 

for PHLs to benchmark themselves by comparing their own laboratory data with those from 

peers with similar testing volumes. Benchmarking may serve as a useful guide for identifying 

testing practices and algorithms that are successful or need examination. 

A few items must be considered when reviewing this report. First, the data are self-reported 

by PHLs. The interpretation of the statistic and the calculation used to derive the reported 

values may differ between laboratories. Second, although the same data were requested 

from all 58 PHL, not every PHL reported complete data. In the future, we expect that all PHLs 

will report data for each variable. Complete reporting is imperative for providing an accurate 

reflection of the work being performed over time to be described in future aggregate reports. 

Third, unless noted otherwise, data are reported on a “per patient” and not “per specimen” 

basis. Lastly, due to the limitations presented above, this report is to be used only as a guide 

and is not intended for other purposes that may be disciplinary in nature. 

The MLB thanks you for your continued dedication and hard work in providing TB laboratory 

testing services. We hope that you find this report both interesting and informative. Please let 

us know if you have any comments, questions, or suggestions that might improve the quality 

of future reports. 

Contact Details 

For inquiries, please contact the laboratory consultant for your jurisdiction. 

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

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

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

Acknowledgements: MLB thanks both Beverly Metchock (Reference Lab Team Lead) and 

Mitch Yakrus for their significant contributions to the aggregate report. 

INSIDE THIS REPORT: 

National Workload Data 2 

Ratio of Specimens 

per Patient 2 

Time for receipt 

of clinical specimens 3 

TAT for AFB smear 

microscopy 3 

Positivity rate 

for direct detection 4 

Methodology for 

Direct Detection 4 

Methodology for ID 4 

TAT for ID 

from clinical specimen 5 

TAT for DST 

from clinical specimen 5 

Positivity of 

Cultures and Isolates 6 

Key Findings 

and Guidance 6 

JUNE 22, 2010 

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

Division of Tuberculosis Elimination 
Ratio of Total Number of Specimens 

to Number of Patients Tested (N=58)

TABLE 1. National Workload Data for 


TB Elimination Cooperative Agreement Recipient Labs in 2008.
 

Variable Total 

number 

Minimum 

number per site 

Maximum 

number per site 

Number labs

reporting 

Clinical specimens receiveda 295,416 306 23,500 58 

Patients for whom a clinical specimen was 118,914 124 10,934 58 

submittedb 

Patients with at least one specimen culture 5,745 1 792 58 

positive for MTBCc 

Patients for whom a reference isolate was 21,250 0 2,575 58 

submittedd 

Patients with at least one reference isolate 3,327 0 276 55 

identified as MTBC 

Patients for whom DSTe

 for first-line drugs 8,255 2 895 58 

was performed 

Patients for whom clinical specimen was 13,232 0 5,855 57 

tested directly with NAATf or other rapid 

detection test 

Patients NAAT positive for MTBC 2,479 0 567 52 

a

 Processed and cultured, not including isolates referred from other laboratories, b Processed and a TB culture inoculated, 
 c Mycobacterium tuberculosis complex, d

 Received to rule out or confirm the identification of MTBC, 
 e

 Drug susceptibility testing, f Nucleic acid amplification test
 

Ratio of Total Number of Specimens 

to Number of Patients Tested (N=58) 

Ratio 

Mean = 2.61 

Standard Dev = 1.004 

Number of Public Health Labs

Percentiles 

10 1.59 

25 1.77 

50 2.33 

75 3.52 

90 4.10 

Figure 1. 

Ratio of total specimens tested to number 

of patients tested. The mean number of 

specimens cultured per patient was 2.61. 

In general, laboratories in high-incidence 

areas have a higher ratio and labs located 

in lower-incidence areas have a lower 

ratio. A value far in excess of the 10th and 

90th percentiles (<1.59 or >4.10 specimens 

cultured per patient) may suggest that a 

review of laboratory policies is indicated. 

2 
Percent of Specimens Received

Within 1, 2, and 3 Days After Collection 

AFB Smear Results Reported within One Day

Percent of Specimens Received 

Within 1, 2, and 3 Days After Collection 

 

 

0% 

100% 

Percent Specimens Received 80% 

60% 

40% 

20% 

Within 1 day Within 2 days Within 3 days 

Time to Specimen Receipt 

State Public Health Labs City Public Health Labs 

 

 

 

Figure 2. 

The current goal of laboratory receipt of 

specimens within 1 day of collection was 

achieved on average 37% of the time in 

state public health labs. Barriers described 

in cooperative agreement narratives 

included lack of a courier system, difficult 

terrain, remote locales, and limited 

education to providers. In addition, receipt 

of specimens can be affected by weekends 

and furlough days. 

AFB Smear Results Reported Within One Day Percent AFB Smear Results Reported 

100% 

90% 

80% 

70% 

60% 

50% 

3rd Quartile = 99.8% 

Median = 95.6% 

1st Quartile = 87.0% 

Mean = 91.3% 

Std. Dev. = 11.4 

N = 50 

Min = 74.6% 

Outlier 2 = 59% 

Outlier 1 = 64% 

Outlier 3 = 54% 

Max = 100% 

Figure 3. 

Box plot display of the percent of AFB 

smear results reported within one day 

of specimen receipt. An overwhelming 

majority of cooperative agreement 

recipient labs reported 87% or more of AFB 

smear results within 1 day of specimen 

receipt. Three laboratories reported values 

that were statistically below the observed 

minimum for other sites. Outliers should 

assess potential reasons for difficulty in 

meeting this objective. 

3 
Positivity of Direct Detection

Stratified by Testing Volume (N = 39 labs)

Rapid Direct DetectionMethods (N = 58) 

ID from Culture, Primary Methods (N = 58)

 

 

 

0 

>500 

Number TB Suspects Screened by Direct Detection 

11–50 51–150 151–500 

2 

4 

6 

8 

10 

12 

14 

16 

Number of Public Health Labs

0%

10%

20%

30%

40%

50%

60%

80%

90%

100%

Mean Percent TB Suspects

(+) by Direct Detection 

70%

No. of Public Health Labs Percentage TB Suspects (+) by Direct Detection 

Positivity of Direct Detection Stratified by 

Testing Volume (N = 39 labs) 

 

Figure 4. 

Overall, approximately 19% of TB suspects 

with a clinical specimen tested by a 

direct detection method were positive 

for MTBC. The positivity rate declined 

with an increasing number of TB suspects 

examined. PHL should work with 

submitters and their TB Control Program 

to determine an appropriate testing 

algorithm for utilization of direct detection 

methodologies. 

Rapid Direct Detection Methods (N = 58) 

D

H

Unknown: 

1 

Lab 

irect 

PLC: 

1 

Referred: 

9 

Developed 

NAAT: 8 

None: 

6 FDA 

Approved

NAAT: 

33 

Figure 5. 

Methods used by public health laboratories 

for rapid direct detection of MTBC from 

clinical specimens. 

ID from Culture, Primary Methods (N = 58) 

Lab Referred: 

developed:

1 Commercially 

available: 

2 

FDA 

Approved 

Probe: 

38 HPLC: 

14 

1 Unknown: 

2 

Figure 6. 

Primary methods used by public health 

laboratories for identification of MTBC 

from culture. 

4 
Percent ID Reported Within 21 Days of Specimen Receipt 

Stratified by Testing Volume (N=49)

Percent First-line DST Reported Within 28 Days 

Percent ID Reported Within 21 Days of Specimen 

Receipt Stratified by Testing Volume (N=49) 

Number of 

public health labs 

Mean Percent ID reported 

within 21 days of specimen receipt 

0 0%

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

Number of TB Suspects with Clinical Specimen Received by Lab 

20%

40%

60%

80%

100%

Mean Percent ID Reported 

ithin 21 days of Specimen Receipt 

2 

4 

6 

8 

10 

12 

14 

16 

18 

Number of Public Health Labs 

W

Figure 7. 

Many PHLs are near to or exceeding 80% of MTBC identifications being reported within 21 days of specimen receipt by the laboratory. 

There were no significant differences in turnaround time based on volume of testing. Some PHLs challenged in meeting this goal 

reported issues with staffing that limit the number of times ID assays can be performed each week. 

Percent First-line DST Reported Within 28 Days of 

Specimen Receipt Stratified by Testing Volume (N=51) of Specimen Receipt Stratified by Testing Volume (N=51) 

Number of 

public health labs 

Percent DST reported 

within 28 days of specimen receipt 

0% 

10% 

20% 

30% 

40% 

50% 

60% 

70% 

80% 

90% 

100% 

0–25 26–50 51–100 101–200 >200 

Number of Patients for Whom DST Performed 

Mean Percent DST Within 28 Days 

0 

2 

4 

6 

8 

10 

12 

14 

Number of Public Health Labs

Figure 8. 

Overall, 55% of first-line DST results are reported within the recommended 28 days of specimen receipt in the laboratory. In general, 

PHLs that performed more DST per year reported a higher percentage of results within 28 days. Barriers to meeting recommended 

TAT should be evaluated to ensure progress of reporting DST results within 28 days of receipt. 

5 
Positivity of Isolates Stratified by Volume

of Patient Isolates Tested 

Positivity of Cultures Stratified by Volume of 

Patient Specimens Tested

Positivity of Cultures Stratified by Volume of 

Patient Specimens Tested 

5.2

4.2

4.2

7.7 

9.6 

Figure 9. 

This figure represents the percent of 

cultures positive for MTBC stratified by 

volume of patients tested (not volume 

of total specimens). Overall, positivity 

declined with increasing volume, except for 

labs testing very high numbers; however 

the differences among volumes were not 

statistically significant (p =.099, Anova test, 

SPSS, v. 17). 

Positivity of Isolates Stratified by Volume 

of Patient Isolates Tested 

0 5 10 15 20 25 30 35

>800

01-800

01-400

00-200

<100

P

Mean Percent Positive for MTBC 

14.4

11.2

24.3

24.8

33.2

Number of

atient Isolates Received 4

2

1

 

 

>4000 

000-3999 

000-1999 

500-999 

<500 

Patient Specimens Cultured 

2

Number of

1

0 2 4 6 8 10 12 

Mean Percent Positive for MTBC 

Figure 10. 

This figure represents the percent of 

reference isolates, positive for MTBC, 

stratified by volume of patients tested. 

Similar to Figure 9, positivity declined 

with increasing volume, except for labs 

testing very high numbers; however the 

differences among volumes were not 

statistically significant (p =0 .25, Anova 

test, SPSS, v. 17). 

Monitoring the positivity of cultures and 

isolates over time (i.e., recovery rate of 

MTBC), is a useful performance indicator 

for the laboratory. 

Summary of Key Findings: 

1.	 Overall, PHLs are meeting the recommended TAT for reporting of smear results in one day, and for identification of MTBC within 21 days 


of specimen receipt. However, meeting the CDC recommended TAT of specimen receipt within one calendar day of collection and the 


provision of first-line DST results within 28 days of specimen receipt remain significant challenges.
 

2.	 Due to reporting variability by PHLs, it is difficult to determine the percent of patients meeting the Healthy People 2010 Goal of reducing 

the average time for a laboratory to confirm and report TB cases (Target: 2 days for 75 percent of cases that are later culture confirmed). 

However, it is evident that PHLs have great difficulty meeting this goal. PHLs should continue to ensure access to direct detection 

methodologies (e.g., nucleic acid amplification tests) for rapid identification of MTBC from clinical specimens. 

3.	 PHL Cooperative Agreement narratives provide insight into existing barriers for meeting TAT goals. For example, large geographical areas, 

inadequacies in postal delivery methods, lack of state-sponsored courier systems, and the practice of batching specimens all contribute 

to difficulties for timely specimen delivery. Additionally, staffing and scheduling issues, lab practices such as the need to wait for growth 

on solid media, and policies that delay reporting of preliminary results have all been identified as contributing to lengthy TAT for DST. 

4.	 Analyzing both aggregate and individual PHL data may help to identify trends and patterns that inform strategies to reduce barriers. 

These data are useful for advocacy of policy changes and reveal opportunities for operational research. Data analysis aids in assessment 

of both national recommendations as well as your own PHL performance objectives to ensure they closely reflect goals that are realistic 

and tied to measurable outcomes. 

CS2225701A

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