Effectiveness of real-time polymerase chain reaction assay for the detection of Mycobacterium tuberculosis in pathological samples
: a systematic review and meta-analysis

  • Emmanuel O. Babafemi

Student thesis: Doctoral Thesis


Background: Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (MTB) and is a major global health problem with an annual mortality of 1.8 million people and being the cause of ill-health among many more millions. Rapid and accurate diagnosis of TB is key to managing the disease, its control and transmission. Many established diagnostic methods suffer from low sensitivity or delays in getting results and are inadequate for rapid detection of MTB in pulmonary and extra-pulmonary clinical samples. This study examined whether real-time polymerase chain reaction (RT-PCR) assay, with a 2 h turn-a-round time, would prove effective for routine detection of MTB in clinical microbiology laboratories.

Methods: A systematic literature search was performed for publications in any language (January 1995–November 2016) on the detection of MTB in pathological samples by RT-PCR assay. The following databases were used: MEDLINE via PUBMED, EMBASE, BIOSIS Citation Index, Web of Science, SCOPUS, ISI Web of Knowledge and Cochrane Infectious Diseases Group Specialised Register, grey literature and the World Health Organization and Centers for Disease Control and Prevention websites. Studies were only included if they met set inclusion criteria. Generated pooled summary estimates (95% CIs) were calculated for sensitivity and specificity by use of random-effects meta-analysis when four or more studies were available. For meta-analysis, the bivariate model was used because it takes into account potential threshold effects and the correlation between sensitivity and specificity. It also allows addition of covariates for investigation of potential sources of heterogeneity. RevMan 5.3 and Meta-Disc software packages were used.

Results: Forty-six studies out of 6,706 citations identified met the inclusion criteria, providing information from 21 countries with high, moderate and low prevalence of TB. Studies included patients with infections identified in primary, secondary and tertiary healthcare settings. There were a total of 35,380 samples: 28,406 from pulmonary TB (PTB) and 6974 from extra-pulmonary (EPTB). Summary estimates for PTB (31 studies) were: sensitivity 0.82; 95% CI, 0.81–0.83; specificity 0.99; 95% CI, 0.99–0.99; positive likelihood ratio 43.00 (28.23–64.81); negative likelihood ratio 0.16 (0.12–0.20), diagnostic odds ratio 324.26 (95% CI 189.08–556.09) and area under curve (AUC) 0.99. Summary estimates for EPTB (25 studies) were: sensitivity 0.70, 95% CI, 0.67–0.72; specificity 0.99, 95% CI, 0.99–0.99; positive likelihood ratio 29.82 (17.86–49.78); negative likelihood ratio 0.33 (0.26–0.42); diagnostic odds ratio 125.20 (95% CI 65.75–238.36) and AUC 0.96. Summary estimates for subgroup analyses by RT-PCR assay type were: with CobasTaqMan as the RTPCR assay (17 studies): sensitivity 0.78, 95% CI, 0.76–0.80; specificity 0.99, 95% CI, 0.99–0.99 and AUC 0.98. With Roche Light cycler as the RT-PCR assay (7 studies): sensitivity 0.85, 95% CI, 0.80–0.88; specificity 0.99, 95% CI, 0.98–0.99 and AUC 0.97. With Cepheid & other types of RT-PCR assay (22 studies): sensitivity 0.78, 95% CI, 0.77–0.80; specificity 0.99, 95% CI, 0.99–0.99 and AUC 0.99. Summary estimates for subgroup analyses by RT-PCR assay target sequence genes were: with IS6110 as the RT-PCR assay target sequence gene (22 studies): sensitivity 0.79, 0.77–0.81, specificity 0.98, 0.98–0.98 and AUC 0.99. With 16SRNA as the RTPCR assay target sequence gene (7 studies): sensitivity 0.69, 0.66–0.71; specificity 0.99, 0.99–0.99 and AUC 0.97. With other genes (17 studies): sensitivity 0.82, 0.80–0.84; specificity 0.99, 0.99–0.99 and AUC 0.98. Summary estimates for subgroup analyses by reference tests were: with solid and liquid media combined (25 studies): sensitivity 0.77, 95% CI, 0.76–0.79; specificity 0.99, 95% CI, 0.99–0.99 and AUC 0.99. With solid media alone (13 studies): sensitivity 0.80, 95% CI, 0.77–0.82; specificity 0.96, 95% CI, 0.96–0.97 and AUC 0.98. With liquid media alone (6 studies): sensitivity 0.81, 95% CI, 0.75–0.86; specificity 0.99, 95% CI, 0.99–1.00 and AUC 0.94.

Conclusions: RT-PCR assay demonstrated a high degree of sensitivity for PTB and good sensitivity for EPTB. It indicated a high degree of specificity for ruling in TB infection from sampling regimes. This was acceptable, but may suggest it as a rule-out add-on diagnostic test. RT-PCR assay’s high degree of sensitivity in pulmonary samples and rapidity of detection of TB is an important factor in achieving effective global control and for patient management in terms of initiating early and appropriate anti-tubercular therapy.

Date of AwardSept 2017
Original languageEnglish
Awarding Institution
  • University of Portsmouth
SupervisorLee Banting (Supervisor) & Graham Mills (Supervisor)

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