Lancet TB Diagnostics - Dr Keshree Pillay Dr Peter Cole 2013

Lancet TB Diagnostics

                Dr Keshree Pillay
                   Dr Peter Cole
                           2013

Background
• SA has a high burden of TB and HIV
• Dx of TB has many challenges including slow TAT’s
       – delays allow continued transmission
• TB dx critically important in HIV co-infected individuals
       – continued transmission especially of MDR
•    % of new TB cases with MDR-TB :              1.8%
•    % of retreatment TB cases with MDR-TB : 6.7%
•    Ideal to perform sensitivity testing on all patients
•    Should be done on all retreatment patients

http://www.who.int/tb/country/data/profiles/en/index.html accessed Nov 2013

South African Stats 2012
• Incidence
       – 1003/100 000 pop. (827-1194)
       – 530 000 cases
   TB patients with known HIV status : 84%
   HIV positive TB patients: 65%
• New cases
       –    40% smear positive
       –    21% smear negative
       –    24% smear unknown
       –    14% extra pulmonary
       Retreatment: 51% relapse

http://www.who.int/tb/country/data/profiles/en/index.html, accessed Nov 2013

• Growth of TB epidemic in Africa is attributable to several
  factors, the most important being the HIV epidemic

http://www.who.int/tb/publications/tb_global_facts_sep05_en.pdf

• Gene-Xpert rapid molecular diagnostic test assesses TB and
  rifampicin resistance ( 2 hrs)
• Lancet private pathology laboratory introduced Gene-Xpert
  rapid molecular TB diagnostic method in 2009
• In December 2010 the WHO convened an expert group that
  concluded the following:
   – "XPert should be used as the initial diagnostic test in individuals suspected of having
     MDR-TB or HIV-associated TB
   – "Xpert may be used as a follow-on test to microscopy where MDR and/or HIV are of
     lesser concern, especially in smear-negative specimens (Conditional recommendation)

• Before NDOH outlined introduction to public sector in 2011
• Modeling studies suggest that use of this test (replacing or
  adding to microscopy) will:
   – Increase TB case finding by 30%
   – Increase MDR-TB case finding by 3-fold
   http://www.medscape.com/viewarticle/745030, Lockman S. A new Era:Molecular Tuberculosis Diagnosis

TESTING ALGORITHM

                                                              Culture     ID & Sensitivity
                                           Negative
                                                             (6 weeks)       (2 weeks)

     Smear           Gene-Xpert                               Culture    ID & Sensitivity (2
                                      Rifampicin resistant
POSITIVE/NEGATIVE   MTB/Rif (2 hrs)                          (6 weeks)        weeks)

                                      Rifampicin sensitive

Scope of TB and related diagnostic
       tests within Lancet
                       Rapid Diagnostics

   • GeneXpert MTB/RIF
      
 Two 16 module instruments
      
 Average of 1500 tests per month
      
 Performed on Direct sample or as Culture confirmation

   • Hain Genotype MTBDRplus
      
 Average of 300 tests per month
      
 Performed on direct decontaminated sputum with smear P1
        or greater
      
 Performed on culture positive samples

Scope of TB and related diagnostic
       tests within Lancet
                       Culture
   • Bactec MGIT 960
      
 Average of 5000 tests per month
      
 15 Bactec 960 instruments
           Interfaced to EpiCenter

   • Bactec FX
      
 Average of 200 tests per month
      
 Performed on blood cultures

TB Fingerprinting
        •   Use a MIRU-VNTR Assay

        •   Sensitive and specific methodology
            to determine mTB strain.

        •   Strain differentiation is used by
            examining 24 different loci, except
            in Beijing strain where 28 loci are
            used.

        •   Assay is a useful tool to determine
            relapse or re-infection by identifying
            clusters.

        •   Useful to determine best infection
            control practises.

Determination of TB Resistance

                                      •   Lancet has population
                                          based sequencing
                                          capacity to amplify and
                                          sequence the 11 genes of
                                          the TB genome.

                                      •   The population-based
                                          sequences obtained are
                                          used to identify known
                                          mutations, which result in
                                          decreased susceptibility
                                          to antibiotics used in TB
                                          treatment.
Farhat et al., Nature Genetics 2013

Snapshot analysis of Lancet TB
                data
   – July 2009-January 2012

   – KZN + Gauteng

• Limited socio-demographic data

• Sub-set with associated HIV data

   – HIV ELISA, CD4 count, RNA Viral load

• Personal identifiers removed for analysis

Results
• 51,075 tests in total
   – 24,969 in 2011
   – 2.7% patients had > 1 Gene-Xpert test

                    2.7%       0.2%

                                             single GE
                                             2 GE: 2.7%
                                             3 GE: 0.2%
                               97.1%

Socio-Demographics
  Parameter                Results
Sex           Female                 51.2%
              Male                   48.8%
Age           Mean 37.2 yrs
              0-5 yrs:                9.4%
              30-49 yrs:             46.4%
Province      GP                     49.9%
              KZN                    50.1%
Status        In patient             71.8%
              Outpatient             21.2%
Source        Pulmonary              83.7%
              Extra Pulmonary        16.0%

Gene-Xpert MTB Results
                   MTB +ve      Significance

Total
                        21.6%
(n=51,075)
Males                   23.9%
                                     p

MTB+ve by Region
GAUTENG: 22.26%    KZN: 21.03%

                          p=0.001

Rifampicin Susceptibility
          87.0%

100.0%

 80.0%

 60.0%

 40.0%                 12.7%
                                     0.3%
 20.0%

  0.0%
         Sensitive   Resistant   Indeterminate

Rifampicin Resistance and HIV
               MTB +ve      Significance

HIV negative         8.7%
                                 p=0.328
HIV positive        10.5%

CD4 0-50            14.3%

CD4 51-350          13.3%        p=0.337

CD4 >350            10.6%

Significant Predictors
            Odds ratios in multiple regression
                             MTB         Rifampicin
         Comparison
                             +ve         Resistance
Female
                                   0.8                1.5
 vs Male
Adult
                                   4.1                NS
 vs Child
Pulmonary
                                   2.1                NS
 vs Extra-pulmonary
KZN                                NS                 1.9
 vs GT
HIV positive
                                   1.8                NS
 vs HIV negative

Conclusions
• Gene-Xpert test does play a significant role in MTB and MDR
  diagnosis

• HIV increased likelihood of MTB positivity but not rifampicin
  resistance in this cohort

• Rifampicin resistance was significantly higher in KZN

• Private laboratory data is useful in investigating patterns of
  MTB positivity and rifampicin resistance in South Africa

Challenges
•   Funding limitations –
     -sub optimal methods for dx
           smear only
           limited susceptibilties
     - sub optimal TAT
       eg initial test culture based diagnostics rather than rapid molecular {best
       practice}
•   Co ordination and communication between public and private sector

•   Standardisation of testing ideally

•   Waste of scare resources by repeat testing between facilities