Defining Discordance

• “A state of non-harmony or non-agreement”

• Non-agreement between:

Different genotypic tests – Xpert and LPA

Genotypic and phenotypic tests - Xper/LPA and

MGIT culture

1 or more of genotypic and/or phenotypic tests and

clinical response to treatment

 Resistance

• Genotypic resistance

• Phenotypic resistance

• Clinical resistance
 Patient fails to respond to therapy with the drug
 Detected by failure of smear conversion,
treatment failure or relapse
 Genotypic Resistance

• Genetic mutation gives rise to resistance

• Detected by molecular testing – Xpert, LPA, gene

sequencing
Xpert
LPA
 What can go wrong with Xpert?
• False resistance
 Lab will check Xpert readout

 VL bacterial load

 Drop out vs delay

 Ct value 4.1 – 4.9

• False susceptible
 Mixed infection of resistant and susceptible MTB population
in the same specimen/patient

 If resistant population less < 65 – 100%

 Xpert susceptibility drops to below 80% in mixed infections

 What can go wrong with LPA?

• False resistance
 Cross contamination

 Procedural error

 Scanner/Observer error

• False susceptible
 Some mutations at very end of amplified sequence can be
missed

 Disputed mutilations may be missed

 Procedural error

 Scanner/observer
 Phenotypic Resistance

• MTB fails to grow or survives in the presence of

antibiotic

• Detected by culture based methods e.g. MGIT

 MGIT
(Mycobacteria Growth Incubator Tube)
 What can go wrong with Phenotypic
DST?
• False resistance

 Contamination with NTM

 Technical error: incorrect inoculum of bacteria, incorrect

amount of drug added, loss of potency of the drug

• False susceptible

 Incorrect critical concentration

 Technical error: incorrect inoculum of bacteria, incorrect

amount of drug added, loss of potency of the drug

 Heteroresistance

• Sensitive and resistant MTB population in a single

clinical sample/patient

• Due to:

mixed infection with two or more MTB strains

resistance mutations arise from a single clone

 Impact of Heteroresistance
Culture based DST (MGIT)
• In one sample/patient there can be co-existence of sub-populations

with different levels of resistance

• Assumption that the MTB population in MGIT culture is the same

• To obtain a measure of heterogenicity of TB infection, several

independent bacterial isolates should be examined from each

patient sample

Xpert/LPA
• Xpert: increase risk for false susceptible result

• LPA: better at detecting it, but will be missed if disputed mutations

are present
Commonly Encountered Discordant DST
Results
Rifampicin
Genotypic vs. genotypic
• Xpert Rif-R and LPA Rif-S

• Xpert Rif-S and LPA-R

Genotypic vs phenotypic
• Xpert Rif-R (Xpert and LPA agree) vs phenotypic Rif-S

• Genotypic Rif-S vs phenotypic Rif-R

INH
Genotypic INH-S vs phenotypic INH-R
How does the laboratory deal with
discordance?
 How does the laboratory deal with
discordance?
• Detected
 History checks on Xpert Rif-R results – not always possible
because of patient identifiers
 Call from clinician
• Check if no sample mix up in the lab

• Check the Xpert graph and Ct values to rule out possible false
Xpert resistance

• Check LPA results (check bands and sometimes do Xpert directly on

MGIT culture)

• If truly discordant – phenotypic test +/- Second Line LPA

• Enter comment on laboratory report

 Example of Comment Entered on
Laboratory Report
The discordant rifampicin result between the Xpert (12.10.17 – Rifampicin
resistant; UH00935910) and the previous LPA performed on a cultured isolate
(18.08.17– Rifampicin susceptible; UH00959822) for this patient is noted. The
Xpert and LPA results have been checked. This discordant result may be due
to mixed infection (one susceptible and one resistant MTB strain in same
specimen / patient) which requires management by a Specialist TB Physician.
Correlate clinically and with results of repeat specimens submitted for Xpert
and culture + DST. Please call the laboratory on (041) 395 6163/6170 for
further information if required.
 Acknowledgements

• Cindy Hayes, PE NHLS

• Dr Natalie Baylis, Groote Schuur NHLS
• Yonas Ghebrekristos, Groote Schuur
NHLS