TB genotyping update, with particular reference to 24 locus MIRU

1
TB genotyping update, with particular reference
to24 locus MIRU

• CTCA 2009
• Ed Desmond
• Calif. Dept. of Public Health

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MIRU-VNTR12 ? MIRU-VNTR 24
miru02
miru39
miru04
miru40
miru10
miru31
miru16
miru27
miru26
miru24
miru20
miru23
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C. Allix-Beguec, JCM Aug 2008, p. 2692Testing of
802 population-based European cultures
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Mokrousov, I. JCM Nov 08, p 357648 Beijing
spoligotype isolates from Russia
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Jiao, WW, JCM Mar 2008, p 104572 Beijing
genotype isolates from Beijing, China
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Discriminatory power of 24 locus MIRU with Manila
genotype

• ?

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16 capillary ABI 3130xl
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384 well plate for expanded MIRU
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Robotic pipettor for 384 well plates
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Naming clusters with MIRU 24

• For the past five years, the results of the
  MIRU-VNTR assay were reported as a 12 character
  string. When at least two isolates within the
  state program had identical spoligotype and MIRU
  patterns they were assigned a cluster name.
• Isolate Spoligotype MIRU
  Cluster name
• 1 777777777760771 111111111111
  CA_01
• 2 777777777760771 111111111111
  CA_01
• 3 777777777760771 211111111111

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Naming clusters with MIRU 24, contd

• Beginning in April 2009, the genotyping labs will
  be performing a second MIRU-VNTR assay on all
  isolates submitted for genotyping. The original
  assay will be referred to as MIRU1 and the new
  assay as MIRU2. The MIRU2 result is also a 12
  character string.
• Isolate Spoligotype MIRU1
  MIRU2 Cluster
• 
  name
• 1 777777777760771 111111111111
  555555555555 CA_01
• 2 777777777760771 111111111111
  555555555558 CA_01
• 3 777777777760771 211111111111
  555555555555

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• So that you may compare your new results with
  results obtained prior to April 2009,clusters
  will continue to be named based on spoligotype
  and MIRU1. As MIRU2 subclusters are identified
  within each primary cluster, the cluster name
  will be updated with a suffix.
• Isolate Spoligotype MIRU1
  MIRU2 Cluster
• 
  
  name
• 1 777777777760771 111111111111
  555555555555 CA_001-001
• 2 777777777760771 111111111111
  555555555558 CA_001
• 3 777777777760771 211111111111
  555555555555
• 4 777777777760771 111111111111
  555555555555 CA_001-001

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• In June 2009, we will be changing the current PCR
  type field to PCRtype1 and introducing a new
  field, PCRtype2. PCRtype2 will be the type name
  given to each spoligotype_MIRU1_MIRU2 result as
  it is identified within the National TB
  Genotyping Service. PCRtype2 names will be based
  on sub-types within PCRtype1.
• Spoligotype MIRU1 MIRU2
  PCRtype1 PCRtype2
• 777777777760771 111111111111 555555555555
  PCR00001 PCR00001-001
• 777777777760771 111111111111 555555555556
  PCR00001 PCR00001-002
• Note PCR type is a national designation,
  enabling comparison of strains from different
  states.

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Shipping cultures for genotyping 10 CA counties
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Staffing notes

• Steven Yuspoligotyping and database
• Laura CruzMIRU
• Terry WeberDNA prep, culture maintenance, RFLP
  analysis
• Jane WengerRFLP, DNA prep, culture work
• Lucy Pham(half-time) DNA prep, RFLP, culture
  maintenance