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v2 Discrete Microbiology

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Doing the Culture

  • A sample is collected and cultured for several days in a petri dish to see if anything grows
  • If nothing grows, the culture is “negative” and gets reported in a relatively simple v2 message
  • If something grows, then observations are collected and more tests are done
    • Observations can include:
      • “normal flora”
      • Growth quantity
      • Gram stain (bacteria can largely split into two categories – Gram Positive and Gram Negative)
      • The actual identified organism(s) (E. coli, Salmonella, etc)
    • These observations are typically just returned as OBX segments under the OBR

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Doing the Culture

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Doing the Culture (Gram Stain)

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Doing the Susceptibility Test

  • Also sometimes called sensitivity tests
  • Organisms of interest are tested to see which antibiotics they are sensitive (or resistant) to
  • There are different ways to do these tests (MIC, Kirby Bauer, etc) but ultimately they end up with an “interpretation” of sensitive or resistant
    • Some tests yield an actual result value as well
  • Susceptibility results are returned in a different way in the v2 message

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Doing the Susceptibility Test

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v2 Message Structure

  • MSH
  • PID/PV1 etc
  • ORC/OBR – culture
  • OBX – culture level observations
  • ORC/OBR – susceptibility (organism) 1
  • OBX – antibiotic observations
  • ORC/OBR – susceptibility (organism) 2
  • OBX – antibiotic observations
  • …

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v2 Message Structure (Culture Results)

  • ORC|RE|ORD723222-4^NIST EHR|R-783274-4^NIST Lab Filler|GORD874211^NIST EHR||||||||57422^Radon^Nicholas^^^^^^NIST-AA-1^L^^^NPI
  • OBR|1|ORD723222-4^NIST EHR|R-783274-4^NIST Lab Filler|625-4^Bacteria identified in Stool by Culture^LN^3456543^CULTURE STOOL^99USI^^^Stool Culture|||20110530123551-0500||||||787.91^DIARRHEA^I9CDX^^^^^^DIARRHEA|||57422^Radon^Nicholas^^^^^^NIST-AA-1^L^^^NPI||||||20110531140428-0500|||F
  • OBX|1|CWE|625-4^Bacteria identified in Stool by Culture^LN^^^^^^Stool Culture|1|103429008^Enterohemorrhagic Escherichia coli, serotype O157:H7^SCT^^^^^^Shiga toxin producing E. coli O157:H7 isolated|||A|||F|||20110530123551-0500|||||20110531130655-0500||||Century Hospital^^^^^NIST HCAA-1^XX^^^987|2070 Test Park^^Los Angeles^CA^90067^^B|9876543^Slide^Stan^S^^^^^NIST HCAA-1^L^^^NPI
  • OBX|2|CWE|625-4^Bacteria identified in Stool by Culture^LN^^^^^^Stool Culture|2|398567006^Salmonella I, group O:4^SCT^^^^^^Salmonella I, group O:4 isolated|||A|||F|||20110530123551-0500|||||20110531130655-0500||||Century Hospital^^^^^NIST HCAA-1^XX^^^987|2070 Test Park^^Los Angeles^CA^90067^^B|9876543^Slide^Stan^S^^^^^NIST HCAA-1^L^^^NPI
  • OBX|3|ST|664-3^Gram Stain^LN^^^^^^Gram Stain|3|Many Gram Negative Rods|||A|||F|||20110530123551-0500|||||20110531130655-0500||||Century Hospital^^^^^NIST HCAA-1^XX^^^987|2070 Test Park^^Los Angeles^CA^90067^^B|9876543^Slide^Stan^S^^^^^NIST HCAA-1^L^^^NPI

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v2 Message Structure (Susceptibility Results)

  • ORC|RE||R-783274-5^NIST Lab Filler|GORD874211^NIST EHR||||||||57422^Radon^Nicholas^^^^^^NIST-AA-1^L^^^NPI
  • OBR|2||R-783274-5^NIST Lab Filler|50545-3^Bacterial susceptibility panel in Isolate by Minimum inhibitory concentration (MIC)^LN^^^^^^Bacteria susceptibility|||20110530123551-0500||||G|||||57422^Radon^Nicholas^^^^^^NIST-AA-1^L^^^NPI||||||20110601140428-0500|||F|625-4&Bacteria identified in Stool by Culture&LN&&&&&&Stool Culture^1|||ORD723222-4&NIST EHR^R-783274-4&NIST Lab Filler
  • OBX|1|SN|28-1^Ampicillin [Susceptibility] by Minimum inhibitory concentration (MIC)^LN^^^^^^AMPICILLIN|1|<^0.06|ug/mL^^UCUM||S|||F|||20110530123551-0500|||||20110601130655-0500||||Century Hospital^^^^^NIST HCAA-1^XX^^^987|2070 Test Park^^Los Angeles^CA^90067^^B|9876543^Slide^Stan^S^^^^^NIST HCAA-1^L^^^NPI
  • OBX|2|SN|267-5^Gentamicin [Susceptibility] by Minimum inhibitory concentration (MIC)^LN^^^^^^GENTAMICIN|1|^0.05|ug/mL^^UCUM||S|||F|||20110530123551-0500|||||20110601130655-0500||||Century Hospital^^^^^NIST HCAA-1^XX^^^987|2070 Test Park^^Los Angeles^CA^90067^^B|9876543^Slide^Stan^S^^^^^NIST HCAA-1^L^^^NPI

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v2 Message Structure (Susceptibility Results)

  • ORC|RE||R-783274-6^NIST Lab Filler|GORD874211^NIST EHR||||||||57422^Radon^Nicholas^^^^^^NIST-AA-1^L^^^NPI
  • OBR|3||R-783274-6^NIST Lab Filler|50545-3^Bacterial susceptibility panel in Isolate by Minimum inhibitory concentration (MIC)^LN^^^^^^Bacteria susceptibility|||20110530123551-0500||||G|||||57422^Radon^Nicholas^^^^^^NIST-AA-1^L^^^NPI||||||20110601140428-0500|||F|625-4&Bacteria identified in Stool by Culture&LN&&&&&&Stool Culture^2|||ORD723222-4&NIST EHR^R-783274-4&NIST Lab Filler
  • OBX|1|SN|28-1^Ampicillin [Susceptibility] by Minimum inhibitory concentration (MIC)^LN^^^^^^AMPICILLIN|1|<^0.06|ug/mL^^UCUM||S|||F|||20110530123551-0500|||||20110601130655-0500||||Century Hospital^^^^^NIST HCAA-1^XX^^^987|2070 Test Park^^Los Angeles^CA^90067^^B|9876543^Slide^Stan^S^^^^^NIST HCAA-1^L^^^NPI
  • OBX|2|SN|267-5^Gentamicin [Susceptibility] by Minimum inhibitory concentration (MIC)^LN^^^^^^GENTAMICIN|1|^0.05|ug/mL^^UCUM||S|||F|||20110530123551-0500|||||20110601130655-0500||||Century Hospital^^^^^NIST HCAA-1^XX^^^987|2070 Test Park^^Los Angeles^CA^90067^^B|9876543^Slide^Stan^S^^^^^NIST HCAA-1^L^^^NPI

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v2 Message Structure (Susceptibility Results)

  • OBR|1|ORD723222-4^NIST EHR|R-783274-4^NIST Lab Filler|625-4^Bacteria identified in Stool by Culture^LN^3456543^CULTURE STOOL^99USI^^^Stool Culture|||20110530123551-0500||||||787.91^DIARRHEA^I9CDX^^^^^^DIARRHEA|||57422^Radon^Nicholas^^^^^^NIST-AA-1^L^^^NPI||||||20110531140428-0500|||F
  • OBX|1|CWE|625-4^Bacteria identified in Stool by Culture^LN^^^^^^Stool Culture|1|103429008^Enterohemorrhagic Escherichia coli, serotype O157:H7^SCT^^^^^^Shiga toxin producing E. coli O157:H7 isolated|||A|||F|||20110530123551-0500|||||20110531130655-0500||||Century Hospital^^^^^NIST HCAA-1^XX^^^987|2070 Test Park^^Los Angeles^CA^90067^^B|9876543^Slide^Stan^S^^^^^NIST HCAA-1^L^^^NPI
  • OBX|2|CWE|625-4^Bacteria identified in Stool by Culture^LN^^^^^^Stool Culture|2|398567006^Salmonella I, group O:4^SCT^^^^^^Salmonella I, group O:4 isolated|||A|||F|||20110530123551-0500|||||20110531130655-0500||||Century Hospital^^^^^NIST HCAA-1^XX^^^987|2070 Test Park^^Los Angeles^CA^90067^^B|9876543^Slide^Stan^S^^^^^NIST HCAA-1^L^^^NPI

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  • Susceptibility #1
  • OBR|2||R-783274-5^NIST Lab Filler|50545-3^Bacterial susceptibility panel in Isolate by Minimum inhibitory concentration (MIC)^LN^^^^^^Bacteria susceptibility|||20110530123551-0500||||G|||||57422^Radon^Nicholas^^^^^^NIST-AA-1^L^^^NPI||||||20110601140428-0500|||F|625-4&Bacteria identified in Stool by Culture&LN&&&&&&Stool Culture^1|||ORD723222-4&NIST EHR^R-783274-4&NIST Lab Filler

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  • Susceptibility #2
  • OBR|3||R-783274-6^NIST Lab Filler|50545-3^Bacterial susceptibility panel in Isolate by Minimum inhibitory concentration (MIC)^LN^^^^^^Bacteria susceptibility|||20110530123551-0500||||G|||||57422^Radon^Nicholas^^^^^^NIST-AA-1^L^^^NPI||||||20110601140428-0500|||F|625-4&Bacteria identified in Stool by Culture&LN&&&&&&Stool Culture^2|||ORD723222-4&NIST EHR^R-783274-4&NIST Lab Filler

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FHIR Micro Structure #1

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FHIR Micro Structure #2

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FHIR Micro Structure #2

Resource List

  • DiagnosticReport
  • Observation (gramstain1)
  • Observation (gramstain2)
  • Observation (growth1)
  • Observation (growth2)
  • Observation (org2-amp)
  • Observation (org2-cip)
  • Observation (organism1)
  • Observation (organism2)

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http://hl7.org/implement/standards/fhir/diagnosticreport-example-lri.xml.html

Resource Linkages

  • DiagnosticReport.result points to:
    • Observation (gramstain1)
    • Observation (gramstain2)
    • Observation (organism1)
    • Observation (organism2)
  • Observation(organism1).hasMember points to:
    • Observation (growth1)
  • Observation(organism2).hasMember points to:
    • Observation (growth2)
    • Observation (org2-amp)
    • Observation (org2-cip)

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v2 Message Structure to FHIR

  • https://docs.google.com/spreadsheets/d/1MXb3yDwHQYMjzoOzQRj1AaSYFwu1uRpqur-y51-Qtgo/edit#gid=0
  • MSH
  • PID/PV1 etc
  • ORC/OBR – culture => DiagnosticReport
  • OBX – culture level observations => Observation via DiagnosticReport.value (culture specific or organism identification) or Observation.hasMember (organism specific)
  • ORC/OBR – susceptibility 1 => Lookup DiagnosticReport and Observation
  • OBX – antibiotic observations => Observation via Observation.hasMember
  • ORC/OBR – susceptibility 2 => Lookup DiagnosticReport and Observation
  • OBX – antibiotic observations => Observation via Observation.hasMember

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