COVID 19 Webinar for Case Investigation and Follow up What is ELR? - - PowerPoint PPT Presentation

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COVID 19 Webinar for Case Investigation and Follow up What is ELR? - - PowerPoint PPT Presentation

Apr 11, 2023 153 likes •304 views

COVID 19 Webinar for Case Investigation and Follow up What is ELR? June 9, 2020 Sita Smith Bureau of Infectious Disease and Laboratory Sciences MA Department of Public Health ELR Things to know 2 Scale of reporting March 2020 90

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SLIDE 1

COVID‐19 Webinar for Case Investigation and Follow‐up

What is ELR?

Sita Smith Bureau of Infectious Disease and Laboratory Sciences MA Department of Public Health

June 9, 2020

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SLIDE 2

ELR Things to know

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SLIDE 3

Scale of reporting

March 2020

  • 90 MA clinical labs and reference labs
  • Around 2000 lab reports/day

June 2020

  • 200 clinical labs, reference labs, urgent care

centers, point of care centers

  • From 10000 – 18000 reports/day

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SLIDE 4

Anna Jaques Hospital Lahey Clinic Brockton Hospital ARUP Addison Gilbert Hospital

  • St. Luke's Hospital

Baystate Medical Center Beverly Hospital Charlton Hospital Berkshire Health Systems Winchester Hospital Tobey Hospital Fairview Hospital Lawrence General Hospital South Shore Hospital Beth Israel Milton Hospital Lowell General Hospital Saint Vincents Hospital Beth Israel Plymouth Lowell General Saints Campus Steward Carney Hospital Beth‐Israel Deaconess Medical Center Mayo Clinic Good Samaritan Medical Center Beth‐Israel Deaconess Needham Mercy Medical Center Holy Family Hospital Boston Children Hospital Metrowest Medical Center, Merrimack Valley Hospital Boston Medical Center Milford Regional Medical Center Morton Hospital Broad Institute Mount Auburn Hospital Nashoba Hospital Falmouth Hospital New England Baptist Hospital Norwood Hospital Cape Cod Hospital Brigham and Women's Hospital Saint Anne's Hospital Cambridge Health Alliance Laboratory Brigham And Women's Faulkner Hospital

  • St. Elizabeth's Medical Center

Whidden Hospital Dana‐Farber Cancer Institute Excell Clinical Labs Emerson Hospital Newton Wellesley Hospital New England Sinai Hospital Lawrence Memorial MGH Sturdy Memorial Hospital Melrose Wakefield North Shore Hospital Tufts Medical Center Harrington Memorial Hospital Martha's Vineyard Hospital UMass Memorial Medical Center Heywood Hospital Nantucket Cottage Hospital HealthAlliance Holyoke Medical Center Spaulding Rehabilitation Hospital State Laboratory Instititute Imugen Cooley Dickinson Hospital Quest Laboratory Corporation of America Massachusetts Eye & Ear BioReference

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Routine infectious disease reporting

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SLIDE 5

AccessDX CareOne ‐ Brookline Encompass NEDS Aegis CareOne ‐ Concord etruenorth One Medical AFC Methuen, Stoneham, Waltham, N Andover CareOne ‐ Lexington Exact Sciences BROAD AFC Marlboro CareOne ‐ Lowell Excelsior ORDRS Houston/MD TOX AFC Saugus CareOne ‐ Needham ExosomeDx_Biotechne‐eurofin Orig3n, Inc. AFC Springfield CareOne ‐ Newton Fallon Pangea AFC Swampscott CareOne ‐ Wilmington Fulgent Pediatric Associates of Greater Salem AFC UC @Natick CareOne at Essex Park GeneSyS PerkinElmer AFC Waltham, Patriots CareOne at Millbury Genetworx Pine Street (Boston Homeless) Alliance at Devereux House CareOne at New Bedford Genomic Expression pmaonline Ammon CareOne at Peabody Greater Lawrence Family Health Center PrimaCare Arcpoint CareOne at Weymouth Integrity PWN Health Assurance Carewell UC Jackson Labs QDX Pathology Services Atrius Center for motivation & change John Dewey Academy Sparrow Healthcare Bedford Research CHAlliance Nursing Homes kbmo diagnostics Tempus Biocerna Color Lab USA Haverhill Tewkesbury Hospital Biogen IDEC ConvenientMD Lafayette Rehabilitation The Horowitz Medical Group (THMG) BioReference cQuentia Lemuel Shattuck Trident US Labs at Brockton Boston Heart Diagnostics. Curative Leonard Florence Center for Living VA Bedford and Boston Boston Home CVS Linden Ponds VA Central Western MA Brandon Woods of Dartmouth Davita Mako Medical Veritas Genetics Brandon Woods of New Bedford Dispatch Meadow Green Nursing and Rehab Center Vikor Cambridge Biomedical East Boston FHC Middleton Family Medicine Viracor Capstone East Side Clinical Lab (Sonicare) + Sunrise MIT Walden Behavioral Health

Additional COVID only reporting

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SLIDE 6

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  • Faxes ‐ manual data entry (how many?) ~ 250 day
  • Team of 8 manually entering into Maven
  • Electronic laboratory reporting (ELR)
  • Vast majority of what we receive ~ 12000/day
  • Team of 4 monitoring and correcting
  • Simple Excel spreadsheets, received via sftp or

secure mail ~ 2500/day

  • Team of 4 epidemiologists processing

How are we receiving labs?

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SLIDE 7

Electronic Laboratory Reporting

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MAVEN

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SLIDE 8

Not real time

  • We receive reports for everything resulted the day

before

  • Usually one batch per day
  • Reports feed into Maven within half an hour of

entering the portal

  • Having to correct errors will delay the process

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SLIDE 9

HL7 message

  • FHS|^~\&|Lab Facility^2.16.840.1.114222.4.1.220759^ISO|Lab Facility^05D0000000^CLIA|MA‐MDPH^2.16.840.1.113883.19.3.2^ISO|MA‐

MDPH^0000000^CLIA|20200603130950‐0800||MA‐MDPH||MA‐MDPH:20200603130950‐0800

  • BHS|^~\&|Lab Facility^2.16.840.1.114222.4.1.220759^ISO|Lab Facility^05D0000000^CLIA|MA‐MDPH^2.16.840.1.113883.19.3.2^ISO|MA‐

MDPH^0000000^CLIA|20200603130950‐0800||MA‐MDPH||MA‐MDPH:20200603130950‐0800

  • MSH|^~\&|Lab Facility^2.16.840.1.114222.4.1.220759^ISO|2.16.840.1.114222.4.1.220759^Lab Facility^05D0000000^CLIA|MA‐

MDPH^2.16.840.1.113883.19.3.2^ISO|MA‐MDPH^0000000^CLIA|20200603131238‐0800||ORU^R01^ORU_R01|D‐ 4861207191202006032112953627|P|2.5.1|||NE|NE|USA||||PHLabReportNoAck^^2.16.840.1.113883.9.10^ISO

  • SFT|Lab Facility|1.0|Lab Facility|Binary Id Unknown
  • PID|1||110596808^^^Lab Facility&2.16.840.1.114222.4.1.220759&ISO^PI||Mouse^Mickey||19870501|M||2028‐9^Asian^CDCREC^^^^3.1.0|00 Fake

street^^Disney^MA^02130^USA^H||^PRN^PH^^1^617^9834370|||||||||2186‐5^Not Hispanic or Latino^CDCREC^^^^3.1.0

  • ORC|RE|3631467^Lab Facility^2.16.840.1.114222.4.1.220759^ISO|3631467^Lab

Facility^2.16.840.1.114222.4.1.220759^ISO||CM|||||||1962476994^Mouse^Minnie^^^^^^NPI&2.16.840.1.113883.4.6&ISO^^^^NPI|||||||||Ordering Facility^D|00 Main St.^^Tunes^MA^02130^USA^O|^WPN^PH^^1^617^9834370|25 Fake Street^Building E23^Tunes^MA^02130^USA^O

  • OBR|1|3631467^Lab Facility^2.16.840.1.114222.4.1.220759^ISO|3631467^Lab Facility^2.16.840.1.114222.4.1.220759^ISO|94309‐

2^^LN|||20200522075702‐0800|||||||||1962476994^Mouse^Minnie^^^^^^NPI&2.16.840.1.113883.4.6&ISO^^^^NPI||||||20200523065409‐0800|||F

  • OBX|1|CWE|94309‐2^SARS coronavirus 2 RNA:PrThr:Pt:XXX:Ord:Probe.amp.tar^LN|1|260415000^Not detected^SCT||Not

detected|N^Normal^HL70078^^^^2.5.1|||F||||05D0000000^Performing Lab Facility^CLIA^2.16.840.1.114222.4.1.220759&ISO||||20200523022020‐ 0800||||Testing Institute^D^^^^CLIA&2.16.840.1.113883.19.4.6&ISO^XX^^^22D0000001|320 Fake St.^^Tunes^MA^02130^USA^B

  • SPM|1|D‐4861207191&Lab Facility&2.16.840.1.114222.4.1.220759&ISO^D‐4861207191&Lab

Facility&2.16.840.1.114222.4.1.220759&ISO||697989009^Anterior nares swab (specimen)^SCT^^^^3.1.0||373067005^No (qualifier value)^SCT^^^^3.1.0|||||||||||20200522075702‐0800|20200522075703‐0800

  • BTS|1
  • FTS|1

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SLIDE 10

Reports vs Maven Events

  • Number of reports is not equal to the number of events
  • Reports are not deduplicated in the portal ‐ that happens

in Maven, and is based on full name, date of birth and

  • addresses. Reports that feed in without address can take

longer to deduplicate

  • One person can have many tests
  • We do receive out‐of‐state reports from some MA

facilities that we have to redirect

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SLIDE 11

Spreadsheet processing

  • 2000 – 2500 a day
  • Spreadsheets come in via secure email or sftp
  • Team cleans files
  • Runs location specific code to format the files
  • Imports them into Maven
  • Intense activity at beginning and end of each day

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Spreadsheet variables

Last_Name Specimen_Date First_Name Specimen_Source Middle_Name Specimen_number Sex Test Race Result Ethnicity (Hispanic/non‐Hispanic) Lab_Facility DOB Ordering_Facility ADDRESS1 Ordering_Provider CITY Ordering_Provider_Address ZIP Ordering_Provider_City STATE Ordering_Provider_Zip Patient_phone Ordering_Provider_State STAFF/RESIDENT Ordering_Provider_Phone

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SLIDE 13

Ongoing improvements

  • Move away from manual data entry to spreadsheets
  • Move away from spreadsheets to true ELR
  • Consolidate the ELR portal, expand capability
  • Consolidate Maven, expand capability
  • Bring on more epidemiologist and analyst support
  • Environmental scan ‐ who exactly is processing tests for

MA residents?

  • Work with new sites to ensure that we get the

demographic data we need

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SLIDE 14

Thank you

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