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 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 • 3
Routine infectious disease reporting 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 4 Holyoke Medical Center Spaulding Rehabilitation Hospital State Laboratory Instititute Imugen Cooley Dickinson Hospital Quest Laboratory Corporation of America Massachusetts Eye & Ear BioReference
Additional COVID only reporting CareOne ‐ Brookline Encompass AccessDX NEDS CareOne ‐ Concord etruenorth Aegis One Medical CareOne ‐ Lexington Exact Sciences AFC Methuen, Stoneham, Waltham, N Andover BROAD AFC Marlboro CareOne ‐ Lowell Excelsior ORDRS Houston/MD TOX AFC Saugus CareOne ‐ Needham Orig3n, Inc. ExosomeDx_Biotechne ‐ eurofin AFC Springfield CareOne ‐ Newton Pangea Fallon AFC Swampscott CareOne ‐ Wilmington Pediatric Associates of Greater Salem Fulgent AFC UC @Natick CareOne at Essex Park PerkinElmer GeneSyS AFC Waltham, Patriots CareOne at Millbury Pine Street (Boston Homeless) Genetworx Alliance at Devereux House CareOne at New Bedford pmaonline Genomic Expression Ammon CareOne at Peabody Greater Lawrence Family Health Center PrimaCare CareOne at Weymouth Integrity Arcpoint PWN Health Assurance Carewell UC Jackson Labs QDX Pathology Services Atrius John Dewey Academy Center for motivation & change Sparrow Healthcare CHAlliance Nursing Homes kbmo diagnostics Bedford Research Tempus Color Lab USA Haverhill Tewkesbury Hospital Biocerna ConvenientMD Lafayette Rehabilitation The Horowitz Medical Group (THMG) Biogen IDEC cQuentia Lemuel Shattuck Trident US Labs at Brockton BioReference Curative Leonard Florence Center for Living VA Bedford and Boston Boston Heart Diagnostics. Linden Ponds VA Central Western MA Boston Home CVS 5 Mako Medical Veritas Genetics Brandon Woods of Dartmouth Davita Brandon Woods of New Bedford Dispatch Meadow Green Nursing and Rehab Center Vikor Cambridge Biomedical East Boston FHC Middleton Family Medicine Viracor East Side Clinical Lab (Sonicare) + Sunrise MIT Capstone Walden Behavioral Health
How are we receiving labs? • 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 6
Electronic Laboratory Reporting MAVEN 7
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 8
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 9 BTS|1 • FTS|1 •
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 10
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 11
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 12 Patient_phone Ordering_Provider_State STAFF/RESIDENT Ordering_Provider_Phone
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 13 demographic data we need
Thank you 14
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