3/20/2017. Winter is Coming: An Overview of the DoD s Multidrug Resistant Organism Repository and Surveillance Network (MRSN) Disclaimer

Transcription

1 Winter is Coming: An Overview of the DoD s Multidrug Resistant Organism Repository and Surveillance Network (MRSN) CPT Joshua G. Martinez, MT(AMT) Laboratory Manager/Quality Assurance Manager Disclaimer The views expressed in this presentation are those of the speaker and authors, and do not reflect the official policy of the Department of Army, Department of Defense, or U.S. Government Learning Objectives Understand the role of the MRSN and how it is involved in infection control Understand the importance of participating in a MDRO surveillance program to reduce potential future MDROs and/or outbreaks Understand the concept of antibiotic stewardship and how the MRSN can play a significant role within any medical treatment facility 1

2 Source: Source: Source: Why Are We Concerned about AMR? Source: CDC, (2015), 2

3 3

4 Source: CDC, (2015), 4

5 MRSN-WRAIR U.S. Federal Recognition of AMR Signed in July

6 MRSN Target Organisms ESKAPE pathogens Enterococcus faecium (vancomycin-resistant) Staphylococcus aureus (methicillin-resistant) Klebsiella pneumoniae Acinetobacter spp Pseudomonas aeruginosa Enterobacter spp, Escherichia coli Carbapenem-resistant Gram negative bacteria Clostridium difficile MDRO Identified MTF MDRO sub-cultured on MRSN supplied media Shipped to MRSN MRSN Testing Tracking Storage Clinical Micro. Analyzers Molecular Micro. Testing Sequencing Analysis ARMoR-D Entry Surveillance Report Generation On & Off-Site Cryopreservation ARMOR-D MRSN Test Workflow ARMOR-D Specimen Routine Sample Processing Room 2W106 Historical Sequencing Clinical Microbiology Room GW50 Microscan ID/AST Vitek 2 ID/AST Urgent Clinical Microbiology Room GW50 Outbreak Clinical Microbiology Room GW50 + CARBA-NP qpcr BD Phoenix ID/AST Microscan ID/AST Microscan ID/AST DNA Extraction Trek Sensititre Bruker MS Vitek MS Vitek 2 ID/AST BD Phoenix ID/AST Trek Sensititre Bruker MS LIMS LIMS Vitek 2 ID/AST BD Phoenix ID/AST Trek Sensititre Bruker MS NextSeq Sequencer Bioinformatics Pipeline Vitek MS Vitek MS If required + CARBA-NP qpcr DNA Extraction + CARBA-NP Urgent Outbreak DNA Extraction MiSeq Sequencer MiSeq Sequencer If required PacBio RSII Long Read Sequencer MiSeq Sequencer If required PacBio RSII Long Read Sequencer Bioinformatics Pipeline ARMOR-D Bioinformatics Pipeline -Optional Testing 6

7 Specimen Submission TSA Slant Do not obscure slant Take sample from ID/AST purity check plate, when possible Specimen submission manual MRSN Clinical Microbiology Laboratory Initial specimen processing; creation and storage of repository sample BD Phoenix with Bruker MALDI-TOF Biomerieux Vitek 2 with MS Microscan with Bruker MALDI-TOF Trek Sensititre ARIS 2X Biomerieux E-Test With permission of MRSN personnel MRSN Molecular Microbiology Lab Multiplex PCR assays (Biorad CFX96) MRSA (meca, mup, qac A/B, pvl) Carbapenem-resistant GNR (bla KPC, bla IMP, bla NDM, bla OXA 48-like, bla VIM ) 16s methylases (arma, npm, rmta-h) MDR Acinetobacter (bla OXA 23, 24, 58 ) Benchtop short-read sequencers (Illumina MiSeq and NextSeq ) Pacific BioSciences RS-II long-read sequencer (SMRT analysis) Automated liquid handlers for DNA and library prep Design, validate and test primers and/or probes for specific genes upon request ~1 week turnaround time to design and validate the assay With permission of MRSN personnel 7

8 MRSN Bioinformatics Automated software pipeline for analysis of DNA sequencing data End products: 16s species confirmation, resistance and virulence gene content, MLST derivation, plasmid finder, relatedness/phylogeny Accomplishments Generated >2200 genomes on MiSeq and NextSeq platforms 30 genomes from PacBio long-read sequencer >950 genomes submitted to GenBank ( ) 48 hr turn-around time from colony growth to genomic determination of strain relatedness for potential outbreak investigations MRSN High Throughput Sequencing Data Analysis Pipeline Illumina Sequence Data Processing PacBio Sequence Merge Overlapping FLASH Reads Read Quality Btrim Trimming De Novo Assembly Newbler Data Processing Semi-Automated Analysis Outbreak Identification SNP and InDel Identification Gene Loss and Acquisition Rearrangement / Transposition Resistance Mechanism Detection SNP and InDel Identification Rearrangement / Transposition Automated Process Assembly Quality Control Read Coverage Contig N50 Contamination Detection SMRT Analysis Software Package Resistance Transfer Mechanisms Transposon Structure and Function Plasmid Transfer Mechanisms Species ID ABR Genes WG Annotation WG Phylogeny Outbreak ID Automated Search of 16S Database MLST Multilocus Sequence Typing Database Antibiotic Resistance Gene Annotation Plasmid Typing Plasmid Replicon Typing Database Whole Genome Annotation RAST/Prokka VIR Genes Virulence Gene Annotation Align Reads to Reference Genome Extract SNPs/Indels and Filter Bayesian Inference of Phylogeny Complete Genome/Plasmid Comparison Identify SNPs, InDels, and rearrangements Genome Sequencing Database Antimicrobial Resistance Monitoring and Research- Database (ARMoR-D) Clinical and demographic data for each isolate Identification and susceptibility results from 3 platforms + any additional testing needed Multiplex PCR results Sequence data (AMR and virulence genes) All personal identifying information (PII) will be separated, encrypted, and securely stored in accordance with the Army Information Assurance regulation As of January 2017: 42,653 isolates from 30,126 patients 112 facilities throughout the world 1,103,492 tests performed 3,011,932 results 8

9 ARMoR-D 9

10 MRSN Reports Outbreak/Case Reports Hospitals/providers Infection control Aggregate reports & antibiograms DoD medical providers Surveillance activities Armed Forces Health Surveillance Branch (AFHSB) U.S. Army Pharmacovigiliance Center (USAPVC) U.S. Navy and Marine Corps Public Health Center Epi-Data Center (USNPHC EDC) DoD and Federal policymakers Future Projects ARMoR website DoD, specified partners/collaborators; eventually public-facing Individual user accounts with level of access based on needs & approvals Promote awareness & education about antimicrobial resistance with links to ARMoR documents and related information Quarterly Conference Webinar Updates and Reports LIMS Biorepository CAP accreditation Next Generation Sequencing CAP accreditation 10

11 Antibiotic Stewardship Right antibiotic for the right infection for the right time The Joint Commission standard- MM Starting January 2017 Multidisciplinary team Infectious Disease Physician, Infection Preventionist, Pharmacist, Practitioner, Microbiologist Evaluate antibiotic use in the hospital Establish appropriate dosing Determine when deescalate course of treatment Decrease in hospital costs by as much as $51,000 Decrease in mortality by 12% Antibiotic Stewardship Programs Source: 11

12 Summary Be prepared! The MRSN/ARMoR program is the only large-scale repository of MDR bacterial isolates within the U.S. DoD, derived mainly from patients within the MHS located throughout the world. CAP-certified clinical laboratory; molecular lab with DNA sequencing and bioinformatics capabilities. Produce specific and aggregate reports, including 48hr support for outbreak investigations; unique collaborations allow for correlation of MRSN isolate data with AMR and antibiotic use metadata. Public-facing website in development for access to ARMoR-D. Ensure your facility has an antibiotic stewardship program and make sure you have a seat at the table Acknowledgements Partners and Supporters COL (ret) Emil Lesho AFHSC-GEIS LTC Paige Waterman CDR Franca Jones Ms. June Early Bacterial Disease Branch LTC Stuart Tyner WRAIR Command COL Deborah Witmer COL Michael Zapor COL Kevin Pitzer Questions? Command and Management Director: LTC Kate Hinkle mary.k.hinkle.mil@mail.mil Deputy Director: MAJ Anthony Jones anthony.r.jones14.mil@mail.mil Laboratory Manager: CPT Joshua Martinez joshua.g.martinez6.mil@mail.mil Microbiology Lab Mimi Kwak Lan Preston Ligia Flores Melissa Ly Katherine Lane Mekuria Bint Kinati Feyissa SPC Ramiro Chavez SPC Josh Rosadomendez Molecular / Sequencing Lab Dr. Patrick Mc Gann Kathy Ong Rosslyn Maybank Brendan Corey Dr. Madeline Galac CPT Amanda Roth Bioinformatics Dr. Robert Clifford Erik Snesrud Fatma Onmus-Leone Lakshmi Appalla Jason Stam Kalpana Dommaraju Database and Informatics Michael Julius Jacob Padilla Gerald Ward Travis Curtis Stephen Hooley Off-Site MRSN Team Members Eric Steele Doug Richesson Henry Dao Brandi Chandler JibranMarquez 12