title: The Challenges of Implementing Next Generation Sequencing Across a Large Healthcare System, and the Molecular Epidemiology and Antibiotic Susceptibilities of Carbapenemase-Producing Bacteria in the Healthcare System of the U.S. Department of Defense.
abstract: We sought to: 1) provide an overview of the genomic epidemiology of an extensive collection of carbapenemase-producing bacteria (CPB) collected in the U.S. Department of Defense health system; 2) increase awareness of the public availability of the sequences, isolates, and customized antimicrobial resistance database of that system; and 3) illustrate challenges and offer mitigations for implementing next generation sequencing (NGS) across large health systems.
  
  
  
  Prospective surveillance and system-wide implementation of NGS.
  
  
  
  288-hospital healthcare network.
  
  
  
  All phenotypically carbapenem resistant bacteria underwent CarbaNP® testing and PCR, followed by NGS. Commercial (Newbler and Geneious), on-line (ResFinder), and open-source software (Btrim, FLASh, Bowtie2, an Samtools) were used for assembly, SNP detection and clustering. Laboratory capacity, throughput, and response time were assessed.
  
  
  
  From 2009 through 2015, 27,000 multidrug-resistant Gram-negative isolates were submitted. 225 contained carbapenemase-encoding genes (most commonly blaKPC, blaNDM, and blaOXA23). These were found in 15 species from 146 inpatients in 19 facilities. Genetically related CPB were found in more than one hospital. Other clusters or outbreaks were not clonal and involved genetically related plasmids, while some involved several unrelated plasmids. Relatedness depended on the clustering algorithm used. Transmission patterns of plasmids and other mobile genetic elements could not be determined without ultra-long read, single-molecule real-time sequencing. 80% of carbapenem-resistant phenotypes retained susceptibility to aminoglycosides, and 70% retained susceptibility to fluoroquinolones. However, among the CPB-confirmed genotypes, fewer than 25% retained susceptibility to aminoglycosides or fluoroquinolones.
  
  
  
  Although NGS is increasingly acclaimed to revolutionize clinical practice, resource-constrained environments, large or geographically dispersed healthcare networks, and military or government-funded public health laboratories are likely to encounter constraints and challenges as they implement NGS across their health systems. These include lack of standardized definitions and quality control metrics, limitations of short-read sequencing, insufficient bandwidth, and the current limited availability of very expensive and scarcely available sequencing platforms. Possible solutions and mitigations are also proposed.
authors.affiliation: Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America.
authors.forename: Emil
authors.initials: E
authors.lastname: Lesho
authors.affiliation: Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America.
authors.forename: Robert
authors.initials: R
authors.lastname: Clifford
authors.affiliation: Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America.
authors.forename: Fatma
authors.initials: F
authors.lastname: Onmus-Leone
authors.affiliation: Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America.
authors.forename: Lakshmi
authors.initials: L
authors.lastname: Appalla
authors.affiliation: Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America.
authors.forename: Erik
authors.initials: E
authors.lastname: Snesrud
authors.affiliation: Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America.
authors.forename: Yoon
authors.initials: Y
authors.lastname: Kwak
authors.affiliation: Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America.
authors.forename: Ana
authors.initials: A
authors.lastname: Ong
authors.affiliation: Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America.
authors.forename: Rosslyn
authors.initials: R
authors.lastname: Maybank
authors.affiliation: Global Emerging Infectious Disease Surveillance and Response Section, Armed Forces Health Surveillance Section, Silver Spring, MD, United States of America.
authors.forename: Paige
authors.initials: P
authors.lastname: Waterman
authors.affiliation: Epidemiology and Analysis Section, Armed Forces Health Surveillance Center, Silver Spring, MD, United States of America.
authors.forename: Patricia
authors.initials: P
authors.lastname: Rohrbeck
authors.affiliation: Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America.
authors.forename: Michael
authors.initials: M
authors.lastname: Julius
authors.affiliation: Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America.
authors.forename: Amanda
authors.initials: A
authors.lastname: Roth
authors.affiliation: Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America.
authors.forename: Joshua
authors.initials: J
authors.lastname: Martinez
authors.affiliation: Department of Laboratory Medicine, San Antonio Military Medical Center, San Antonio, TX, United States of America.
authors.forename: Lindsey
authors.initials: L
authors.lastname: Nielsen
authors.affiliation: Department of Laboratory Medicine, San Antonio Military Medical Center, San Antonio, TX, United States of America.
authors.forename: Eric
authors.initials: E
authors.lastname: Steele
authors.affiliation: Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America.
authors.forename: Patrick
authors.initials: P
authors.lastname: McGann
authors.affiliation: Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America.
authors.forename: Mary
authors.initials: M
authors.lastname: Hinkle
mesh_terms: D000150:Acinetobacter / Q000235:genetics; D000900:Anti-Bacterial Agents / Q000627:therapeutic use*; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D015780:Carbapenems / Q000627:therapeutic use*; D016494:Computer Security; D003199:Computer Systems; D030541:Databases, Genetic; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006772:Hospitals, Military; D006801:Humans; D007709:Klebsiella / Q000235:genetics; D008490:Medical Informatics / Q000379:methods; D008826:Microbial Sensitivity Tests; D017720:Molecular Epidemiology / Q000379:methods*; D010641:Phenotype; D010957:Plasmids / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D014481:United States; D059030:United States Department of Defense; D001618:beta-Lactamases / Q000378:metabolism
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D015780:Carbapenems; D001618:beta-Lactamases; C063912:carbapenemase