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Bacteriology

Evaluation of the FilmArray Blood Culture Identification Panel: Results of a Multicenter Controlled Trial

Hossein Salimnia, Marilynn R. Fairfax, Paul R. Lephart, Paul Schreckenberger, Sharon M. DesJarlais, J. Kristie Johnson, Gwen Robinson, Karen C. Carroll, Amy Greer, Margie Morgan, Raymond Chan, Michael Loeffelholz, Frances Valencia-Shelton, Stephen Jenkins, Audrey N. Schuetz, Judy A. Daly, Trenda Barney, Andrew Hemmert, Kristen J. Kanack
S. S. Richter, Editor
Hossein Salimnia
aDepartment of Pathology, Wayne State University School of Medicine, Detroit, Michigan, USA
bDMC University Laboratories, Detroit, Michigan, USA
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Marilynn R. Fairfax
aDepartment of Pathology, Wayne State University School of Medicine, Detroit, Michigan, USA
bDMC University Laboratories, Detroit, Michigan, USA
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Paul R. Lephart
bDMC University Laboratories, Detroit, Michigan, USA
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Paul Schreckenberger
cLoyola University Medical Center, Chicago, Illinois, USA
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Sharon M. DesJarlais
cLoyola University Medical Center, Chicago, Illinois, USA
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J. Kristie Johnson
dDepartment of Pathology, University of Maryland, Baltimore, Maryland, USA
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Gwen Robinson
dDepartment of Pathology, University of Maryland, Baltimore, Maryland, USA
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Karen C. Carroll
eDivision of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Amy Greer
eDivision of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Margie Morgan
fCedars-Sinai Medical Center, Los Angeles, California, USA
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Raymond Chan
fCedars-Sinai Medical Center, Los Angeles, California, USA
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Michael Loeffelholz
gDepartment of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
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Frances Valencia-Shelton
gDepartment of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
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Stephen Jenkins
hNew York-Presbyterian Hospital, Weill-Cornell Medical Center, New York, New York, USA
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Audrey N. Schuetz
hNew York-Presbyterian Hospital, Weill-Cornell Medical Center, New York, New York, USA
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Judy A. Daly
iDepartment of Pathology, University of Utah, and Primary Children's Medical Center, Salt Lake City, Utah, USA
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Trenda Barney
iDepartment of Pathology, University of Utah, and Primary Children's Medical Center, Salt Lake City, Utah, USA
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Andrew Hemmert
jBioFire Diagnostics LLC, Salt Lake City, Utah, USA
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Kristen J. Kanack
jBioFire Diagnostics LLC, Salt Lake City, Utah, USA
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S. S. Richter
Roles: Editor
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DOI: 10.1128/JCM.01679-15
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Tables

  • TABLE 1

    FilmArray BCID panel targets and prevalence of positive results by age group for the prospective clinical study arm

    FilmArray BCID resultaNo. (%) of patients
    TotalcPediatricdAdulte
    Gram-positive bacteria
        Enterococcus102 (7)5 (3)97 (7)
        Listeria monocytogenes0 (0)0 (0)0 (0)
        Staphylococcus780 (50)74 (50)706 (50)
        S. aureus257 (16)25 (17)232 (16)
        Streptococcus140 (9)21 (14)119 (8)
        S. agalactiae (GBS)18 (1)2 (1)16 (1)
        S. pneumoniae26 (2)3 (2)23 (2)
        S. pyogenes (GAS)8 (1)2 (1)6 (<1)
    Gram-negative bacteria
        A. baumannii16 (1)1 (1)15 (1)
        Enterobacteriaceae307 (20)27 (18)280 (20)
        Enterobacter cloacaeb24 (2)4 (3)20 (1)
        Escherichia coli149 (10)16 (11)133 (9)
        Klebsiella oxytoca6 (<1)1 (1)5 (<1)
        Klebsiella pneumoniae74 (5)5 (3)69 (5)
        Proteus22 (1)0 (0)22 (2)
        Serratia marcescens22 (1)1 (1)21 (1)
        Haemophilus influenzae8 (1)3 (2)5 (<1)
        Neisseria meningitidis1 (<1)0 (0)1 (0)
        P. aeruginosa52 (3)4 (3)48 (3)
    Yeast
        Candida albicans20 (1)1 (1)19 (1)
        Candida glabrata14 (1)0 (0)14 (1)
        Candida krusei4 (<1)1 (1)3 (<1)
        Candida parapsilosis8 (1)0 (0)8 (1)
        Candida tropicalis3 (<1)0 (0)3 (<1)
    Antimicrobial resistance genes
        mecA491 (31)46 (31)445 (31)
        vanA/B36 (2)0 (0)36 (3)
        blaKPC6 (<1)0 (0)6 (<1)
    • ↵a Regardless of results of comparator assays.

    • ↵b E. cloacae complex. Individual members are not separated.

    • ↵c n = 1,568 (100%).

    • ↵d Those <18 years old; n = 149 (10% of the total).

    • ↵e Those ≥18 years old; n = 1,419 (90% of the total).

  • TABLE 2

    OPOs not targeted by BCID and identified in the prospective clinical arm only

    OPONo. of isolatesOPONo. of isolates
    Abiotrophia or Granulicatella speciesa7bLactobacillus species3
    Achromobacter xylosoxidans1Micrococcus species27
    Acinetobacter species (not A. baumannii)23cMoraxella catarrhalis1
    Actinomyces odontolyticus2Moraxella species2
    Actinomyces species1Mycobacterium fortuitum complex1
    Aerococcus species3Neisseria species2
    Aeromonas sobria1Paenibacillus species1
    Bacillus cereus19Pasteurella multocida2
    Bacillus species14Pasteurella species1
    Brevibacterium species2Pasteurella stomatis1d
    Brevundimonas species2Propionibacterium species1
    Burkholderia cepacia complex2Pseudomonas species5
    Candida kefyr1Pseudomonas stutzeri1d
    Capnocytophaga species1Raoultella ornithinolytica4d
    Chryseobacterium meningosepticum1Raoultella planticola1d
    Chryseobacterium indologenes1Rhizobium radiobacter1
    Chryseomonas luteola1Rhodococcus species1
    Corynebacterium jeikeium1Rothia (Stomatococcus) mucilaginosa4
    Corynebacterium species/diphtheroids48Sphingomonas mucosissima1
    Cryptococcus neoformans2Staphylococcus pettenkoferi16e
    Flavobacterium species1Stenotrophomonas maltophilia10
    Fusarium species1Weeksella virosa1
    Kocuria kristinae1
    • ↵a Formerly nutritionally deficient streptococci.

    • ↵b One of seven Abiotrophia spp. was identified by 16S rRNA gene sequencing during discrepancy investigations. It had been misidentified phenotypically as a Streptococcus species.

    • ↵c Of 23 isolates, 17 were Acinetobacter spp. not A. baumannii and 10 were phenotypically A. baumannii. The latter were revealed to be A. pittii, A. nosocomialis, A. bereziniae, and A. radioresistens by 16S rRNA gene sequencing.

    • ↵d Other organisms identified during the resolution of discrepancies between BCID and the phenotypic comparator assays included one Pasteurella stomatis isolate (phenotypic ID, E. coli), one Pseudomonas stutzeri isolate (phenotypic ID, P. aeruginosa), one Raoultella planticola isolate (phenotypic ID, K. pneumoniae), and four R. ornithinolytica isolates (phenotypic ID, K. oxytoca).

    • ↵e Although all Staphylococcus spp. are intended to be detected by the panel, these species do not react with either of the Staphylococcus sp. target assays. Several less common Staphylococcus spp. are not detected or are detected with lower sensitivity (18).

  • TABLE 3

    Performance summary of the BCID panel versus the comparator assays for bacteria in both clinical and seeded positive blood cultures combined

    OrganismIsolates detecteda: BCID/comparatorNo. of results: BCID/comparatorSensitivity or PPAb: TP/(TP + FN) (%)95% CISpecificity or NPAb: TN/(TN + FP) (%)95% CI
    Clinical armSeeded armTP +/+FP +/−FN −/+TN −/−
    Gram-positive bacteria
        Enterococcus102/10129/29127432,073127/130 (97.7)93.4–99.52,073/2,077 (99.8)99.5–99.9
        L. monocytogenes0/036/3636002,17136/36 (100)90.3–1002,171/2,171 (100)99.8–100
        Staphylococcus780/7972/177012281,397770/798 (96.5)95.0–97.71,397/1,409 (99.1)98.5–99.6
        S. aureus257/2570/0253441,946253/257 (98.4)96.1–99.61,946/1,950 (99.8)99.5–99.9
        Streptococcus140/14163/62198551,999198/203 (97.5)94.3–99.21,999/2,004 (99.8)99.4–99.9
        S. agalactiae (group B)18/1818/1836002,17136/36 (100)90.3–1002,171/2,171 (100)99.8–100
        S. pneumoniae26/2512/1236212,16836/37 (97.3)85.8–99.92,168/2,170 (99.9)99.7–100
        S. pyogenes (group A)8/731/3138102,16838/38 (100)90.7–1002,168/2,169 (99.9)99.7–100
        Total1,331/1,346191/1891,494284116,0931,494/1,535 (97.3)96.4–98.116,093/16,121 (99.8)99.7–99.9
    Gram-negative bacteria
        A. baumannii16/1440/3751502,15151/51 (100)93.0–1002,151/2,156 (99.8)99.5–99.9
        Enterobacteriaceae307/310187/188490481,705490/498 (98.4)96.9–99.31,705/1,709 (99.8)99.4–99.9
        E. cloacae complex24/2217/1738312,16538/39 (97.4)86.5–99.92,165/2,168 (99.9)99.6–100
        E. coli149/1486/5150532,049150/153 (98.0)94.4–99.62,049/2,054 (99.8)99.4–99.9
        K. oxytoca6/654/5859152,14259/64 (92.2)c82.7–97.42,142/2,143 (99.9)99.7–100
        K. pneumoniae74/7137/34102932,093102/105 (97.1)91.9–99.42,093/2,102 (99.6)99.2–99.8
        Proteus22/2217/1739002,16839/39 (100)91.0–1002,168/2,168 (100)99.8–100
        S. marcescens22/2255/5576112,12976/77 (98.7)93.0–1002,129/2,130 (99.9)99.7–100
        H. influenzae8/835/3543002,16443/43 (100)91.8–1002,164/2,164 (100)99.8–100
        N. meningitidis1/135/3536002,17136/36 (100)90.3–1002,171/2,171 (100)99.8–100
        P. aeruginosa52/520/051112,15451/52 (98.1)89.7–1002,154/2,155 (99.9)99.7–100
        Total681/676483/4811135292223,0911,135/1,157 (98.1)97.1–98.823,091/23,120 (99.9)99.8–99.9
    • ↵a Culture or culture and 16S rRNA gene sequencing for A. baumannii.

    • ↵b The data in these columns are based on the combined results from the clinical and seeded specimens. Sensitivity refers to performance with clinical specimens, while PPA refers to performance with seeded specimens. Despite the differences in names and usage, they were calculated identically. Likewise, specificity refers to performance with prospective samples, while NPA is used for seeded specimens. They were also calculated identically. These data were obtained in the initial analyses and have not been changed to reflect subsequent investigations of discordant results. Investigations of discordant results are described in Results and summarized in Table 5.

    • ↵c K. oxytoca is the only organism that apparently failed to meet the prespecified criterion of a sensitivity of >95%. However, this was due to an unavoidable error in phenotypic identification. When this was resolved, the sensitivity for this organism exceeded 98.3%.

  • TABLE 4

    Performance summary of the FilmArray BCID panel versus culture for Candida spp. in positive blood cultures

    OrganismIsolates detected: BCID/comparatorNo. of results: BCID/comparatorSensitivity or PPAa: TP/(TP + FN) (%)95% CISpecificity or NPAa: TN/(TN + FP) (%)95% CI
    Clinical armSeeded armTP +/+FP +/−FN −/+TN −/−
    Candida albicans20/1648/4864402,13964/64 (100)94.4–1002,139/2,143 (99.8)99.5–99.9
    Candida glabrata14/1237/3749202,15649/49 (100)92.7–1002,156/2,158 (99.9)99.7–100
    Candida krusei4/433/3337002,17037/37 (100)90.5–1002,170/2,170 (100)99.8–100
    Candida parapsilosis9/752/5459222,14459/61 (96.7)88.7–99.62,144/2,146 (99.9)99.7–100
    Candida tropicalis3/336/3639002,16839/39 (100)91.0–1002,168/2,168 (100)99.8–100
        All yeast isolates49/42207/2082488210,777248/250 (99.2)97.1–99.910,777/10,785 (99.9)99.9–100
    • ↵a Sensitivity and specificity refer to performance with the prospective specimens only. PPA and NPA refer to performance with the seeded specimens. These are unresolved data and do not reflect the further investigations discussed in Results.

  • TABLE 5

    Summary of outcomes of discordant organism result investigations

    Result and analyteNo. of resultsNo. of investigationsa
    Comparator result confirmedFilmArray result confirmedBoth results incorrectbInconclusive
    BCID FP results
        Enterococcus413
        Staphylococcus12111
        S. aureus4013
        Streptococcus5113
        S. pneumoniae211
        S. pyogenes11
        A. baumannii55
        Enterobacteriaceae413
        E. cloacae complex312
        E. coli5122
        K. pneumoniae9432
        K. oxytoca11
        S. marcescens11
        P. aeruginosa11
        C. albicans44
        C. glabrata22
        C. parapsilosis22
        Total651218530
        % of total FP results1828846
    BCID FN results
        Enterococcus33
        Staphylococcus282017
        S. aureus4121
        Streptococcus532
        S. pneumoniae11
        Enterobacteriaceae8431
        E. cloacae complex11
        E. coli33
        K. pneumoniae3111
        K. oxytoca514
        S. marcescens11
        P. aeruginosa11
        C. parapsilosis22
        Total653418112
        % of total FN results5228218
    • ↵a The method used was investigation of possible sample mix-ups, reculturing from frozen aliquots of the blood culture bottle fluid, sequencing directly from the bottle if isolated organisms were expected, or sequencing from resubcultured isolated organisms if more than one isolate per bottle was present. For bacterial resolution, 16S rRNA gene sequences were analyzed and for yeast, ITS1 was analyzed. See Materials and Methods for further information. Three apparent blood culture bottle mix-ups and one apparent bottle selection error were resolved in favor of BCID.

    • ↵b See Results for further information regarding the indicated organism.

  • TABLE 6

    Comparison of FilmArray BCID resistance gene results to the prespecified comparator assay (PCR/sequencing directly from blood culture bottle)

    Antimicrobial resistance gene(s)Isolates detected: BCID/comparatorNo. of results: BCID/comparatorSensitivity or PPAa: TP/(TP + FN) (%)95% CISpecificity or NPAa: TN/(TN + FP) (%)95% CI
    Clinical armSeeded armTP +/+FP +/−FN −/+TN −/−
    mecA in association with:
        All Staphylococcus isolates detectedb491/4942/248858281488/496 (98.4)96.8–99.3281/286 (98.3)96.0–99.4
        Staphylococcus and S. aureus isolates detected137/1390/013702118137/139 (98.6)94.9–99.8118/118 (100)96.9–100
    vanA/B in association with Enterococcus isolates detected36/3628/2864006764/64 (100)c94.4–10067/67 (100)94.6–100
    blaKPC in association with Enterobacteriaceae and/or A. baumannii and/or P. aeruginosa isolates detected6/6d33/33390055839/39 (100)e91.0–100558/558 (100)99.3–100
    • ↵a Sensitivity and specificity refer to performance with the prospective specimens only. PPA and NPA refer to performance with the seeded specimens. These are unresolved data.

    • ↵b Either Staphylococcus or S. aureus isolates detected or both.

    • ↵c Of the 64 Enterococcus isolates, 11 (17.2%) carried the vanB gene as determined by bidirectional sequence analysis.

    • ↵d All six isolates were identified as K. pneumoniae.

    • ↵e These isolates included 30 of K. pneumoniae, 2 of E. cloacae, and 1 of E. coli.

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Evaluation of the FilmArray Blood Culture Identification Panel: Results of a Multicenter Controlled Trial
Hossein Salimnia, Marilynn R. Fairfax, Paul R. Lephart, Paul Schreckenberger, Sharon M. DesJarlais, J. Kristie Johnson, Gwen Robinson, Karen C. Carroll, Amy Greer, Margie Morgan, Raymond Chan, Michael Loeffelholz, Frances Valencia-Shelton, Stephen Jenkins, Audrey N. Schuetz, Judy A. Daly, Trenda Barney, Andrew Hemmert, Kristen J. Kanack
Journal of Clinical Microbiology Feb 2016, 54 (3) 687-698; DOI: 10.1128/JCM.01679-15

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Evaluation of the FilmArray Blood Culture Identification Panel: Results of a Multicenter Controlled Trial
Hossein Salimnia, Marilynn R. Fairfax, Paul R. Lephart, Paul Schreckenberger, Sharon M. DesJarlais, J. Kristie Johnson, Gwen Robinson, Karen C. Carroll, Amy Greer, Margie Morgan, Raymond Chan, Michael Loeffelholz, Frances Valencia-Shelton, Stephen Jenkins, Audrey N. Schuetz, Judy A. Daly, Trenda Barney, Andrew Hemmert, Kristen J. Kanack
Journal of Clinical Microbiology Feb 2016, 54 (3) 687-698; DOI: 10.1128/JCM.01679-15
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    • ABSTRACT
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