Research ArticleNosocomial Infection

Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing

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Science Translational Medicine  22 Aug 2012:
Vol. 4, Issue 148, pp. 148ra116
DOI: 10.1126/scitranslmed.3004129
  • Fig. 1

    Patient location and overlap during the outbreak. (A) Timeline of first positive cultures of the outbreak strain for the 18 affected patients. (B) Patient traces for each of the 18 patients shown in (A). Black lines, first positive culture; blue lines, medical ICU; yellow lines, cohorted areas; other colors represent specific wards at the NIH Clinical Center. (C) Graph of possible transmission links among patients. Patient IDs are within the circles. An arrow is present from one patient to another if the two patients overlapped in the same unit before the potential recipient culturing positive. Red links, the transmission event is predicted by the analysis reported here (see Fig. 3).

  • Fig. 2

    SNVs identified in K. pneumoniae genomes. (A) DNA sequence variation among isolates taken from patient 1 while at the NIH Clinical Center is shown as a heat map, with isolates in chronological order on the y axis and variants on the x axis. Gray, ancestral K. pneumoniae alleles present in the previously sequenced NTUH-K2044 strain; black, variants found in at least one of the isolates. (B) Variants among all outbreak genomes are shown in a clustered heat map, with patients shown on the y axis and variable positions in their respective genomes on the x axis. Blue and green, the two major patient clusters identified on the basis of shared variants.

  • Fig. 3

    Putative map of K. pneumoniae transmission during outbreak. The transmission map was constructed with genetic and patient trace data, as detailed in Materials and Methods. Nodes represent patients, and arrows indicate a transmission event directly or indirectly from one patient to another. Blue, cluster I; green, cluster II (from Fig. 2B). Red arrows, opportunity for a direct transmission event from patients overlapping in the same ward before the recipient culturing positive; black arrows, transmission events that cannot be explained by patient overlap (may result from a more complicated transmission route or an intermediate patient or environmental source); dashed lines, at least one other equally parsimonious transmission link exists leading to the given patient.

  • Fig. 4

    Patient trace for patients 1 and 4 and all patients who could have acted as transmission intermediates between them. Patient traces for the 1115 patients present in the hospital during the outbreak were mined to identify those patients whose location in the hospital could have allowed them to act as an intermediary in a transmission event between patients 1 and 4. Patients who overlapped with patient 1 after her arrival to the hospital and overlapped with patient 4 before his first positive culture were selected. The patient traces for patients 1 and 4 and the five patients (patients A to E) fitting the criteria of potential transmission intermediate are shown. Locations of patients in different hospital wards are indicated by different colors.

  • Table 1

    Clinical histories of patients colonized with the outbreak of KPC-producing K. pneumonia strain. KPC, died of KPC infection; underlying, died of underlying disease; MUD, matched unrelated donor; MRD, matched related donor; NA, not applicable.

    Date of
    Culture typeLocation of
    1Pulmonary alveolar
    F436/14/11Sputum, urineICULungNoAlive
    2Solid tumorM348/5/11Tracheal aspirateICUNAYesDied (KPC)
    F278/15/11Throat, groin
    ICUMUDYesDied (KPC)
    4LymphomaM298/23/11Peritoneal fluidICUNAYesDied
    5Solid tumorM548/29/11Groin surveillanceICUNANoDied
    6LymphomaM659/15/11Rectal surveillanceICUMUDYesDied (KPC)
    7Aplastic anemiaM299/19/11Rectal surveillanceICUMRDYesDied (KPC)
    8LymphomaM719/22/11Rectal surveillanceFloorMRDNoAlive
    9BronchiectasisF599/26/11Rectal surveillanceICUNANoAlive
    10Solid tumorF7210/6/11Rectal surveillanceICUNAYesDied (KPC)
    11LymphomaM5010/17/11Throat, groin
    12Solid tumorM4510/17/11Rectal surveillanceICUNANoDied
    13Solid tumorM3911/3/11Throat, groin
    M1911/10/11Throat, groin,
    rectal surveillance
    ICUMUDYesDied (KPC)
    15BronchiectasisF6011/17/11Rectal surveillanceFloorNANoAlive
    M5911/18/11Rectal surveillanceFloorNANoAlive
    17Aplastic anemiaM3411/27/11Rectal surveillanceFloorNAYesDied
    18Sickle cell diseaseF3712/14/11Rectal surveillanceFloorNANoAlive
  • Table 2

    Mutations unique to colistin-resistant isolates.

    StrainUnique mutations
    Patient 2 (resistant)Coding indel in query: GA at position 321
    of 1221 in KPNIH1_08595 (microcin
    B17 transporter)
    Noncoding SNP: G→A, between KPNIH1_06013
    (hypothetical protein) and KPNIH1_06008
    (putative acid phosphatase)
    Patient 8 (initial)Coding SNP: CTG→ATG (L→M) at 130 of 309
    in KPNIH1_18808 (putative membrane
    Coding SNP: ACC→ATC (T→I) at 1106 of 1119
    in KPNIH1_07189 (L-Ala-D/L-Glu epimerase)
    (methyl viologen resistance protein SmvA)
    Noncoding SNP: G→T, between KPNIH1_24168
    (putative phosphatase) and KPNIH1_24173
    (hypothetical protein)
    Coding SNP: GGC→TGC (G→C) at 811 of 1110
    in KPNIH1_05438 (putative transport protein)
    Coding SNP: CTT→CCT (L→P) at 941 of 1476
    in KPNIH1_07179
    Noncoding SNP: G→T, between KPNIH1_15985
    (aspartate kinase III) and KPNIH1_15980
    (glucose-6-phosphate isomerase)

Additional Files

  • Supplementary Materials for:

    Tracking a Hospital Outbreak of Carbapenem-Resistant Klebsiella pneumoniae with Whole-Genome Sequencing

    Evan S. Snitkin, Adrian M. Zelazny, Pamela J. Thomas, Frida Stock, NISC Comparative Sequencing Program, David K. Henderson, Tara N. Palmore,* Julia A. Segre*

    *To whom correspondence should be addressed. E-mail: tpalmore{at} (T.N.P.); jsegre{at} (J.A.S.)

    Published 22 August 2012, Sci. Transl. Med. 4, 148ra116 (2012)
    DOI: 10.1126/scitranslmed.3004129

    This PDF file includes:

    • Methods
    • Fig. S1. Repetitive element PCR and pulsed-field gels of representative outbreak isolates.
    • Fig. S2. Surveillance cultures for outbreak patients.
    • Fig. S3. Transmission opportunities between patients when using negative rectal surveillance to exclude patient colonization.
    • Fig. S4. Predicted transmission chart based only on genetic data.
    • Fig. S5. Predicted transmission chart based only on epidemiological data.
    • Fig. S6. Computing epidemiological distances between patients.
    • Table S1. Genome sequencing statistics.
    • Table S2. Characteristics of patients who acquired outbreak strain.
    • Table S3. MICs for antibiotic susceptibility of outbreak isolates.
    • Table S4. Mutations identified among outbreak genomes.

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