Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines

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Standard

Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines. / Carlos, C.C.; Masim, M.A.L.; Lagrada, M.L.; Gayeta, J.M.; Macaranas, P.K.V.; Sia, S.B.; Facun, M.A.M.; Palarca, J.F.C.; Olorosa, A.M.; Cueno, G.A.C.; Abrudan, M.; Abudahab, K.; Argimón, S.; Kekre, M.; Stelling, J.; Aanensen, D.M.; Harste, H.; Muddyman, D.; Taylor, B.; Wheeler, N.; Donado-Godoy, P.; Bernal, J.F.; Arevalo, A.; Valencia, M.F.; Ravikumar, K.L.; Nagaraj, G.; Shamanna, V.; Govindan, V.; Prabhu, A.; Sravani, D.; Shincy, M.R.; Ravishankar, K.N.; Okeke, I.N.; Oaikhena, A.O.; Afolayan, A.O.; Ajiboye, J.J.; Odih, E.E.; Molloy, A.; Vegvari, C.

In: Clinical Infectious Diseases, Vol. 73, No. S4, 2021, p. S316–S324.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Carlos, CC, Masim, MAL, Lagrada, ML, Gayeta, JM, Macaranas, PKV, Sia, SB, Facun, MAM, Palarca, JFC, Olorosa, AM, Cueno, GAC, Abrudan, M, Abudahab, K, Argimón, S, Kekre, M, Stelling, J, Aanensen, DM, Harste, H, Muddyman, D, Taylor, B, Wheeler, N, Donado-Godoy, P, Bernal, JF, Arevalo, A, Valencia, MF, Ravikumar, KL, Nagaraj, G, Shamanna, V, Govindan, V, Prabhu, A, Sravani, D, Shincy, MR, Ravishankar, KN, Okeke, IN, Oaikhena, AO, Afolayan, AO, Ajiboye, JJ, Odih, EE, Molloy, A & Vegvari, C 2021, 'Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines', Clinical Infectious Diseases, vol. 73, no. S4, pp. S316–S324. https://doi.org/10.1093/cid/ciab776

APA

Carlos, C. C., Masim, M. A. L., Lagrada, M. L., Gayeta, J. M., Macaranas, P. K. V., Sia, S. B., Facun, M. A. M., Palarca, J. F. C., Olorosa, A. M., Cueno, G. A. C., Abrudan, M., Abudahab, K., Argimón, S., Kekre, M., Stelling, J., Aanensen, D. M., Harste, H., Muddyman, D., Taylor, B., ... Vegvari, C. (2021). Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines. Clinical Infectious Diseases, 73(S4), S316–S324. https://doi.org/10.1093/cid/ciab776

Vancouver

Carlos CC, Masim MAL, Lagrada ML, Gayeta JM, Macaranas PKV, Sia SB et al. Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines. Clinical Infectious Diseases. 2021;73(S4):S316–S324. https://doi.org/10.1093/cid/ciab776

Author

Carlos, C.C. ; Masim, M.A.L. ; Lagrada, M.L. ; Gayeta, J.M. ; Macaranas, P.K.V. ; Sia, S.B. ; Facun, M.A.M. ; Palarca, J.F.C. ; Olorosa, A.M. ; Cueno, G.A.C. ; Abrudan, M. ; Abudahab, K. ; Argimón, S. ; Kekre, M. ; Stelling, J. ; Aanensen, D.M. ; Harste, H. ; Muddyman, D. ; Taylor, B. ; Wheeler, N. ; Donado-Godoy, P. ; Bernal, J.F. ; Arevalo, A. ; Valencia, M.F. ; Ravikumar, K.L. ; Nagaraj, G. ; Shamanna, V. ; Govindan, V. ; Prabhu, A. ; Sravani, D. ; Shincy, M.R. ; Ravishankar, K.N. ; Okeke, I.N. ; Oaikhena, A.O. ; Afolayan, A.O. ; Ajiboye, J.J. ; Odih, E.E. ; Molloy, A. ; Vegvari, C. / Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines. In: Clinical Infectious Diseases. 2021 ; Vol. 73, No. S4. pp. S316–S324.

Bibtex

@article{b441bf6a683c47349e28cd5901f3ea4f,
title = "Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines",
abstract = "BackgroundKlebsiella pneumoniae is a critically important pathogen in the Philippines. Isolates are commonly resistant to at least 2 classes of antibiotics, yet mechanisms and spread of its resistance are not well studied.MethodsA retrospective sequencing survey was performed on carbapenem-, extended spectrum beta-lactam-, and cephalosporin-resistant Klebsiella pneumoniae isolated at 20 antimicrobial resistance (AMR) surveillance sentinel sites from 2015 through 2017. We characterized 259 isolates using biochemical methods, antimicrobial susceptibility testing, and whole-genome sequencing (WGS). Known AMR mechanisms were identified. Potential outbreaks were investigated by detecting clusters from epidemiologic, phenotypic, and genome-derived data.ResultsPrevalent AMR mechanisms detected include blaCTX-M-15 (76.8%) and blaNDM-1 (37.5%). An epidemic IncFII(Yp) plasmid carrying blaNDM-1 was also detected in 46 isolates from 6 sentinel sites and 14 different sequence types (STs). This plasmid was also identified as the main vehicle of carbapenem resistance in 2 previously unrecognized local outbreaks of ST348 and ST283 at 2 different sentinel sites. A third local outbreak of ST397 was also identified but without the IncFII(Yp) plasmid. Isolates in each outbreak site showed identical STs and K- and O-loci, and similar resistance profiles and AMR genes. All outbreak isolates were collected from blood of children aged < 1 year.ConclusionWGS provided a better understanding of the epidemiology of multidrug resistant Klebsiella in the Philippines, which was not possible with only phenotypic and epidemiologic data. The identification of 3 previously unrecognized Klebsiella outbreaks highlights the utility of WGS in outbreak detection, as well as its importance in public health and in implementing infection control programs.",
author = "C.C. Carlos and M.A.L. Masim and M.L. Lagrada and J.M. Gayeta and P.K.V. Macaranas and S.B. Sia and M.A.M. Facun and J.F.C. Palarca and A.M. Olorosa and G.A.C. Cueno and M. Abrudan and K. Abudahab and S. Argim{\'o}n and M. Kekre and J. Stelling and D.M. Aanensen and H. Harste and D. Muddyman and B. Taylor and N. Wheeler and P. Donado-Godoy and J.F. Bernal and A. Arevalo and M.F. Valencia and K.L. Ravikumar and G. Nagaraj and V. Shamanna and V. Govindan and A. Prabhu and D. Sravani and M.R. Shincy and K.N. Ravishankar and I.N. Okeke and A.O. Oaikhena and A.O. Afolayan and J.J. Ajiboye and E.E. Odih and A. Molloy and C. Vegvari",
year = "2021",
doi = "10.1093/cid/ciab776",
language = "English",
volume = "73",
pages = "S316–S324",
journal = "Clinical Infectious Diseases",
issn = "1058-4838",
publisher = "Oxford University Press",
number = "S4",

}

RIS

TY - JOUR

T1 - Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines

AU - Carlos, C.C.

AU - Masim, M.A.L.

AU - Lagrada, M.L.

AU - Gayeta, J.M.

AU - Macaranas, P.K.V.

AU - Sia, S.B.

AU - Facun, M.A.M.

AU - Palarca, J.F.C.

AU - Olorosa, A.M.

AU - Cueno, G.A.C.

AU - Abrudan, M.

AU - Abudahab, K.

AU - Argimón, S.

AU - Kekre, M.

AU - Stelling, J.

AU - Aanensen, D.M.

AU - Harste, H.

AU - Muddyman, D.

AU - Taylor, B.

AU - Wheeler, N.

AU - Donado-Godoy, P.

AU - Bernal, J.F.

AU - Arevalo, A.

AU - Valencia, M.F.

AU - Ravikumar, K.L.

AU - Nagaraj, G.

AU - Shamanna, V.

AU - Govindan, V.

AU - Prabhu, A.

AU - Sravani, D.

AU - Shincy, M.R.

AU - Ravishankar, K.N.

AU - Okeke, I.N.

AU - Oaikhena, A.O.

AU - Afolayan, A.O.

AU - Ajiboye, J.J.

AU - Odih, E.E.

AU - Molloy, A.

AU - Vegvari, C.

PY - 2021

Y1 - 2021

N2 - BackgroundKlebsiella pneumoniae is a critically important pathogen in the Philippines. Isolates are commonly resistant to at least 2 classes of antibiotics, yet mechanisms and spread of its resistance are not well studied.MethodsA retrospective sequencing survey was performed on carbapenem-, extended spectrum beta-lactam-, and cephalosporin-resistant Klebsiella pneumoniae isolated at 20 antimicrobial resistance (AMR) surveillance sentinel sites from 2015 through 2017. We characterized 259 isolates using biochemical methods, antimicrobial susceptibility testing, and whole-genome sequencing (WGS). Known AMR mechanisms were identified. Potential outbreaks were investigated by detecting clusters from epidemiologic, phenotypic, and genome-derived data.ResultsPrevalent AMR mechanisms detected include blaCTX-M-15 (76.8%) and blaNDM-1 (37.5%). An epidemic IncFII(Yp) plasmid carrying blaNDM-1 was also detected in 46 isolates from 6 sentinel sites and 14 different sequence types (STs). This plasmid was also identified as the main vehicle of carbapenem resistance in 2 previously unrecognized local outbreaks of ST348 and ST283 at 2 different sentinel sites. A third local outbreak of ST397 was also identified but without the IncFII(Yp) plasmid. Isolates in each outbreak site showed identical STs and K- and O-loci, and similar resistance profiles and AMR genes. All outbreak isolates were collected from blood of children aged < 1 year.ConclusionWGS provided a better understanding of the epidemiology of multidrug resistant Klebsiella in the Philippines, which was not possible with only phenotypic and epidemiologic data. The identification of 3 previously unrecognized Klebsiella outbreaks highlights the utility of WGS in outbreak detection, as well as its importance in public health and in implementing infection control programs.

AB - BackgroundKlebsiella pneumoniae is a critically important pathogen in the Philippines. Isolates are commonly resistant to at least 2 classes of antibiotics, yet mechanisms and spread of its resistance are not well studied.MethodsA retrospective sequencing survey was performed on carbapenem-, extended spectrum beta-lactam-, and cephalosporin-resistant Klebsiella pneumoniae isolated at 20 antimicrobial resistance (AMR) surveillance sentinel sites from 2015 through 2017. We characterized 259 isolates using biochemical methods, antimicrobial susceptibility testing, and whole-genome sequencing (WGS). Known AMR mechanisms were identified. Potential outbreaks were investigated by detecting clusters from epidemiologic, phenotypic, and genome-derived data.ResultsPrevalent AMR mechanisms detected include blaCTX-M-15 (76.8%) and blaNDM-1 (37.5%). An epidemic IncFII(Yp) plasmid carrying blaNDM-1 was also detected in 46 isolates from 6 sentinel sites and 14 different sequence types (STs). This plasmid was also identified as the main vehicle of carbapenem resistance in 2 previously unrecognized local outbreaks of ST348 and ST283 at 2 different sentinel sites. A third local outbreak of ST397 was also identified but without the IncFII(Yp) plasmid. Isolates in each outbreak site showed identical STs and K- and O-loci, and similar resistance profiles and AMR genes. All outbreak isolates were collected from blood of children aged < 1 year.ConclusionWGS provided a better understanding of the epidemiology of multidrug resistant Klebsiella in the Philippines, which was not possible with only phenotypic and epidemiologic data. The identification of 3 previously unrecognized Klebsiella outbreaks highlights the utility of WGS in outbreak detection, as well as its importance in public health and in implementing infection control programs.

U2 - 10.1093/cid/ciab776

DO - 10.1093/cid/ciab776

M3 - Journal article

C2 - 34850834

VL - 73

SP - S316–S324

JO - Clinical Infectious Diseases

JF - Clinical Infectious Diseases

SN - 1058-4838

IS - S4

ER -

ID: 323555286