Whole-Genome Sequencing to Determine Origin of Multinational Outbreak of Sarocladium Kiliense Bloodstream Infections

Overview

Journal Emerg Infect Dis

Specialty Infectious Diseases

Date 2016 Feb 19

PMID 26891230

Citations 26

Authors

Kizee A Etienne

Chandler C Roe

Rachel M Smith

Snigdha Vallabhaneni

Carolina Duarte

Patricia Escadon

Elizabeth Castaneda

Beatriz L Gomez

Catalina De Bedout

Luisa F Lopez

Valentina Salas

Luz Maria Hederra

Jorge Fernandez

Paola Pidal

Juan Carlos Hormazabel

Fernando Otaiza

Fredrik O Vannberg

John Gillece

Darrin Lemmer

Elizabeth M Driebe

David M Englethaler

Anastasia P Litvintseva

Affiliations

Soon will be listed here.

Abstract

We used whole-genome sequence typing (WGST) to investigate an outbreak of Sarocladium kiliense bloodstream infections (BSI) associated with receipt of contaminated antinausea medication among oncology patients in Colombia and Chile during 2013-2014. Twenty-five outbreak isolates (18 from patients and 7 from medication vials) and 11 control isolates unrelated to this outbreak were subjected to WGST to elucidate a source of infection. All outbreak isolates were nearly indistinguishable (<5 single-nucleotide polymorphisms), and >21,000 single-nucleotide polymorphisms were identified from unrelated control isolates, suggesting a point source for this outbreak. S. kiliense has been previously implicated in healthcare-related infections; however, the lack of available typing methods has precluded the ability to substantiate point sources. WGST for outbreak investigation caused by eukaryotic pathogens without reference genomes or existing genotyping methods enables accurate source identification to guide implementation of appropriate control and prevention measures.

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References

Litvintseva A, Hurst S, Gade L, Frace M, Hilsabeck R, Schupp J . Whole-genome analysis of Exserohilum rostratum from an outbreak of fungal meningitis and other infections. J Clin Microbiol. 2014; 52(9):3216-22. PMC: 4313140. DOI: 10.1128/JCM.00936-14. View

Manamgoda D, Rossman A, Castlebury L, Crous P, Madrid H, Chukeatirote E . The genus Bipolaris. Stud Mycol. 2014; 79:221-88. PMC: 4255534. DOI: 10.1016/j.simyco.2014.10.002. View

Wilgenbusch J, Swofford D . Inferring evolutionary trees with PAUP*. Curr Protoc Bioinformatics. 2008; Chapter 6:Unit 6.4. DOI: 10.1002/0471250953.bi0604s00. View

Fridkin S, Kremer F, Bland L, Padhye A, McNeil M, Jarvis W . Acremonium kiliense endophthalmitis that occurred after cataract extraction in an ambulatory surgical center and was traced to an environmental reservoir. Clin Infect Dis. 1996; 22(2):222-7. DOI: 10.1093/clinids/22.2.222. View

Pham C, Purfield A, Fader R, Pascoe N, Lockhart S . Development of a Multilocus Sequence Typing System for Medically Relevant Bipolaris Species. J Clin Microbiol. 2015; 53(10):3239-46. PMC: 4572541. DOI: 10.1128/JCM.01546-15. View

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A . The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010; 20(9):1297-303. PMC: 2928508. DOI: 10.1101/gr.107524.110. View

Gillece J, Schupp J, Arunmozhi Balajee S, Harris J, Pearson T, Yan Y . Whole genome sequence analysis of Cryptococcus gattii from the Pacific Northwest reveals unexpected diversity. PLoS One. 2011; 6(12):e28550. PMC: 3233577. DOI: 10.1371/journal.pone.0028550. View

Walker B, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S . Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014; 9(11):e112963. PMC: 4237348. DOI: 10.1371/journal.pone.0112963. View

Repetto E, Giacomazzi C, Castelli F . Hospital-related outbreaks due to rare fungal pathogens: a review of the literature from 1990 to June 2011. Eur J Clin Microbiol Infect Dis. 2012; 31(11):2897-904. DOI: 10.1007/s10096-012-1661-3. View

10.

. Exophiala infection from contaminated injectable steroids prepared by a compounding pharmacy--United States, July-November 2002. MMWR Morb Mortal Wkly Rep. 2003; 51(49):1109-12. View

11.

Mikosz C, Smith R, Kim M, Tyson C, Lee E, Adams E . Fungal endophthalmitis associated with compounded products. Emerg Infect Dis. 2014; 20(2):248-56. PMC: 3901475. DOI: 10.3201/eid2002.131257. View

12.

Litvintseva A, Brandt M, Mody R, Lockhart S . Investigating fungal outbreaks in the 21st century. PLoS Pathog. 2015; 11(5):e1004804. PMC: 4440772. DOI: 10.1371/journal.ppat.1004804. View

13.

Summerbell R, Gueidan C, Schroers H, de Hoog G, Starink M, Rosete Y . Acremonium phylogenetic overview and revision of Gliomastix, Sarocladium, and Trichothecium. Stud Mycol. 2011; 68:139-62. PMC: 3065988. DOI: 10.3114/sim.2011.68.06. View

14.

Simpson J, Wong K, Jackman S, Schein J, Jones S, Birol I . ABySS: a parallel assembler for short read sequence data. Genome Res. 2009; 19(6):1117-23. PMC: 2694472. DOI: 10.1101/gr.089532.108. View

15.

Cheng V, Chan J, Ngan A, To K, Leung S, Tsoi H . Outbreak of intestinal infection due to Rhizopus microsporus. J Clin Microbiol. 2009; 47(9):2834-43. PMC: 2738128. DOI: 10.1128/JCM.00908-09. View

16.

Das S, Saha R, Dar S, Ramachandran V . Acremonium species: a review of the etiological agents of emerging hyalohyphomycosis. Mycopathologia. 2010; 170(6):361-75. DOI: 10.1007/s11046-010-9334-1. View

17.

Engelthaler D, Hicks N, Gillece J, Roe C, Schupp J, Driebe E . Cryptococcus gattii in North American Pacific Northwest: whole-population genome analysis provides insights into species evolution and dispersal. mBio. 2014; 5(4):e01464-14. PMC: 4161256. DOI: 10.1128/mBio.01464-14. View

18.

Ioakimidou A, Vyzantiadis T, Sakellari I, Arabatzis M, Smias C, Douka V . An unusual cluster of Acremonium kiliense fungaemias in a haematopoietic cell transplantation unit. Diagn Microbiol Infect Dis. 2013; 75(3):313-6. DOI: 10.1016/j.diagmicrobio.2012.11.015. View

19.

. Notes from the field: Multistate outbreak of postprocedural fungal endophthalmitis associated with a single compounding pharmacy - United States, March-April 2012. MMWR Morb Mortal Wkly Rep. 2012; 61(17):310-1. View

20.

Guinea J, Garcia de Viedma D, Pelaez T, Escribano P, Munoz P, Meis J . Molecular epidemiology of Aspergillus fumigatus: an in-depth genotypic analysis of isolates involved in an outbreak of invasive aspergillosis. J Clin Microbiol. 2011; 49(10):3498-503. PMC: 3187310. DOI: 10.1128/JCM.01159-11. View