Kristine Wylie, Ph.D.  kwylie@wustl.edu

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Assistant Professor of Pediatrics, Infectious Diseases
Infectious Diseases

phone: (314) 454-6050

Clinical Interests

Dr. Kristine Wylie is an Assistant Professor in the Department of Pediatrics at Washington University School of Medicine and the McDonnell Genome Institute. Her main research interest is the study of the dynamics of the microbiome and microbial infections during pregnancy. During Dr. Wylie’s postdoctoral work, she developed methods for analyzing high-throughput metagenomic shotgun sequence data sets to study the human virome, the viral component of the microbiome. Dr. Wylie analyzed the human virome (eukaryotic viruses) in the healthy subjects from the Human Microbiome Project, providing the first analysis of the commensal virome in a large cohort of generally healthy, asymptomatic people. She and her colleagues developed a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from eukaryotic DNA and RNA viruses from 34 families that infect vertebrate hosts. This approach greatly enhances the study of eukaryotic viruses using metagenomic sequencing. Using these methods, she and her colleagues have found that characteristics of the eukaryotic virome in the vagina associate with preterm birth. They are currently studying the dynamic associations between the vaginal microbiome (viruses and bacteria) and host response in a larger cohort of pregnant women and carrying out in vitro experiments to understand the mechanisms underlying associations with preterm birth.

Education

  • BA, Southern Illinois University1996
  • PhD, Saint Louis University2009

Training

  • Postdoctoral Research Associate, Washington University School of Medicine2009 - 2013

Honors and Awards

  • Michael R. Levy Award in Cellular and Molecular Biology, Southern Illinois University at Edwardsville1996
  • Sigma Xi, Saint Louis University2004
  • Presidential Fellowship, Saint Louis University2004 - 2008
  • Student travel award, American Society for Virology 27th Annual Meeting2008
  • Alpha Sigma Nu Jesuit Honor Society2009
  • Student travel award, American Society for Virology 28th Annual Meeting2009
  • Graduate Student of the Year, Molecular Microbiology and Immunology, Saint Louis University2009 - 2010
  • NHGRI Genome Advance of the Month, The Human Microbiome Project: Extending the definition of what constitutes a human2012

Recent Publications view all (70)


  1. Comparison of Metagenomic Sequencing and the NanoString nCounter Analysis System for the Characterization of Bacterial and Viral Communities in Vaginal Samples. mSphere. 2022;e0019722. PMID:36000741 
  2. Longitudinal Dynamics of Skin Bacterial Communities in the Context of Staphylococcus aureus Decolonization. Microbiol Spectr. 2022;10(2):e0267221. PMCID:PMC9045213  PMID:35384711 
  3. Helping others enhances graduate student wellness and mental health. Nat Biotechnol. 2022;40(4):618-619. PMCID:PMC9074398  PMID:35418639 
  4. Association of the human semen DNA virome with successful in vitro fertilization. F S Sci. 2022;3(1):2-9. PMID:35559992 
  5. Fecal microbiome and bile acid metabolome in adult short bowel syndrome. Am J Physiol Gastrointest Liver Physiol. 2022;322(1):G154-G168. PMCID:PMC8793869  PMID:34816756 
  6. Chronic villitis of unknown etiology: Investigations into viral pathogenesis. Placenta. 2021;107:24-30. PMCID:PMC8101289  PMID:33730616 
  7. ViroMatch: A Computational Pipeline for the Detection of Viral Sequences from Complex Metagenomic Data. Microbiol Resour Announc. 2021;10(9). PMCID:PMC7936641  PMID:33664143 
  8. Association of vaginal bacterial communities and reproductive outcomes with prophylactic antibiotic exposure in a subfertile population undergoing in vitro fertilization: a prospective exploratory study. F S Sci. 2021;2(1):71-79. PMCID:PMC8494411  PMID:34632426 
  9. A Protein Epitope Targeted by the Antibody Response to Kawasaki Disease. J Infect Dis. 2020;222(1):158-168. PMCID:PMC7296860  PMID:32052021 
  10. Association of the eukaryotic vaginal virome with prophylactic antibiotic exposure and reproductive outcomes in a subfertile population undergoing in vitro fertilisation: a prospective exploratory study. BJOG. 2020;127(2):208-216. PMCID:PMC6910962  PMID:31529767 
  11. A virome sequencing approach to feline oral squamous cell carcinoma to evaluate viral causative factors. Vet Microbiol. 2020;240:108491. PMCID:PMC7117531  PMID:31902496 
  12. The upper-airway microbiota and loss of asthma control among asthmatic children Nat Commun. 2019;10(1):5714. doi:10.1038/s41467-019-13698-x  PMCID:PMC6915697  PMID:31844063 
  13. Impaired Chylomicron Assembly Modifies Hepatic Metabolism Through Bile Acid-Dependent and Transmissible Microbial Adaptations. Hepatology. 2019;70(4):1168-1184. doi:10.1002/hep.30669  PMCID:PMC6783349  PMID:31004524 
  14. Genome Organization of Canada Goose Coronavirus, A Novel Species Identified in a Mass Die-off of Canada Geese. Sci Rep. 2019;9(1):5954. PMCID:PMC6459860  PMID:30976080 
  15. Dynamic host immune response in virus-associated cancers. Commun Biol. 2019;2:109. PMCID:PMC6430765  PMID:30911684 
  16. Metagenomic analysis of DNA viruses from posttransplant lymphoproliferative disorders Cancer Med. 2019;8(3):1013-23. doi:10.1002/cam4.1985  PMCID:PMC6434222  PMID:30697958 
  17. Whole-Genome Sequencing of Klebsiella pneumoniae Isolates to Track Strain Progression in a Single Patient With Recurrent Urinary Tract Infection. Front Cell Infect Microbiol. 2019;9:14. PMCID:PMC6375827  PMID:30800643 
  18. Differences in the lower airway microbiota of infants with and without cystic fibrosis. J Cyst Fibros. 2018. PMID:30580994 
  19. Detection of Viruses in Clinical Samples by Use of Metagenomic Sequencing and Targeted Sequence Capture. J Clin Microbiol. 2018;56(12). PMCID:PMC6258860  PMID:30232133 
  20. Evaluation of patient- versus provider-collected vaginal swabs for microbiome analysis during pregnancy. BMC Res Notes. 2018;11(1):706. PMCID:PMC6173906  PMID:30290831 
  21. Carriage of the Toxic Shock Syndrome Toxin Gene by Contemporary Community-Associated Staphylococcus aureus Isolates. J Pediatric Infect Dis Soc. 2018. PMID:30285124 
  22. Remnant Small Bowel Length in Pediatric Short Bowel Syndrome and the Correlation with Intestinal Dysbiosis and Linear Growth. J Am Coll Surg. 2018. PMID:30077861 
  23. The vaginal eukaryotic DNA virome and preterm birth. Am J Obstet Gynecol. 2018. PMID:29738749 
  24. Nucleotide resolution mapping of influenza A virus nucleoprotein-RNA interactions reveals RNA features required for replication. Nat Commun. 2018;9(1):465. PMCID:PMC5792457  PMID:29386621 
  25. BreakPoint Surveyor: A Pipeline for Structural Variant Visualization. Bioinformatics. 2017. PMID:28582538 
  26. Association of Antibiotics, Airway Microbiome and Inflammation in Infants with Cystic Fibrosis. Ann Am Thorac Soc. 2017. PMID:28708417 
  27. Early pregnancy vaginal microbiome trends and preterm birth. Am J Obstet Gynecol. 2017. PMID:28549981 
  28. The lower airway microbiota in early cystic fibrosis lung disease: a longitudinal analysis. Thorax. 2017. PMID:28280235 
  29. Genome Sequence of Enterovirus D68 from St. Louis, Missouri, USA, 2016. Genome Announc. 2017;5(9). PMCID:PMC5334578  PMID:28254971 
  30. The Virome of the Human Respiratory Tract. Clin Chest Med. 2017;38(1):11-19. PMID:28159153 
  31. Resurgence of Rotavirus Genotype G12 in St. Louis During the 2014-2015 Rotavirus Season. J Pediatric Infect Dis Soc. 2016. PMID:27988496 
  32. Environmental Enteric Dysfunction and the Fecal Microbiota in Malawian Children. Am J Trop Med Hyg. 2016. PMID:27956653 
  33. Tissue polymerase chain reaction for the diagnosis of cytomegalovirus disease after allogeneic stem cell transplantation. Am J Hematol. 2016. PMID:27859620 
  34. Divergent viral presentation among human tumors and adjacent normal tissues Sci Rep. 2016;6:28294. doi:10.1038/srep28294  PMCID:MC4919655  PMID:27339696 
  35. Azithromycin therapy during respiratory syncytial virus bronchiolitis: Upper airway microbiome alterations and subsequent recurrent wheeze J Allergy Clin Immunol. 2016;pii:S0091-6749(16)30288-3. doi:10.116/j.jaci.2016.03.054 [Epub ahead of print]  PMID:27339392 
  36. High-throughput sequencing of cerebrospinal fluid for diagnosis of chronic Propionibacterium acnes meningitis in an allogeneic stem cell transplant recipient. Transpl Infect Dis. 2016;18(2):227-33. PMID:26895706 
  37. Metagenomic approach for identification of the pathogens associated with diarrhea in stool specimens. J Clin Microbiol. 2016;54(2):368-75. doi:0.1128/JCM.01965-15 Epub 2015 Dec 4  PMCID:PMC4733167  PMID:26637379 
  38. The transcriptional profile of coronary arteritis in Kawasaki disease. BMC Genomics. 2015;16:1076. PMCID:PMC4683744  PMID:26679344 
  39. Emergence of Rotavirus G12P[8] in St. Louis During the 2012-2013 Rotavirus Season. J Pediatric Infect Dis Soc. 2015;4(4):e84-9. PMCID:PMC4681384  PMID:26513823 
  40. Enhanced virome sequencing using targeted sequence capture. Genome Res. 2015;25(12):1910-20. doi:10.1101/gr.191049.115  PMID:26395152 
  41. mBLAST: Keeping up with the sequencing explosion for (meta)genome analysis. J Data Mining Genomics Proteomics. 2015;4(3):135. doi:Epub 2013 Jul 31  PMCID:PMC4612494  PMID:26500804 
  42. Development and Evaluation of an Enterovirus D68 Real-Time Reverse Transcriptase PCR Assay. J Clin Microbiol. 2015;53(8):2641-7. doi:10.1128/JCM.00923-15  PMCID:PMC4508392  PMID:26063859 
  43. Enterovirus D68-associated acute respiratory distress syndrome in adult, United States, 2014. Emerg Infect Dis. 2015;21(5):914-6. doi:10.3201/eid2105.142033  PMCID:PMC4412249  PMID:25897542 
  44. Genome sequence of enterovirus D68 from St. Louis, Missouri, USA. Emerg Infect Dis. 2015;21(1):184-6. doi:10.3201/eid2101.141605  PMCID:PMC4285240  PMID:25532062 
  45. Metagenomic analysis of double-stranded DNA viruses in healthy adults. BMC Biol. 2014;12(1):71. doi:10.1186/s12915-014-0071-7  PMCID:PMC4177058  PMID:25212266 
  46. Exploration of bacterial community classes in major human habitats. Genome Biol. 2014;15(5):R66. doi:10.1186/gb-2014-15-5-r66  PMCID:PMC4073010  PMID:24887286 
  47. Virome genomics: a tool for defining the human virome. Curr Opin Microbiol. 2013;16(4):479-84. doi:10.1016/j.mib.2013.04.006  PMCID:PMC3755052  PMID:23706900 
  48. A proautophagic antiviral role for the cellular prion protein identified by infection with a herpes simplex virus 1 ICP34.5 mutant. J Virol. 2013;87(10):5882-94. doi:10.1128/JVI.02559-12  PMCID:PMC3648145  PMID:23487467 
  49. Biogeography of the ecosystems of the healthy human body. Genome Biol. 2013;14(1):R1. doi:10.1186/gb-2013-14-1-r1  PMCID:PMC4054670  PMID:23316946 
  50. Emerging view of the human virome. Transl Res. 2012;160(4):283-90. doi:10.1016/j.trsl.2012.03.006  PMCID:PMC3701101  PMID:22683423 
  51. A framework for human microbiome research. Nature. 2012;486(7402):215-21. doi:10.1038/nature11209  PMCID:PMC3377744  PMID:22699610 
  52. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207-14. doi:10.1038/nature11234  PMCID:PMC3564958  PMID:22699609 
  53. Sequence analysis of the human virome in febrile and afebrile children. PLoS One. 2012;7(6):e27735. doi:10.1371/journal.pone.0027735  PMCID:PMC3374612  PMID:22719819 
  54. Novel bacterial taxa in the human microbiome. PLoS One. 2012;7(6):e35294. doi:10.1371/journal.pone.0035294  PMCID:PMC3374617  PMID:22719826 
  55. Increased prevalence of anellovirus in pediatric patients with fever. PLoS One. 2012;7(11):e50937. doi:10.1371/journal.pone.0050937  PMCID:PMC3511395  PMID:23226428 
  56. The "most wanted" taxa from the human microbiome for whole genome sequencing. PLoS One. 2012;7(7):e41294. doi:10.1371/journal.pone.0041294  PMCID:PMC3406062  PMID:22848458 
  57. Astrovirus MLB2 viremia in febrile child. Emerg Infect Dis. 2011;17(11):2050-2. doi:10.3201/eid1711.110496  PMCID:PMC3310569  PMID:22099095 
  58. Herpes simplex virus 2 UL13 protein kinase disrupts nuclear lamins. Virology. 2009;392(1):137-47. doi:10.1016/j.virol.2009.06.051  PMCID:PMC2769575  PMID:19640559 
  59. Increased eIF2alpha phosphorylation attenuates replication of herpes simplex virus 2 vhs mutants in mouse embryonic fibroblasts and correlates with reduced accumulation of the PKR antagonist ICP34.5. J Virol. 2009;83(18):9151-62. doi:10.1128/JVI.00886-09  PMCID:PMC2738226  PMID:19587046 
  60. Herpes simplex virus virion host shutoff attenuates establishment of the antiviral state. J Virol. 2008;82(11):5527-35. doi:10.1128/JVI.02047-07  PMCID:PMC2395185  PMID:18367525 
  61. Selective ablation of virion host shutoff protein RNase activity attenuates herpes simplex virus 2 in mice. J Virol. 2008;82(7):3642-53. doi:10.1128/JVI.02409-07  PMCID:PMC2268463  PMID:18234805 
  62. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature. 2005;434(7034):724-31. doi:10.1038/nature03466  PMID:15815621 
  63. A physical map of the chicken genome. Nature. 2004;432(7018):761-4. doi:10.1038/nature03030  PMID:15592415 
  64. Finishing the euchromatic sequence of the human genome. Nature. 2004;431(7011):931-45. doi:10.1038/nature03001  PMID:15496913 
  65. The DNA sequence of human chromosome 7. Nature. 2003;424(6945):157-64. doi:10.1038/nature01782  PMID:12853948 
  66. A physical map of the mouse genome. Nature. 2002;418(6899):743-50. doi:10.1038/nature00957  PMID:12181558 
  67. The LN54 radiation hybrid map of zebrafish expressed sequences. Genome Res. 2001;11(12):2127-32. doi:10.1101/gr.210601  PMCID:PMC311215  PMID:11731504 
  68. A physical map of the human Y chromosome. Nature. 2001;409(6822):943-5. doi:10.1038/35057170  PMID:11237016 
  69. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860-921. doi:10.1038/35057062  PMID:11237011 
  70. A physical map of the human genome. Nature. 2001;409(6822):934-41. doi:10.1038/35057157  PMID:11237014 
Last updated: 09/25/2022
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