1
|
Schaefer EAF, Chu S, Wylie KM, Wylie TN, Griffith OL, Pearce JW, Johnson GC, Bryan JN, Flesner BK. Metagenomic Analysis of DNA Viruses with Targeted Sequence Capture of Canine Lobular Orbital Adenomas and Normal Conjunctiva. Microorganisms 2023; 11:1163. [PMID: 37317137 DOI: 10.3390/microorganisms11051163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 06/16/2023] Open
Abstract
Our study aims are: (1) to evaluate phenotypically normal canine conjunctival and orbital tissue and tissue from canine lobular orbital adenomas (CLOAs) for the presence of viral genomic material and (2) phylogenetically classify detected DNA viruses to determine if a DNA virus is associated with CLOAs. A total of 31 formalin fixed paraffin embedded CLOA tissue samples, 4 papillomas or sarcoid, and 10 fresh clinically normal conjunctival tissues were included in this study. Genomic DNA was isolated from all samples and sequencing libraries were prepared. The libraries were molecularly indexed and pooled and viral DNA was enriched via targeted sequence capture utilizing ViroCap. The libraries were sequenced on the Illumina HiSeq platform and compared to known viral DNA reference genomes to identify viral DNA. Carnivore parvovirus was identified in 6.4% and 20% of CLOA tissue and normal conjunctival samples, respectively. This study showed that conjunctival tissue from healthy dogs and CLOAs uncommonly harbor DNA viruses, and no DNA virus was associated with these tumors. Further studies are needed to evaluate the etiologic cause of CLOAs.
Collapse
Affiliation(s)
- Elizabeth A F Schaefer
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Shirley Chu
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Kristine M Wylie
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA
- Department of Pediatrics, Washington University, St. Louis, MO 63110, USA
| | - Todd N Wylie
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA
- Department of Pediatrics, Washington University, St. Louis, MO 63110, USA
| | - Obi L Griffith
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA
- Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Jacqueline W Pearce
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Gayle C Johnson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Jeffrey N Bryan
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Brian K Flesner
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| |
Collapse
|
2
|
Galardi MM, Sowa GM, Crockett CD, Rudock R, Smith AE, Shwe EE, San T, Linn K, Aye AMM, Ramachandran PS, Zia M, Wapniarski AE, Hawes IA, Hlaing CS, Kyu EH, Thair C, Mar YY, Nway N, Storch GA, Wylie KM, Wylie TN, Dalmau J, Wilson MR, Mar SS. Pathogen and Antibody Identification in Children with Encephalitis in Myanmar. Ann Neurol 2023; 93:615-628. [PMID: 36443898 DOI: 10.1002/ana.26560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 10/22/2022] [Accepted: 11/20/2022] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Prospective studies of encephalitis are rare in regions where encephalitis is prevalent, such as low middle-income Southeast Asian countries. We compared the diagnostic yield of local and advanced tests in cases of pediatric encephalitis in Myanmar. METHODS Children with suspected subacute or acute encephalitis at Yangon Children's Hospital, Yangon, Myanmar, were prospectively recruited from 2016-2018. Cohort 1 (n = 65) had locally available diagnostic testing, whereas cohort 2 (n = 38) had advanced tests for autoantibodies (ie, cell-based assays, tissue immunostaining, studies with cultured neurons) and infections (ie, BioFire FilmArray multiplex Meningitis/Encephalitis multiplex PCR panel, metagenomic sequencing, and pan-viral serologic testing [VirScan] of cerebrospinal fluid). RESULTS A total of 20 cases (13 in cohort 1 and 7 in cohort 2) were found to have illnesses other than encephalitis. Of the 52 remaining cases in cohort 1, 43 (83%) had presumed infectious encephalitis, of which 2 cases (4%) had a confirmed infectious etiology. Nine cases (17%) had presumed autoimmune encephalitis. Of the 31 cases in cohort 2, 23 (74%) had presumed infectious encephalitis, of which one (3%) had confirmed infectious etiology using local tests only, whereas 8 (26%) had presumed autoimmune encephalitis. Advanced tests confirmed an additional 10 (32%) infections, 4 (13%) possible infections, and 5 (16%) cases of N-methyl-D-aspartate receptor antibody encephalitis. INTERPRETATION Pediatric encephalitis is prevalent in Myanmar, and advanced technologies increase identification of treatable infectious and autoimmune causes. Developing affordable advanced tests to use globally represents a high clinical and research priority to improve the diagnosis and prognosis of encephalitis. ANN NEUROL 2023;93:615-628.
Collapse
Affiliation(s)
- Maria M Galardi
- Department of Neurology, Washington University School of Medicine, St. Louis, MO
| | - Gavin M Sowa
- Department of Medicine, McGaw Medical Center of Northwestern University, Chicago, IL
| | - Cameron D Crockett
- Department of Neurology, Washington University School of Medicine, St. Louis, MO
| | - Robert Rudock
- Department of Neurology, Washington University School of Medicine, St. Louis, MO
| | - Alyssa E Smith
- Department of Neurology, Washington University School of Medicine, St. Louis, MO
| | - Ei E Shwe
- Department of Pathology, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Thidar San
- Department of Pathology, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Kyaw Linn
- Department of Pediatrics, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Aye Mya M Aye
- Department of Pediatrics, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Prashanth S Ramachandran
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Maham Zia
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Anne E Wapniarski
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Isobel A Hawes
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Chaw S Hlaing
- Department of Pediatrics, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Ei H Kyu
- Department of Pediatrics, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Cho Thair
- Department of Pediatrics, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Yi Y Mar
- Department of Pediatrics, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Nway Nway
- Department of Pediatrics, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Gregory A Storch
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO
| | - Kristine M Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO
| | - Todd N Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO
| | - Josep Dalmau
- Neuroimmunology Program, Institut d'Investigacions Biomèdiques August Pi i Sunyer Hospital Clínic, University of Barcelona, Barcelona, Spain.,Department of Neurology, University of Pennsylvania, Philadelphia, PA.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Michael R Wilson
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Soe S Mar
- Department of Neurology, Washington University School of Medicine, St. Louis, MO
| |
Collapse
|
3
|
Stout MJ, Brar AK, Herter BN, Rankin A, Wylie KM. The plasma virome in longitudinal samples from pregnant patients. Front Cell Infect Microbiol 2023; 13:1061230. [PMID: 36844406 PMCID: PMC9949529 DOI: 10.3389/fcimb.2023.1061230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction Nucleic acid from viruses is common in peripheral blood, even in asymptomatic individuals. How physiologic changes of pregnancy impact host-virus dynamics for acute, chronic, and latent viral infections is not well described. Previously we found higher viral diversity in the vagina during pregnancy associated with preterm birth (PTB) and Black race. We hypothesized that higher diversity and viral copy numbers in the plasma would show similar trends. Methods To test this hypothesis, we evaluated longitudinally collected plasma samples from 23 pregnant patients (11 term and 12 preterm) using metagenomic sequencing with ViroCap enrichment to enhance virus detection. Sequence data were analyzed with the ViroMatch pipeline. Results We detected nucleic acid from at least 1 virus in at least 1 sample from 87% (20/23) of the maternal subjects. The viruses represented 5 families: Herpesviridae, Poxviridae, Papillomaviridae, Anelloviridae, and Flaviviridae. We analyzed cord plasma from 18 of the babies from those patients and found nucleic acid from viruses in 33% of the samples (6/18) from 3 families: Herpesviridae, Papillomaviridae, and Anelloviridae. Some viral genomes were found in both maternal plasma and cord plasma from maternal-fetal pairs (e.g. cytomegalovirus, anellovirus). We found that Black race associated with higher viral richness (number of different viruses detected) in the maternal blood samples (P=0.003), consistent with our previous observations in vaginal samples. We did not detect associations between viral richness and PTB or the trimester of sampling. We then examined anelloviruses, a group of viruses that is ubiquitous and whose viral copy numbers fluctuate with immunological state. We tested anellovirus copy numbers in plasma from 63 pregnant patients sampled longitudinally using qPCR. Black race associated with higher anellovirus positivity (P<0.001) but not copy numbers (P=0.1). Anellovirus positivity and copy numbers were higher in the PTB group compared to the term group (P<0.01, P=0.003, respectively). Interestingly, these features did not occur at the time of delivery but appeared earlier in pregnancy, suggesting that although anelloviruses were biomarkers for PTB they were not triggering parturition. Discussion These results emphasize the importance of longitudinal sampling and diverse cohorts in studies of virome dynamics during pregnancy.
Collapse
Affiliation(s)
- Molly J. Stout
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Anoop K. Brar
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
| | - Brandi N. Herter
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
| | - Ananda Rankin
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
| | - Kristine M. Wylie
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States,The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, United States,*Correspondence: Kristine M. Wylie,
| |
Collapse
|
4
|
Garand M, Huang SSY, Goessling LS, Wan F, Santillan DA, Santillan MK, Brar A, Wylie TN, Wylie KM, Eghtesady P. Virome Analysis and Association of Positive Coxsackievirus B Serology during Pregnancy with Congenital Heart Disease. Microorganisms 2023; 11:262. [PMID: 36838226 PMCID: PMC9963073 DOI: 10.3390/microorganisms11020262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/09/2023] [Accepted: 01/15/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND We have previously shown coxsackievirus B (CVB) to be a potent inducer of congenital heart disease (CHD) in mice. The clinical relevance of these findings in humans and the roles of other viruses in the pathogenesis of CHD remain unknown. METHODS We obtained plasma samples, collected at all trimesters, from 89 subjects (104 pregnancies), 73 healthy controls (88 pregnancies), and 16 with CHD-affected birth (16 pregnancies), from the Perinatal Family Tissue Bank (PFTB). We performed CVB IgG/IgM serological assays on plasma. We also used ViroCap sequencing and PCR to test for viral nucleic acid in plasma, circulating leukocytes from the buffy coat, and in the media of a co-culture system. RESULTS CVB IgG/IgM results indicated that prior exposure was 7.8 times more common in the CHD group (95% CI, 1.14-54.24, adj. p-value = 0.036). However, the CVB viral genome was not detected in plasma, buffy coat, or co-culture supernatant by molecular assays, although other viruses were detected. CONCLUSION Detection of viral nucleic acid in plasma was infrequent and specifically no CVB genome was detected. However, serology demonstrated that prior CVB exposure is higher in CHD-affected pregnancies. Further studies are warranted to understand the magnitude of the contribution of the maternal blood virome to the pathogenesis of CHD.
Collapse
Affiliation(s)
- Mathieu Garand
- Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susie S. Y. Huang
- Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lisa S. Goessling
- Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Fei Wan
- Department of Public Health Sciences and Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Donna A. Santillan
- Department of Obstetrics and Gynecology, University of Iowa, Iowa City, IA 52242, USA
| | - Mark K. Santillan
- Department of Obstetrics and Gynecology, University of Iowa, Iowa City, IA 52242, USA
| | - Anoop Brar
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Todd N. Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kristine M. Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Pirooz Eghtesady
- Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| |
Collapse
|
5
|
Fritz SA, Wylie TN, Gula H, Hogan PG, Boyle MG, Muenks CE, Sullivan ML, Burnham CAD, Wylie KM. Longitudinal Dynamics of Skin Bacterial Communities in the Context of Staphylococcus aureus Decolonization. Microbiol Spectr 2022; 10:e0267221. [PMID: 35384711 PMCID: PMC9045213 DOI: 10.1128/spectrum.02672-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/15/2022] [Indexed: 11/22/2022] Open
Abstract
Decolonization with topical antimicrobials is frequently prescribed in health care and community settings to prevent Staphylococcus aureus infection. However, effects on commensal skin microbial communities remains largely unexplored. Within a household affected by recurrent methicillin-resistant S. aureus skin and soft tissue infections (SSTI), skin swabs were collected from the anterior nares, axillae, and inguinal folds of 14 participants at 1- to 3-month intervals over 24 months. Four household members experienced SSTI during the first 12-months (observational period) and were prescribed a 5-day decolonization regimen with intranasal mupirocin and bleach water baths at the 12-month study visit. We sequenced the 16S rRNA gene V1-V2 region and compared bacterial community characteristics between the pre- and post-intervention periods and between younger and older subjects. The median Shannon diversity index was stable during the 12-month observational period at all three body sites. Bacterial community characteristics (diversity, stability, and taxonomic composition) varied with age. Among all household members, not exclusively among the four performing decolonization, diversity was unstable throughout the year post-intervention. In the month after decolonization, bacterial communities were changed. Although communities largely returned to their baseline states, relative abundance of some taxa remained changed throughout the year following decolonization (e.g., more abundant Bacillus; less abundant Cutibacterium). This 5-day decolonization regimen caused disruption of skin bacteria, and effects differed in younger and older subjects. Some effects were observed throughout the year post-intervention, which emphasizes the need for better understanding of the collateral effects of decolonization for S. aureus eradication. IMPORTANCE Decolonization with topical antimicrobials is frequently prescribed to prevent Staphylococcus aureus infection, but the effects on commensal skin bacteria are undetermined. We found that decolonization with mupirocin and bleach water baths leads to sustained disruption of bacterial communities.
Collapse
Affiliation(s)
- Stephanie A. Fritz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Todd N. Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Haley Gula
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Patrick G. Hogan
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Mary G. Boyle
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carol E. Muenks
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Melanie L. Sullivan
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carey-Ann D. Burnham
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kristine M. Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| |
Collapse
|
6
|
Hermanstyne TO, Johnson L, Wylie KM, Skeath JB. Helping others enhances graduate student wellness and mental health. Nat Biotechnol 2022; 40:618-619. [PMID: 35418639 PMCID: PMC9074398 DOI: 10.1038/s41587-022-01275-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Tracey O Hermanstyne
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lauren Johnson
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Kristine M Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
| | - James B Skeath
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
7
|
Gunderson S, Eskew AM, Stoutenburg D, Riley JK, Stout MJ, Schrimpf J, Jungheim ES, Wylie KM. Association of the human semen DNA virome with successful in vitro fertilization. F S Sci 2022; 3:2-9. [PMID: 35559992 DOI: 10.1016/j.xfss.2021.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 06/15/2023]
Abstract
OBJECTIVE To comprehensively characterize the DNA virome in semen samples collected for in vitro fertilization (IVF). DESIGN A descriptive clinical study. SETTING Single academic fertility center. PATIENT(S) Twenty-four male partners from couples undergoing IVF. INTERVENTION(S) Couples were randomized to receive 1 g of azithromycin (standard of care) or no azithromycin at the time of baseline IVF assessment. Semen samples were collected at the time of the female partners' egg retrieval, and 100 μL of the sample was used for the virome analysis. MAIN OUTCOME MEASURE(S) Detection of viruses by ViroCap enrichment of viral nucleic acid and sequencing. Association between the virome, semen parameters, and pregnancy outcomes. RESULT(S) We detected viruses in 58% of the participants. Viruses included polyomaviruses, papillomaviruses, herpesviruses, and anelloviruses. Viromes detected in semen had little overlap with the viromes detected in vaginal samples from their female partners collected at the time of embryo transfer, which were analyzed in a previous study. A lower viral diversity in semen samples was positively associated with pregnancy (Hodges-Lehmann estimate of difference, 1; 95% confidence interval, 2-0.00003). There was no association between viral diversity and sperm concentration, motility, or fertilization rates. CONCLUSION(S) This comprehensive characterization of the DNA virome in semen reveals an association between virome diversity and pregnancy in couples undergoing IVF. However, no association was found with specific semen parameters or fertilization rates, suggesting that viral exposure may negatively affect pregnancy after fertilization. Future studies should be undertaken to evaluate the associations between the semen virome with IVF outcomes in larger cohorts.
Collapse
Affiliation(s)
- Stephanie Gunderson
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, Missouri
| | - Ashley M Eskew
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, Missouri
| | - Dylan Stoutenburg
- Department of Pediatrics, Division of Infectious Diseases, Washington University in St Louis, St. Louis, Missouri
| | - Joan K Riley
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, Missouri
| | - Molly J Stout
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Washington University in St Louis, St. Louis, Missouri
| | - Jane Schrimpf
- Department of Pediatrics, Division of Infectious Diseases, Washington University in St Louis, St. Louis, Missouri
| | - Emily S Jungheim
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, Missouri
| | - Kristine M Wylie
- Department of Pediatrics, Division of Infectious Diseases, Washington University in St Louis, St. Louis, Missouri; McDonnell Genome Institute, Washington University in St Louis, St Louis, Missouri.
| |
Collapse
|
8
|
Boutte HJ, Chen J, Wylie TN, Wylie KM, Xie Y, Geisman M, Prabu A, Gazit V, Tarr PI, Levin MS, Warner BW, Davidson NO, Rubin DC. Fecal microbiome and bile acid metabolome in adult short bowel syndrome. Am J Physiol Gastrointest Liver Physiol 2022; 322:G154-G168. [PMID: 34816756 PMCID: PMC8793869 DOI: 10.1152/ajpgi.00091.2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Loss of functional small bowel surface area causes short bowel syndrome (SBS), intestinal failure, and parenteral nutrition (PN) dependence. The gut adaptive response following resection may be difficult to predict, and it may take up to 2 yr to determine which patients will wean from PN. Here, we examined features of gut microbiota and bile acid (BA) metabolism in determining adaptation and ability to wean from PN. Stool and sera were collected from healthy controls and from patients with SBS (n = 52) with ileostomy, jejunostomy, ileocolonic, and jejunocolonic anastomoses fed with PN plus enteral nutrition or who were exclusively enterally fed. We undertook 16S rRNA gene sequencing, BA profiling, and 7α-hydroxy-4-cholesten-3-one (C4) quantitation with LC-MS/MS and serum amino acid analyses. Patients with SBS exhibited altered gut microbiota with reduced gut microbial diversity compared with healthy controls. We observed differences in the microbiomes of patients with SBS with ileostomy versus jejunostomy, jejunocolonic versus ileocolonic anastomoses, and PN dependence compared with those who weaned from PN. Stool and serum BA composition and C4 concentrations were also altered in patients with SBS, reflecting adaptive changes in enterohepatic BA cycling. Stools from patients who were weaned from PN were enriched in secondary BAs including deoxycholic acid and lithocholic aicd. Shifts in gut microbiota and BA metabolites may generate a favorable luminal environment in select patients with SBS, promoting the ability to wean from PN. Proadaptive microbial species and select BA may provide novel targets for patient-specific therapies for SBS.NEW & NOTEWORTHY Loss of intestinal surface area causes short bowel syndrome, intestinal failure, and parenteral nutrition dependence. We analyzed the gut microbiota and bile acid metabolome of a large cohort of short bowel syndrome adult patients with different postsurgical anatomies. We report a novel analysis of the microbiome of patients with ileostomy and jejunostomy. Enrichment of specific microbial and bile acid species may be associated with the ability to wean from parenteral nutrition.
Collapse
Affiliation(s)
- Harold J. Boutte
- 1Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Jacqueline Chen
- 1Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Todd N. Wylie
- 2Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri,3McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Kristine M. Wylie
- 2Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri,3McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Yan Xie
- 1Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Mackenzie Geisman
- 1Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Anirudh Prabu
- 1Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Vered Gazit
- 1Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Phillip I. Tarr
- 2Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri,4Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri
| | - Marc S. Levin
- 1Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri,7Veterans Administration Saint Louis Health Care System, St. Louis, Missouri
| | - Brad W. Warner
- 5Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, Missouri
| | - Nicholas O. Davidson
- 1Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri,6Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri
| | - Deborah C. Rubin
- 1Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri,6Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri
| |
Collapse
|
9
|
Eskew AM, Stout MJ, Bedrick BS, Riley JK, Herter BN, Gula H, Jungheim ES, Wylie KM. Association of vaginal bacterial communities and reproductive outcomes with prophylactic antibiotic exposure in a subfertile population undergoing in vitro fertilization: a prospective exploratory study. ACTA ACUST UNITED AC 2021; 2:71-79. [PMID: 34632426 PMCID: PMC8494411 DOI: 10.1016/j.xfss.2021.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Objective: To determine whether prophylactic azithromycin is associated with the vaginal bacterial microbiome and clinical outcomes in subfertile women undergoing in vitro fertilization (IVF). Design: Prospective exploratory cohort study. Setting: Single academic fertility center. Patients: Subfertile women aged 18–43 years undergoing their first IVF cycle and fresh embryo transfer. Intervention: Primary exposure to prophylactic azithromycin (1 g orally) once at baseline. Main Outcome Measures: The primary outcome was the effect of azithromycin on the vaginal microbiome compared with a no-azithromycin group at 3 time points throughout the IVF cycle (baseline, retrieval, and embryo transfer). The secondary outcomes were associations of vaginal bacterial communities with clinical outcomes. Results: A planned a priori exploratory cohort of 27 subjects (12 in the azithromycin treatment group and 15 in the no-azithromycin group) contributed 79 vaginal swabs for the analysis as part of an ongoing randomized, controlled noninferiority trial. No specific taxa were associated with azithromycin or pregnancy at any time point. Azithromycin did not affect alpha diversity or community stability. Although there were trends of a lower bacterial load and higher percentage of Lactobacillus species in the azithromycin group at the time of transfer, these were not statistically significant. In women who did not become pregnant, the percentage of Lactobacillus species was lower (P = .048; Hodges-Lehmann estimate of difference, 0.41; 95% confidence interval, 0.08–0.65) and the change in community composition over time was higher. The percentage of Lactobacillus species at baseline was not predictive of the percentage of Lactobacillus species at the time of embryo transfer. Conclusions: Prophylactic azithromycin at baseline is not associated with changes in vaginal bacterial communities. Bacterial community features at the time of embryo transfer are associated with pregnancy. Bacterial community structures at baseline are not predictive of those at the time of embryo transfer. Clinical Trial Registration Number: NCT03386227.
Collapse
Affiliation(s)
- Ashley M Eskew
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Washington University in St. Louis, St. Louis, Missouri.,Atrium Health, Women's Institute, Charlotte, North Carolina
| | - Molly J Stout
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Washington University in St. Louis, St. Louis, Missouri.,Division of Maternal Fetal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Bronwyn S Bedrick
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Washington University in St. Louis, St. Louis, Missouri.,Department of Obstetrics and Gynecology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Joan K Riley
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Washington University in St. Louis, St. Louis, Missouri
| | - Brandi N Herter
- Division of Infectious Diseases, Department of Pediatrics, Washington University in St. Louis, St. Louis, Missouri
| | - Haley Gula
- Division of Infectious Diseases, Department of Pediatrics, Washington University in St. Louis, St. Louis, Missouri
| | - Emily S Jungheim
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Washington University in St. Louis, St. Louis, Missouri.,Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Kristine M Wylie
- Division of Infectious Diseases, Department of Pediatrics, Washington University in St. Louis, St. Louis, Missouri.,McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri
| |
Collapse
|
10
|
Ernst LM, Bockoven C, Freedman A, Wang V, Pellerite M, Wylie TN, Wylie KM. Chronic villitis of unknown etiology: Investigations into viral pathogenesis. Placenta 2021; 107:24-30. [PMID: 33730616 DOI: 10.1016/j.placenta.2021.02.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/02/2021] [Accepted: 02/25/2021] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Chronic villitis of unknown etiology (VUE) is a chronic inflammatory lesion of third trimester placenta, which contributes to major adverse obstetric outcomes. However, the inciting factors and mechanisms by which VUE contributes to adverse outcomes are poorly understood. This limits our ability to develop preventions or interventions. Our goals were to determine whether viruses can be detected in placental tissues with VUE and to determine whether gene expression profiles support an antiviral response. METHODS We extracted RNA and DNA from 20 placentas with high-grade chronic villitis and 20 control placentas without inflammation. Viruses were assessed using ViroCap viral nucleic acid enrichment coupled with metagenomic sequencing. RNA sequencing was used to evaluate the inflammatory gene expression profiles in each placenta. RESULTS We detected at least 1 virus in 50% of the samples tested. We found that herpesviruses, were found more frequently in cases compared with controls (P = 0.01). Antiviral pathways, including defense response to virus, interferon gamma response, and IFN alpha/beta response, were upregulated in cases. We observed two clusters of gene expression profiles in the VUE cases, suggesting multiple inflammatory profiles are associated with VUE. DISCUSSION These data support a viral etiology for some cases of VUE. Furthermore, gene expression profiles suggest the possibility of more than one cause or manifestation of VUE. Viral mechanisms should be explored as potential targets for prevention or intervention in VUE.
Collapse
Affiliation(s)
- Linda M Ernst
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, IL, USA; University of Chicago Pritzker School of Medicine, Chicago, IL, USA.
| | - Crystal Bockoven
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, IL, USA; University of Chicago Pritzker School of Medicine, Chicago, IL, USA
| | - Alexa Freedman
- Institute for Policy Research, Northwestern University, Evanston, IL, USA; Department of Obstetrics and Gynecology, NorthShore University HealthSystem, Evanston, IL, USA
| | - Vivien Wang
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Matthew Pellerite
- Department of Pediatrics, NorthShore University HealthSystem, Evanston, IL, USA
| | - Todd N Wylie
- Department of Pediatrics, Washington University, St. Louis, MO, USA
| | - Kristine M Wylie
- Department of Pediatrics, Washington University, St. Louis, MO, USA
| |
Collapse
|
11
|
Rowley AH, Baker SC, Arrollo D, Gruen LJ, Bodnar T, Innocentini N, Hackbart M, Cruz-Pulido YE, Wylie KM, Kim KYA, Shulman ST. A Protein Epitope Targeted by the Antibody Response to Kawasaki Disease. J Infect Dis 2020; 222:158-168. [PMID: 32052021 PMCID: PMC7296860 DOI: 10.1093/infdis/jiaa066] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 02/07/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Kawasaki disease (KD) is the leading cause of childhood acquired heart disease in developed nations and can result in coronary artery aneurysms and death. Clinical and epidemiologic features implicate an infectious cause but specific antigenic targets of the disease are unknown. Peripheral blood plasmablasts are normally highly clonally diverse but the antibodies they encode are approximately 70% antigen-specific 1-2 weeks after infection. METHODS We isolated single peripheral blood plasmablasts from children with KD 1-3 weeks after onset and prepared 60 monoclonal antibodies (mAbs). We used the mAbs to identify their target antigens and assessed serologic response among KD patients and controls to specific antigen. RESULTS Thirty-two mAbs from 9 of 11 patients recognize antigen within intracytoplasmic inclusion bodies in ciliated bronchial epithelial cells of fatal cases. Five of these mAbs, from 3 patients with coronary aneurysms, recognize a specific peptide, which blocks binding to inclusion bodies. Sera from 5/8 KD patients day ≥ 8 after illness onset, compared with 0/17 infant controls (P < .01), recognized the KD peptide antigen. CONCLUSIONS These results identify a protein epitope targeted by the antibody response to KD and provide a means to elucidate the pathogenesis of this important worldwide pediatric problem.
Collapse
Affiliation(s)
- Anne H Rowley
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Microbiology/Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Susan C Baker
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, Illinois, USA
| | - David Arrollo
- Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Leah J Gruen
- Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Tetyana Bodnar
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Nancy Innocentini
- Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Matthew Hackbart
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, Illinois, USA
| | - Yazmin E Cruz-Pulido
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, Illinois, USA
| | - Kristine M Wylie
- Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri, USA
| | - Kwang-Youn A Kim
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Stanford T Shulman
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| |
Collapse
|
12
|
|
13
|
Parrish KL, Wylie KM, Reich PJ, Hogan PG, Wylie TN, Kennedy CR, Lainhart W, Hunstad DA, Burnham CAD, Fritz SA. Carriage of the Toxic Shock Syndrome Toxin Gene by Contemporary Community-Associated Staphylococcus aureus Isolates. J Pediatric Infect Dis Soc 2019; 8:470-473. [PMID: 30285124 PMCID: PMC6831934 DOI: 10.1093/jpids/piy098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/13/2018] [Indexed: 01/02/2023]
Abstract
We report here the prevalence of the tst-1 gene among 252 methicillin-susceptible Staphylococcus aureus (MSSA) isolates and 458 methicillin-resistant S aureus (MRSA) isolates collected from 531 subjects between 2008 and 2017, one of which was recovered from a child with MRSA toxic shock syndrome. tst-1 was encoded by 43 (6%) S aureus isolates overall: 42 (16.7%) MSSA isolates and 1 (0.2%) MRSA isolate (P < .001).
Collapse
Affiliation(s)
- Katelyn L Parrish
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Kristine M Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Patrick J Reich
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Patrick G Hogan
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Todd N Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Colleen R Kennedy
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - William Lainhart
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - David A Hunstad
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri
| | - Carey-Ann D Burnham
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri
| | - Stephanie A Fritz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| |
Collapse
|
14
|
Eskew AM, Stout MJ, Bedrick BS, Riley JK, Omurtag KR, Jimenez PT, Odem RR, Ratts VS, Keller SL, Jungheim ES, Wylie KM. 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 2019; 127:208-216. [PMID: 31529767 DOI: 10.1111/1471-0528.15951] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The objective of this study was to use high-throughput sequencing to describe the vaginal eukaryotic DNA virome in patients undergoing in vitro fertilisation (IVF) to examine associations between the vaginal virome, antibiotic exposure and IVF outcomes. DESIGN Prospective exploratory study. SETTING Single academic fertility centre. POPULATION Subfertile women age 18-43 years undergoing their first IVF cycle with a fresh embryo transfer. METHODS The primary exposure was prophylactic azithromycin or no azithromycin before IVF. A mid-vaginal swab was obtained at the time of embryo transfer for virome analysis. MAIN OUTCOME MEASURES The primary outcomes compared between exposure groups were characteristics of vaginal virome and clinical pregnancy rates. Secondary outcomes were virome associations with number of oocytes retrieved, number of blastocysts and implantation rate. RESULTS Twenty-six women contributed a vaginal swab before embryo transfer. There were no significant differences in IVF outcomes between azithromycin groups. There was no association between viral diversity and clinical pregnancy overall. A higher diversity of herpesviruses and α-papillomaviruses was observed in samples from the azithromycin-treated group compared with the no azithromycin group (P = 0.04). In women that received azithromycin, viral diversity was higher in the group that did not achieve clinical pregnancy compared with those who did (P = 0.06). CONCLUSIONS We demonstrate that the vaginal eukaryotic virome in women undergoing IVF is associated with antibiotic exposure. Additionally, we demonstrate an inverse trend between viral diversity and pregnancy, with a higher number of viruses detected associated with failure to achieve clinical pregnancy in the azithromycin group. TWEETABLE ABSTRACT Higher viral diversity is associated with prophylactic antibiotic exposure in subfertile women undergoing IVF.
Collapse
Affiliation(s)
- A M Eskew
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, MO, USA
| | - M J Stout
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Washington University in St Louis, St Louis, MO, USA
| | - B S Bedrick
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, MO, USA
| | - J K Riley
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, MO, USA
| | - K R Omurtag
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, MO, USA
| | - P T Jimenez
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, MO, USA
| | - R R Odem
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, MO, USA
| | - V S Ratts
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, MO, USA
| | - S L Keller
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, MO, USA
| | - E S Jungheim
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Washington University in St Louis, St Louis, MO, USA
| | - K M Wylie
- Department of Pediatrics, Division of Infectious Diseases, Washington University in St Louis, St Louis, MO, USA.,McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| |
Collapse
|
15
|
Xie Y, Matsumoto H, Kennedy S, Newberry EP, Moritz W, DeBosch BJ, Moley KH, Rubin DC, Warner BW, Kau AL, Tarr PI, Wylie TN, Wylie KM, Davidson NO. Impaired Chylomicron Assembly Modifies Hepatic Metabolism Through Bile Acid-Dependent and Transmissible Microbial Adaptations. Hepatology 2019; 70:1168-1184. [PMID: 31004524 PMCID: PMC6783349 DOI: 10.1002/hep.30669] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/15/2019] [Indexed: 01/05/2023]
Abstract
The mechanisms by which alterations in intestinal bile acid (BA) metabolism improve systemic glucose tolerance and hepatic metabolic homeostasis are incompletely understood. We examined metabolic adaptations in mice with conditional intestinal deletion of the abetalipoproteinemia (ABL) gene microsomal triglyceride transfer protein (Mttp-IKO), which blocks chylomicron assembly and impairs intestinal lipid transport. Mttp-IKO mice exhibit improved hepatic glucose metabolism and augmented insulin signaling, without weight loss. These adaptations included decreased BA excretion, increased pool size, altered BA composition, and increased fibroblast growth factor 15 production. Mttp-IKO mice absorb fructose normally but are protected against dietary fructose-induced hepatic steatosis, without weight loss or changes in energy expenditure. In addition, Mttp-IKO mice exhibit altered cecal microbial communities, both at baseline and following fructose feeding, including increased abundance of Bacteroides and Lactobacillus genera. Transplantation of cecal microbiota from chow-fed Mttp-IKO mice into antibiotic-treated wild-type recipients conferred transmissible protection against fructose-induced hepatic steatosis in association with a bloom in Akkermansia and increased Clostridium XIVa genera, whose abundance was positively correlated with fecal coprostanol and total neutral sterol excretion in recipient mice. However, antibiotic-treated Mttp-IKO mice were still protected against fructose-induced hepatic steatosis, suggesting that changes in microbiota are not required for this phenotype. Nevertheless, we found increased abundance of fecal Akkermansia from two adult ABL subjects with MTTP mutations compared to their heterozygous parents and within the range noted in six healthy control subjects. Furthermore, Akkermansia abundance across all subjects was positively correlated with fecal coprostanol excretion. Conclusion: The findings collectively suggest multiple adaptive pathways of metabolic regulation following blocked chylomicron assembly, including shifts in BA signaling and altered microbial composition that confer a transmissible phenotype.
Collapse
Affiliation(s)
- Yan Xie
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hitoshi Matsumoto
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susan Kennedy
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Elizabeth P. Newberry
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - William Moritz
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brian J. DeBosch
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kelle H. Moley
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Deborah C. Rubin
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brad W. Warner
- Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew L. Kau
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Phillip I. Tarr
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Todd N. Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA,Department of McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kristine M. Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA,Department of McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicholas O. Davidson
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA,Lead contact
| |
Collapse
|
16
|
Cao S, Wylie KM, Wyczalkowski MA, Karpova A, Ley J, Sun S, Mashl RJ, Liang WW, Wang X, Johnson K, DiPersio JF, Gay H, Ratner L, Chen F, Adkins DR, Ding L. Dynamic host immune response in virus-associated cancers. Commun Biol 2019; 2:109. [PMID: 30911684 PMCID: PMC6430765 DOI: 10.1038/s42003-019-0352-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 02/07/2019] [Indexed: 02/06/2023] Open
Abstract
Viruses drive carcinogenesis in human cancers through diverse mechanisms that have not been fully elucidated but include promoting immune escape. Here we investigated associations between virus-positivity and immune pathway alteration for 2009 tumors across six virus-related cancer types. Analysis revealed that for 3 of 72 human papillomavirus (HPV)-positive head and neck squamous cell carcinoma (HNSC) the HPV genome integrated in immune checkpoint genes PD-L1 or PD-L2, driving elevated expression in the corresponding gene. In addition to the previously described upregulation of the PD-1 immunosuppressive pathway in Epstein-Barr virus (EBV)-positive stomach tumors, we also observed upregulation of the PD-1 pathway in cytomegalovirus (CMV)-positive tumors. Furthermore, we found signatures of T-cell and B-cell response in HPV-positive HNSC and EBV-positive stomach tumors and HPV-positive HNSC patients were associated with better survival when T-cell signals were detected. Our work reveals that viral infection may recruit immune effector cells, and upregulate PD-1 and CTLA-4 immunosuppressive pathways.
Collapse
Affiliation(s)
- Song Cao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110 USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108 USA
| | - Kristine M. Wylie
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108 USA
- Department of Pediatrics, Washington University in St. Louis, St. Louis, MO 63110 USA
| | - Matt A. Wyczalkowski
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110 USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108 USA
| | - Alla Karpova
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110 USA
| | - Jessica Ley
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110 USA
| | - Sam Sun
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110 USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108 USA
| | - R. Jay Mashl
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110 USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108 USA
| | - Wen-Wei Liang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110 USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108 USA
| | - Xiaowei Wang
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, MO 63110 USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63110 USA
| | - Kimberly Johnson
- Brown School Master of Public Health Program, Washington University in St. Louis, St. Louis, MO 63130 USA
| | - John F. DiPersio
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110 USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110 USA
| | - Hiram Gay
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110 USA
| | - Lee Ratner
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110 USA
| | - Feng Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110 USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110 USA
| | - Douglas R. Adkins
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110 USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110 USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110 USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108 USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110 USA
- Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110 USA
| |
Collapse
|
17
|
Wylie KM, Wylie TN, Minx PJ, Rosen DA. 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. [PMID: 30800643 PMCID: PMC6375827 DOI: 10.3389/fcimb.2019.00014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/17/2019] [Indexed: 01/19/2023] Open
Abstract
Klebsiella pneumoniae is an important uropathogen that increasingly harbors broad-spectrum antibiotic resistance determinants. Evidence suggests that some same-strain recurrences in women with frequent urinary tract infections (UTIs) may emanate from a persistent intravesicular reservoir. Our objective was to analyze K. pneumoniae isolates collected over weeks from multiple body sites of a single patient with recurrent UTI in order to track ordered strain progression across body sites, as has been employed across patients in outbreak settings. Whole-genome sequencing of 26 K. pneumoniae isolates was performed utilizing the Illumina platform. PacBio sequencing was used to create a refined reference genome of the original urinary isolate (TOP52). Sequence variation was evaluated by comparing the 26 isolate sequences to the reference genome sequence. Whole-genome sequencing of the K. pneumoniae isolates from six different body sites of this patient with recurrent UTI demonstrated 100% chromosomal sequence identity of the isolates, with only a small P2 plasmid deletion in a minority of isolates. No single nucleotide variants were detected. The complete absence of single-nucleotide variants from 26 K. pneumoniae isolates from multiple body sites collected over weeks from a patient with recurrent UTI suggests that, unlike in an outbreak situation with strains collected from numerous patients, other methods are necessary to discern strain progression within a single host over a relatively short time frame.
Collapse
Affiliation(s)
- Kristine M Wylie
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, United States
| | - Todd N Wylie
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, United States.,Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States
| | - Patrick J Minx
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, United States
| | - David A Rosen
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States
| |
Collapse
|
18
|
Wylie KM, Blankenship SA, Tuuli MG, Macones GA, Stout MJ. Evaluation of patient- versus provider-collected vaginal swabs for microbiome analysis during pregnancy. BMC Res Notes 2018; 11:706. [PMID: 30290831 PMCID: PMC6173906 DOI: 10.1186/s13104-018-3809-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/27/2018] [Indexed: 11/10/2022] Open
Abstract
Objective We aimed to evaluate if patient- and provider-collected vaginal swabs in pregnant women reflect similar bacterial community characteristics. Pregnant patients performed a self-collected vaginal swab, then underwent a provider-collected swab via speculum exam. DNA pyrosequencing of the 16S rRNA gene V1V3 and V3V5 variable regions was performed. Relative abundance of taxa, alpha diversity, and beta diversity of patient- and provider-collected swabs were compared. Results Ninety-four vaginal swabs from 47 women were analyzed. On non-metric multi-dimensional scaling plots, paired patient- and provider-collected swabs clustered closely. The median Pearson correlation coefficient was 0.993 (interquartile range 0.951–0.999) for V1V3 and 0.987 (interquartile range 0.902–0.999) for V3V5. Among paired V1V3 and V3V5 sequences, 83.0% and 73.9% showed strong Pearson correlation (> 0.9), respectively, between patient- and provider-collected swabs; V1V3 and V3V5 sequences with weaker Pearson correlation (< 0.9) had correlation coefficients 0.57–0.89 and 0.49–0.89, respectively. No taxa were preferentially detected by sampling method, with relative abundance of taxa highly conserved. No significant difference in Shannon diversity for V1V3 (p = 0.22) and V3V5 (p = 0.11) sequences among paired samples was seen. We demonstrate that bacterial communities defined from patient- and provider-collected vaginal swabs in pregnant women are similar, validating utilization of patient-collected swabs for vaginal bacterial microbiome sampling during pregnancy.
Collapse
Affiliation(s)
- Kristine M Wylie
- Department of Pediatrics, Washington University School in St. Louis School of Medicine, St. Louis, MO, USA.,The McDonnell Genome Institute, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Stephanie A Blankenship
- Department of Obstetrics and Gynecology, Washington University in St. Louis School of Medicine, 660 S. Euclid, Box 8064, St. Louis, MO, 63110, USA
| | - Methodius G Tuuli
- Department of Obstetrics and Gynecology, Washington University in St. Louis School of Medicine, 660 S. Euclid, Box 8064, St. Louis, MO, 63110, USA
| | - George A Macones
- Department of Obstetrics and Gynecology, Washington University in St. Louis School of Medicine, 660 S. Euclid, Box 8064, St. Louis, MO, 63110, USA
| | - Molly J Stout
- Department of Obstetrics and Gynecology, Washington University in St. Louis School of Medicine, 660 S. Euclid, Box 8064, St. Louis, MO, 63110, USA.
| |
Collapse
|
19
|
Wyczalkowski MA, Wylie KM, Cao S, McLellan MD, Flynn J, Huang M, Ye K, Fan X, Chen K, Wendl MC, Ding L. BreakPoint Surveyor: a pipeline for structural variant visualization. Bioinformatics 2018; 33:3121-3122. [PMID: 28582538 DOI: 10.1093/bioinformatics/btx362] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 06/01/2017] [Indexed: 11/14/2022] Open
Abstract
Summary BreakPoint Surveyor (BPS) is a computational pipeline for the discovery, characterization, and visualization of complex genomic rearrangements, such as viral genome integration, in paired-end sequence data. BPS facilitates interpretation of structural variants by merging structural variant breakpoint predictions, gene exon structure, read depth, and RNA-sequencing expression into a single comprehensive figure. Availability and implementation Source code and sample data freely available for download at https://github.com/ding-lab/BreakPointSurveyor, distributed under the GNU GPLv3 license, implemented in R, Python and BASH scripts, and supported on Unix/Linux/OS X operating systems. Contact lding@wustl.edu. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
| | | | - Song Cao
- Oncology Division, Department of Medicine.,McDonnell Genome Institute
| | | | | | - Mo Huang
- Oncology Division, Department of Medicine.,McDonnell Genome Institute
| | - Kai Ye
- McDonnell Genome Institute
| | - Xian Fan
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA
| | - Michael C Wendl
- Oncology Division, Department of Medicine.,McDonnell Genome Institute.,Department of Genetics.,Department of Mathematics, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Li Ding
- Oncology Division, Department of Medicine.,McDonnell Genome Institute.,Department of Genetics.,Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| |
Collapse
|
20
|
Williams GD, Townsend D, Wylie KM, Kim PJ, Amarasinghe GK, Kutluay SB, Boon ACM. Nucleotide resolution mapping of influenza A virus nucleoprotein-RNA interactions reveals RNA features required for replication. Nat Commun 2018; 9:465. [PMID: 29386621 PMCID: PMC5792457 DOI: 10.1038/s41467-018-02886-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 01/04/2018] [Indexed: 02/03/2023] Open
Abstract
Influenza A virus nucleoprotein (NP) association with viral RNA (vRNA) is essential for packaging, but the pattern of NP binding to vRNA is unclear. Here we applied photoactivatable ribonucleoside enhanced cross-linking and immunoprecipitation (PAR-CLIP) to assess the native-state of NP-vRNA interactions in infected human cells. NP binds short fragments of RNA (~12 nucleotides) non-uniformly and without apparent sequence specificity. Moreover, NP binding is reduced at specific locations within the viral genome, including regions previously identified as required for viral genome segment packaging. Synonymous mutations designed to alter the predicted RNA structures in these low-NP-binding regions impact genome packaging and result in virus attenuation, whereas control mutations or mutagenesis of NP-bound regions have no effect. Finally, we demonstrate that the sequence conservation of low-NP-binding regions is required in multiple genome segments for propagation of diverse mammalian and avian IAV in host cells.
Collapse
Affiliation(s)
- Graham D Williams
- Department of Medicine at Washington University School of Medicine, St Louis, MO, 63110, USA
- Department of Molecular Microbiology at Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Dana Townsend
- Department of Molecular Microbiology at Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Kristine M Wylie
- Department of Pediatrics at Washington University School of Medicine, St Louis, MO, 63110, USA
- The McDonnell Genome Institute at Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Preston J Kim
- Department of Pathology and Immunology at Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology at Washington University School of Medicine, St Louis, MO, 63110, USA
- Department of Biochemistry and Biophysics at Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Sebla B Kutluay
- Department of Molecular Microbiology at Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Adrianus C M Boon
- Department of Medicine at Washington University School of Medicine, St Louis, MO, 63110, USA.
- Department of Molecular Microbiology at Washington University School of Medicine, St Louis, MO, 63110, USA.
- Department of Pathology and Immunology at Washington University School of Medicine, St Louis, MO, 63110, USA.
| |
Collapse
|
21
|
|
22
|
Wylie KM, Stanley KM, TeKippe EM, Mihindukulasuriya K, Storch GA. Resurgence of Rotavirus Genotype G12 in St. Louis During the 2014-2015 Rotavirus Season. J Pediatric Infect Dis Soc 2017; 6:346-351. [PMID: 27988496 PMCID: PMC5907883 DOI: 10.1093/jpids/piw065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/27/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND Rotaviruses are a leading cause of gastroenteritis. Rotavirus vaccination has dramatically reduced rotavirus occurrence; however, we have noticed mild to moderate recurrences in the St. Louis area in alternate years. In 2013, we found rotavirus genotype G12 to be the dominant strain in the St. Louis region. In this study, we again determined the distribution of genotypes and ascertained vaccine history in patients infected with rotavirus G12 during the 2014-15 season. METHODS Samples submitted to the St. Louis Children's Hospital Microbiology Laboratory were tested for rotavirus using an antigen assay. We determined the VP7 genotype using amplicon sequence analysis. We determined genome sequences using high-throughput sequencing. We evaluated rotavirus immunization records when available. RESULTS Of 30 typed viruses from 2014-15, 29 were G12 (97%). Whole-genome sequencing revealed few changes from G12 viruses analyzed in 2012-13. VP4 and VP7 sequences were >99% identical to previously sequenced G12 strains from St. Louis, and immune epitopes were conserved. Vaccination histories were available from 17 patients. Of these, 4 had been vaccinated, 3 had received incomplete vaccination or had a vaccine history that could not be confirmed, and 10 had not been vaccinated. CONCLUSIONS G12 re-emerged as the predominant rotavirus genotype in 2014-15, comprising a higher percentage of cases than in 2012-13. The majority of patients with G12 and available vaccination histories were unvaccinated. There was no genomic evidence to indicate that the G12 strains in St. Louis had evolved to escape vaccine protection. Our work emphasizes the need for continued surveillance.
Collapse
Affiliation(s)
- Kristine M Wylie
- Department of Pediatrics,The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | | | - Erin McElvania TeKippe
- Departments of Pathology and Pediatrics, University of Texas Southwestern, Dallas, Texas
| | | | - Gregory A Storch
- Department of Pediatrics,Correspondence: G. A. Storch, MD, The Department of Pediatrics, Washington University School of Medicine Campus Box 8208, 660 S. Euclid Avenue, St. Louis, MO 63110 ()
| |
Collapse
|
23
|
Frayman KB, Armstrong DS, Carzino R, Ferkol TW, Grimwood K, Storch GA, Teo SM, Wylie KM, Ranganathan SC. The lower airway microbiota in early cystic fibrosis lung disease: a longitudinal analysis. Thorax 2017; 72:1104-1112. [PMID: 28280235 DOI: 10.1136/thoraxjnl-2016-209279] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 01/19/2017] [Accepted: 02/02/2017] [Indexed: 11/03/2022]
Abstract
RATIONALE In infants and young children with cystic fibrosis, lower airway infection and inflammation are associated with adverse respiratory outcomes. However, the role of lower airway microbiota in the pathogenesis of early cystic fibrosis lung disease remains uncertain. OBJECTIVES To assess the development of the lower airway microbiota over time in infants and young children with cystic fibrosis, and to explore its association with airway inflammation and pulmonary function at age 6 years. METHODS Serial, semi-annual bronchoscopies and bronchoalveolar lavage (BAL) procedures were performed in infants newly diagnosed with cystic fibrosis following newborn screening. Quantitative microbiological cultures and inflammatory marker (interleukin 8 and neutrophil elastase) measurements were undertaken contemporaneously. 16S ribosomal RNA gene sequencing was conducted on stored BAL samples. Spirometry results recorded at 6 years of age were extracted from medical records. MEASUREMENTS AND MAIN RESULTS Ninety-five BAL samples provided 16S ribosomal RNA gene data. These were collected from 48 subjects aged 1.2-78.3 months, including longitudinal samples from 27 subjects and 13 before age 6 months. The lower airway microbiota varied, but diversity decreased with advancing age. Detection of recognised cystic fibrosis bacterial pathogens was associated with reduced microbial diversity and greater lower airway inflammation. There was no association between the lower airway microbiota and pulmonary function at age 6 years. CONCLUSIONS In infants with cystic fibrosis, the lower airway microbiota is dynamic. Dominance of the microbiota by recognised cystic fibrosis bacterial pathogens is associated with increased lower airway inflammation, however early microbial diversity is not associated with pulmonary function at 6 years of age.
Collapse
Affiliation(s)
- Katherine B Frayman
- Department of Respiratory and Sleep Medicine, Royal Children's Hospital, Parkville, Victoria, Australia.,Respiratory Diseases Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - David S Armstrong
- Department of Respiratory Medicine, Monash Children's Hospital, Clayton, Victoria, Australia.,Department of Paediatrics, Monash University, Clayton, Victoria, Australia
| | - Rosemary Carzino
- Department of Respiratory and Sleep Medicine, Royal Children's Hospital, Parkville, Victoria, Australia.,Respiratory Diseases Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Thomas W Ferkol
- Department of Pediatrics, Washington University, St Louis, Missouri, USA.,Department of Cell Biology and Physiology, Washington University, St Louis, Missouri, USA
| | - Keith Grimwood
- Menzies Health Institute Queensland, Griffith University and Gold Coast Health, Gold Coast, Queensland, Australia
| | - Gregory A Storch
- Department of Pediatrics, Washington University, St Louis, Missouri, USA
| | - Shu Mei Teo
- Centre for System Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Kristine M Wylie
- Department of Pediatrics, Washington University, St Louis, Missouri, USA.,McDonnell Genome Institute, Washington University, St Louis, Missouri, USA
| | - Sarath C Ranganathan
- Department of Respiratory and Sleep Medicine, Royal Children's Hospital, Parkville, Victoria, Australia.,Respiratory Diseases Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| |
Collapse
|
24
|
Rashidi A, Vij KR, Buller RS, Wylie KM, Storch GA, DiPersio JF. Tissue polymerase chain reaction for the diagnosis of cytomegalovirus disease after allogeneic hematopoietic cell transplantation. Am J Hematol 2017; 92:E19-E20. [PMID: 27859620 DOI: 10.1002/ajh.24609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 11/14/2016] [Indexed: 01/28/2023]
Affiliation(s)
- Armin Rashidi
- Bone Marrow Transplantation and Leukemia Section, Division of Oncology; Washington University School of Medicine; St. Louis Missouri
| | - Kiran R. Vij
- Bone Marrow Transplantation and Leukemia Section, Division of Oncology; Washington University School of Medicine; St. Louis Missouri
- Department of Pathology and Immunology; Washington University School of Medicine; St. Louis Missouri
| | - Richard S. Buller
- Department of Pediatrics; Washington University School of Medicine; St. Louis Missouri
| | - Kristine M. Wylie
- Department of Pediatrics; Washington University School of Medicine; St. Louis Missouri
- The McDonnell Genome Institute, Washington University School of Medicine; St. Louis Missouri
| | - Gregory A. Storch
- Department of Pediatrics; Washington University School of Medicine; St. Louis Missouri
| | - John F. DiPersio
- Bone Marrow Transplantation and Leukemia Section, Division of Oncology; Washington University School of Medicine; St. Louis Missouri
| |
Collapse
|
25
|
Ordiz MI, Stephenson K, Agapova S, Wylie KM, Maleta K, Martin J, Trehan I, Tarr PI, Manary MJ. Environmental Enteric Dysfunction and the Fecal Microbiota in Malawian Children. Am J Trop Med Hyg 2016; 96:473-476. [PMID: 27956653 DOI: 10.4269/ajtmh.16-0617] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 10/23/2016] [Indexed: 01/18/2023] Open
Abstract
Environmental enteric dysfunction (EED) is often measured with a dual sugar absorption test and implicated as a causative factor in childhood stunting. Disturbances in the gut microbiota are hypothesized to be a mechanism by which EED is exacerbated, although this supposition lacks support. We performed 16S ribosomal RNA gene sequencing of fecal samples from 81 rural Malawian children with varying degrees of EED to determine which bacterial taxa were associated with EED. At the phyla level, Proteobacteria abundance is reduced with severe EED. Among bacterial genera, Megasphaera, Mitsuokella, and Sutterella were higher in EED and Succinivibrio, Klebsiella, and Clostridium_XI were lower in EED. Bacterial diversity did not vary with the extent of EED. Though EED is a condition that is typically believed to affect the proximal small bowel, and our focus was on stool, our data do suggest that there are intraluminal microbial differences that reflect, or plausibly lead to, EED.
Collapse
Affiliation(s)
- M Isabel Ordiz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Kevin Stephenson
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Sophia Agapova
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Kristine M Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri.,The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Ken Maleta
- Department of Community Health, College of Medicine, University of Malawi, Malawi, Africa
| | - John Martin
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Indi Trehan
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri.,College of Medicine, University of Malawi, Malawi, Africa
| | - Phillip I Tarr
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Mark J Manary
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri. .,School of Public Health and Family Medicine, University of Malawi, Blantyre, Malawi.,United States Department of Agriculture/Agricultural Research Service Childrens Nutrition Research Center, Houston, Texas
| |
Collapse
|
26
|
Farrell JJ, Ikladios O, Wylie KM, O'Rourke LM, Lowery KS, Cromwell JS, Wylie TN, Melendez ELV, Makhoul Y, Sampath R, Bonomo RA, Storch GA. Enterovirus D68-associated acute respiratory distress syndrome in adult, United States, 2014. Emerg Infect Dis 2016; 21:914-6. [PMID: 25897542 PMCID: PMC4412249 DOI: 10.3201/eid2105.142033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
|
27
|
Rowley AH, Wylie KM, Kim KYA, Pink AJ, Yang A, Reindel R, Baker SC, Shulman ST, Orenstein JM, Lingen MW, Weinstock GM, Wylie TN. The transcriptional profile of coronary arteritis in Kawasaki disease. BMC Genomics 2015; 16:1076. [PMID: 26679344 PMCID: PMC4683744 DOI: 10.1186/s12864-015-2323-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 12/15/2015] [Indexed: 12/31/2022] Open
Abstract
Background Kawasaki Disease (KD) can cause potentially life-threatening coronary arteritis in young children, and has a likely infectious etiology. Transcriptome profiling is a powerful approach to investigate gene expression in diseased tissues. RNA sequencing of KD coronary arteries could elucidate the etiology and the host response, with the potential to improve KD diagnosis and/or treatment. Methods Deep RNA sequencing was performed on KD (n = 8) and childhood control (n = 7) coronary artery tissues, revealing 1074 differentially expressed mRNAs. Non-human RNA sequences were subjected to a microbial discovery bioinformatics platform, and microbial sequences were analyzed by Metastats for association with KD. Results T lymphocyte activation, antigen presentation, immunoglobulin production, and type I interferon response were significantly upregulated in KD arteritis, while the tumor necrosis factor α pathway was not differentially expressed. Transcripts from known infectious agents were not specifically associated with KD coronary arteritis. Conclusions The immune transcriptional profile in KD coronary artery tissues has features of an antiviral immune response such as activated cytotoxic T lymphocyte and type I interferon-induced gene upregulation. These results provide new insights into the pathogenesis of KD arteritis that can guide selection of new immunomodulatory therapies for high-risk KD patients, and provide direction for future etiologic studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2323-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Anne H Rowley
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, 310 E Superior Street, Morton 4-685B, Chicago, IL, 60611, USA. .,Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. .,Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA.
| | - Kristine M Wylie
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO, USA.,The McDonnell Genome Institute at Washington University, Washington University School of Medicine, Saint Louis, MO, USA
| | - Kwang-Youn A Kim
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Adam J Pink
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, 310 E Superior Street, Morton 4-685B, Chicago, IL, 60611, USA
| | - Amy Yang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Rebecca Reindel
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, 310 E Superior Street, Morton 4-685B, Chicago, IL, 60611, USA.,Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA.,Present address: AbbVie, Inc, North Chicago, IL, USA
| | - Susan C Baker
- Department of Microbiology/Immunology, Loyola University Stritch School of Medicine, Maywood, IL, USA
| | - Stanford T Shulman
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, 310 E Superior Street, Morton 4-685B, Chicago, IL, 60611, USA.,Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Jan M Orenstein
- Department of Pathology, George Washington University School of Medicine, Washington, DC, USA
| | - Mark W Lingen
- Department of Pathology, University of Chicago Pritzker School of Medicine, Chicago, IL, USA
| | - George M Weinstock
- The McDonnell Genome Institute at Washington University, Washington University School of Medicine, Saint Louis, MO, USA.,Present address: The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Todd N Wylie
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO, USA.,The McDonnell Genome Institute at Washington University, Washington University School of Medicine, Saint Louis, MO, USA
| |
Collapse
|
28
|
Wylie KM, Weinstock GM, Storch GA. Emergence of Rotavirus G12P[8] in St. Louis During the 2012-2013 Rotavirus Season. J Pediatric Infect Dis Soc 2015; 4:e84-9. [PMID: 26513823 PMCID: PMC4681384 DOI: 10.1093/jpids/piu090] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 08/18/2014] [Indexed: 01/13/2023]
Abstract
BACKGROUND We observed an increase in the number of rotavirus cases in the St. Louis area during the 2012-2013 rotavirus season compared with recent seasons. We aimed to determine whether the rotavirus cases during the 2012-2013 rotavirus season were of types not included in licensed vaccines. METHODS Microbiology laboratories of 3 children's hospitals in St. Louis provided samples that were positive using rapid antigen tests from 2010 to 2013. The majority of samples were from St. Louis Children's Hospital. We determined rotavirus genotypes by polymerase chain reaction tests and further characterized a subset of viruses by genome sequencing and comparative sequence analysis. RESULTS Eighty-six percent (24 of 28) of typed viruses analyzed from the 2012-2013 rotavirus season were G12. We performed whole genome sequencing on 8 G12 viruses, all of which were VP4 type P[8]. The sequenced viruses showed differences from vaccine strains in major antigenic epitopes on the VP7 protein, but most epitopes on VP4 were conserved. Rotavirus vaccine histories were available for 11 G12 cases, of whom 10 had not been vaccinated. CONCLUSIONS G12 was a dominant community-wide genotype in 2013. Most of the G12 cases for whom vaccine histories were available had not received rotavirus vaccine. The experience demonstrates the potential for rapid shifts in rotavirus genotype distribution and underscores the need for vigilant surveillance to detect unusual genotypes that might escape from vaccine protection.
Collapse
Affiliation(s)
- Kristine M. Wylie
- The Department of Pediatrics,The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - George M. Weinstock
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | | |
Collapse
|
29
|
Abstract
Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ∼1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications.
Collapse
Affiliation(s)
- Todd N Wylie
- The Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri 63110, USA; McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Kristine M Wylie
- The Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri 63110, USA; McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Brandi N Herter
- The Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Gregory A Storch
- The Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| |
Collapse
|
30
|
Wylie KM, Wylie TN, Orvedahl A, Buller RS, Herter BN, Magrini V, Wilson RK, Storch GA. Genome sequence of enterovirus D68 from St. Louis, Missouri, USA. Emerg Infect Dis 2015; 21:184-6. [PMID: 25532062 PMCID: PMC4285240 DOI: 10.3201/eid2101.141605] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
|
31
|
Wylie KM, Mihindukulasuriya KA, Zhou Y, Sodergren E, Storch GA, Weinstock GM. Metagenomic analysis of double-stranded DNA viruses in healthy adults. BMC Biol 2014; 12:71. [PMID: 25212266 PMCID: PMC4177058 DOI: 10.1186/s12915-014-0071-7] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The Human Microbiome Project (HMP) was undertaken with the goal of defining microbial communities in and on the bodies of healthy individuals using high-throughput, metagenomic sequencing analysis. The viruses present in these microbial communities, the 'human virome', are an important aspect of the human microbiome that is particularly understudied in the absence of overt disease. We analyzed eukaryotic double-stranded DNA (dsDNA) viruses, together with dsDNA replicative intermediates of single-stranded DNA viruses, in metagenomic sequence data generated by the HMP. 706 samples from 102 subjects were studied, with each subject sampled at up to five major body habitats: nose, skin, mouth, vagina, and stool. Fifty-one individuals had samples taken at two or three time points 30 to 359 days apart from at least one of the body habitats. RESULTS We detected an average of 5.5 viral genera in each individual. At least 1 virus was detected in 92% of the individuals sampled. These viruses included herpesviruses, papillomaviruses, polyomaviruses, adenoviruses, anelloviruses, parvoviruses, and circoviruses. Each individual had a distinct viral profile, demonstrating the high interpersonal diversity of the virome. Some components of the virome were stable over time. CONCLUSIONS This study is the first to use high-throughput DNA sequencing to describe the diversity of eukaryotic dsDNA viruses in a large cohort of normal individuals who were sampled at multiple body sites. Our results show that the human virome is a complex component of the microbial flora. Some viruses establish long-term infections that may be associated with increased risk or possibly with protection from disease. A better understanding of the composition and dynamics of the virome may hold important keys to human health.
Collapse
|
32
|
Zhou Y, Mihindukulasuriya KA, Gao H, La Rosa PS, Wylie KM, Martin JC, Kota K, Shannon WD, Mitreva M, Sodergren E, Weinstock GM. Exploration of bacterial community classes in major human habitats. Genome Biol 2014; 15:R66. [PMID: 24887286 PMCID: PMC4073010 DOI: 10.1186/gb-2014-15-5-r66] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 05/07/2014] [Indexed: 01/28/2023] Open
Abstract
Background Determining bacterial abundance variation is the first step in understanding bacterial similarity between individuals. Categorization of bacterial communities into groups or community classes is the subsequent step in describing microbial distribution based on abundance patterns. Here, we present an analysis of the groupings of bacterial communities in stool, nasal, skin, vaginal and oral habitats in a healthy cohort of 236 subjects from the Human Microbiome Project. Results We identify distinct community group patterns in the anterior nares, four skin sites, and vagina at the genus level. We also confirm three enterotypes previously identified in stools. We identify two clusters with low silhouette values in most oral sites, in which bacterial communities are more homogeneous. Subjects sharing a community class in one habitat do not necessarily share a community class in another, except in the three vaginal sites and the symmetric habitats of the left and right retroauricular creases. Demographic factors, including gender, age, and ethnicity, significantly influence community composition in several habitats. Community classes in the vagina, retroauricular crease and stool are stable over approximately 200 days. Conclusion The community composition, association of demographic factors with community classes, and demonstration of community stability deepen our understanding of the variability and dynamics of human microbiomes. This also has significant implications for experimental designs that seek microbial correlations with clinical phenotypes.
Collapse
|
33
|
Abstract
High throughput, deep sequencing assays are powerful tools for gaining insights into virus-host interactions. Sequencing assays can discover novel viruses and describe the genomes of novel and known viruses. Genomic information can predict viral proteins that can be characterized, describe important genes in the host that control infections, and evaluate gene expression of viruses and hosts during infection. Sequencing can also describe variation and evolution of viruses during replication and transmission. This review recounts some of the major advances in the studies of virus-host interactions from the last two years, and discusses the uses of sequencing technologies relating to these studies.
Collapse
Affiliation(s)
- Kristine M Wylie
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St. Louis, MO 63108, United States.
| | | | | |
Collapse
|
34
|
Davis C, Kota K, Baldhandapani V, Gong W, Abubucker S, Becker E, Martin J, Wylie KM, Khetani R, Hudson ME, Weinstock GM, Mitreva M. mBLAST: Keeping up with the sequencing explosion for (meta)genome analysis. ACTA ACUST UNITED AC 2013; 4. [PMID: 26500804 DOI: 10.4172/2153-0602.1000135] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Recent advances in next-generation sequencing technologies require alignment algorithms and software that can keep pace with the heightened data production. Standard algorithms, especially protein similarity searches, represent significant bottlenecks in analysis pipelines. For metagenomic approaches in particular, it is now often necessary to search hundreds of millions of sequence reads against large databases. Here we describe mBLAST, an accelerated search algorithm for translated and/or protein alignments to large datasets based on the Basic Local Alignment Search Tool (BLAST) and retaining the high sensitivity of BLAST. The mBLAST algorithms achieve substantial speed up over the National Center for Biotechnology Information (NCBI) programs BLASTX, TBLASTX and BLASTP for large datasets, allowing analysis within reasonable timeframes on standard computer architectures. In this article, the impact of mBLAST is demonstrated with sequences originating from the microbiota of healthy humans from the Human Microbiome Project. mBLAST is designed as a plug-in replacement for BLAST for any study that involves short-read sequences and includes high-throughput analysis. The mBLAST software is freely available to academic users at www.multicorewareinc.com.
Collapse
Affiliation(s)
- Curtis Davis
- MultiCoreWare, St. Louis, MO 63108, United States
| | - Karthik Kota
- The Genome Institute, Washington University, St. Louis, MO 63108, United States
| | | | - Wei Gong
- MultiCoreWare, St. Louis, MO 63108, United States
| | - Sahar Abubucker
- The Genome Institute, Washington University, St. Louis, MO 63108, United States
| | - Eric Becker
- The Genome Institute, Washington University, St. Louis, MO 63108, United States
| | - John Martin
- The Genome Institute, Washington University, St. Louis, MO 63108, United States
| | - Kristine M Wylie
- The Genome Institute, Washington University, St. Louis, MO 63108, United States
| | - Radhika Khetani
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Matthew E Hudson
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - George M Weinstock
- The Genome Institute, Washington University, St. Louis, MO 63108, United States ; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, United States
| | - Makedonka Mitreva
- The Genome Institute, Washington University, St. Louis, MO 63108, United States ; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, United States ; Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63108, United States
| |
Collapse
|
35
|
Abstract
The human virome is the collection of all viruses that are found in or on humans, including both eukaryotic and prokaryotic viruses. Eukaryotic viruses clearly have important effects on human health, ranging from mild, self-limited acute or chronic infections to those with serious or fatal consequences. Prokaryotic viruses can also influence human health by affecting bacterial community structure and function. Therefore, definition of the virome is an important step toward understanding how microbes affect human health and disease. We review progress in virome analysis, which has been driven by advances in high-throughput, deep sequencing technology. Highlights from these studies include the association of viruses with clinical phenotypes and description of novel viruses that may be important pathogens. Together these studies indicate that analysis of the human virome is critical as we aim to understand how microbial communities influence human health and disease. Descriptions of the human virome will stimulate future work to understand how the virome affects long-term human health, immunity, and response to coinfections. Analysis of the virome ultimately may affect the treatment of patients with a variety of clinical syndromes.
Collapse
Affiliation(s)
- Kristine M Wylie
- The Genome Insititute, Washington University School of Medicine, St Louis, MO, USA
| | | | | |
Collapse
|
36
|
Fodor AA, DeSantis TZ, Wylie KM, Badger JH, Ye Y, Hepburn T, Hu P, Sodergren E, Liolios K, Huot-Creasy H, Birren BW, Earl AM. The "most wanted" taxa from the human microbiome for whole genome sequencing. PLoS One 2012; 7:e41294. [PMID: 22848458 PMCID: PMC3406062 DOI: 10.1371/journal.pone.0041294] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 06/19/2012] [Indexed: 11/24/2022] Open
Abstract
The goal of the Human Microbiome Project (HMP) is to generate a comprehensive catalog of human-associated microorganisms including reference genomes representing the most common species. Toward this goal, the HMP has characterized the microbial communities at 18 body habitats in a cohort of over 200 healthy volunteers using 16S rRNA gene (16S) sequencing and has generated nearly 1,000 reference genomes from human-associated microorganisms. To determine how well current reference genome collections capture the diversity observed among the healthy microbiome and to guide isolation and future sequencing of microbiome members, we compared the HMP's 16S data sets to several reference 16S collections to create a 'most wanted' list of taxa for sequencing. Our analysis revealed that the diversity of commonly occurring taxa within the HMP cohort microbiome is relatively modest, few novel taxa are represented by these OTUs and many common taxa among HMP volunteers recur across different populations of healthy humans. Taken together, these results suggest that it should be possible to perform whole-genome sequencing on a large fraction of the human microbiome, including the 'most wanted', and that these sequences should serve to support microbiome studies across multiple cohorts. Also, in stark contrast to other taxa, the 'most wanted' organisms are poorly represented among culture collections suggesting that novel culture- and single-cell-based methods will be required to isolate these organisms for sequencing.
Collapse
Affiliation(s)
- Anthony A. Fodor
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Todd Z. DeSantis
- Bioinformatics Department, Second Genome, Inc., San Bruno, California, United States of America
| | - Kristine M. Wylie
- Department of Genetics, The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jonathan H. Badger
- Microbial and Environmental Genomics Department. J. Craig Venter Institute, San Diego, California, United States of America
| | - Yuzhen Ye
- School of Informatics and Computing, Indiana University, Bloomington, Indiana, United States of America
| | - Theresa Hepburn
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Ping Hu
- Earth Science Division, Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Erica Sodergren
- Department of Genetics, The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Konstantinos Liolios
- Microbial Genomics and Metagenomics Program, Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Heather Huot-Creasy
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Bruce W. Birren
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Ashlee M. Earl
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| |
Collapse
|
37
|
Wylie KM, Truty RM, Sharpton TJ, Mihindukulasuriya KA, Zhou Y, Gao H, Sodergren E, Weinstock GM, Pollard KS. Novel bacterial taxa in the human microbiome. PLoS One 2012; 7:e35294. [PMID: 22719826 PMCID: PMC3374617 DOI: 10.1371/journal.pone.0035294] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 03/14/2012] [Indexed: 12/21/2022] Open
Abstract
The human gut harbors thousands of bacterial taxa. A profusion of metagenomic sequence data has been generated from human stool samples in the last few years, raising the question of whether more taxa remain to be identified. We assessed metagenomic data generated by the Human Microbiome Project Consortium to determine if novel taxa remain to be discovered in stool samples from healthy individuals. To do this, we established a rigorous bioinformatics pipeline that uses sequence data from multiple platforms (Illumina GAIIX and Roche 454 FLX Titanium) and approaches (whole-genome shotgun and 16S rDNA amplicons) to validate novel taxa. We applied this approach to stool samples from 11 healthy subjects collected as part of the Human Microbiome Project. We discovered several low-abundance, novel bacterial taxa, which span three major phyla in the bacterial tree of life. We determined that these taxa are present in a larger set of Human Microbiome Project subjects and are found in two sampling sites (Houston and St. Louis). We show that the number of false-positive novel sequences (primarily chimeric sequences) would have been two orders of magnitude higher than the true number of novel taxa without validation using multiple datasets, highlighting the importance of establishing rigorous standards for the identification of novel taxa in metagenomic data. The majority of novel sequences are related to the recently discovered genus Barnesiella, further encouraging efforts to characterize the members of this genus and to study their roles in the microbial communities of the gut. A better understanding of the effects of less-abundant bacteria is important as we seek to understand the complex gut microbiome in healthy individuals and link changes in the microbiome to disease.
Collapse
Affiliation(s)
- Kristine M. Wylie
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail: (KMW); (RMT)
| | - Rebecca M. Truty
- Gladstone Institutes, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (KMW); (RMT)
| | - Thomas J. Sharpton
- Gladstone Institutes, University of California San Francisco, San Francisco, California, United States of America
| | - Kathie A. Mihindukulasuriya
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Yanjiao Zhou
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Hongyu Gao
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Erica Sodergren
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - George M. Weinstock
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Katherine S. Pollard
- Gladstone Institutes, University of California San Francisco, San Francisco, California, United States of America
- Division of Biostatistics, Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| |
Collapse
|
38
|
Abstract
Astroviruses cause diarrhea, but it is not known whether they circulate in human plasma. Astrovirus MLB2 was recently discovered in diarrhea samples from children. We detected MLB2 in the plasma of a febrile child, which suggests that MLB2 has broader tropism than expected and disease potential beyond the gastrointestinal tract.
Collapse
Affiliation(s)
- Lori R Holtz
- Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | | | | | | | | | | | | | | |
Collapse
|
39
|
Cano-Monreal GL, Wylie KM, Cao F, Tavis JE, Morrison LA. Herpes simplex virus 2 UL13 protein kinase disrupts nuclear lamins. Virology 2009; 392:137-47. [PMID: 19640559 PMCID: PMC2769575 DOI: 10.1016/j.virol.2009.06.051] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 06/16/2009] [Accepted: 06/30/2009] [Indexed: 02/05/2023]
Abstract
Herpesviruses must cross the inner nuclear membrane and underlying lamina to exit the nucleus. HSV-1 US3 and PKC can phosphorylate lamins and induce their dispersion but do not elicit all of the phosphorylated lamin species produced during infection. UL13 is a serine threonine protein kinase conserved among many herpesviruses. HSV-1 UL13 phosphorylates US3 and thereby controls UL31 and UL34 nuclear rim localization, indicating a role in nuclear egress. Here, we report that HSV-2 UL13 alone induced conformational changes in lamins A and C and redistributed lamin B1 from the nuclear rim to intranuclear granular structures. HSV-2 UL13 directly phosphorylated lamins A, C, and B1 in vitro, and the lamin A1 tail domain. HSV-2 infection recapitulated the lamin alterations seen upon expression of UL13 alone, and other alterations were also observed, indicating that additional viral and/or cellular proteins cooperate with UL13 to alter lamins during HSV-2 infection to allow nuclear egress.
Collapse
Affiliation(s)
| | - Kristine M. Wylie
- Department of Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO 63104, United States
| | - Feng Cao
- Department of Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO 63104, United States
| | - John E. Tavis
- Department of Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO 63104, United States
| | - Lynda A. Morrison
- Department of Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO 63104, United States
| |
Collapse
|