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Salazar-Hamm PS, Johnson WL, Nofchissey RA, Salazar JR, Gonzalez P, Goodfellow SM, Dunnum JL, Bradfute SB, Armién B, Cook JA, Domman DB, Dinwiddie DL. Choclo virus (CHOV) recovered from deep metatranscriptomics of archived frozen tissues in natural history biorepositories. PLoS Negl Trop Dis 2024; 18:e0011672. [PMID: 38215158 PMCID: PMC10810438 DOI: 10.1371/journal.pntd.0011672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/25/2024] [Accepted: 01/03/2024] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Hantaviruses are negative-stranded RNA viruses that can sometimes cause severe disease in humans; however, they are maintained in mammalian host populations without causing harm. In Panama, sigmodontine rodents serve as hosts to transmissible hantaviruses. Due to natural and anthropogenic forces, these rodent populations are having increased contact with humans. METHODS We extracted RNA and performed Illumina deep metatranscriptomic sequencing on Orthohantavirus seropositive museum tissues from rodents. We acquired sequence reads mapping to Choclo virus (CHOV, Orthohantavirus chocloense) from heart and kidney tissue of a two-decade old frozen museum sample from a Costa Rican pygmy rice rat (Oligoryzomys costaricensis) collected in Panama. Reads mapped to the CHOV reference were assembled and then validated by visualization of the mapped reads against the assembly. RESULTS We recovered a 91% complete consensus sequence from a reference-guided assembly to CHOV with an average of 16X coverage. The S and M segments used in our phylogenetic analyses were nearly complete (98% and 99%, respectively). There were 1,199 ambiguous base calls of which 93% were present in the L segment. Our assembled genome varied 1.1% from the CHOV reference sequence resulting in eight nonsynonymous mutations. Further analysis of all publicly available partial S segment sequences support a clear relationship between CHOV clinical cases and O. costaricensis acquired strains. CONCLUSIONS Viruses occurring at extremely low abundances can be recovered from deep metatranscriptomics of archival tissues housed in research natural history museum biorepositories. Our efforts resulted in the second CHOV genome publicly available. This genomic data is important for future surveillance and diagnostic tools as well as understanding the evolution and pathogenicity of CHOV.
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Affiliation(s)
- Paris S. Salazar-Hamm
- Clinical and Translational Science Center, University of New Mexico, Albuquerque, New Mexico, United States of America
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - William L. Johnson
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Robert A. Nofchissey
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Jacqueline R. Salazar
- Department of Research in Emerging and Zoonotic Infectious Diseases, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Publio Gonzalez
- Department of Research in Emerging and Zoonotic Infectious Diseases, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Samuel M. Goodfellow
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Jonathan L. Dunnum
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Steven B. Bradfute
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Blas Armién
- Department of Research in Emerging and Zoonotic Infectious Diseases, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Sistema Nacional de Investigación (SNI), Secretaria Nacional de Ciencia, Tecnología e Innovacion (SENACYT), Panama City, Panama
| | - Joseph A. Cook
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Daryl B. Domman
- Clinical and Translational Science Center, University of New Mexico, Albuquerque, New Mexico, United States of America
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Darrell L. Dinwiddie
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
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Daly GT, Pastukh VM, Tan YB, Francis CM, Aggen CZ, Groark SC, Edwards C, Mulekar MS, Hamo M, Simmons JD, Kutcher ME, Hartsell EM, Dinwiddie DL, Turpin ZM, Bass HW, Roberts JT, Gillespie MN, Langley RJ. Novel attributes of cell-free plasma mitochondrial DNA in traumatic injury. Clin Transl Med 2022; 12:e1055. [PMID: 36245326 PMCID: PMC9574491 DOI: 10.1002/ctm2.1055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/22/2022] [Accepted: 09/29/2022] [Indexed: 01/28/2023] Open
Affiliation(s)
- Grant T. Daly
- Department of PharmacologyUniversity of South Alabama College of MedicineMobileAlabamaUSA
| | - Viktor M. Pastukh
- Department of PharmacologyUniversity of South Alabama College of MedicineMobileAlabamaUSA
| | - Yong B. Tan
- Department of SurgeryUniversity of South Alabama Colleges of MedicineMobileAlabamaUSA
| | - C. Michael Francis
- Department of Physiology and Cell BiologyUniversity of South Alabama College of MedicineMobileAlabamaUSA
| | - C. Zack Aggen
- Department of PharmacologyUniversity of South Alabama College of MedicineMobileAlabamaUSA
| | - S. Chris Groark
- Department of PharmacologyUniversity of South Alabama College of MedicineMobileAlabamaUSA
| | - Carson Edwards
- Department of PharmacologyUniversity of South Alabama College of MedicineMobileAlabamaUSA
| | - Madhuri S. Mulekar
- Department of Mathematics and StatisticsUniversity of South Alabama Colleges of Medicine and Arts and SciencesMobileAlabamaUSA
| | - Mohammad Hamo
- Department of PharmacologyUniversity of South Alabama College of MedicineMobileAlabamaUSA
| | - Jon D. Simmons
- Department of SurgeryUniversity of South Alabama Colleges of MedicineMobileAlabamaUSA
| | - Matthew E. Kutcher
- Department of SurgeryUniversity of Mississippi School of MedicineJacksonMississippiUSA
| | - Emily M. Hartsell
- Department of PharmacologyUniversity of South Alabama College of MedicineMobileAlabamaUSA
| | - Darrell L. Dinwiddie
- Department of PediatricsUniversity of New Mexico School of MedicineAlbuquerqueNew MexicoUSA
| | - Zachary M. Turpin
- Department of Biological Science, College of Arts and SciencesFlorida State UniversityTallahasseeFloridaUSA
| | - Hank W. Bass
- Department of Biological Science, College of Arts and SciencesFlorida State UniversityTallahasseeFloridaUSA
| | - Justin T. Roberts
- Department of PharmacologyUniversity of South Alabama College of MedicineMobileAlabamaUSA
| | - Mark N. Gillespie
- Department of PharmacologyUniversity of South Alabama College of MedicineMobileAlabamaUSA
| | - Raymond J. Langley
- Department of PharmacologyUniversity of South Alabama College of MedicineMobileAlabamaUSA
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3
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Dinwiddie DL, Kaukis N, Pham S, Hardin O, Stoner AN, Kincaid JC, Caid K, Kirkpatrick C, Pomeroy K, Putt C, Schwalm KC, Thompson TM, Storm E, Perry TT, Kennedy JL. Viral infection and allergy status impact severity of asthma symptoms in children with asthma exacerbations. Ann Allergy Asthma Immunol 2022; 129:319-326.e3. [PMID: 35750292 PMCID: PMC10091837 DOI: 10.1016/j.anai.2022.06.017] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND While viral infection is known to be associated with asthma exacerbations, prior research has not identified reliable predictors of acute symptom severity in virus-related asthma exacerbations (VRAE). OBJECTIVE To determine the effect of asthma control and viral infection on the severity of current illness and evaluate biomarkers related to acute symptoms during asthma exacerbations. METHODS We prospectively enrolled 120 children with physician diagnosed asthma and current wheezing who presented to Arkansas Children's Hospital Emergency Department. The Asthma Control Test (ACT) stratified controlled (ACT>19) and uncontrolled (ACT≤19) asthma, while Pediatric Respiratory Symptoms (PRS) scores assessed symptoms. Nasopharyngeal swabs were obtained for viral analysis, and inflammatory mediators were evaluated by nasal filter paper and Luminex assays. RESULTS There were 33 controlled and 87 uncontrolled asthmatics. In uncontrolled asthmatics, 77% were infected with viruses during VRAE compared to 58% of WC. Uncontrolled subjects with VRAE demonstrated more acute symptoms compared to controlled with VRAE or uncontrolled without a virus. Uncontrolled with VRAE and allergy had the highest acute symptom scores (3.363 point PRS; p=0.041). Asthmatics with higher symptom scores had more periostin (p=0.028). CONCLUSION Detection of respiratory viruses is frequent in uncontrolled asthmatics. Uncontrolled subjects with viruses have more acute symptoms during exacerbations, especially in those with allergy. Periostin was highest in subjects with the most acute symptoms, regardless of control status. Taken together, these data imply synergy between viral infection and allergy in subjects with uncontrolled asthma when considering acute asthma symptoms and nasal inflammation during an exacerbation of asthma.
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Affiliation(s)
- Darrell L Dinwiddie
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; Clinical Translational Sciences Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Nicholas Kaukis
- Department of Biostatistics, University of Arkansas for Medical Sciences
| | - Sarah Pham
- Department of Pediatrics, Division of Allergy and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Olga Hardin
- Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Ashley N Stoner
- Department of Pediatrics, Division of Allergy and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR
| | - John C Kincaid
- Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Katherine Caid
- Department of Pediatrics, Division of Allergy and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR
| | | | - Kelsi Pomeroy
- Arkansas Children's Research Institute, Little Rock, AR
| | - Claire Putt
- Department of Pediatrics, Division of Allergy and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Kurt C Schwalm
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Tonya M Thompson
- Department of Emergency Medicine, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Elizabeth Storm
- Department of Emergency Medicine, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Tamara T Perry
- Department of Pediatrics, Division of Allergy and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR; Arkansas Children's Research Institute, Little Rock, AR
| | - Joshua L Kennedy
- Department of Pediatrics, Division of Allergy and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR; Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, AR; Arkansas Children's Research Institute, Little Rock, AR.
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4
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Goodfellow SM, Nofchissey RA, Schwalm KC, Cook JA, Dunnum JL, Guo Y, Ye C, Mertz GJ, Chandran K, Harkins M, Domman DB, Dinwiddie DL, Bradfute SB. Tracing Transmission of Sin Nombre Virus and Discovery of Infection in Multiple Rodent Species. J Virol 2021; 95:e0153421. [PMID: 34549977 PMCID: PMC8577387 DOI: 10.1128/jvi.01534-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 12/23/2022] Open
Abstract
Sin Nombre orthohantavirus (SNV), a negative-sense, single-stranded RNA virus that is carried and transmitted by the North American deer mouse Peromyscus maniculatus, can cause infection in humans through inhalation of aerosolized excreta from infected rodents. This infection can lead to hantavirus cardiopulmonary syndrome (HCPS), which has an ∼36% case-fatality rate. We used reverse transcriptase quantitative PCR (RT-qPCR) to confirm SNV infection in a patient and identified SNV in lung tissues in wild-caught rodents from potential sites of exposure. Using viral whole-genome sequencing (WGS), we identified the likely site of transmission and discovered SNV in multiple rodent species not previously known to carry the virus. Here, we report, for the first time, the use of SNV WGS to pinpoint a likely site of human infection and identify SNV simultaneously in multiple rodent species in an area of known host-to-human transmission. These results will impact epidemiology and infection control for hantaviruses by tracing zoonotic transmission and investigating possible novel host reservoirs. IMPORTANCE Orthohantaviruses cause severe disease in humans and can be lethal in up to 40% of cases. Sin Nombre orthohantavirus (SNV) is the main cause of hantavirus disease in North America. In this study, we sequenced SNV from an infected patient and wild-caught rodents to trace the location of infection. We also discovered SNV in rodent species not previously known to carry SNV. These studies demonstrate for the first time the use of virus sequencing to trace the transmission of SNV and describe infection in novel rodent species.
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Affiliation(s)
- Samuel M. Goodfellow
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Robert A. Nofchissey
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Kurt C. Schwalm
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Joseph A. Cook
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, New Mexico, USA
| | - Jonathan L. Dunnum
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, New Mexico, USA
| | - Yan Guo
- Comprehensive Cancer Center, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Chunyan Ye
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Gregory J. Mertz
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Kartik Chandran
- Albert Einstein College of Medicine, Department of Microbiology and Immunology, Bronx, New York, USA
| | - Michelle Harkins
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Daryl B. Domman
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Darrell L. Dinwiddie
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Steven B. Bradfute
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
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5
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Merkley SD, Goodfellow SM, Guo Y, Wilton ZER, Byrum JR, Schwalm KC, Dinwiddie DL, Gullapalli RR, Deretic V, Jimenez Hernandez A, Bradfute SB, In JG, Castillo EF. Non-autophagy Role of Atg5 and NBR1 in Unconventional Secretion of IL-12 Prevents Gut Dysbiosis and Inflammation. J Crohns Colitis 2021; 16:259-274. [PMID: 34374750 PMCID: PMC8864635 DOI: 10.1093/ecco-jcc/jjab144] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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] [Indexed: 12/23/2022]
Abstract
Intestinal myeloid cells play a critical role in balancing intestinal homeostasis and inflammation. Here, we report that expression of the autophagy-related 5 [Atg5] protein in myeloid cells prevents dysbiosis and excessive intestinal inflammation by limiting IL-12 production. Mice with a selective genetic deletion of Atg5 in myeloid cells [Atg5ΔMye] showed signs of dysbiosis preceding colitis, and exhibited severe intestinal inflammation upon colitis induction that was characterised by increased IFNγ production. The exacerbated colitis was linked to excess IL-12 secretion from Atg5-deficient myeloid cells and gut dysbiosis. Restoration of the intestinal microbiota or genetic deletion of IL-12 in Atg5ΔMye mice attenuated the intestinal inflammation in Atg5ΔMye mice. Additionally, Atg5 functions to limit IL-12 secretion through modulation of late endosome [LE] acidity. Last, the autophagy cargo receptor NBR1, which accumulates in Atg5-deficient cells, played a role by delivering IL-12 to LE. In summary, Atg5 expression in intestinal myeloid cells acts as an anti-inflammatory brake to regulate IL-12, thus preventing dysbiosis and uncontrolled IFNγ-driven intestinal inflammation.
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Affiliation(s)
- Seth D Merkley
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Samuel M Goodfellow
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Yan Guo
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Zoe E R Wilton
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Janie R Byrum
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Kurt C Schwalm
- Department of Pediatrics, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Darrell L Dinwiddie
- Department of Pediatrics, University of New Mexico Health Sciences, Albuquerque, NM, USA,Clinical and Translational Science Center, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Rama R Gullapalli
- Department of Pathology, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Vojo Deretic
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences, Albuquerque, NM, USA,Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Anthony Jimenez Hernandez
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Steven B Bradfute
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences, Albuquerque, NM, USA
| | - Julie G In
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of New Mexico Health Sciences, Albuquerque, NM, USA,Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eliseo F Castillo
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of New Mexico Health Sciences, Albuquerque, NM, USA,Clinical and Translational Science Center, University of New Mexico Health Sciences, Albuquerque, NM, USA,Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences, Albuquerque, NM, USA,Corresponding author: Eliseo F. Castillo, PhD, Department of Internal Medicine, MSC 10 550, 1 University of New Mexico, Albuquerque, New Mexico 87131, USA.
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6
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Hodcroft EB, Domman DB, Snyder DJ, Oguntuyo KY, Van Diest M, Densmore KH, Schwalm KC, Femling J, Carroll JL, Scott RS, Whyte MM, Edwards MW, Hull NC, Kevil CG, Vanchiere JA, Lee B, Dinwiddie DL, Cooper VS, Kamil JP. Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. medRxiv 2021:2021.02.12.21251658. [PMID: 33594385 PMCID: PMC7885944 DOI: 10.1101/2021.02.12.21251658] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein (S) plays critical roles in host cell entry. Non-synonymous substitutions affecting S are not uncommon and have become fixed in a number of SARS-CoV-2 lineages. A subset of such mutations enable escape from neutralizing antibodies or are thought to enhance transmission through mechanisms such as increased affinity for the cell entry receptor, angiotensin-converting enzyme 2 (ACE2). Independent genomic surveillance programs based in New Mexico and Louisiana contemporaneously detected the rapid rise of numerous clade 20G (lineage B.1.2) infections carrying a Q677P substitution in S. The variant was first detected in the US on October 23, yet between 01 Dec 2020 and 19 Jan 2021 it rose to represent 27.8% and 11.3% of all SARS-CoV-2 genomes sequenced from Louisiana and New Mexico, respectively. Q677P cases have been detected predominantly in the south central and southwest United States; as of 03 Feb 2021, GISAID data show 499 viral sequences of this variant from the USA. Phylogenetic analyses revealed the independent evolution and spread of at least six distinct Q677H sub-lineages, with first collection dates ranging from mid-August to late November 2020. Four 677H clades from clade 20G (B.1.2), 20A (B.1.234), and 20B (B.1.1.220, and B.1.1.222) each contain roughly 100 or fewer sequenced cases, while a distinct pair of clade 20G clusters are represented by 754 and 298 cases, respectively. Although sampling bias and founder effects may have contributed to the rise of S:677 polymorphic variants, the proximity of this position to the polybasic cleavage site at the S1/S2 boundary are consistent with its potential functional relevance during cell entry, suggesting parallel evolution of a trait that may confer an advantage in spread or transmission. Taken together, our findings demonstrate simultaneous convergent evolution, thus providing an impetus to further evaluate S:677 polymorphisms for effects on proteolytic processing, cell tropism, and transmissibility.
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Affiliation(s)
- Emma B Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
| | - Daryl B Domman
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Daniel J Snyder
- Microbial Genome Sequencing Center, LLC, Pittsburgh, PA, USA
| | | | - Maarten Van Diest
- Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA
| | - Kenneth H Densmore
- Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA
| | - Kurt C Schwalm
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Jon Femling
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Jennifer L Carroll
- Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA
| | - Rona S Scott
- Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA
| | | | | | - Noah C Hull
- Wyoming Public Health Laboratory, Cheyenne, WY, USA
| | - Christopher G Kevil
- Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA
| | - John A Vanchiere
- Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA
| | - Benhur Lee
- Microbial Genome Sequencing Center, LLC, Pittsburgh, PA, USA
| | | | - Vaughn S Cooper
- University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Jeremy P Kamil
- Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA
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Dehority W, Spence D, Dinwiddie DL. Severe Acute Respiratory Syndrome Coronavirus 2: Genomic Observations and Emerging Therapies. Pediatr Allergy Immunol Pulmonol 2020; 33:49-52. [PMID: 35921576 PMCID: PMC8443257 DOI: 10.1089/ped.2020.1179] [Citation(s) in RCA: 1] [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] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of the disease COVID-19, first emerged in late December 2019 in China, and has subsequently become a pandemic with unprecedented clinical impact. The virus appears to more severely affect older individuals and those with co-morbid medical conditions, specifically those with chronic lung disease, obesity, heart failure and diabetes. Fortunately, children appear to be less severely affected, though mortality and severe disease have been reported. In addition, children's role in spreading the disease (potentially through asymptomatic shedding of the virus) remains an important area requiring further investigation. The emergence of SARS-CoV-2 has highlighted the importance of metagenomic next generation sequencing as a tool for pandemic investigation. Though no proven therapeutic options currently exist, ongoing genomic and clinical trial data may help inform the identification and development of both repurposed and novel therapeutic agents for use in this disease.
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Affiliation(s)
- Walter Dehority
- Department of Pediatrics, Division of Infectious Diseases, The University of New Mexico School of Medicine, Albuquerque, New Mexico, USA
- Address correspondence to: Walter Dehority, MD, MSc, Department of Pediatrics, Division of Infectious Diseases, The University of New Mexico Health Sciences Center, MSC10 5590, 1 University of New Mexico, Albuquerque, NM 87131-0001, USA
| | - Dominique Spence
- Clinical and Translational Science Center, The University of New Mexico School of Medicine, Albuquerque, New Mexico, USA
| | - Darrell L. Dinwiddie
- Clinical and Translational Science Center, The University of New Mexico School of Medicine, Albuquerque, New Mexico, USA
- Department of Pediatrics, The University of New Mexico School of Medicine, Albuquerque, New Mexico, USA
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8
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Komesu YM, Dinwiddie DL, Richter HE, Lukacz ES, Sung VW, Siddiqui NY, Zyczynski HM, Ridgeway B, Rogers RG, Arya LA, Mazloomdoost D, Levy J, Carper B, Gantz MG. Defining the relationship between vaginal and urinary microbiomes. Am J Obstet Gynecol 2020; 222:154.e1-154.e10. [PMID: 31421123 DOI: 10.1016/j.ajog.2019.08.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/24/2019] [Accepted: 08/02/2019] [Indexed: 12/23/2022]
Abstract
BACKGROUND Although the vaginal and urinary microbiomes have been increasingly well-characterized in health and disease, few have described the relationship between these neighboring environments. Elucidating this relationship has implications for understanding how manipulation of the vaginal microbiome may affect the urinary microbiome and treatment of common urinary conditions. OBJECTIVE To describe the relationship between urinary and vaginal microbiomes using 16S rRNA gene sequencing. We hypothesized that the composition of the urinary and vaginal microbiomes would be significantly associated, with similarities in predominant taxa. STUDY DESIGN This multicenter study collected vaginal swabs and catheterized urine samples from 186 women with mixed urinary incontinence enrolled in a parent study and 84 similarly aged controls. Investigators decided a priori that if vaginal and/or urinary microbiomes differed between continent and incontinent women, the groups would be analyzed separately; if similar, samples from continent and incontinent women would be pooled and analyzed together. A central laboratory sequenced variable regions 1-3 (v1-3) and characterized bacteria to the genus level. Operational taxonomic unit abundance was described for paired vaginal and urine samples. Pearson's correlation characterized the relationship between individual operational taxonomic units of paired samples. Canonical correlation analysis evaluated the association between clinical variables (including mixed urinary incontinence and control status) and vaginal and urinary operational taxonomic units, using the Canonical correlation analysis function in the Vegan package (R version 3.5). Linear discriminant analysis effect size was used to find taxa that discriminated between vaginal and urinary samples. RESULTS Urinary and vaginal samples were collected from 212 women (mean age 53±11 years) and results from 197 paired samples were available for analysis. As operational taxonomic units in mixed urinary incontinence and control samples were related in canonical correlation analysis and since taxa did not discriminate between mixed urinary incontinence or controls in either vagina or urine, mixed urinary incontinence and control samples were pooled for further analysis. Canonical correlation analysis of vaginal and urinary samples indicated that that 60 of the 100 most abundant operational taxonomic units in the samples largely overlapped. Lactobacillus was the most abundant genus in both urine and vagina (contributing on average 53% to an individual's urine sample and 64% to an individual's vaginal sample) (Pearson correlation r=0.53). Although less abundant than Lactobacillus, other bacteria with high Pearson correlation coefficients also commonly found in vagina and urine included: Gardnerella (r=0.70), Prevotella (r=0.64), and Ureaplasma (r=0.50). Linear discriminant analysis effect size analysis identified Tepidimonas and Flavobacterium as bacteria that distinguished the urinary environment for both mixed urinary incontinence and controls as these bacteria were absent in the vagina (Tepidimonas effect size 2.38, P<.001, Flavobacterium effect size 2.15, P<.001). Although Lactobacillus was the most abundant bacteria in both urine and vagina, it was more abundant in the vagina (linear discriminant analysis effect size effect size 2.72, P<.001). CONCLUSION Significant associations between vaginal and urinary microbiomes were demonstrated, with Lactobacillus being predominant in both urine and vagina. Abundance of other bacteria also correlated highly between the vagina and urine. This inter-relatedness has implications for studying manipulation of the urogenital microbiome in treating conditions such as urgency urinary incontinence and urinary tract infections.
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9
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Stoner A, Pham S, Hardin O, Dinwiddie DL, Kincaid JC, Putt C, Kennedy JL. Nasal IL-15 levels are similar between asthmatics and controls during asthma exacerbations and viral upper respiratory infections. J Allergy Clin Immunol 2019. [DOI: 10.1016/j.jaci.2018.12.364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Pham S, Hardin O, Dinwiddie DL, Bhattacharyya S, Stoner A, Kincaid JC, Kirkpatrick C, Putt C, Kennedy JL. Nasal Periostin Levels and Acute Symptoms in Asthmatics during Viral-induced Exacerbations. J Allergy Clin Immunol 2019. [DOI: 10.1016/j.jaci.2018.12.629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Dinwiddie DL, Denson JL, Kennedy JL. Role of the Airway Microbiome in Respiratory Infections and Asthma in Children. Pediatr Allergy Immunol Pulmonol 2018; 31:236-240. [PMID: 30595952 DOI: 10.1089/ped.2018.0958] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/17/2018] [Indexed: 12/13/2022]
Abstract
The respiratory tract can be colonized with bacterial, fungal, and viral microorganisms, and the whole of the microbiota, their genes, and the surrounding environment is collectively termed the microbiome. Increasing evidence indicates that the respiratory microbiome has an important role in respiratory health and disease and is both impacted by and potentially contributes to the severity of symptomatic respiratory viral infections and asthma in children. A deeper understanding of the complex interactions between bacteria, viruses, and the host will provide further comprehension into the drivers and mechanisms of respiratory health and disease and will impart opportunities for clinical therapies.
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Affiliation(s)
- Darrell L Dinwiddie
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico.,Clinical Translational Sciences Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Jesse L Denson
- Department of Pharmaceutical Sciences, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Joshua L Kennedy
- Department of Pediatrics, Arkansas Children's Research Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas.,Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
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12
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Komesu YM, Richter HE, Carper B, Dinwiddie DL, Lukacz ES, Siddiqui NY, Sung VW, Zyczynski HM, Ridgeway B, Rogers RG, Arya LA, Mazloomdoost D, Gantz MG. The urinary microbiome in women with mixed urinary incontinence compared to similarly aged controls. Int Urogynecol J 2018; 29:1785-1795. [PMID: 29909556 PMCID: PMC6295358 DOI: 10.1007/s00192-018-3683-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [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: 02/22/2018] [Accepted: 05/28/2018] [Indexed: 01/18/2023]
Abstract
INTRODUCTION & HYPOTHESIS Previous studies have suggested that women with urinary incontinence have an altered urinary microbiome. We hypothesized that the microbiome in women with mixed urinary incontinence (MUI) differed from controls and tested this hypothesis using bacterial gene sequencing techniques. METHODS This multicenter study compared the urinary microbiome in women with MUI and similarly aged controls. Catheterized urine samples were obtained; v4-6 regions of the 16S rRNA gene were sequenced to identify bacteria. Bacterial predominance (> 50% of an individual's genera) was compared between MUI and controls. Bacterial sequences were categorized into "community types" using Dirichlet multinomial mixture (DMM) methods. Generalized linear mixed models predicted MUI/control status based on clinical characteristics and community type. Post-hoc analyses were performed in women < 51 and ≥ 51 years. Sample size estimates required 200 samples to detect a 20% difference in Lactobacillus predominance with P < 0.05. RESULTS Of 212 samples, 97.6% were analyzed (123 MUI/84 controls, mean age 53 ± 11 years). Overall Lactobacillus predominance did not differ between MUI and controls (45/123 = 36.6% vs. 36/84 = 42.9%, P = 0.36). DMM analyses revealed six community types; communities differed by age (P = 0.001). A High-Lactobacillus (89.2% Lactobacillus) community had a greater proportion of controls (19/84 = 22.6%, MUI 11/123 = 8.9%). Overall, bacterial community types did not differ in MUI and controls. However, post-hoc analysis of women < 51 years found that bacterial community types distinguished MUI from controls (P = 0.041); Moderate-Lactobacillus (aOR 7.78, CI 1.85-32.62) and Mixed (aOR 7.10, CI 1.32-38.10) community types were associated with MUI. Community types did not differentiate MUI and controls in women ≥ 51 years (P = 0.94). CONCLUSIONS Women with MUI and controls did not differ in overall Lactobacillus predominance. In younger women, urinary bacterial community types differentiated MUI from controls.
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Affiliation(s)
- Yuko M Komesu
- Department of Obstetrics and Gynecology, University of New Mexico Health Sciences Center, MSC 10 5580 1 University of New Mexico, Albuquerque, NM, 87131-0001, USA.
| | - Holly E Richter
- Obstetrics & Gynecology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Benjamin Carper
- Social, Statistical & Environmental Sciences, RTI International, Research Triangle Park, NC, USA
| | - Darrell L Dinwiddie
- Pediatrics and Clinical Translational Science Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Emily S Lukacz
- Department of Reproductive Medicine, University of California San Diego, San Diego, CA, USA
| | | | - Vivian W Sung
- Obstetrics & Gynecology, Alpert Medical School of Brown University, Providence, RI, USA
| | - Halina M Zyczynski
- Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Beri Ridgeway
- Obstetrics & Gynecology, Cleveland Clinic, Cleveland, OH, USA
| | - Rebecca G Rogers
- Department of Obstetrics and Gynecology, University of New Mexico Health Sciences Center, MSC 10 5580 1 University of New Mexico, Albuquerque, NM, 87131-0001, USA
- Obstetrics & Gynecology, Dell Medical School University of Texas Austin, Austin, TX, USA
| | - Lily A Arya
- Obstetrics & Gynecology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Donna Mazloomdoost
- Gynecologic Health and Disease Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) National Institutes of Health (NIH), Bethesda, MD, USA
| | - Marie G Gantz
- Social, Statistical & Environmental Sciences, RTI International, Research Triangle Park, NC, USA
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13
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O'Flaherty BM, Li Y, Tao Y, Paden CR, Queen K, Zhang J, Dinwiddie DL, Gross SM, Schroth GP, Tong S. Comprehensive viral enrichment enables sensitive respiratory virus genomic identification and analysis by next generation sequencing. Genome Res 2018; 28:869-877. [PMID: 29703817 PMCID: PMC5991510 DOI: 10.1101/gr.226316.117] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [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: 06/16/2017] [Accepted: 04/10/2018] [Indexed: 01/01/2023]
Abstract
Next generation sequencing (NGS) technologies have revolutionized the genomics field and are becoming more commonplace for identification of human infectious diseases. However, due to the low abundance of viral nucleic acids (NAs) in relation to host, viral identification using direct NGS technologies often lacks sufficient sensitivity. Here, we describe an approach based on two complementary enrichment strategies that significantly improves the sensitivity of NGS-based virus identification. To start, we developed two sets of DNA probes to enrich virus NAs associated with respiratory diseases. The first set of probes spans the genomes, allowing for identification of known viruses and full genome sequencing, while the second set targets regions conserved among viral families or genera, providing the ability to detect both known and potentially novel members of those virus groups. Efficiency of enrichment was assessed by NGS testing reference virus and clinical samples with known infection. We show significant improvement in viral identification using enriched NGS compared to unenriched NGS. Without enrichment, we observed an average of 0.3% targeted viral reads per sample. However, after enrichment, 50%–99% of the reads per sample were the targeted viral reads for both the reference isolates and clinical specimens using both probe sets. Importantly, dramatic improvements on genome coverage were also observed following virus-specific probe enrichment. The methods described here provide improved sensitivity for virus identification by NGS, allowing for a more comprehensive analysis of disease etiology.
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Affiliation(s)
- Brigid M O'Flaherty
- Centers for Disease Control and Prevention, NCIRD, DVD, Atlanta, Georgia 30329, USA.,Oak Ridge Institute for Science Education, Oak Ridge, Tennessee 37830, USA
| | - Yan Li
- Centers for Disease Control and Prevention, NCIRD, DVD, Atlanta, Georgia 30329, USA
| | - Ying Tao
- Centers for Disease Control and Prevention, NCIRD, DVD, Atlanta, Georgia 30329, USA
| | - Clinton R Paden
- Centers for Disease Control and Prevention, NCIRD, DVD, Atlanta, Georgia 30329, USA.,Oak Ridge Institute for Science Education, Oak Ridge, Tennessee 37830, USA
| | - Krista Queen
- Centers for Disease Control and Prevention, NCIRD, DVD, Atlanta, Georgia 30329, USA.,Oak Ridge Institute for Science Education, Oak Ridge, Tennessee 37830, USA
| | - Jing Zhang
- Centers for Disease Control and Prevention, NCIRD, DVD, Atlanta, Georgia 30329, USA.,IHRC Incorporated, Atlanta, Georgia 30346, USA
| | - Darrell L Dinwiddie
- Department of Pediatrics, Clinical Translational Science Center, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | | | - Gary P Schroth
- Illumina, Incorporated, San Diego, California 92122, USA
| | - Suxiang Tong
- Centers for Disease Control and Prevention, NCIRD, DVD, Atlanta, Georgia 30329, USA
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14
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Stoner A, Dinwiddie DL, Putt CC, Schwalm K, Kincaid JC, Bell M, Abramo TJ, Thompson TM, Jones SM, Kurten RC, Kennedy JL. Rhinovirus causes increased acute symptoms in children with first time wheezing compared to either controls with cold symptoms or children with first time wheezing and Respiratory Syncytial Virus. J Allergy Clin Immunol 2018. [DOI: 10.1016/j.jaci.2017.12.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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15
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Hardin O, Dinwiddie DL, Bhattacharyya S, Luo C, Stoner A, Kincaid JC, Schwalm K, Abramo TJ, Thompson TM, Jones SM, Kurten RC, Kennedy JL. Asthma Control, Viral Infections, and Severity of Asthma Exacerbation Symptoms in Children Seen in the Emergency Department. J Allergy Clin Immunol 2018. [DOI: 10.1016/j.jaci.2017.12.693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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16
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Kothari A, Burgess MJ, Crescencio JCR, Kennedy JL, Denson JL, Schwalm KC, Stoner AN, Kincaid JC, Davies FE, Dinwiddie DL. The role of next generation sequencing in infection prevention in human parainfluenza virus 3 infections in immunocompromised patients. J Clin Virol 2017; 92:53-55. [PMID: 28531552 DOI: 10.1016/j.jcv.2017.05.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 03/13/2017] [Revised: 05/03/2017] [Accepted: 05/10/2017] [Indexed: 11/16/2022]
Abstract
BACKGROUND Respiratory viral infections are a significant problem in patients with hematologic malignancies. We report a cluster of HPIV 3 infections in our myeloma patients, and describe the utility of next generation sequencing (NGS) to identify transmission linkages which can assist in infection prevention. OBJECTIVES To evaluate the utility of NGS to track respiratory viral infection outbreaks and delineate between community acquired and nosocomial infections in our cancer units. STUDY DESIGN Retrospective chart review conducted at a single site. All patients diagnosed with multiple myeloma who developed symptoms suggestive of upper respiratory tract infection (URTI) or lower respiratory tract infection (LRTI) along with a respiratory viral panel (RVP) test positive for HPIV 3 between April 1, 2016, to June 30, 2016, were included. Sequencing was performed on the Illumina MiSeq™. To gain understanding regarding community strains of HPIV 3 during the same season, we also performed NGS on HPIV3 strains isolated from pediatric cases. RESULTS We saw a cluster of 13 cases of HPIV3 infections in the myeloma unit. Using standard epidemiologic criteria, 3 cases were considered community acquired, 7 cases developed infection during treatment in the cancer infusion center, while an additional 3 developed infections during hospital stay. Seven patients required hospitalization for a median duration of 20days. NGS enabled sensitive discrimination of the relatedness of the isolates obtained during the outbreak and provided evidence for source of transmission. Two hospital onset infections could be tracked to an index case; the genome sequences of HPIV 3 strains from these 3 patients only differed by a single nucleotide. CONCLUSIONS NGS offers a significantly higher discriminatory value as an epidemiologic tool, and can be used to gather real-time information and identification of transmission linkages to assist in infection prevention in immunocompromised patients.
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Affiliation(s)
- Atul Kothari
- Division of Infectious Diseases, Department of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| | - Mary J Burgess
- Division of Infectious Diseases, Department of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Juan Carlos Rico Crescencio
- Division of Infectious Diseases, Department of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Joshua L Kennedy
- Division of Allergy and Immunology, Department of Medicine and Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jesse L Denson
- Department of Pharmaceutical Sciences, University of New Mexico College of Pharmacy, Albuquerque, NM, USA
| | - Kurt C Schwalm
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Ashley N Stoner
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Faith E Davies
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Darrell L Dinwiddie
- Clinical Translational Sciences Center, Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
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17
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Komesu YM, Richter HE, Dinwiddie DL, Siddiqui NY, Sung VW, Lukacz ES, Ridgeway B, Arya LA, Zyczynski HM, Rogers RG, Gantz M. Methodology for a vaginal and urinary microbiome study in women with mixed urinary incontinence. Int Urogynecol J 2017; 28:711-720. [PMID: 27738739 PMCID: PMC5391306 DOI: 10.1007/s00192-016-3165-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/19/2016] [Indexed: 12/11/2022]
Abstract
INTRODUCTION AND HYPOTHESIS We describe the rationale and methods of a study designed to compare vaginal and urinary microbiomes in women with mixed urinary incontinence (MUI) and similarly aged, asymptomatic controls. METHODS This paper delineates the methodology of a supplementary microbiome study nested in an ongoing randomized controlled trial comparing a standardized perioperative behavioral/pelvic floor exercise intervention plus midurethral sling versus midurethral sling alone for MUI. Women in the parent study had at least "moderate bother" from urgency and stress urinary incontinence symptoms (SUI) on validated questionnaire and confirmed MUI on bladder diary. Controls had no incontinence symptoms. All participants underwent vaginal and urine collection for DNA analysis and conventional urine culture. Standardized protocols were designed, and a central lab received samples for subsequent polymerase chain reaction (PCR) amplification and sequencing of the bacterial16S ribosomal RNA (rRNA) gene. The composition of bacterial communities will be determined by dual amplicon sequencing of variable regions 1-3 and 4-6 from vaginal and urine specimens to compare the microbiome of patients with controls. Sample-size estimates determined that 126 MUI and 84 control participants were sufficient to detect a 20 % difference in predominant urinary genera, with 80 % power and 0.05 significance level. RESULTS Specimen collection commenced January 2015 and finished April 2016. DNA was extracted and stored for subsequent evaluation. CONCLUSIONS Methods papers sharing information regarding development of genitourinary microbiome studies, particularly with control populations, are few. We describe the rigorous methodology developed for a novel urogenital microbiome study in women with MUI.
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Affiliation(s)
- Yuko M Komesu
- Division of Female Pelvic Medicine and Reconstructive Surgery, Department of Obstetrics and Gynecology MSC10-5580, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131-0001, USA.
| | - Holly E Richter
- Division of Urogynecology and Pelvic Reconstructive Surgery, Department of Obstetrics and Gynecology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Darrell L Dinwiddie
- Clinical Translational Sciences Center and Department of Pediatrics, University of New Mexico of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Nazema Y Siddiqui
- Division of Urogynecology and Reconstructive Pelvic Surgery, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Vivian W Sung
- Division of Urogynecology and Reconstructive Pelvic Surgery, Department of Obstetrics and Gynecology, Alpert Medical School of Brown University, Providence, RI, USA
| | - Emily S Lukacz
- Division of Female Pelvic Medicine and Reconstructive Surgery, Department of Reproductive Medicine, UC San Diego Health System, San Diego, CA, USA
| | - Beri Ridgeway
- Center for Urogynecology and Reconstructive Pelvic Surgery, Obstetrics and Gynecology and Women's Health Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Lily A Arya
- Division of Urogynecology and Reconstructive Pelvic Surgery, Hospital of University of Pennsylvania, Philadelphia, PA, USA
| | - Halina M Zyczynski
- Division of Urogynecology and Reconstructive Pelvic Surgery, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Rebecca G Rogers
- Division of Female Pelvic Medicine and Reconstructive Surgery, Department of Obstetrics and Gynecology MSC10-5580, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131-0001, USA
| | - Marie Gantz
- Social, Statistical and Environmental Sciences, RTI International, Research Triangle Park, Durham, NC, USA
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18
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Dinwiddie DL, Kennedy J, Dehority WN, Schwalm K, Langley RJ, Young SA. Unbiased RNA Sequencing of Acute Respiratory Syncytial Virus Infection Reveals Gene Expression Signatures that Provide Insight into Pathogenesis. J Allergy Clin Immunol 2017. [DOI: 10.1016/j.jaci.2016.12.871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Twist GP, Gaedigk A, Miller NA, Farrow EG, Willig LK, Dinwiddie DL, Petrikin JE, Soden SE, Herd S, Gibson M, Cakici JA, Riffel AK, Leeder JS, Dinakarpandian D, Kingsmore SF. Erratum: Constellation: a tool for rapid, automated phenotype assignment of a highly polymorphic pharmacogene, CYP2D6, from whole-genome sequences. NPJ Genom Med 2017; 2:16039. [PMID: 29266105 PMCID: PMC5685321 DOI: 10.1038/npjgenmed.2016.39] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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20
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Dehority WN, Eickman MM, Schwalm KC, Gross SM, Schroth GP, Young SA, Dinwiddie DL. Complete genome sequence of a KI polyomavirus isolated from an otherwise healthy child with severe lower respiratory tract infection. J Med Virol 2016; 89:926-930. [PMID: 27704585 DOI: 10.1002/jmv.24706] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [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: 10/04/2016] [Indexed: 11/11/2022]
Abstract
Unbiased, deep sequencing of a nasal specimen from an otherwise healthy 13-month-old boy hospitalized in intensive care revealed high gene expression and the complete genome of a novel isolate of KI polyomavirus (KIPyV). Further investigation detected minimal gene expression of additional viruses, suggesting that KIPyV was potentially the causal agent. Analysis of the complete genome of isolate NMKI001 revealed it is different from all previously reported genomes and contains two amino acid differences as compared to the closest virus isolate, Stockholm 380 (EF127908). J. Med. Virol. 89:926-930, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Walter N Dehority
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Megan M Eickman
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Kurt C Schwalm
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | | | | | | | - Darrell L Dinwiddie
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico.,Clinical Translational Science Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
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21
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Denson JL, Kennedy JL, Dehority WN, Eickman MM, Schwalm KS, Stoner AN, Kincaid JC, Abramo TJ, Thompson TM, Ulloa EM, Burchiel SW, Young SA, Dinwiddie DL. Complete Genome Sequences of Two Novel Isolates of Human Parainfluenza Virus 1 Associated with Acute Respiratory Infection. Genome Announc 2016; 4:e01154-16. [PMID: 27738046 PMCID: PMC5064119 DOI: 10.1128/genomea.01154-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 08/25/2016] [Indexed: 11/20/2022]
Abstract
Using target capture of viral nucleic acid and next-generation sequencing, we generated the complete genomes of two novel human parainfluenza virus 1 isolates. Isolates AR001 (accession no. KX570602) and NM001 (accession no. KX639498) were collected 3 months apart from pediatric patients with acute respiratory infection from Arkansas and New Mexico, respectively.
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Affiliation(s)
- J L Denson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - J L Kennedy
- Department of Pediatrics, Arkansas Children's Research Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA Clinical and Translational Sciences Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - W N Dehority
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - M M Eickman
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - K S Schwalm
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - A N Stoner
- Department of Pediatrics, Arkansas Children's Research Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - J C Kincaid
- Department of Pediatrics, Arkansas Children's Research Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - T J Abramo
- Department of Pediatrics, Arkansas Children's Research Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - T M Thompson
- Department of Pediatrics, Arkansas Children's Research Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - E M Ulloa
- Department of Pediatrics, Arkansas Children's Research Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - S W Burchiel
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - S A Young
- TriCore Reference Laboratories, Albuquerque, New Mexico, USA
| | - D L Dinwiddie
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA Clinical Translational Sciences Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
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22
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Miller NA, Farrow EG, Gibson M, Willig LK, Twist G, Yoo B, Marrs T, Corder S, Krivohlavek L, Walter A, Petrikin JE, Saunders CJ, Thiffault I, Soden SE, Smith LD, Dinwiddie DL, Herd S, Cakici JA, Catreux S, Ruehle M, Kingsmore SF. A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases. Genome Med 2015; 7:100. [PMID: 26419432 PMCID: PMC4588251 DOI: 10.1186/s13073-015-0221-8] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [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: 05/15/2015] [Accepted: 09/10/2015] [Indexed: 12/14/2022] Open
Abstract
While the cost of whole genome sequencing (WGS) is approaching the realm of routine medical tests, it remains too tardy to help guide the management of many acute medical conditions. Rapid WGS is imperative in light of growing evidence of its utility in acute care, such as in diagnosis of genetic diseases in very ill infants, and genotype-guided choice of chemotherapy at cancer relapse. In such situations, delayed, empiric, or phenotype-based clinical decisions may meet with substantial morbidity or mortality. We previously described a rapid WGS method, STATseq, with a sensitivity of >96 % for nucleotide variants that allowed a provisional diagnosis of a genetic disease in 50 h. Here improvements in sequencing run time, read alignment, and variant calling are described that enable 26-h time to provisional molecular diagnosis with >99.5 % sensitivity and specificity of genotypes. STATseq appears to be an appropriate strategy for acutely ill patients with potentially actionable genetic diseases.
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Affiliation(s)
- Neil A Miller
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Emily G Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA.,Department of Pediatrics, Children's Mercy, Kansas City, MO, 64108, USA.,Department of Pathology, Children's Mercy, Kansas City, MO, 64108, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Margaret Gibson
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Laurel K Willig
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA.,Department of Pediatrics, Children's Mercy, Kansas City, MO, 64108, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Greyson Twist
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Byunggil Yoo
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Tyler Marrs
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Shane Corder
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Lisa Krivohlavek
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Adam Walter
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Josh E Petrikin
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA.,Department of Pediatrics, Children's Mercy, Kansas City, MO, 64108, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA.,Department of Pediatrics, Children's Mercy, Kansas City, MO, 64108, USA.,Department of Pathology, Children's Mercy, Kansas City, MO, 64108, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA.,Department of Pathology, Children's Mercy, Kansas City, MO, 64108, USA
| | - Sarah E Soden
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA.,Department of Pediatrics, Children's Mercy, Kansas City, MO, 64108, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Laurie D Smith
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA.,Department of Pediatrics, Children's Mercy, Kansas City, MO, 64108, USA.,Department of Pathology, Children's Mercy, Kansas City, MO, 64108, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Darrell L Dinwiddie
- Deparment of Pediatrics, and Clinical Translational Science Center, University of New Mexico Health Science Center, Albuquerque, NM, 87131, USA
| | - Suzanne Herd
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Julie A Cakici
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Severine Catreux
- Edico Genome, Inc., 3344 North Torrey Pines Court, Plaza Level, La Jolla, CA, 92037, USA
| | - Mike Ruehle
- Edico Genome, Inc., 3344 North Torrey Pines Court, Plaza Level, La Jolla, CA, 92037, USA
| | - Stephen F Kingsmore
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA. .,Department of Pediatrics, Children's Mercy, Kansas City, MO, 64108, USA. .,Department of Pathology, Children's Mercy, Kansas City, MO, 64108, USA. .,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA. .,Rady Pediatric Genomics and Systems Medicine Institute, Rady Chlildren's Hospital, 3020 Children's Way, San Diego, CA, 92123, USA.
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23
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Soden SE, Saunders CJ, Willig LK, Farrow EG, Smith LD, Petrikin JE, LePichon JB, Miller NA, Thiffault I, Dinwiddie DL, Twist G, Noll A, Heese BA, Zellmer L, Atherton AM, Abdelmoity AT, Safina N, Nyp SS, Zuccarelli B, Larson IA, Modrcin A, Herd S, Creed M, Ye Z, Yuan X, Brodsky RA, Kingsmore SF. Effectiveness of exome and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders. Sci Transl Med 2015; 6:265ra168. [PMID: 25473036 DOI: 10.1126/scitranslmed.3010076] [Citation(s) in RCA: 384] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Neurodevelopmental disorders (NDDs) affect more than 3% of children and are attributable to single-gene mutations at more than 1000 loci. Traditional methods yield molecular diagnoses in less than one-half of children with NDD. Whole-genome sequencing (WGS) and whole-exome sequencing (WES) can enable diagnosis of NDD, but their clinical and cost-effectiveness are unknown. One hundred families with 119 children affected by NDD received diagnostic WGS and/or WES of parent-child trios, wherein the sequencing approach was guided by acuity of illness. Forty-five percent received molecular diagnoses. An accelerated sequencing modality, rapid WGS, yielded diagnoses in 73% of families with acutely ill children (11 of 15). Forty percent of families with children with nonacute NDD, followed in ambulatory care clinics (34 of 85), received diagnoses: 33 by WES and 1 by staged WES then WGS. The cost of prior negative tests in the nonacute patients was $19,100 per family, suggesting sequencing to be cost-effective at up to $7640 per family. A change in clinical care or impression of the pathophysiology was reported in 49% of newly diagnosed families. If WES or WGS had been performed at symptom onset, genomic diagnoses may have been made 77 months earlier than occurred in this study. It is suggested that initial diagnostic evaluation of children with NDD should include trio WGS or WES, with extension of accelerated sequencing modalities to high-acuity patients.
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Affiliation(s)
- Sarah E Soden
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA.
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA. Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Laurel K Willig
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Emily G Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA. Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Laurie D Smith
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Josh E Petrikin
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Jean-Baptiste LePichon
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Neil A Miller
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA. Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Darrell L Dinwiddie
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA. Clinical and Translational Science Center, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Greyson Twist
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Aaron Noll
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Bryce A Heese
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Lee Zellmer
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Andrea M Atherton
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Ahmed T Abdelmoity
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Nicole Safina
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Sarah S Nyp
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Britton Zuccarelli
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Ingrid A Larson
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Ann Modrcin
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Suzanne Herd
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Mitchell Creed
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Zhaohui Ye
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Xuan Yuan
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Robert A Brodsky
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Stephen F Kingsmore
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA. Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
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24
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Tsalik EL, Langley RJ, Dinwiddie DL, Miller NA, Yoo B, van Velkinburgh JC, Smith LD, Thiffault I, Jaehne AK, Valente AM, Henao R, Yuan X, Glickman SW, Rice BJ, McClain MT, Carin L, Corey GR, Ginsburg GS, Cairns CB, Otero RM, Fowler VG, Rivers EP, Woods CW, Kingsmore SF. An integrated transcriptome and expressed variant analysis of sepsis survival and death. Genome Med 2014; 6:111. [PMID: 25538794 PMCID: PMC4274761 DOI: 10.1186/s13073-014-0111-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [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: 08/11/2014] [Accepted: 11/14/2014] [Indexed: 12/13/2022] Open
Abstract
Background Sepsis, a leading cause of morbidity and mortality, is not a homogeneous disease but rather a syndrome encompassing many heterogeneous pathophysiologies. Patient factors including genetics predispose to poor outcomes, though current clinical characterizations fail to identify those at greatest risk of progression and mortality. Methods The Community Acquired Pneumonia and Sepsis Outcome Diagnostic study enrolled 1,152 subjects with suspected sepsis. We sequenced peripheral blood RNA of 129 representative subjects with systemic inflammatory response syndrome (SIRS) or sepsis (SIRS due to infection), including 78 sepsis survivors and 28 sepsis non-survivors who had previously undergone plasma proteomic and metabolomic profiling. Gene expression differences were identified between sepsis survivors, sepsis non-survivors, and SIRS followed by gene enrichment pathway analysis. Expressed sequence variants were identified followed by testing for association with sepsis outcomes. Results The expression of 338 genes differed between subjects with SIRS and those with sepsis, primarily reflecting immune activation in sepsis. Expression of 1,238 genes differed with sepsis outcome: non-survivors had lower expression of many immune function-related genes. Functional genetic variants associated with sepsis mortality were sought based on a common disease-rare variant hypothesis. VPS9D1, whose expression was increased in sepsis survivors, had a higher burden of missense variants in sepsis survivors. The presence of variants was associated with altered expression of 3,799 genes, primarily reflecting Golgi and endosome biology. Conclusions The activation of immune response-related genes seen in sepsis survivors was muted in sepsis non-survivors. The association of sepsis survival with a robust immune response and the presence of missense variants in VPS9D1 warrants replication and further functional studies. Trial registration ClinicalTrials.gov NCT00258869. Registered on 23 November 2005. Electronic supplementary material The online version of this article (doi:10.1186/s13073-014-0111-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ephraim L Tsalik
- Emergency Medicine Service, Durham Veterans Affairs Medical Center, Durham, North Carolina 27705 USA ; Department of Medicine, Duke University Medical Center, Durham, NC 27710 USA
| | - Raymond J Langley
- National Center for Genome Resources, Santa Fe, NM 87505 USA ; Department of Immunology, Lovelace Respiratory Research Institute, Albuquerque, NM 87108 USA
| | - Darrell L Dinwiddie
- National Center for Genome Resources, Santa Fe, NM 87505 USA ; Department of Pediatrics, Center for Translational Sciences, University of New Mexico, Albuquerque, NM 87131 USA
| | - Neil A Miller
- National Center for Genome Resources, Santa Fe, NM 87505 USA ; Center for Pediatric Genomic Medicine, Children's Mercy Hospitals and Clinic, Kansas City, MO 64108 USA
| | - Byunggil Yoo
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals and Clinic, Kansas City, MO 64108 USA
| | | | - Laurie D Smith
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals and Clinic, Kansas City, MO 64108 USA
| | - Isabella Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals and Clinic, Kansas City, MO 64108 USA
| | - Anja K Jaehne
- Department of Emergency Medicine, Henry Ford Hospital, Detroit, Michigan 48202 USA
| | - Ashlee M Valente
- Department of Medicine, Duke University Medical Center, Durham, NC 27710 USA
| | - Ricardo Henao
- Department of Electrical & Computer Engineering, Duke University, Durham, NC 27710 USA
| | - Xin Yuan
- Department of Electrical & Computer Engineering, Duke University, Durham, NC 27710 USA
| | - Seth W Glickman
- Department of Emergency Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599 USA
| | - Brandon J Rice
- National Center for Genome Resources, Santa Fe, NM 87505 USA
| | - Micah T McClain
- Department of Medicine, Duke University Medical Center, Durham, NC 27710 USA ; Medicine Service, Durham Veterans Affairs Medical Center, Durham, NC 27705 USA
| | - Lawrence Carin
- Department of Electrical & Computer Engineering, Duke University, Durham, NC 27710 USA
| | - G Ralph Corey
- Department of Medicine, Duke University Medical Center, Durham, NC 27710 USA ; Medicine Service, Durham Veterans Affairs Medical Center, Durham, NC 27705 USA
| | - Geoffrey S Ginsburg
- Department of Medicine, Duke University Medical Center, Durham, NC 27710 USA
| | - Charles B Cairns
- Department of Emergency Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599 USA
| | - Ronny M Otero
- Department of Emergency Medicine, Henry Ford Hospital, Detroit, Michigan 48202 USA ; Department of Emergency Medicine, University of Michigan, Ann Arbor, MI 48109 USA
| | - Vance G Fowler
- Department of Medicine, Duke University Medical Center, Durham, NC 27710 USA
| | - Emanuel P Rivers
- Department of Emergency Medicine, Henry Ford Hospital, Detroit, Michigan 48202 USA
| | - Christopher W Woods
- Department of Medicine, Duke University Medical Center, Durham, NC 27710 USA ; Medicine Service, Durham Veterans Affairs Medical Center, Durham, NC 27705 USA
| | - Stephen F Kingsmore
- National Center for Genome Resources, Santa Fe, NM 87505 USA ; Department of Pediatrics, Center for Translational Sciences, University of New Mexico, Albuquerque, NM 87131 USA
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25
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Raje N, Soden S, Swanson D, Ciaccio CE, Kingsmore SF, Dinwiddie DL. Utility of next generation sequencing in clinical primary immunodeficiencies. Curr Allergy Asthma Rep 2014; 14:468. [PMID: 25149170 DOI: 10.1007/s11882-014-0468-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Primary immunodeficiencies (PIDs) are a group of genetically heterogeneous disorders that present with very similar symptoms, complicating definitive diagnosis. More than 240 genes have hitherto been associated with PIDs, of which more than 30 have been identified in the last 3 years. Next generation sequencing (NGS) of genomes or exomes of informative families has played a central role in the discovery of novel PID genes. Furthermore, NGS has the potential to transform clinical molecular testing for established PIDs, allowing all PID differential diagnoses to be tested at once, leading to increased diagnostic yield, while decreasing both the time and cost of obtaining a molecular diagnosis. Given that treatment of PID varies by disease gene, early achievement of a molecular diagnosis is likely to enhance treatment decisions and improve patient outcomes.
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Affiliation(s)
- Nikita Raje
- Children's Mercy Hospital, 2401 Gillham Road, Kansas City, MO, 64108, USA,
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26
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Caracciolo S, Moratto D, Giacomelli M, Negri S, Lougaris V, Porta F, Pajno G, Salpietro A, Montin D, Dinwiddie DL, Kingsmore SF, Plebani A, Badolato R. Expansion of CCR4+ activated T cells is associated with memory B cell reduction in DOCK8-deficient patients. Clin Immunol 2014; 152:164-70. [DOI: 10.1016/j.clim.2014.03.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 03/11/2014] [Accepted: 03/12/2014] [Indexed: 10/25/2022]
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Dinwiddie DL, Soden SE, Saunders CJ, Miller NA, Farrow EG, Smith LD, Kingsmore SF. De novo frameshift mutation in ASXL3 in a patient with global developmental delay, microcephaly, and craniofacial anomalies. BMC Med Genomics 2013; 6:32. [PMID: 24044690 PMCID: PMC3851682 DOI: 10.1186/1755-8794-6-32] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 09/11/2013] [Indexed: 12/23/2022] Open
Abstract
Background Currently, diagnosis of affected individuals with rare genetic disorders can be lengthy and costly, resulting in a diagnostic odyssey and in many patients a definitive molecular diagnosis is never achieved despite extensive clinical investigation. The recent advent and use of genomic medicine has resulted in a paradigm shift in the clinical molecular genetics of rare diseases and has provided insight into the causes of numerous rare genetic conditions. In particular, whole exome and genome sequencing of families has been particularly useful in discovering de novo germline mutations as the cause of both rare diseases and complex disorders. Case presentation We present a six year old, nonverbal African American female with microcephaly, autism, global developmental delay, and metopic craniosynostosis. Exome sequencing of the patient and her two parents revealed a heterozygous two base pair de novo deletion, c.1897_1898delCA, p.Gln633ValfsX13 in ASXL3, predicted to result in a frameshift at codon 633 with substitution of a valine for a glutamine and introduction of a premature stop codon. Conclusions We provide additional evidence that, truncating and frameshifting mutations in the ASXL3 gene are the cause of a newly recognized disorder characterized by severe global developmental delay, short stature, microcephaly, and craniofacial anomalies. Furthermore, we expand the knowledge about disease causing mutations and the genotype-phenotype relationships in ASXL3 and provide evidence that rare, nonsynonymous, damaging mutations are not associated with developmental delay or microcephaly.
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Affiliation(s)
- Darrell L Dinwiddie
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA.
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28
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Langley RJ, Tsalik EL, van Velkinburgh JC, Glickman SW, Rice BJ, Wang C, Chen B, Carin L, Suarez A, Mohney RP, Freeman DH, Wang M, You J, Wulff J, Thompson JW, Moseley MA, Reisinger S, Edmonds BT, Grinnell B, Nelson DR, Dinwiddie DL, Miller NA, Saunders CJ, Soden SS, Rogers AJ, Gazourian L, Fredenburgh LE, Massaro AF, Baron RM, Choi AMK, Corey GR, Ginsburg GS, Cairns CB, Otero RM, Fowler VG, Rivers EP, Woods CW, Kingsmore SF. An integrated clinico-metabolomic model improves prediction of death in sepsis. Sci Transl Med 2013; 5:195ra95. [PMID: 23884467 DOI: 10.1126/scitranslmed.3005893] [Citation(s) in RCA: 322] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Sepsis is a common cause of death, but outcomes in individual patients are difficult to predict. Elucidating the molecular processes that differ between sepsis patients who survive and those who die may permit more appropriate treatments to be deployed. We examined the clinical features and the plasma metabolome and proteome of patients with and without community-acquired sepsis, upon their arrival at hospital emergency departments and 24 hours later. The metabolomes and proteomes of patients at hospital admittance who would ultimately die differed markedly from those of patients who would survive. The different profiles of proteins and metabolites clustered into the following groups: fatty acid transport and β-oxidation, gluconeogenesis, and the citric acid cycle. They differed consistently among several sets of patients, and diverged more as death approached. In contrast, the metabolomes and proteomes of surviving patients with mild sepsis did not differ from survivors with severe sepsis or septic shock. An algorithm derived from clinical features together with measurements of five metabolites predicted patient survival. This algorithm may help to guide the treatment of individual patients with sepsis.
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29
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Dinwiddie DL, Kingsmore SF, Caracciolo S, Rossi G, Moratto D, Mazza C, Sabelli C, Bacchetta R, Passerini L, Magri C, Bell CJ, Miller NA, Hateley SL, Saunders CJ, Zhang L, Schroth GP, Barlati S, Badolato R. Combined DOCK8 and CLEC7A mutations causing immunodeficiency in 3 brothers with diarrhea, eczema, and infections. J Allergy Clin Immunol 2013; 131:594-7.e1-3. [PMID: 23374272 DOI: 10.1016/j.jaci.2012.10.062] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Revised: 10/29/2012] [Accepted: 10/31/2012] [Indexed: 11/25/2022]
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30
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Dinwiddie DL, Smith LD, Miller NA, Atherton AM, Farrow EG, Strenk ME, Soden SE, Saunders CJ, Kingsmore SF. Diagnosis of mitochondrial disorders by concomitant next-generation sequencing of the exome and mitochondrial genome. Genomics 2013; 102:148-56. [PMID: 23631824 DOI: 10.1016/j.ygeno.2013.04.013] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/18/2013] [Accepted: 04/19/2013] [Indexed: 01/22/2023]
Abstract
Mitochondrial diseases are notoriously difficult to diagnose due to extreme locus and allelic heterogeneity, with both nuclear and mitochondrial genomes potentially liable. Using exome sequencing we demonstrate the ability to rapidly and cost effectively evaluate both the nuclear and mitochondrial genomes to obtain a molecular diagnosis for four patients with three distinct mitochondrial disorders. One patient was found to have Leigh syndrome due to a mutation in MT-ATP6, two affected siblings were discovered to be compound heterozygous for mutations in the NDUFV1 gene, which causes mitochondrial complex I deficiency, and one patient was found to have coenzyme Q10 deficiency due to compound heterozygous mutations in COQ2. In all cases conventional diagnostic testing failed to identify a molecular diagnosis. We suggest that additional studies should be conducted to evaluate exome sequencing as a primary diagnostic test for mitochondrial diseases, including those due to mtDNA mutations.
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Affiliation(s)
- Darrell L Dinwiddie
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA.
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Lamour KH, Mudge J, Gobena D, Hurtado-Gonzales OP, Schmutz J, Kuo A, Miller NA, Rice BJ, Raffaele S, Cano LM, Bharti AK, Donahoo RS, Finley S, Huitema E, Hulvey J, Platt D, Salamov A, Savidor A, Sharma R, Stam R, Storey D, Thines M, Win J, Haas BJ, Dinwiddie DL, Jenkins J, Knight JR, Affourtit JP, Han CS, Chertkov O, Lindquist EA, Detter C, Grigoriev IV, Kamoun S, Kingsmore SF. Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici. Mol Plant Microbe Interact 2012; 25:1350-60. [PMID: 22712506 PMCID: PMC3551261 DOI: 10.1094/mpmi-02-12-0028-r] [Citation(s) in RCA: 181] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diverse isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30% of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.
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Kingsmore SF, Dinwiddie DL, Miller NA, Soden SE, Saunders CJ. Adopting orphans: comprehensive genetic testing of Mendelian diseases of childhood by next-generation sequencing. Expert Rev Mol Diagn 2012; 11:855-68. [PMID: 22022947 DOI: 10.1586/erm.11.70] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Orphan diseases are individually uncommon but collectively contribute significantly to pediatric morbidity, mortality and healthcare costs. Current molecular testing for rare genetic disorders is often a lengthy and costly endeavor, and in many cases a molecular diagnosis is never achieved despite extensive testing. Diseases with locus heterogeneity or overlapping signs and symptoms are especially challenging owing to the number of potential targets. Consequently, there is immense need for scalable, economical, rapid, multiplexed diagnostic testing for rare Mendelian diseases. Recent advances in next-generation sequencing and bioinformatic technologies have the potential to change the standard of care for the diagnosis of rare genetic disorders. These advances will be reviewed in the setting of a recently developed test for 592 autosomal recessive and X-linked diseases.
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Affiliation(s)
- Stephen F Kingsmore
- Children's Mercy Hospital & Clinics, 2401 Gillham Road, Kansas City, MO 64108, USA.
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Kingsmore SF, Lantos JD, Dinwiddie DL, Miller NA, Soden SE, Farrow EG, Saunders CJ. Next-generation community genetics for low- and middle-income countries. Genome Med 2012; 4:25. [PMID: 22458566 PMCID: PMC3446275 DOI: 10.1186/gm324] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A recent report by the World Health Organization calls for implementation of community genetics programs in low- and middle-income countries (LMICs). Their focus is prevention of congenital disorders and genetic diseases at the population level, in addition to providing genetics services, including diagnosis and counseling. The proposed strategies include both newborn screening and population screening for carrier detection, in addition to lowering the incidence of congenital disorders and genetic diseases through the removal of environmental factors. In this article, we consider the potential impact of such testing on global health and highlight the near-term relevance of next-generation sequencing (NGS) and bioinformatic approaches to their implementation. Key attributes of NGS for community genetics programs are homogeneous approach, high multiplexing of diseases and samples, as well as rapidly falling costs of new technologies. In the near future, we estimate that appropriate use of population-specific test panels could cost as little as $10 for 10 Mendelian disorders and could have a major impact on diseases that currently affect 2% of children worldwide. However, the successful deployment of this technological innovation in LMICs will require high value for human life, thoughtful implementation, and autonomy of individual decisions, supported by appropriate genetic counseling and community education.
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Affiliation(s)
- Stephen F Kingsmore
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals and Clinics, 2401 Gilham Road, Kansas City, MO 64108, USA
| | - John D Lantos
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals and Clinics, 2401 Gilham Road, Kansas City, MO 64108, USA
| | - Darrell L Dinwiddie
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals and Clinics, 2401 Gilham Road, Kansas City, MO 64108, USA
| | - Neil A Miller
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals and Clinics, 2401 Gilham Road, Kansas City, MO 64108, USA
| | - Sarah E Soden
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals and Clinics, 2401 Gilham Road, Kansas City, MO 64108, USA
| | - Emily G Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals and Clinics, 2401 Gilham Road, Kansas City, MO 64108, USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals and Clinics, 2401 Gilham Road, Kansas City, MO 64108, USA
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Jie Z, Dinwiddie DL, Senft AP, Harrod KS. Regulation of STAT signaling in mouse bone marrow derived dendritic cells by respiratory syncytial virus. Virus Res 2011; 156:127-33. [PMID: 21255624 DOI: 10.1016/j.virusres.2011.01.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 01/11/2011] [Accepted: 01/13/2011] [Indexed: 10/18/2022]
Abstract
BACKGROUND/AIMS Dendritic cells (DCs) act as a portal for virus invasion as well as potent antigen-presenting cells (APCs) involved in the antiviral host response. Interferons (IFNs) are produced in response to bacterial and viral infection and activate innate immune responses to efficiently counteract and remove pathogenic invaders. Respiratory syncytial virus (RSV) could inhibit IFN-mediated signaling pathway in epithelial cells; however, the effects of RSV on IFN signaling in the dendritic cells (DCs) are still unknown. METHODS Mouse bone marrow derived DCs (BMDCs) were mock or infected with RSV at different multiplicity of infection (MOI) for 24h, and then treated with different cytokines such as interferon-β (IFN-β), IFN-γ or interleukin-10 (IL-10). The mRNA expression of RSV nonstructural protein-1 (NS-1) and NS-2 was detected by RT-PCR. The expression of Janus family kinase-signal transducer and activator of transcription (JAK/STAT) signaling proteins was assessed by immunoblotting assays. The nuclear localization of specific signaling proteins was determined by immunofluorescence assay. RESULTS Increasing amounts of NS-1 or NS-2 mRNA expression in BMDCs were observed with infected RSV at increasing MOI, suggesting BMDCs were permissive for viral gene expression. Further examination of the IFN-β signaling cascade showed RSV infection increased the total cellular levels of STAT1 and STAT2 in BMDCs, but impaired the IFN-β-dependent phosphorylation and nuclear localization of STAT1 and STAT2. The inhibitory effects of RSV on STAT1 and STAT2 phosphorylation and translocation were abolished by UV inactivation. In contrast, RSV did not inhibit the IFN-γ-stimulated STAT1 phosphorylation and nuclear localization. IL-10-stimulated STAT3 phosphorylation was also unaffected by RSV. CONCLUSIONS As well as RSV inhibiting STAT protein levels through degradation mechanisms in epithelial cells, these findings demonstrate that RSV also can specifically inhibit the type I interferon response in BMDCs through regulation of STAT1 and STAT2 phosphorylation and nuclear translocation.
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Affiliation(s)
- Zhijun Jie
- Infectious Diseases Program, Lovelace Respiratory Research Institute, Albuquerque, NM 87108, USA.
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Bell CJ, Dinwiddie DL, Miller NA, Hateley SL, Ganusova EE, Mudge J, Langley RJ, Zhang L, Lee CC, Schilkey FD, Sheth V, Woodward JE, Peckham HE, Schroth GP, Kim RW, Kingsmore SF. Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci Transl Med 2011; 3:65ra4. [PMID: 21228398 PMCID: PMC3740116 DOI: 10.1126/scitranslmed.3001756] [Citation(s) in RCA: 479] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Of 7028 disorders with suspected Mendelian inheritance, 1139 are recessive and have an established molecular basis. Although individually uncommon, Mendelian diseases collectively account for ~20% of infant mortality and ~10% of pediatric hospitalizations. Preconception screening, together with genetic counseling of carriers, has resulted in remarkable declines in the incidence of several severe recessive diseases including Tay-Sachs disease and cystic fibrosis. However, extension of preconception screening to most severe disease genes has hitherto been impractical. Here, we report a preconception carrier screen for 448 severe recessive childhood diseases. Rather than costly, complete sequencing of the human genome, 7717 regions from 437 target genes were enriched by hybrid capture or microdroplet polymerase chain reaction, sequenced by next-generation sequencing (NGS) to a depth of up to 2.7 gigabases, and assessed with stringent bioinformatic filters. At a resultant 160x average target coverage, 93% of nucleotides had at least 20x coverage, and mutation detection/genotyping had ~95% sensitivity and ~100% specificity for substitution, insertion/deletion, splicing, and gross deletion mutations and single-nucleotide polymorphisms. In 104 unrelated DNA samples, the average genomic carrier burden for severe pediatric recessive mutations was 2.8 and ranged from 0 to 7. The distribution of mutations among sequenced samples appeared random. Twenty-seven percent of mutations cited in the literature were found to be common polymorphisms or misannotated, underscoring the need for better mutation databases as part of a comprehensive carrier testing strategy. Given the magnitude of carrier burden and the lower cost of testing compared to treating these conditions, carrier screening by NGS made available to the general population may be an economical way to reduce the incidence of and ameliorate suffering associated with severe recessive childhood disorders.
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Affiliation(s)
- Callum J. Bell
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Darrell L. Dinwiddie
- National Center for Genome Resources, Santa Fe, NM 87505, USA
- Children’s Mercy Hospital, Kansas City, MO 64108, USA
| | - Neil A. Miller
- National Center for Genome Resources, Santa Fe, NM 87505, USA
- Children’s Mercy Hospital, Kansas City, MO 64108, USA
| | | | | | - Joann Mudge
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Ray J. Langley
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Lu Zhang
- Illumina Inc., Hayward, CA 94545, USA
| | | | | | | | | | | | | | - Ryan W. Kim
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Stephen F. Kingsmore
- National Center for Genome Resources, Santa Fe, NM 87505, USA
- Children’s Mercy Hospital, Kansas City, MO 64108, USA
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Li Y, Dinwiddie DL, Harrod KS, Jiang Y, Kim KC. Anti-inflammatory effect of MUC1 during respiratory syncytial virus infection of lung epithelial cells in vitro. Am J Physiol Lung Cell Mol Physiol 2010; 298:L558-63. [PMID: 20081068 DOI: 10.1152/ajplung.00225.2009] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
MUC1 is a transmembrane glycoprotein expressed on the apical surface of airway epithelial cells and plays an anti-inflammatory role during airway bacterial infection. In this study, we determined whether the anti-inflammatory effect of MUC1 is also operative during the respiratory syncytial virus (RSV) infection. The lung epithelial cell line A549 was treated with RSV, and the production of TNFalpha and the levels of MUC1 protein were monitored temporally during the course of infection by ELISA and Western blot analysis. Small inhibitory RNA (siRNA) transfection was utilized to assess the role of MUC1 in regulating RSV-mediated inflammatory responses by lung epithelial cells. Our results revealed that: 1) following RSV infection, an increase in MUC1 level was preceded by an increase in TNFalpha production and completely inhibited by soluble TNF receptor (TNFR); and 2) knockdown of MUC1 using MUC1 siRNA resulted in a greater increase in TNFalpha level following RSV infection compared with control siRNA treatment. We conclude that the RSV-induced increase in the TNFalpha levels upregulates MUC1 through its interaction with TNFR, which in turn suppresses further increase in TNFalpha by RSV, thus forming a negative feedback loop in the control of RSV-induced inflammation. This is the first demonstration showing that MUC1 can suppress the virus-induced inflammatory responses.
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Affiliation(s)
- Yusheng Li
- Department of Physiology and Lung Center, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, USA
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Dinwiddie DL, Harrod KS. Human Metapneumovirus Inhibits IFN-α Signaling through Inhibition of STAT1 Phosphorylation. Am J Respir Cell Mol Biol 2008; 38:661-70. [DOI: 10.1165/rcmb.2007-0285oc] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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