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Erickson DE, Simmons KM, Barrand ZA, Ridenour CL, Hawkinson PB, Lemke L, Sellner SP, Brock BN, Rivas AN, Sheridan K, Lemmer D, Yaglom HD, Porter WT, Belanger M, Torrey RM, Stills AJR, McCormack K, Black M, Holmes W, Rostain D, Mikus J, Sotelo K, Haq E, Neupane R, Weiss J, Johnson J, Collins C, Avalle S, White C, Howard BJ, Maltinsky SA, Whealy RN, Gordon NB, Sahl JW, Pearson T, Fofanov VY, Furstenau T, Driebe EM, Caporaso JG, Barber J, Terriquez J, Engelthaler DM, Hepp CM. Pan-Enterovirus Characterization Reveals Cryptic Circulation of Clinically Relevant Subtypes in Arizona Wastewater. medRxiv 2024:2023.11.20.23297677. [PMID: 38562876 PMCID: PMC10984038 DOI: 10.1101/2023.11.20.23297677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Background Most seasonally circulating enteroviruses result in asymptomatic or mildly symptomatic infections. In rare cases, however, infection with some subtypes can result in paralysis or death. Of the 300 subtypes known, only poliovirus is reportable, limiting our understanding of the distribution of other enteroviruses that can cause clinical disease. Objective The overarching objectives of this study were to: 1) describe the distribution of enteroviruses in Arizona during the late summer and fall of 2022, the time of year when they are thought to be most abundant, and 2) demonstrate the utility of viral pan-assay approaches for semi-agnostic discovery that can be followed up by more targeted assays and phylogenomics. Methods This study utilizes pooled nasal samples collected from school-aged children and long-term care facility residents, and wastewater from multiple locations in Arizona during July-October of 2022. We used PCR to amplify and sequence a region common to all enteroviruses, followed by species-level bioinformatic characterization using the QIIME 2 platform. For Enterovirus-D68 (EV-D68), detection was carried out using RT-qPCR, followed by confirmation using near-complete whole EV-D68 genome sequencing using a newly designed tiled amplicon approach. Results In the late summer and early fall of 2022, multiple enterovirus species were identified in Arizona wastewater, with Coxsackievirus A6, EV-D68, and Coxsackievirus A19 composing 86% of the characterized reads sequenced. While EV-D68 was not identified in pooled human nasal samples, and the only reported acute flaccid myelitis case in Arizona did not test positive for the virus, an in-depth analysis of EV-D68 in wastewater revealed that the virus was circulating from August through mid-October. A phylogenetic analysis on this relatively limited dataset revealed just a few importations into the state, with a single clade indicating local circulation. Significance This study further supports the utility of wastewater-based epidemiology to identify potential public health threats. Our further investigations into EV-D68 shows how these data might help inform healthcare diagnoses for children presenting with concerning neurological symptoms.
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Affiliation(s)
- Daryn E Erickson
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Kyle M Simmons
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Zachary A Barrand
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Chase L Ridenour
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - Paige B Hawkinson
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Lacey Lemke
- Northern Arizona Healthcare, Flagstaff, AZ, USA
| | - Shayne P Sellner
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Breezy N Brock
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Alexis N Rivas
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | | | - Darrin Lemmer
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - Hayley D Yaglom
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - W Tanner Porter
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | | | - Rachel M Torrey
- City of Flagstaff, Water Services Division, Flagstaff, AZ, USA
| | | | - Kiley McCormack
- City of Flagstaff, Water Services Division, Flagstaff, AZ, USA
| | - Matt Black
- City of Flagstaff, Water Services Division, Flagstaff, AZ, USA
| | - Wydale Holmes
- City of Tempe, Municipal Utilities Department, Tempe, AZ, USA
| | - Drew Rostain
- City of Tempe, Municipal Utilities Department, Tempe, AZ, USA
| | - Jeremy Mikus
- City of Tempe, Municipal Utilities Department, Tempe, AZ, USA
| | - Kimberly Sotelo
- City of Tempe, Municipal Utilities Department, Tempe, AZ, USA
| | - Emmen Haq
- City of Tempe, Municipal Utilities Department, Tempe, AZ, USA
| | | | - Joli Weiss
- Arizona Department of Health Services, Phoenix, AZ, USA
| | | | | | - Sarah Avalle
- Arizona Department of Health Services, Phoenix, AZ, USA
| | - Chelsi White
- Maricopa County Department of Public Health, Phoenix, AZ, USA
| | | | - Sara A Maltinsky
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Ryann N Whealy
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Nathaniel B Gordon
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jason W Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Talima Pearson
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Viacheslav Y Fofanov
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Tara Furstenau
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | | | - J Gregory Caporaso
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jarrett Barber
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | | | | | - Crystal M Hepp
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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2
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Bowers JR, Parise KL, Kelley EJ, Lemmer D, Schupp JM, Driebe EM, Engelthaler DM, Keim P, Barker BM. Direct detection of Coccidioides from Arizona soils using CocciENV, a highly sensitive and specific real-time PCR assay. Med Mycol 2019. [PMID: 29534236 DOI: 10.1093/mmy/myy007] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Coccidioides immitis and Coccidioides posadasii are soil fungi endemic to desert regions of the southwestern United States, and the causative agents of valley fever, or coccidioidomycosis. Studies have shown that the distribution of Coccidioides in soils is sporadic and cannot be explained by soil characteristics alone, suggesting that biotic and other abiotic factors should be examined. However, tools to reliably and robustly screen the large number of soils needed to investigate these potential associations have not been available. Thus, we developed a real-time polymerase chain reaction (PCR) assay for testing environmental samples by modifying CocciDx, an assay validated for testing clinical specimens to facilitate coccidioidomycosis diagnosis. For this study, we collected soil samples from previously established locations of C. posadasii in Arizona and new locations in fall 2013 and spring 2014, and screened the extracted DNA with the new assay known as CocciEnv. To verify the presence of Coccidioides in soil using an alternate method, we employed next generation amplicon sequencing targeting the ITS2 region. Results show our modified assay, CocciEnv, is a rapid and robust method for detecting Coccidioides DNA in complex environmental samples. The ability to test a large number of soils for the presence of Coccidioides is a much-needed tool in the understanding of the ecology of the organism and epidemiology of the disease and will greatly improve our understanding of this human pathogen.
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Affiliation(s)
- J R Bowers
- Pathogen Genomics Division, Translational Genomics Research Institute North, Flagstaff, Arizona
| | - K L Parise
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona
| | - E J Kelley
- Pathogen Genomics Division, Translational Genomics Research Institute North, Flagstaff, Arizona
| | - D Lemmer
- Pathogen Genomics Division, Translational Genomics Research Institute North, Flagstaff, Arizona
| | - J M Schupp
- Pathogen Genomics Division, Translational Genomics Research Institute North, Flagstaff, Arizona
| | - E M Driebe
- Pathogen Genomics Division, Translational Genomics Research Institute North, Flagstaff, Arizona
| | - D M Engelthaler
- Pathogen Genomics Division, Translational Genomics Research Institute North, Flagstaff, Arizona
| | - P Keim
- Pathogen Genomics Division, Translational Genomics Research Institute North, Flagstaff, Arizona.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona
| | - B M Barker
- Pathogen Genomics Division, Translational Genomics Research Institute North, Flagstaff, Arizona.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona
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Engelthaler DM, Valentine M, Bowers J, Pistole J, Driebe EM, Terriquez J, Nienstadt L, Carroll M, Schumacher M, Ormsby ME, Brady S, Livar E, Yazzie D, Waddell V, Peoples M, Komatsu K, Keim P. Hypervirulent emm59 Clone in Invasive Group A Streptococcus Outbreak, Southwestern United States. Emerg Infect Dis 2016; 22:734-8. [PMID: 26982330 PMCID: PMC4806960 DOI: 10.3201/eid2204.151582] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The hyper-virulent emm59 genotype of invasive group A Streptococcus was identified in northern Arizona in 2015. Eighteen isolates belonging to a genomic cluster grouped most closely with recently identified isolates in New Mexico. The continued transmission of emm59 in the southwestern United States poses a public health concern.
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4
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Roe CC, Horn KS, Driebe EM, Bowers J, Terriquez JA, Keim P, Engelthaler DM. Whole genome SNP typing to investigate methicillin-resistant Staphylococcus aureus carriage in a health-care provider as the source of multiple surgical site infections. Hereditas 2016; 153:11. [PMID: 28096773 PMCID: PMC5226111 DOI: 10.1186/s41065-016-0017-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/26/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Prevention of nosocomial transmission of infections is a central responsibility in the healthcare environment, and accurate identification of transmission events presents the first challenge. Phylogenetic analysis based on whole genome sequencing provides a high-resolution approach for accurately relating isolates to one another, allowing precise identification or exclusion of transmission events and sources for nearly all cases. We sequenced 24 methicillin-resistant Staphylococcus aureus (MRSA) genomes to retrospectively investigate a suspected point source of three surgical site infections (SSIs) that occurred over a one-year period. The source of transmission was believed to be a surgical team member colonized with MRSA, involved in all surgeries preceding the SSI cases, who was subsequently decolonized. Genetic relatedness among isolates was determined using whole genome single nucleotide polymorphism (SNP) data. RESULTS Whole genome SNP typing (WGST) revealed 283 informative SNPs between the surgical team member's isolate and the closest SSI isolate. The second isolate was 286 and the third was thousands of SNPs different, indicating the nasal carriage strain from the surgical team member was not the source of the SSIs. Given the mutation rates estimated for S. aureus, none of the SSI isolates share a common ancestor within the past 16 years, further discounting any common point source for these infections. The decolonization procedures and resources spent on the point source infection control could have been prevented if WGST was performed at the time of the suspected transmission, instead of retrospectively. CONCLUSIONS Whole genome sequence analysis is an ideal method to exclude isolates involved in transmission events and nosocomial outbreaks, and coupling this method with epidemiological data can determine if a transmission event occurred. These methods promise to direct infection control resources more appropriately.
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Affiliation(s)
- Chandler C. Roe
- Pathogen Genomics Division, Translational Genomics Research Institute, 3051 W. Shamrell Blvd., Suite 106, Flagstaff, AZ 86001 USA
| | | | - Elizabeth M. Driebe
- Pathogen Genomics Division, Translational Genomics Research Institute, 3051 W. Shamrell Blvd., Suite 106, Flagstaff, AZ 86001 USA
| | - Jolene Bowers
- Pathogen Genomics Division, Translational Genomics Research Institute, 3051 W. Shamrell Blvd., Suite 106, Flagstaff, AZ 86001 USA
| | | | - Paul Keim
- Pathogen Genomics Division, Translational Genomics Research Institute, 3051 W. Shamrell Blvd., Suite 106, Flagstaff, AZ 86001 USA
| | - David M. Engelthaler
- Pathogen Genomics Division, Translational Genomics Research Institute, 3051 W. Shamrell Blvd., Suite 106, Flagstaff, AZ 86001 USA
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5
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Etienne KA, Roe CC, Smith RM, Vallabhaneni S, Duarte C, Escadon P, Castaneda E, Gomez BL, de Bedout C, López LF, Salas V, Hederra LM, Fernandez J, Pidal P, Hormazabel JC, Otaiza F, Vannberg FO, Gillece J, Lemmer D, Driebe EM, Englethaler DM, Litvintseva AP. Whole-Genome Sequencing to Determine Origin of Multinational Outbreak of Sarocladium kiliense Bloodstream Infections. Emerg Infect Dis 2016; 22:476-81. [PMID: 26891230 PMCID: PMC4766898 DOI: 10.3201/eid2203.151193] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Next-generation technologies and bioinformatics enabled source attribution and implementation of effective control strategies. We used whole-genome sequence typing (WGST) to investigate an outbreak of Sarocladium kiliense bloodstream infections (BSI) associated with receipt of contaminated antinausea medication among oncology patients in Colombia and Chile during 2013–2014. Twenty-five outbreak isolates (18 from patients and 7 from medication vials) and 11 control isolates unrelated to this outbreak were subjected to WGST to elucidate a source of infection. All outbreak isolates were nearly indistinguishable (<5 single-nucleotide polymorphisms), and >21,000 single-nucleotide polymorphisms were identified from unrelated control isolates, suggesting a point source for this outbreak. S. kiliense has been previously implicated in healthcare-related infections; however, the lack of available typing methods has precluded the ability to substantiate point sources. WGST for outbreak investigation caused by eukaryotic pathogens without reference genomes or existing genotyping methods enables accurate source identification to guide implementation of appropriate control and prevention measures.
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Sahl JW, Lemmer D, Travis J, Schupp JM, Gillece JD, Aziz M, Driebe EM, Drees KP, Hicks ND, Williamson CHD, Hepp CM, Smith DE, Roe C, Engelthaler DM, Wagner DM, Keim P. NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats. Microb Genom 2016; 2:e000074. [PMID: 28348869 DOI: 10.1099/mgen.0.000074] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/17/2016] [Indexed: 12/30/2022] Open
Abstract
Whole-genome sequencing (WGS) of bacterial isolates has become standard practice in many laboratories. Applications for WGS analysis include phylogeography and molecular epidemiology, using single nucleotide polymorphisms (SNPs) as the unit of evolution. NASP was developed as a reproducible method that scales well with the hundreds to thousands of WGS data typically used in comparative genomics applications. In this study, we demonstrate how NASP compares with other tools in the analysis of two real bacterial genomics datasets and one simulated dataset. Our results demonstrate that NASP produces similar, and often better, results in comparison with other pipelines, but is much more flexible in terms of data input types, job management systems, diversity of supported tools and output formats. We also demonstrate differences in results based on the choice of the reference genome and choice of inferring phylogenies from concatenated SNPs or alignments including monomorphic positions. NASP represents a source-available, version-controlled, unit-tested method and can be obtained from tgennorth.github.io/NASP.
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Affiliation(s)
- Jason W Sahl
- 1Translational Genomics Research Institute, Phoenix, Arizona, USA.,2Northern Arizona University, S San Francisco St, Flagstaff, AZ 86011, USA
| | - Darrin Lemmer
- 1Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Jason Travis
- 1Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - James M Schupp
- 1Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - John D Gillece
- 1Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Maliha Aziz
- 3The George Washington University, 2121 I St NW, Washington, DC 20052, USA
| | | | - Kevin P Drees
- 4University of New Hampshire, 105 Main St, Durham, NH 03824, USA
| | | | | | - Crystal M Hepp
- 2Northern Arizona University, S San Francisco St, Flagstaff, AZ 86011, USA
| | - David Earl Smith
- 1Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Chandler Roe
- 1Translational Genomics Research Institute, Phoenix, Arizona, USA
| | | | - David M Wagner
- 2Northern Arizona University, S San Francisco St, Flagstaff, AZ 86011, USA
| | - Paul Keim
- 2Northern Arizona University, S San Francisco St, Flagstaff, AZ 86011, USA
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7
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Bowers JR, Kitchel B, Driebe EM, MacCannell DR, Roe C, Lemmer D, de Man T, Rasheed JK, Engelthaler DM, Keim P, Limbago BM. Genomic Analysis of the Emergence and Rapid Global Dissemination of the Clonal Group 258 Klebsiella pneumoniae Pandemic. PLoS One 2015; 10:e0133727. [PMID: 26196384 PMCID: PMC4510304 DOI: 10.1371/journal.pone.0133727] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 07/01/2015] [Indexed: 11/19/2022] Open
Abstract
Multidrug-resistant Klebsiella pneumoniae producing the KPC carbapenemase have rapidly spread throughout the world, causing severe healthcare-associated infections with limited antimicrobial treatment options. Dissemination of KPC-producing K. pneumoniae is largely attributed to expansion of a single dominant strain, ST258. In this study, we explore phylogenetic relationships and evolution within ST258 and its clonal group, CG258, using whole genome sequence analysis of 167 isolates from 20 countries collected over 17 years. Our results show a common ST258 ancestor emerged from its diverse parental clonal group around 1995 and likely acquired blaKPC prior to dissemination. Over the past two decades, ST258 has remained highly clonal despite diversity in accessory elements and divergence in the capsule polysaccharide synthesis locus. Apart from the large recombination event that gave rise to ST258, few mutations set it apart from its clonal group. However, one mutation occurs in a global transcription regulator. Characterization of outer membrane protein sequences revealed a profile in ST258 that includes a truncated OmpK35 and modified OmpK37. Our work illuminates potential genomic contributors to the pathogenic success of ST258, helps us better understand the global dissemination of this strain, and identifies genetic markers unique to ST258.
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Affiliation(s)
- Jolene R. Bowers
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Brandon Kitchel
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Elizabeth M. Driebe
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Duncan R. MacCannell
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Chandler Roe
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Darrin Lemmer
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Tom de Man
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - J. Kamile Rasheed
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - David M. Engelthaler
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Paul Keim
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Brandi M. Limbago
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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8
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Driebe EM, Sahl JW, Roe C, Bowers JR, Schupp JM, Gillece JD, Kelley E, Price LB, Pearson TR, Hepp CM, Brzoska PM, Cummings CA, Furtado MR, Andersen PS, Stegger M, Engelthaler DM, Keim PS. Using Whole Genome Analysis to Examine Recombination across Diverse Sequence Types of Staphylococcus aureus. PLoS One 2015; 10:e0130955. [PMID: 26161978 PMCID: PMC4498916 DOI: 10.1371/journal.pone.0130955] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [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: 09/06/2013] [Accepted: 05/27/2015] [Indexed: 12/29/2022] Open
Abstract
Staphylococcus aureus is an important clinical pathogen worldwide and understanding this organism's phylogeny and, in particular, the role of recombination, is important both to understand the overall spread of virulent lineages and to characterize outbreaks. To further elucidate the phylogeny of S. aureus, 35 diverse strains were sequenced using whole genome sequencing. In addition, 29 publicly available whole genome sequences were included to create a single nucleotide polymorphism (SNP)-based phylogenetic tree encompassing 11 distinct lineages. All strains of a particular sequence type fell into the same clade with clear groupings of the major clonal complexes of CC8, CC5, CC30, CC45 and CC1. Using a novel analysis method, we plotted the homoplasy density and SNP density across the whole genome and found evidence of recombination throughout the entire chromosome, but when we examined individual clonal lineages we found very little recombination. However, when we analyzed three branches of multiple lineages, we saw intermediate and differing levels of recombination between them. These data demonstrate that in S. aureus, recombination occurs across major lineages that subsequently expand in a clonal manner. Estimated mutation rates for the CC8 and CC5 lineages were different from each other. While the CC8 lineage rate was similar to previous studies, the CC5 lineage was 100-fold greater. Fifty known virulence genes were screened in all genomes in silico to determine their distribution across major clades. Thirty-three genes were present variably across clades, most of which were not constrained by ancestry, indicating horizontal gene transfer or gene loss.
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Affiliation(s)
- Elizabeth M Driebe
- Pathogen Genomics Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Jason W Sahl
- Pathogen Genomics Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Chandler Roe
- Pathogen Genomics Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Jolene R Bowers
- Pathogen Genomics Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - James M Schupp
- Pathogen Genomics Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - John D Gillece
- Pathogen Genomics Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Erin Kelley
- Pathogen Genomics Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Lance B Price
- Pathogen Genomics Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Talima R Pearson
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Crystal M Hepp
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Pius M Brzoska
- Thermo Fisher Scientific, South San Francisco, California, United States of America
| | - Craig A Cummings
- Thermo Fisher Scientific, South San Francisco, California, United States of America
| | - Manohar R Furtado
- Thermo Fisher Scientific, South San Francisco, California, United States of America
| | - Paal S Andersen
- Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - David M Engelthaler
- Pathogen Genomics Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Paul S Keim
- Pathogen Genomics Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America; Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
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9
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Rawat A, Engelthaler DM, Driebe EM, Keim P, Foster JT. MetaGeniE: characterizing human clinical samples using deep metagenomic sequencing. PLoS One 2014; 9:e110915. [PMID: 25365329 PMCID: PMC4218713 DOI: 10.1371/journal.pone.0110915] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 09/19/2014] [Indexed: 11/19/2022] Open
Abstract
With the decreasing cost of next-generation sequencing, deep sequencing of clinical samples provides unique opportunities to understand host-associated microbial communities. Among the primary challenges of clinical metagenomic sequencing is the rapid filtering of human reads to survey for pathogens with high specificity and sensitivity. Metagenomes are inherently variable due to different microbes in the samples and their relative abundance, the size and architecture of genomes, and factors such as target DNA amounts in tissue samples (i.e. human DNA versus pathogen DNA concentration). This variation in metagenomes typically manifests in sequencing datasets as low pathogen abundance, a high number of host reads, and the presence of close relatives and complex microbial communities. In addition to these challenges posed by the composition of metagenomes, high numbers of reads generated from high-throughput deep sequencing pose immense computational challenges. Accurate identification of pathogens is confounded by individual reads mapping to multiple different reference genomes due to gene similarity in different taxa present in the community or close relatives in the reference database. Available global and local sequence aligners also vary in sensitivity, specificity, and speed of detection. The efficiency of detection of pathogens in clinical samples is largely dependent on the desired taxonomic resolution of the organisms. We have developed an efficient strategy that identifies “all against all” relationships between sequencing reads and reference genomes. Our approach allows for scaling to large reference databases and then genome reconstruction by aggregating global and local alignments, thus allowing genetic characterization of pathogens at higher taxonomic resolution. These results were consistent with strain level SNP genotyping and bacterial identification from laboratory culture.
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Affiliation(s)
- Arun Rawat
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- * E-mail: (AR); (JTF)
| | - David M. Engelthaler
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Elizabeth M. Driebe
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Paul Keim
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jeffrey T. Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, United States of America
- * E-mail: (AR); (JTF)
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Litvintseva AP, Marsden-Haug N, Hurst S, Hill H, Gade L, Driebe EM, Ralston C, Roe C, Barker BM, Goldoft M, Keim P, Wohrle R, Thompson GR, Engelthaler DM, Brandt ME, Chiller T. Valley fever: finding new places for an old disease: Coccidioides immitis found in Washington State soil associated with recent human infection. Clin Infect Dis 2014; 60:e1-3. [PMID: 25165087 DOI: 10.1093/cid/ciu681] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We used real-time polymerase chain reaction and culture to demonstrate persistent colonization of soils by Coccidioides immitis, an agent of valley fever, in Washington State linked to recent human infections and located outside the endemic range. Whole-genome sequencing confirmed genetic identity between isolates from soil and one of the case-patients.
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Affiliation(s)
| | | | - Steven Hurst
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Heather Hill
- Benton-Franklin Health District, Kennewick, Washington
| | - Lalitha Gade
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Cindy Ralston
- Benton-Franklin Health District, Kennewick, Washington
| | - Chandler Roe
- Translational Genomics Research Institute, Flagstaff, Arizona
| | | | - Marcia Goldoft
- Washington State Department of Health, Shoreline and Tumwater
| | - Paul Keim
- Translational Genomics Research Institute, Flagstaff, Arizona
| | - Ron Wohrle
- Washington State Department of Health, Shoreline and Tumwater
| | - George R Thompson
- Coccidioidomycosis Serology Laboratory, University of California, Davis
| | | | - Mary E Brandt
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Tom Chiller
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
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Marsden-Haug N, Hill H, Litvintseva AP, Engelthaler DM, Driebe EM, Roe CC, Ralston C, Hurst S, Goldoft M, Gade L, Wohrle R, Thompson GR, Brandt ME, Chiller T. Coccidioides immitis identified in soil outside of its known range - Washington, 2013. MMWR Morb Mortal Wkly Rep 2014; 63:450. [PMID: 24848217 PMCID: PMC4584917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/29/2022]
Abstract
Coccidioidomycosis ("valley fever") is caused by inhaling spores of the soil-dwelling fungi Coccidioides immitis or Coccidioides posadasii. Most infections are subclinical. When clinical manifestations do occur (typically 1-4 weeks after exposure), they are similar to those associated with influenza or community-acquired pneumonia. Disseminated disease is rare. Residual pulmonary nodules can lead to chronic lung disease. Fluconazole or other triazoles often are used for treatment, but mild cases often resolve without specific therapy. A total of 17,802 cases were reported in the United States in 2012.
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Affiliation(s)
- Nicola Marsden-Haug
- Washington State Department of Health,Corresponding author: Nicola Marsden-Haug, , 206-418-5429
| | - Heather Hill
- Benton-Franklin Health District, Kennewick, Washington
| | - Anastasia P. Litvintseva
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC
| | | | | | - Chandler C. Roe
- Translational Genomics Research Institute, Flagstaff, Arizona
| | - Cindy Ralston
- Benton-Franklin Health District, Kennewick, Washington
| | - Steven Hurst
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC
| | | | - Lalitha Gade
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC
| | | | | | - Mary E. Brandt
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC
| | - Tom Chiller
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC
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12
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Kelley EJ, Driebe EM, Etienne K, Brandt ME, Schupp JM, Gillece JD, Trujillo JS, Lockhart SR, Deak E, Keim PS, Engelthaler DM. Real-time PCR assays for genotyping of Cryptococcus gattii in North America. BMC Microbiol 2014; 14:125. [PMID: 24886039 PMCID: PMC4032356 DOI: 10.1186/1471-2180-14-125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 12/17/2013] [Accepted: 05/06/2014] [Indexed: 12/30/2022] Open
Abstract
Background Cryptococcus gattii has been the cause of an ongoing outbreak starting in 1999 on Vancouver Island, British Columbia and spreading to mainland Canada and the US Pacific Northwest. In the course of the outbreak, C. gattii has been identified outside of its previously documented climate, habitat, and host disease. Genotyping of C. gattii is essential to understand the ecological and geographical expansion of this emerging pathogen. Methods We developed and validated a mismatch amplification mutation assay (MAMA) real-time PCR panel for genotyping C. gattii molecular types VGI-VGIV and VGII subtypes a,b,c. Subtype assays were designed based on whole-genome sequence of 20 C. gattii strains. Publically available multilocus sequence typing (MLST) data from a study of 202 strains was used for the molecular type (VGI-VGIV) assay design. All assays were validated across DNA from 112 strains of diverse international origin and sample types, including animal, environmental and human. Results Validation revealed each assay on the panel is 100% sensitive, specific and concordant with MLST. The assay panel can detect down to 0.5 picograms of template DNA. Conclusions The (MAMA) real-time PCR panel for C. gattii accurately typed a collection of 112 diverse strains and demonstrated high sensitivity. This is a time and cost efficient method of genotyping C. gattii best suited for application in large-scale epidemiological studies.
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Affiliation(s)
- Erin J Kelley
- The Translational Genomics Research Institute, 3051 W, Shamrell Blvd, Ste, 106, Flagstaff, AZ 86001, USA.
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13
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Engelthaler DM, Kelley E, Driebe EM, Bowers J, Eberhard CF, Trujillo J, Decruyenaere F, Schupp JM, Mossong J, Keim P, Even J. Rapid and robust phylotyping of spa t003, a dominant MRSA clone in Luxembourg and other European countries. BMC Infect Dis 2013; 13:339. [PMID: 23879266 PMCID: PMC3733620 DOI: 10.1186/1471-2334-13-339] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [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: 01/12/2013] [Accepted: 07/18/2013] [Indexed: 11/10/2022] Open
Abstract
Background spa typing is a common genotyping tool for methicillin-resistant Staphylococcus aureus (MRSA) in Europe. Given the high prevalence of dominant clones, spa-typing is proving to be limited in its ability to distinguish outbreak isolates from background isolates. New molecular tools need to be employed to improve subtyping of dominant local MRSA strains (e.g., spa type t003). Methods Phylogenetically critical, or canonical, SNPs (can-SNPs) were identified as subtyping targets through sequence analysis of 40 MRSA whole genomes from Luxembourg. Real-time PCR assays were designed around target SNPs and validated using a repository of 240 previously sub-typed and epidemiologically characterized Luxembourg MRSA isolates, including 153 community and hospital isolates, 69 isolates from long term care (LTC) facilities, and 21 prospectively analyzed MRSA isolates. Selected isolates were also analyzed by whole genome SNP typing (WGST) for comparison to the SNP assays and other subtyping techniques. Results Fourteen real-time PCR assays were developed and validated, including two assays to determine presence of spa t003 or t008. The other twelve assays successfully provided a high degree of resolution within the t003 subtype. WGST analysis of the LTC facility isolates provided greater resolution than other subtyping tools, identifying clusters indicative of ongoing transmission within LTC facilities. Conclusions canSNP-based PCR assays are useful for local level MRSA phylotyping, especially in the presence of one or more dominant clones. The assays designed here can be easily adapted for investigating t003 MRSA strains in other regions in Western Europe. WGST provides substantially better resolution than other typing methods.
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14
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Thompson GR, Sharma S, Bays DJ, Pruitt R, Engelthaler DM, Bowers J, Driebe EM, Davis M, Libke R, Cohen SH, Pappagianis D. Coccidioidomycosis: adenosine deaminase levels, serologic parameters, culture results, and polymerase chain reaction testing in pleural fluid. Chest 2013. [PMID: 23187746 DOI: 10.1378/chest.12-1312] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
BACKGROUND In a patient with positive serum serology for coccidioidomycosis, the differential diagnosis of concurrent pleural effusions can be challenging. We, therefore, sought to clarify the performance characteristics of biochemical, serologic, and nucleic-acid-based testing in an attempt to avoid invasive procedures. The utility of adenosine deaminase (ADA), coccidioidal serology, and polymerase chain reaction (PCR) in the evaluation of pleuropulmonary coccidioidomycosis has not been previously reported. METHODS Forty consecutive patients evaluated for pleuropulmonary coccidioidomycosis were included. Demographic data, pleural fluid values, culture results, and clinical diagnoses were obtained from patient chart review. ADA testing was performed by ARUP Laboratories, coccidioidal serologic testing was performed by the University of California-Davis coccidioidomycosis serology laboratory, and PCR testing was performed by the Translational Genomics Research Institute using a previously published methodology. RESULTS Fifteen patients were diagnosed with pleuropulmonary coccidioidomycosis by European Organization for the Research and Treatment of Cancer/Mycoses Study Group criteria. Pleural fluid ADA concentrations were < 40 IU/L in all patients (range, < 1.0-28.6 IU/L; median, 4.7). The sensitivity and specificity of coccidioidal serologic testing was 100% in this study. The specificity of PCR testing was high (100%), although the overall sensitivity remained low, and was comparable to the experience of others in the clinical use of PCR for coccidioidal diagnostics. CONCLUSION Contrary to prior speculation, ADA levels in pleuropulmonary coccidioidomycosis were not elevated in this study. The sensitivity and specificity of coccidioidal serologic testing in nonserum samples remained high, but the clinical usefulness of PCR testing in pleural fluid was disappointing and was comparable to pleural fluid culture.
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Affiliation(s)
- George R Thompson
- Department of Medical Microbiology and Immunology, Coccidioidomycosis Serology Laboratory, University of California-Davis, Davis, CA; Department of Internal Medicine, Division of Infectious Diseases, University of California Davis Medical Center, Davis, CA.
| | - Shobha Sharma
- Department of Internal Medicine, Division of Infectious Diseases, University of California at San Francisco-Fresno Medical Center, Fresno, CA
| | - Derek J Bays
- Department of Medical Microbiology and Immunology, Coccidioidomycosis Serology Laboratory, University of California-Davis, Davis, CA
| | - Rachel Pruitt
- Department of Medical Microbiology and Immunology, Coccidioidomycosis Serology Laboratory, University of California-Davis, Davis, CA
| | | | - Jolene Bowers
- Translational Genomics Research Institute, Flagstaff, AZ
| | | | | | - Robert Libke
- Department of Internal Medicine, Division of Infectious Diseases, University of California at San Francisco-Fresno Medical Center, Fresno, CA
| | - Stuart H Cohen
- Department of Internal Medicine, Division of Infectious Diseases, University of California Davis Medical Center, Davis, CA
| | - Demosthenes Pappagianis
- Department of Medical Microbiology and Immunology, Coccidioidomycosis Serology Laboratory, University of California-Davis, Davis, CA
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15
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Sahl JW, Gillece JD, Schupp JM, Waddell VG, Driebe EM, Engelthaler DM, Keim P. Evolution of a pathogen: a comparative genomics analysis identifies a genetic pathway to pathogenesis in Acinetobacter. PLoS One 2013; 8:e54287. [PMID: 23365658 PMCID: PMC3554770 DOI: 10.1371/journal.pone.0054287] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 12/10/2012] [Indexed: 01/20/2023] Open
Abstract
Acinetobacter baumannii is an emergent and global nosocomial pathogen. In addition to A. baumannii, other Acinetobacter species, especially those in the Acinetobacter calcoaceticus-baumannii (Acb) complex, have also been associated with serious human infection. Although mechanisms of attachment, persistence on abiotic surfaces, and pathogenesis in A. baumannii have been identified, the genetic mechanisms that explain the emergence of A. baumannii as the most widespread and virulent Acinetobacter species are not fully understood. Recent whole genome sequencing has provided insight into the phylogenetic structure of the genus Acinetobacter. However, a global comparison of genomic features between Acinetobacter spp. has not been described in the literature. In this study, 136 Acinetobacter genomes, including 67 sequenced in this study, were compared to identify the acquisition and loss of genes in the expansion of the Acinetobacter genus. A whole genome phylogeny confirmed that A. baumannii is a monophyletic clade and that the larger Acb complex is also a well-supported monophyletic group. The whole genome phylogeny provided the framework for a global genomic comparison based on a blast score ratio (BSR) analysis. The BSR analysis demonstrated that specific genes have been both lost and acquired in the evolution of A. baumannii. In addition, several genes associated with A. baumannii pathogenesis were found to be more conserved in the Acb complex, and especially in A. baumannii, than in other Acinetobacter genomes; until recently, a global analysis of the distribution and conservation of virulence factors across the genus was not possible. The results demonstrate that the acquisition of specific virulence factors has likely contributed to the widespread persistence and virulence of A. baumannii. The identification of novel features associated with transcriptional regulation and acquired by clades in the Acb complex presents targets for better understanding the evolution of pathogenesis and virulence in the expansion of the genus.
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Affiliation(s)
- Jason W Sahl
- Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America.
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16
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Bowers JR, Driebe EM, Nibecker JL, Wojack BR, Sarovich DS, Wong AH, Brzoska PM, Hubert N, Knadler A, Watson LM, Wagner DM, Furtado MR, Saubolle M, Engelthaler DM, Keim PS. Dominance of multidrug resistant CC271 clones in macrolide-resistant streptococcus pneumoniae in Arizona. BMC Microbiol 2012; 12:12. [PMID: 22251616 PMCID: PMC3285076 DOI: 10.1186/1471-2180-12-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [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: 10/02/2011] [Accepted: 01/18/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rates of resistance to macrolide antibiotics in Streptococcus pneumoniae are rising around the world due to the spread of mobile genetic elements harboring mef(E) and erm(B) genes and post-vaccine clonal expansion of strains that carry them. RESULTS Characterization of 592 clinical isolates collected in Arizona over a 10 year period shows 23.6% are macrolide resistant. The largest portion of the macrolide-resistant population, 52%, is dual mef(E)/erm(B)-positive. All dual-positive isolates are multidrug-resistant clonal lineages of Taiwan19F-14, mostly multilocus sequence type 320, carrying the recently described transposon Tn2010. The remainder of the macrolide resistant S. pneumoniae collection includes 31% mef(E)-positive, and 9% erm(B)-positive strains. CONCLUSIONS The dual-positive, multidrug-resistant S. pneumoniae clones have likely expanded by switching to non-vaccine serotypes after the heptavalent pneumococcal conjugate vaccine release, and their success limits therapy options. This upsurge could have a considerable clinical impact in Arizona.
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Affiliation(s)
- Jolene R Bowers
- Translational Genomics Research Institute, Flagstaff, AZ, USA.
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17
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Engelthaler DM, Chiller T, Schupp JA, Colvin J, Beckstrom-Sternberg SM, Driebe EM, Moses T, Tembe W, Sinari S, Beckstrom-Sternberg JS, Christoforides A, Pearson JV, Carpten J, Keim P, Peterson A, Terashita D, Balajee SA. Next-generation sequencing of Coccidioides immitis isolated during cluster investigation. Emerg Infect Dis 2011; 17:227-32. [PMID: 21291593 PMCID: PMC3204756 DOI: 10.3201/eid1702.100620] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [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] [Indexed: 12/19/2022] Open
Abstract
Next-generation sequencing enables use of whole-genome sequence typing (WGST) as a viable and discriminatory tool for genotyping and molecular epidemiologic analysis. We used WGST to confirm the linkage of a cluster of Coccidioides immitis isolates from 3 patients who received organ transplants from a single donor who later had positive test results for coccidioidomycosis. Isolates from the 3 patients were nearly genetically identical (a total of 3 single-nucleotide polymorphisms identified among them), thereby demonstrating direct descent of the 3 isolates from an original isolate. We used WGST to demonstrate the genotypic relatedness of C. immitis isolates that were also epidemiologically linked. Thus, WGST offers unique benefits to public health for investigation of clusters considered to be linked to a single source.
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18
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Waters AE, Contente-Cuomo T, Buchhagen J, Liu CM, Watson L, Pearce K, Foster JT, Bowers J, Driebe EM, Engelthaler DM, Keim PS, Price LB. Multidrug-Resistant Staphylococcus aureus in US Meat and Poultry. Clin Infect Dis 2011; 52:1227-30. [PMID: 21498385 PMCID: PMC3079400 DOI: 10.1093/cid/cir181] [Citation(s) in RCA: 167] [Impact Index Per Article: 12.8] [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] [Indexed: 11/18/2022] Open
Abstract
We characterized the prevalence, antibiotic susceptibility profiles, and genotypes of Staphylococcus aureus among US meat and poultry samples (n = 136). S. aureus contaminated 47% of samples, and multidrug resistance was common among isolates (52%). S. aureus genotypes and resistance profiles differed significantly among sample types, suggesting food animal–specific contamination.
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Affiliation(s)
- Andrew E Waters
- Division of Pathogen Genomics, Translational Genomics Research Institute, Northern Arizona University, Flagstaff, USA
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19
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Sheff KW, York ER, Driebe EM, Barker BM, Rounsley SD, Waddell VG, Beckstrom-Sternberg SM, Beckstrom-Sternberg JS, Keim PS, Engelthaler DM. Development of a rapid, cost-effective TaqMan Real-Time PCR Assay for identification and differentiation of Coccidioides immitis and Coccidioides posadasii. Med Mycol 2010; 48:466-9. [PMID: 20370360 DOI: 10.3109/13693780903218990] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Coccidioidomycosis is an infection caused by Coccidioides immitis or C. posadasii. We developed a TaqMan real-time PCR assay that rapidly and accurately differentiates the species. This assay can be used as a tool to improve disease surveillance, increase understanding of the natural history of the infection, and assist in clinical differentiation studies.
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Affiliation(s)
- Kelly W Sheff
- Translational Genomics Research Institute, Pathogen Genomics Division (TGen North), 3051 West Shamrell Boulevard, Flagstaff, Arizona, USA
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20
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Liu CM, Driebe EM, Schupp J, Kelley E, Nguyen JT, McSharry JJ, Weng Q, Engelthaler DM, Keim PS. Rapid quantification of single-nucleotide mutations in mixed influenza A viral populations using allele-specific mixture analysis. J Virol Methods 2010; 163:109-15. [DOI: 10.1016/j.jviromet.2009.09.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2009] [Revised: 08/31/2009] [Accepted: 09/07/2009] [Indexed: 11/16/2022]
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Black CM, Driebe EM, Howard LA, Fajman NN, Sawyer MK, Girardet RG, Sautter RL, Greenwald E, Beck-Sague CM, Unger ER, Igietseme JU, Hammerschlag MR. Multicenter study of nucleic acid amplification tests for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in children being evaluated for sexual abuse. Pediatr Infect Dis J 2009; 28:608-13. [PMID: 19451856 DOI: 10.1097/inf.0b013e31819b592e] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Diagnosis of sexually transmitted infections in children suspected of sexual abuse is challenging due to the medico-legal implications of test results. Currently, the forensic standard for diagnosis of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) infections is culture. In adults, nucleic acid amplification tests (NAATs) are superior to culture for CT, but these tests have been insufficiently evaluated in pediatric populations for forensic purposes. METHODS We evaluated the use of NAATs, using urine and genital swabs versus culture for diagnosis of CT and NG in children evaluated for sexual abuse in 4 US cities. Urine and a genital swab were collected for CT and NG NAATs along with routine cultures. NAAT positives were confirmed by PCR, using an alternate target. RESULTS Prevalence of infection among 485 female children were 2.7% for CT and 3.3% for NG by NAAT. The sensitivity of urine NAATs for CT and NG relative to vaginal culture was 100%. Eight participants with CT-positive and 4 with NG-positive NAATs had negative culture results (P = 0.018 for CT urine NAATs vs. culture). There were 24 of 485 (4.9%) female participants with a positive NAAT for CT or NG or both versus 16 of 485 (3.3%) with a positive culture for either, resulting in a 33% increase in children with a positive diagnosis. CONCLUSIONS These results suggest that NAATs on urine, with confirmation, are adequate for use as a new forensic standard for diagnosis of CT and NG in children suspected of sexual abuse. Urine NAATs offer a clear advantage over culture in sensitivity and are less invasive than swabs, reducing patient trauma and discomfort.
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Affiliation(s)
- Carolyn M Black
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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22
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Girardet RG, Lahoti S, Howard LA, Fajman NN, Sawyer MK, Driebe EM, Lee F, Sautter RL, Greenwald E, Beck-Sagué CM, Hammerschlag MR, Black CM. Epidemiology of sexually transmitted infections in suspected child victims of sexual assault. Pediatrics 2009; 124:79-86. [PMID: 19564286 DOI: 10.1542/peds.2008-2947] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE The objective of this study was to describe the epidemiology of Neisseria gonorrhoeae, Chlamydia trachomatis, Trichomonas vaginalis, Treponema pallidum, HIV, and herpes simplex virus type 2 (HSV-2) infection diagnosed by culture or by serologic or microscopic tests and by nucleic acid amplification tests in children who are evaluated for sexual victimization. METHODS Children aged 0 to 13 years, evaluated for sexual victimization, who required sexually transmissible infection (STI) testing were enrolled at 4 US tertiary referral centers. Specimens for N gonorrhoeae and C trachomatis cultures, wet mounts for detection of T vaginalis, and serologic tests for syphilis and HIV were collected and processed according to study sites' protocols. Nucleic acid amplification tests for C trachomatis and N gonorrhoeae and serologic tests for HSV-2 were performed blinded to other data. RESULTS Of 536 children enrolled, 485 were female. C trachomatis was detected in 15 (3.1%) and N gonorrhoeae in 16 (3.3%) girls. T vaginalis was identified in 5 (5.9%) of 85 girls by wet mount, 1 (0.3%) of 384 children had a positive serologic screen for syphilis, and 0 of 384 had serologic evidence of HIV infection. Of 12 girls who had a specimen for HSV-2 culture, 5 (41.7%) had a positive result; 7 (2.5%) of 283 had antibody evidence of HSV-2 infection. Overall, 40 (8.2%) of 485 girls and 0 of 51 boys (P = .02) had >or=1 STI. Girls with vaginal discharge were more likely to test positive for an STI (13 [24.5%] of 53) than other girls (27 [6.3%] of 432; prevalence ratio = 3.9; P < .001), although 10 girls with STIs had normal physical examinations. Most girls (27 [67.5%]) with a confirmed STI had normal or nonspecific findings on anogenital examination. CONCLUSIONS The prevalence of each STI among sexually victimized children is <10%, even when highly sensitive detection methods are used. Most children with STIs have normal or nonspecific findings on physical examination.
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Affiliation(s)
- Rebecca G Girardet
- Department of Pediatrics, University of Texas-Houston Medical School, Houston, Texas 77030, USA.
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