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Williamson CHD, Roe CC, Terriquez J, Hornstra H, Lucero S, Nunnally AE, Vazquez AJ, Vinocur J, Plude C, Nienstadt L, Stone NE, Celona KR, Wagner DM, Keim P, Sahl JW. A local-scale One Health genomic surveillance of Clostridioides difficile demonstrates highly related strains from humans, canines, and the environment. Microb Genom 2023; 9. [PMID: 37347682 DOI: 10.1099/mgen.0.001046] [Citation(s) in RCA: 1] [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] [Indexed: 06/24/2023] Open
Abstract
Although infections caused by Clostridioides difficile have historically been attributed to hospital acquisition, growing evidence supports the role of community acquisition in C. difficile infection (CDI). Symptoms of CDI can range from mild, self-resolving diarrhoea to toxic megacolon, pseudomembranous colitis, and death. In this study, we sampled C. difficile from clinical, environmental, and canine reservoirs in Flagstaff, Arizona, USA, to understand the distribution and transmission of the pathogen in a One Health framework; Flagstaff is a medium-sized, geographically isolated city with a single hospital system, making it an ideal site to characterize genomic overlap between sequenced C. difficile isolates across reservoirs. An analysis of 562 genomes from Flagstaff isolates identified 65 sequence types (STs), with eight STs being found across all three reservoirs and another nine found across two reservoirs. A screen of toxin genes in the pathogenicity locus identified nine STs where all isolates lost the toxin genes needed for CDI manifestation (tcdB, tcdA), demonstrating the widespread distribution of non-toxigenic C. difficile (NTCD) isolates in all three reservoirs; 15 NTCD genomes were sequenced from symptomatic, clinical samples, including two from mixed infections that contained both tcdB+ and tcdB- isolates. A comparative single nucleotide polymorphism (SNP) analysis of clinically derived isolates identified 78 genomes falling within clusters separated by ≤2 SNPs, indicating that ~19 % of clinical isolates are associated with potential healthcare-associated transmission clusters; only symptomatic cases were sampled in this study, and we did not sample asymptomatic transmission. Using this same SNP threshold, we identified genomic overlap between canine and soil isolates, as well as putative transmission between environmental and human reservoirs. The core genome of isolates sequenced in this study plus a representative set of public C. difficile genomes (n=136), was 2690 coding region sequences, which constitutes ~70 % of an individual C. difficile genome; this number is significantly higher than has been published in some other studies, suggesting that genome data quality is important in understanding the minimal number of genes needed by C. difficile. This study demonstrates the close genomic overlap among isolates sampled across reservoirs, which was facilitated by maximizing the genomic search space used for comprehensive identification of potential transmission events. Understanding the distribution of toxigenic and non-toxigenic C. difficile across reservoirs has implications for surveillance sampling strategies, characterizing routes of infections, and implementing mitigation measures to limit human infection.
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Affiliation(s)
| | - Chandler C Roe
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Heidie Hornstra
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Samantha Lucero
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Amalee E Nunnally
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Adam J Vazquez
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | | | | | - Nathan E Stone
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Kimberly R Celona
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - David M Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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2
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Roe CC, Holiday O, Upshaw-Bia K, Benally G, Williamson CHD, Urbanz J, Verocai GG, Ridenour CL, Nottingham R, Ford MA, Lake DP, Kennedy TA, Hepp CM, Sahl JW. Biting midges (Diptera: Ceratopogonidae) as putative vectors of zoonotic Onchocerca lupi (Nematoda: Onchocercidae) in northern Arizona and New Mexico, southwestern United States. Front Vet Sci 2023; 10:1167070. [PMID: 37256003 PMCID: PMC10225701 DOI: 10.3389/fvets.2023.1167070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/28/2023] [Indexed: 06/01/2023] Open
Abstract
Onchocerca lupi (Rodonaja, 1967) is an understudied, vector-borne, filarioid nematode that causes ocular onchocercosis in dogs, cats, coyotes, wolves, and is also capable of infecting humans. Onchocercosis in dogs has been reported with increasing incidence worldwide. However, despite the growing number of reports describing canine O. lupi cases as well as zoonotic infections globally, the disease prevalence in endemic areas and vector species of this parasite remains largely unknown. Here, our study aimed to identify the occurrence of O. lupi infected dogs in northern Arizona, New Mexico, and Utah, United States and identify the vector of this nematode. A total of 532 skin samples from randomly selected companion animals with known geographic locations within the Navajo Reservation were collected and molecularly surveyed by PCR for the presence of O. lupi DNA (September 2019-June 2022) using previously published nematode primers (COI) and DNA sequencing. O. lupi DNA was detected in 50 (9.4%) sampled animals throughout the reservation. Using positive animal samples to target geographic locations, pointed hematophagous insect trapping was performed to identify potential O. lupi vectors. Out of 1,922 insects screened, 38 individual insects and 19 insect pools tested positive for the presence of O. lupi, all of which belong to the Diptera family. This increased surveillance of definitive host and biological vector/intermediate host is the first large scale prevalence study of O. lupi in companion animals in an endemic area of the United States, and identified an overall prevalence of 9.4% in companion animals as well as multiple likely biological vector and putative vector species in the southwestern United States. Furthermore, the identification of these putative vectors in close proximity to human populations coupled with multiple, local zoonotic cases highlight the One Health importance of O. lupi.
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Affiliation(s)
- Chandler C. Roe
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States
| | - Olivia Holiday
- Navajo Nation Veterinary Management Program, Window Rock, AZ, United States
| | - Kelly Upshaw-Bia
- Navajo Nation Veterinary Management Program, Window Rock, AZ, United States
| | - Gaven Benally
- Navajo Nation Veterinary Management Program, Window Rock, AZ, United States
| | - Charles H. D. Williamson
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | | | - Guilherme G. Verocai
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Chase L. Ridenour
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Roxanne Nottingham
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Morgan A. Ford
- U.S. Geological Survey, Southwest Biological Science Center, Flagstaff, AZ, United States
| | - Derek P. Lake
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Theodore A. Kennedy
- U.S. Geological Survey, Southwest Biological Science Center, Flagstaff, AZ, United States
| | - Crystal M. Hepp
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Jason W. Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
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3
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Roe CC, Urbanz J, Auten C, Verocai GG, Upshaw-Bia K, Holiday O, Hepp C, Sahl JW. LupiQuant: A real-time PCR based assay for determining host-to-parasite DNA ratios of Onchocerca lupi and host Canis lupus from onchocercosis samples. PLoS One 2022; 17:e0276916. [PMID: 36409718 PMCID: PMC9678315 DOI: 10.1371/journal.pone.0276916] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/15/2022] [Indexed: 11/22/2022] Open
Abstract
Onchocerca lupi is a filarial nematode that causes ocular onchocercosis in canines globally including North America and areas of Europe, North Africa, and the Middle East. Reported incidence of this parasite in canines has continued to steadily escalate since the early 21st century and was more recently documented in humans. Whole genome sequencing (WGS) of this parasite can provide insight into gene content, provide novel surveillance targets, and elucidate the origin and range expansion. However, past attempts of whole genome sequencing of other Onchocerca species reported a substantial portion of their data unusable due to the variable over-abundance of host DNA in samples. Here, we have developed a method to determine the host-to-parasite DNA ratio using a quantitative PCR (qPCR) approach that relies on two standard plasmids each of which contains a single copy gene specific to the parasite genus Onchocerca (major body wall myosin gene, myosin) or a single copy gene specific to the canine host (polycystin-1 precursor, pkd1). These plasmid standards were used to determine the copy number of the myosin and pkd1 genes within a sample to calculate the ratio of parasite and host DNA. Furthermore, whole genome sequence (WGS) data for three O. lupi isolates were consistent with our host-to-parasite DNA ratio results. Our study demonstrates, despite unified DNA extraction methods, variable quantities of host DNA within any one sample which will likely affect downstream WGS applications. Our quantification assay of host-to-parasite genome copy number provides a robust and accurate method of assessing canine host DNA load in an O. lupi specimen that will allow informed sample selection for WGS. This study has also provided the first whole genome draft sequence for this species. This approach is also useful for future focused WGS studies of other parasites.
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Affiliation(s)
- Chandler C. Roe
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States of America
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States of America
- * E-mail:
| | - Jennifer Urbanz
- Eye Care for Animals, Scottsdale, AZ, United States of America
| | - Candace Auten
- Eye Care for Animals, Albuquerque, NM, United States of America
| | - Guilherme G. Verocai
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States of America
| | - Kelly Upshaw-Bia
- Navajo Nation Veterinary Management Program, Window Rock, NM, United States of America
| | - Olivia Holiday
- Navajo Nation Veterinary Management Program, Window Rock, NM, United States of America
| | - Crystal Hepp
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States of America
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States of America
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - Jason W. Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States of America
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Fernandes LGV, Stone NE, Roe CC, Goris MGA, van der Linden H, Sahl JW, Wagner DM, Nally JE. Leptospira sanjuanensis sp. nov., a pathogenic species of the genus Leptospira isolated from soil in Puerto Rico. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two spirochetes (designated strains LGVF01 and LGVF02T) were isolated from soil samples in San Juan, Puerto Rico in HAN media after selection using a combination of ELISA, agar plating, and colony screening by Fluorescent Antibody Testing (FAT) and PCR for lipL32 and secY. Isolates were helix-shaped, aerobic, fast-growing, and highly motile. Genome sequence analysis indicated that both strains should be classified as members of a novel species within the pathogenic (P1) clade of the genus
Leptospira
. The average nucleotide identity between the two strains was 99.2 %, but below 93.2 % when compared to any previously described leptospiral species. Serotyping of strain LGVF02T indicates that it does not belong within any serogroup of
Leptospira
suggesting it also represents a new serovar. Collectively, strains LGVF01 and LGVF02T represent a new species of pathogenic leptospires for which the name Leptospira sanjuanensis sp. nov. is proposed. The type strain is LGVF02T (=NVSL-LGVF02T=KIT0302T).
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Affiliation(s)
- Luis G. V. Fernandes
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo 05503-900, Brazil
- Infectious Bacterial Diseases Research Unit, ARS, United States Department of Agriculture, Ames, IA, USA
| | - Nathan E. Stone
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Chandler C. Roe
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Marga G. A. Goris
- Department of Medical Microbiology and Infection Prevention, OIE and National Collaborating Centre for Reference and Research on Leptospirosis, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Hans van der Linden
- Department of Medical Microbiology and Infection Prevention, OIE and National Collaborating Centre for Reference and Research on Leptospirosis, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Jason W. Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - David M. Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jarlath E. Nally
- Infectious Bacterial Diseases Research Unit, ARS, United States Department of Agriculture, Ames, IA, USA
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5
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Williamson CHD, Stone NE, Nunnally AE, Roe CC, Vazquez AJ, Lucero SA, Hornstra H, Wagner DM, Keim P, Rupnik M, Janezic S, Sahl JW. Identification of novel, cryptic Clostridioides species isolates from environmental samples collected from diverse geographical locations. Microb Genom 2022; 8. [PMID: 35166655 PMCID: PMC8942030 DOI: 10.1099/mgen.0.000742] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile is a pathogen often associated with hospital-acquired infection or antimicrobial-induced disease; however, increasing evidence indicates infections can result from community or environmental sources. Most genomic sequencing of C. difficile has focused on clinical strains, although evidence is growing that C. difficile spores are widespread in soil and water in the environment. In this study, we sequenced 38 genomes collected from soil and water isolates in Flagstaff (AZ, USA) and Slovenia in an effort targeted towards environmental surveillance of C. difficile. At the average nucleotide identity (ANI) level, the genomes were divergent to C. difficile at a threshold consistent with different species. A phylogenetic analysis of these divergent genomes together with Clostridioides genomes available in public repositories confirmed the presence of three previously described, cryptic Clostridioides species and added two additional clades. One of the cryptic species (C-III) was almost entirely composed of Arizona and Slovenia genomes, and contained distinct sub-groups from each region (evidenced by SNP and gene-content differences). A comparative genomics analysis identified multiple unique coding sequences per clade, which can serve as markers for subsequent environmental surveys of these cryptic species. Homologues to the C. difficile toxin genes, tcdA and tcdB, were found in cryptic species genomes, although they were not part of the typical pathogenicity locus observed in C. difficile, and in silico PCR suggested that some would not amplify with widely used PCR diagnostic tests. We also identified gene homologues in the binary toxin cluster, including some present on phage and, for what is believed to be the first time, on a plasmid. All isolates were obtained from environmental samples, so the function and disease potential of these toxin homologues is currently unknown. Enzymatic profiles of a subset of cryptic isolates (n=5) demonstrated differences, suggesting that these isolates contain substantial metabolic diversity. Antimicrobial resistance (AMR) was observed across a subset of isolates (n=4), suggesting that AMR mechanisms are intrinsic to the genus, perhaps originating from a shared environmental origin. This study greatly expands our understanding of the genomic diversity of Clostridioides. These results have implications for C. difficile One Health research, for more sensitive C. difficile diagnostics, as well as for understanding the evolutionary history of C. difficile and the development of pathogenesis.
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Affiliation(s)
| | - Nathan E Stone
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Amalee E Nunnally
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Chandler C Roe
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Adam J Vazquez
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Samantha A Lucero
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Heidie Hornstra
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - David M Wagner
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Maja Rupnik
- National Laboratory for Health, Environment and Food, Prvomajska Ulica 1, 2000 Maribor, Slovenia
| | - Sandra Janezic
- Faculty of Medicine, University of Maribor, Taborska 8, 2000 Maribor, Slovenia
| | - Jason William Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
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Roe CC, Urbanz J, Andrews L, Verocai GG, Engelthaler DM, Hepp CM, Sahl JW. Complete mitochondrial genome of Onchocerca lupi (Nematoda, Onchocercidae). Mitochondrial DNA B Resour 2021; 6:2572-2574. [PMID: 34377832 PMCID: PMC8344259 DOI: 10.1080/23802359.2021.1960211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Onchocerca lupi, Rodonaja 1967, is an emerging, zoonotic filarial nematode parasite that causes ocular disease in dogs, cats, wild canids, and humans. It is the causative agent of ocular onchocercosis in canines with increasing incidence in both North America and the Old World during the early twenty-first century. We report the complete mitochondrial genome of an O. lupi isolate from a dog from Arizona, southwestern USA, and its genetic differentiation from related Onchocerca species. The whole mitochondrial genome was obtained from whole genome sequencing of genomic DNA isolated from an adult worm. This mitogenome is 13,766 bp in size and contains 36 genes and a control region. This mitogenome provides a valuable resource for future studies involving epidemiological surveillance, population genetics, phylogeography, and comparative mitogenomics of this emerging pathogen and other parasitic nematodes.
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Affiliation(s)
- Chandler C Roe
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.,Translational Genomics Research Institute, Flagstaff, AZ, USA
| | | | - Lela Andrews
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Guilherme G Verocai
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | | | - Crystal M Hepp
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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Bowers JR, Monroy-Nieto J, Gade L, Travis J, Refojo N, Abrantes R, Santander J, French C, Dignani MC, Hevia AI, Roe CC, Lemmer D, Lockhart SR, Chiller T, Litvintseva AP, Clara L, Engelthaler DM. Rhizopus microsporus Infections Associated with Surgical Procedures, Argentina, 2006-2014. Emerg Infect Dis 2021; 26:937-944. [PMID: 32310081 PMCID: PMC7181922 DOI: 10.3201/eid2605.191045] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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
Rhizopus spp. fungi are ubiquitous in the environment and a rare but substantial cause of infection in immunosuppressed persons and surgery patients. During 2005–2017, an abnormally high number of Rhizopus infections in surgery patients, with no apparent epidemiologic links, were reported in Argentina. To determine the likelihood of a common source of the cluster, we performed whole-genome sequencing on samples collected during 2006–2014. Most isolates were separated by >60 single-nucleotide polymorphisms, and we found no evidence for recombination or nonneutral mutation accumulation; these findings do not support common source or patient-to-patient transmission. Assembled genomes of most isolates were ≈25 Mbp, and multiple isolates had substantially larger assembled genomes (43–51 Mbp), indicative of infections with strain types that underwent genome expansion. Whole-genome sequencing has become an essential tool for studying epidemiology of fungal infections. Less discriminatory techniques may miss true relationships, possibly resulting in inappropriate attribution of point source.
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8
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Ridenour CL, Cocking J, Poidmore S, Erickson D, Brock B, Valentine M, Roe CC, Young SJ, Henke JA, Hung KY, Wittie J, Stefanakos E, Sumner C, Ruedas M, Raman V, Seaton N, Bendik W, Hornstra O’Neill HM, Sheridan K, Centner H, Lemmer D, Fofanov V, Smith K, Will J, Townsend J, Foster JT, Keim PS, Engelthaler DM, Hepp CM. St. Louis Encephalitis Virus in the Southwestern United States: A Phylogeographic Case for a Multi-Variant Introduction Event. Front Genet 2021; 12:667895. [PMID: 34168675 PMCID: PMC8217752 DOI: 10.3389/fgene.2021.667895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/28/2021] [Indexed: 11/14/2022] Open
Abstract
Since the reemergence of St. Louis Encephalitis (SLE) Virus (SLEV) in the Southwest United States, identified during the 2015 outbreak in Arizona, SLEV has been seasonally detected within Culex spp. populations throughout the Southwest United States. Previous work revealed the 2015 outbreak was caused by an importation of SLEV genotype III, which had only been detected previously in Argentina. However, little is known about when the importation occurred or the transmission and genetic dynamics since its arrival into the Southwest. In this study, we sought to determine whether the annual detection of SLEV in the Southwest is due to enzootic cycling or new importations. To address this question, we analyzed 174 SLEV genomes (142 sequenced as part of this study) using Bayesian phylogenetic analyses to estimate the date of arrival into the American Southwest and characterize the underlying population structure of SLEV. Phylogenetic clustering showed that SLEV variants circulating in Maricopa and Riverside counties form two distinct populations with little evidence of inter-county transmission since the onset of the outbreak. Alternatively, it appears that in 2019, Yuma and Clark counties experienced annual importations of SLEV that originated in Riverside and Maricopa counties. Finally, the earliest representatives of SLEV genotype III in the Southwest form a polytomy that includes both California and Arizona samples. We propose that the initial outbreak most likely resulted from the importation of a population of SLEV genotype III variants, perhaps in multiple birds, possibly multiple species, migrating north in 2013, rather than a single variant introduced by one bird.
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Affiliation(s)
- Chase L. Ridenour
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Jill Cocking
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Samuel Poidmore
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Daryn Erickson
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Breezy Brock
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Michael Valentine
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Chandler C. Roe
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Steven J. Young
- Vector Control Division, Maricopa County Environmental Services Department, Phoenix, AZ, United States
| | - Jennifer A. Henke
- Coachella Valley Mosquito and Vector Control District, Indio, CA, United States
| | - Kim Y. Hung
- Coachella Valley Mosquito and Vector Control District, Indio, CA, United States
| | - Jeremy Wittie
- Coachella Valley Mosquito and Vector Control District, Indio, CA, United States
| | | | - Chris Sumner
- Yuma County Pest Abatement District, Yuma, AZ, United States
| | - Martha Ruedas
- Yuma County Pest Abatement District, Yuma, AZ, United States
| | - Vivek Raman
- Southern Nevada Health District, Las Vegas, NV, United States
| | - Nicole Seaton
- Southern Nevada Health District, Las Vegas, NV, United States
| | - William Bendik
- Southern Nevada Health District, Las Vegas, NV, United States
| | | | - Krystal Sheridan
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Heather Centner
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Darrin Lemmer
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Viacheslav Fofanov
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Kirk Smith
- Vector Control Division, Maricopa County Environmental Services Department, Phoenix, AZ, United States
| | - James Will
- Vector Control Division, Maricopa County Environmental Services Department, Phoenix, AZ, United States
| | - John Townsend
- Vector Control Division, Maricopa County Environmental Services Department, Phoenix, AZ, United States
| | - Jeffrey T. Foster
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Paul S. Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | | | - Crystal M. Hepp
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, United States
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
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9
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Roe CC, Yaglom H, Howard A, Urbanz J, Verocai GG, Andrews L, Harrison V, Barnes R, Lyons T, Bowers JR, Engelthaler DM. Coyotes as Reservoirs for Onchocerca lupi, United States, 2015-2018. Emerg Infect Dis 2021; 26:2989-2993. [PMID: 33219658 PMCID: PMC7706981 DOI: 10.3201/eid2612.190136] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 12/22/2022] Open
Abstract
The Onchocerca lupi nematode infects dogs, cats, and humans, but whether it can be spread by coyotes has been unknown. We conducted surveillance for O. lupi nematode infection in coyotes in the southwestern United States. We identified multiple coyote populations in Arizona and New Mexico as probable reservoirs for this species.
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10
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Mead HL, Roe CC, Higgins Keppler EA, Van Dyke MCC, Laux KL, Funke AL, Miller KJ, Bean HD, Sahl JW, Barker BM. Defining Critical Genes During Spherule Remodeling and Endospore Development in the Fungal Pathogen, Coccidioides posadasii. Front Genet 2020; 11:483. [PMID: 32499817 PMCID: PMC7243461 DOI: 10.3389/fgene.2020.00483] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/17/2020] [Indexed: 12/18/2022] Open
Abstract
Coccidioides immitis and C. posadasii are soil dwelling dimorphic fungi found in North and South America. Inhalation of aerosolized asexual conidia can result in asymptomatic, acute, or chronic respiratory infection. In the United States there are approximately 350,000 new infections per year. The Coccidioides genus is the only known fungal pathogen to make specialized parasitic spherules, which contain endospores that are released into the host upon spherule rupture. The molecular determinants involved in this key step of infection remain largely elusive as 49% of genes are hypothetical with unknown function. An attenuated mutant strain C. posadasii Δcts2/Δard1/Δcts3 in which chitinase genes 2 and 3 were deleted was previously created for vaccine development. This strain does not complete endospore development, which prevents completion of the parasitic lifecycle. We sought to identify pathways active in the wild-type strain during spherule remodeling and endospore formation that have been affected by gene deletion in the mutant. We compared the transcriptome and volatile metabolome of the mutant Δcts2/Δard1/Δcts3 to the wild-type C735. First, the global transcriptome was compared for both isolates using RNA sequencing. The raw reads were aligned to the reference genome using TOPHAT2 and analyzed using the Cufflinks package. Genes of interest were screened in an in vivo model using NanoString technology. Using solid phase microextraction (SPME) and comprehensive two-dimensional gas chromatography - time-of-flight mass spectrometry (GC × GC-TOFMS) volatile organic compounds (VOCs) were collected and analyzed. Our RNA-Seq analyses reveal approximately 280 significantly differentially regulated transcripts that are either absent or show opposite expression patterns in the mutant compared to the parent strain. This suggests that these genes are tied to networks impacted by deletion and may be critical for endospore development and/or spherule rupture in the wild-type strain. Of these genes, 14 were specific to the Coccidioides genus. We also found that the wild-type and mutant strains differed significantly in their production versus consumption of metabolites, with the mutant displaying increased nutrient scavenging. Overall, our results provide the first targeted list of key genes that are active during endospore formation and demonstrate that this approach can define targets for functional assays in future studies.
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Affiliation(s)
- H L Mead
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States
| | - C C Roe
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States
| | - E A Higgins Keppler
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - M C Caballero Van Dyke
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States
| | - K L Laux
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States
| | - A L Funke
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States.,Imaging Histology Core Facility, Northern Arizona University, Flagstaff AZ, United States
| | - K J Miller
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States
| | - H D Bean
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - J W Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States
| | - B M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff AZ, United States
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11
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Hall CM, Jaramillo S, Jimenez R, Stone NE, Centner H, Busch JD, Bratsch N, Roe CC, Gee JE, Hoffmaster AR, Rivera-Garcia S, Soltero F, Ryff K, Perez-Padilla J, Keim P, Sahl JW, Wagner DM. Burkholderia pseudomallei, the causative agent of melioidosis, is rare but ecologically established and widely dispersed in the environment in Puerto Rico. PLoS Negl Trop Dis 2019; 13:e0007727. [PMID: 31487287 PMCID: PMC6748447 DOI: 10.1371/journal.pntd.0007727] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/17/2019] [Accepted: 08/23/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Burkholderia pseudomallei is a soil-dwelling bacterium and the causative agent of melioidosis. The global burden and distribution of melioidosis is poorly understood, including in the Caribbean. B. pseudomallei was previously isolated from humans and soil in eastern Puerto Rico but the abundance and distribution of B. pseudomallei in Puerto Rico as a whole has not been thoroughly investigated. METHODOLOGY/PRINCIPAL FINDINGS We collected 600 environmental samples (500 soil and 100 water) from 60 sites around Puerto Rico. We identified B. pseudomallei by isolating it via culturing and/or using PCR to detect its DNA within complex DNA extracts. Only three adjacent soil samples from one site were positive for B. pseudomallei with PCR; we obtained 55 isolates from two of these samples. The 55 B. pseudomallei isolates exhibited fine-scale variation in the core genome and contained four novel genomic islands. Phylogenetic analyses grouped Puerto Rico B. pseudomallei isolates into a monophyletic clade containing other Caribbean isolates, which was nested inside a larger clade containing all isolates from Central/South America. Other Burkholderia species were commonly observed in Puerto Rico; we cultured 129 isolates from multiple soil and water samples collected at numerous sites around Puerto Rico, including representatives of B. anthina, B. cenocepacia, B. cepacia, B. contaminans, B. glumae, B. seminalis, B. stagnalis, B. ubonensis, and several unidentified novel Burkholderia spp. CONCLUSIONS/SIGNIFICANCE B. pseudomallei was only detected in three soil samples collected at one site in north central Puerto Rico with only two of those samples yielding isolates. All previous human and environmental B. pseudomallei isolates were obtained from eastern Puerto Rico. These findings suggest B. pseudomallei is ecologically established and widely dispersed in the environment in Puerto Rico but rare. Phylogeographic patterns suggest the source of B. pseudomallei populations in Puerto Rico and elsewhere in the Caribbean may have been Central or South America.
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Affiliation(s)
- Carina M. Hall
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Sierra Jaramillo
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Rebecca Jimenez
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, San Juan, Puerto Rico, United States of America
| | - Nathan E. Stone
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Heather Centner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Joseph D. Busch
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Nicole Bratsch
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Chandler C. Roe
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jay E. Gee
- Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Alex R. Hoffmaster
- Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Sarai Rivera-Garcia
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, San Juan, Puerto Rico, United States of America
| | - Fred Soltero
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, San Juan, Puerto Rico, United States of America
| | - Kyle Ryff
- Dengue Branch, Centers for Disease Control and Prevention, San Juan, Puerto Rico, United States of America
| | - Janice Perez-Padilla
- Dengue Branch, Centers for Disease Control and Prevention, San Juan, Puerto Rico, United States of America
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jason W. Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - David M. Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail:
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12
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Oltean HN, Etienne KA, Roe CC, Gade L, McCotter OZ, Engelthaler DM, Litvintseva AP. Utility of Whole-Genome Sequencing to Ascertain Locally Acquired Cases of Coccidioidomycosis, Washington, USA. Emerg Infect Dis 2019; 25:501-506. [PMID: 30789132 PMCID: PMC6390764 DOI: 10.3201/eid2503.181155] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 12/13/2022] Open
Abstract
Coccidioidomycosis is an emerging fungal infection in Washington, USA, and the epidemiology of the disease in this state is poorly understood. We used whole-genome sequencing to differentiate locally acquired cases in Washington on the basis of the previously identified phylogeographic population structure of Coccidioides spp. Clinical isolates from coccidioidomycosis cases involving possible Washington soil exposure were included. Of 17 human infections with epidemiologic evidence of possible local acquisition, 4 were likely locally acquired infections and 13 were likely acquired outside Washington. Isolates from locally acquired cases clustered within the previously established Washington clade of C. immitis. Genetic differences among these strains suggest multiple environmental reservoirs of C. immitis in the state.
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13
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Williamson CHD, Stone NE, Nunnally AE, Hornstra HM, Wagner DM, Roe CC, Vazquez AJ, Nandurkar N, Vinocur J, Terriquez J, Gillece J, Travis J, Lemmer D, Keim P, Sahl JW. A global to local genomics analysis of Clostridioides difficile ST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network. Microb Genom 2019; 5:e000271. [PMID: 31107202 PMCID: PMC6700662 DOI: 10.1099/mgen.0.000271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 04/04/2019] [Indexed: 12/15/2022] Open
Abstract
Clostridioides difficile is a ubiquitous, diarrhoeagenic pathogen often associated with healthcare-acquired infections that can cause a range of symptoms from mild, self-limiting disease to toxic megacolon and death. Since the early 2000s, a large proportion of C. difficile cases have been attributed to the ribotype 027 (RT027) lineage, which is associated with sequence type 1 (ST1) in the C. difficile multilocus sequence typing scheme. The spread of ST1 has been attributed, in part, to resistance to fluoroquinolones used to treat unrelated infections, which creates conditions ideal for C. difficile colonization and proliferation. In this study, we analysed 27 isolates from a healthcare network in northern Arizona, USA, and 1352 publicly available ST1 genomes to place locally sampled isolates into a global context. Whole genome, single nucleotide polymorphism analysis demonstrated that at least six separate introductions of ST1 were observed in healthcare facilities in northern Arizona over an 18-month sampling period. A reconstruction of transmission networks identified potential nosocomial transmission of isolates, which were only identified via whole genome sequence analysis. Antibiotic resistance heterogeneity was observed among ST1 genomes, including variability in resistance profiles among locally sampled ST1 isolates. To investigate why ST1 genomes are so common globally and in northern Arizona, we compared all high-quality C. difficile genomes and identified that ST1 genomes have gained and lost a number of genomic regions compared to all other C. difficile genomes; analyses of other toxigenic C. difficile sequence types demonstrate that this loss may be anomalous and could be related to niche specialization. These results suggest that a combination of antimicrobial resistance and gain and loss of specific genes may explain the prominent association of this sequence type with C. difficile infection cases worldwide. The degree of genetic variability in ST1 suggests that classifying all ST1 genomes into a quinolone-resistant hypervirulent clone category may not be appropriate. Whole genome sequencing of clinical C. difficile isolates provides a high-resolution surveillance strategy for monitoring persistence and transmission of C. difficile and for assessing the performance of infection prevention and control strategies.
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Affiliation(s)
| | - Nathan E. Stone
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Amalee E. Nunnally
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Heidie M. Hornstra
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - David M. Wagner
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Chandler C. Roe
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Adam J. Vazquez
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Nivedita Nandurkar
- Northern Arizona Healthcare, Flagstaff Medical Center, Flagstaff, AZ 86001, USA
| | - Jacob Vinocur
- Northern Arizona Healthcare, Flagstaff Medical Center, Flagstaff, AZ 86001, USA
| | - Joel Terriquez
- Northern Arizona Healthcare, Flagstaff Medical Center, Flagstaff, AZ 86001, USA
| | - John Gillece
- Translational Genomics Research Institute, Flagstaff, AZ 86001, USA
| | - Jason Travis
- Translational Genomics Research Institute, Flagstaff, AZ 86001, USA
| | - Darrin Lemmer
- Translational Genomics Research Institute, Flagstaff, AZ 86001, USA
| | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jason W. Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
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Abstract
We conducted molecular clock analysis of whole-genome sequences from a set of autochthonous isolates of Cryptococcus gattii sensu stricto from the southeastern United States. Our analysis indicates that C. gattii arrived in the southeastern United States approximately 9,000–19,000 years ago, long before its arrival in the Pacific Northwest.
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15
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McCotter OZ, Benedict K, Engelthaler DM, Komatsu K, Lucas KD, Mohle-Boetani JC, Oltean H, Vugia D, Chiller TM, Sondermeyer Cooksey GL, Nguyen A, Roe CC, Wheeler C, Sunenshine R. Update on the Epidemiology of coccidioidomycosis in the United States. Med Mycol 2019; 57:S30-S40. [PMID: 30690599 DOI: 10.1093/mmy/myy095] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 10/18/2018] [Indexed: 01/25/2023] Open
Abstract
The incidence of reported coccidioidomycosis in the past two decades has increased greatly; monitoring its changing epidemiology is essential for understanding its burden on patients and the healthcare system and for identifying opportunities for prevention and education. We provide an update on recent coccidioidomycosis trends and public health efforts nationally and in Arizona, California, and Washington State. In Arizona, enhanced surveillance shows that coccidioidomycosis continues to be associated with substantial morbidity. California reported its highest yearly number of cases ever in 2016 and has implemented interventions to reduce coccidioidomycosis in the prison population by excluding certain inmates from residing in prisons in high-risk areas. Coccidioidomycosis is emerging in Washington State, where phylogenetic analyses confirm the existence of a unique Coccidioides clade. Additional studies of the molecular epidemiology of Coccidioides will improve understanding its expanding endemic range. Ongoing public health collaborations and future research priorities are focused on characterizing geographic risk, particularly in the context of environmental change; identifying further risk reduction strategies for high-risk groups; and improving reporting of cases to public health agencies.
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Affiliation(s)
- Orion Z McCotter
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kaitlin Benedict
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Ken Komatsu
- Arizona Department of Health Services, Phoenix, Arizona, USA
| | - Kimberley D Lucas
- California Correctional Healthcare Services, Elk Grove, California, USA
| | | | - Hanna Oltean
- Washington State Department of Health, Shoreline, Washington, USA
| | - Duc Vugia
- California Department of Public Health, Richmond and Sacramento, California, USA
| | - Tom M Chiller
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Alyssa Nguyen
- California Department of Public Health, Richmond and Sacramento, California, USA
| | - Chandler C Roe
- Translational Genomics Research Institute, Flagstaff, Arizona, USA.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Charlotte Wheeler
- California Correctional Healthcare Services, Elk Grove, California, USA
| | - Rebecca Sunenshine
- Maricopa County Department of Public Health, Phoenix, Arizona, USA.,Office of Public Health Preparedness and Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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16
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Roe CC, Vazquez AJ, Esposito EP, Zarrilli R, Sahl JW. Diversity, Virulence, and Antimicrobial Resistance in Isolates From the Newly Emerging Klebsiella pneumoniae ST101 Lineage. Front Microbiol 2019; 10:542. [PMID: 31001209 PMCID: PMC6454207 DOI: 10.3389/fmicb.2019.00542] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/01/2019] [Indexed: 11/13/2022] Open
Abstract
The global dissemination of Klebsiella pneumoniae and Klebsiella pneumoniae carbapenemase (KPC) has been largely attributed to a few high-risk sequence types (STs) (ST258, ST11, ST512) associated with human disease. ST101 is an emerging clone that has been identified in different parts of the world with the potential to become a global, persistent public health threat. Recent research suggests the ST101 lineage is associated with an 11% increase in mortality rate in comparison to non-ST101 infections. In this study, we generated a high-quality, near-finished genome assembly of a multidrug-resistant (MDR) isolate from Italy (isolate 4743) that is a single locus variant of ST101 (ST1685). We demonstrate that the 4743 genome contains virulence features such as an integrative conjugative element carrying the yersiniabactin siderophore (ICEKp3), the mannose-resistant Klebsiella-like (type III) fimbriae cluster (mrkABCDFHIJ), the ferric uptake system (kfuABC), the yersiniabactin receptor gene fyuA, a capsular K type K17, and an O antigen type of O1. K. pneumoniae 4743 carries the blaKPC-2 carbapenemase gene along with genes conferring resistance to aminoglycosides, beta-lactams, fluoroquinolones, fosfomycin, macrolides, lincosamides, and streptogramin B. A comparative genomics analysis of 44 ST101 genomes as well as newly sequenced isolate 4743 identified variable antimicrobial resistance (AMR) resistance profiles and incompatibility plasmid types, but similar virulence factor profiles. Using Bayesian methodologies, we estimate the common ancestor for the ST101 lineage emerged in 1990 (95% HPD: 1965 to 2007) and isolates within the lineage acquired bla KPC after the divergence from its parental clonal group and dissemination. The identification of virulence factors and antibiotic resistance genes acquired by this newly emerging clone provides insight into the reported increased mortality rates and highlights its potential success as a persistent nosocomial pathogen. With a combination of both colistin resistance, carbapenem resistance, and several known virulence factors, the ST101 genetic repertoire may be a "perfect storm" allowing for a newly emerging, high-risk, extensively antibiotic resistant clone. This high-risk clone appears adept at acquiring resistance and may perpetuate the dissemination of extensive antimicrobial resistance. Greater focus on the acquisition of virulence factors and antibiotic resistance genes is crucial for understanding the spread of antibiotic resistance.
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Affiliation(s)
- Chandler C. Roe
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Adam J. Vazquez
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Eliana Pia Esposito
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Jason W. Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
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17
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Vu K, Thompson GR, Roe CC, Sykes JE, Dreibe EM, Lockhart SR, Meyer W, Engelthaler DM, Gelli A. Flucytosine resistance in Cryptococcus gattii is indirectly mediated by the FCY2-FCY1-FUR1 pathway. Med Mycol 2018; 56:857-867. [PMID: 29554336 PMCID: PMC10905989 DOI: 10.1093/mmy/myx135] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 06/12/2017] [Revised: 10/12/2017] [Indexed: 11/14/2022] Open
Abstract
Cryptococcosis is an opportunistic fungal infection caused by members of the two sibling species complexes: Cryptococcus neoformans and Cryptococcus gattii. Flucytosine (5FC) is one of the most widely used antifungals against Cryptococcus spp., yet very few studies have looked at the molecular mechanisms responsible for 5FC resistance in this pathogen. In this study, we examined 11 C. gattii clinical isolates of the major molecular type VGIII based on differential 5FC susceptibility and asked whether there were genomic changes in the key genes involved in flucytosine metabolism. Susceptibility assays and sequencing analysis revealed an association between a point mutation in the cytosine deaminase gene (FCY1) and 5FC resistance in two of the studied 5FC resistant C. gattii VGIII clinical isolates, B9322 and JS5. This mutation results in the replacement of arginine for histidine at position 29 and occurs within a variable stretch of amino acids. Heterologous expression of FCY1 and spot sensitivity assays, however, demonstrated that this point mutation did not have any effect on FCY1 activities and was not responsible for 5FC resistance. Comparative sequence analysis further showed that no changes in the amino acid sequence and no genomic alterations were observed within 1 kb of the upstream and downstream sequences of either cytosine permeases (FCY2-4) or uracil phosphoribosyltransferase (FUR1) genes in 5FC resistant and 5FC susceptible C. gattii VGIII isolates. The herein obtained results suggest that the observed 5FC resistance in the isolates B9322 and JS5 is due to changes in unknown protein(s) or pathway(s) that regulate flucytosine metabolism.
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Affiliation(s)
- Kiem Vu
- Department of Pharmacology, University of California, Davis, California, USA
| | - George R Thompson
- Department of Medical Microbiology and Immunology, University of California, Davis, California, USA
- Department of Internal Medicine, Division of Infectious Diseases, University of California Davis Medical Center, Davis, California, USA
| | - Chandler C Roe
- Translational Genomics Research Institute, Flagstaff, Arizona, USA
| | - Jane E Sykes
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, California, USA
| | | | - Shawn R Lockhart
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia USA
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Center for Infectious Diseases and Microbiology, Marie Bashir Institute for Emerging Infectious Diseases and Biosecurity, Westmead Clinical School, Sydney Medical School, Westmead Hospital, The University of Sydney, Westmead Institute for Medical Research, Sydney, Australia
| | | | - Angie Gelli
- Department of Pharmacology, University of California, Davis, California, USA
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18
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Abstract
Cryptococcus gattii is a recognized pathogenic fungus along the Pacific coast of the United States from California to Washington. Here we report that C. gattii may also be endemic to the southeastern United States and has probably been present there longer than in the Pacific Northwest.
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19
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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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20
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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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Firacative C, Roe CC, Malik R, Ferreira-Paim K, Escandón P, Sykes JE, Castañón-Olivares LR, Contreras-Peres C, Samayoa B, Sorrell TC, Castañeda E, Lockhart SR, Engelthaler DM, Meyer W. MLST and Whole-Genome-Based Population Analysis of Cryptococcus gattii VGIII Links Clinical, Veterinary and Environmental Strains, and Reveals Divergent Serotype Specific Sub-populations and Distant Ancestors. PLoS Negl Trop Dis 2016; 10:e0004861. [PMID: 27494185 PMCID: PMC4975453 DOI: 10.1371/journal.pntd.0004861] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 06/29/2016] [Indexed: 12/13/2022] Open
Abstract
The emerging pathogen Cryptococcus gattii causes life-threatening disease in immunocompetent and immunocompromised hosts. Of the four major molecular types (VGI-VGIV), the molecular type VGIII has recently emerged as cause of disease in otherwise healthy individuals, prompting a need to investigate its population genetic structure to understand if there are potential genotype-dependent characteristics in its epidemiology, environmental niche(s), host range and clinical features of disease. Multilocus sequence typing (MLST) of 122 clinical, environmental and veterinary C. gattii VGIII isolates from Australia, Colombia, Guatemala, Mexico, New Zealand, Paraguay, USA and Venezuela, and whole genome sequencing (WGS) of 60 isolates representing all established MLST types identified four divergent sub-populations. The majority of the isolates belong to two main clades, corresponding either to serotype B or C, indicating an ongoing species evolution. Both major clades included clinical, environmental and veterinary isolates. The C. gattii VGIII population was genetically highly diverse, with minor differences between countries, isolation source, serotype and mating type. Little to no recombination was found between the two major groups, serotype B and C, at the whole and mitochondrial genome level. C. gattii VGIII is widespread in the Americas, with sporadic cases occurring elsewhere, WGS revealed Mexico and USA as a likely origin of the serotype B VGIII population and Colombia as a possible origin of the serotype C VGIII population. Serotype B isolates are more virulent than serotype C isolates in a murine model of infection, causing predominantly pulmonary cryptococcosis. No specific link between genotype and virulence was observed. Antifungal susceptibility testing against six antifungal drugs revealed that serotype B isolates are more susceptible to azoles than serotype C isolates, highlighting the importance of strain typing to guide effective treatment to improve the disease outcome. Cryptococcus gattii, which is classically divided into four major molecular types (VGI-VGIV), and two serotypes B and C, is the second most important cause of cryptococcosis. The rising incidence of human and animal cryptococcosis cases caused by molecular type VGIII highlights the need for increased vigilance. In this study, we characterized a large set of C. gattii VGIII isolates. Genetic analysis revealed four diverging sub-populations, which were primarily associated with serotype B or C, and very likely originated from endemic regions in Colombia, Mexico and the USA. Differences in virulence and antifungal susceptibility between serotypes may result in different disease outcomes since serotype B isolates were more virulent in mice than serotype C isolates, but serotype C isolates were less susceptible to azoles, the primary treatment for uncomplicated cryptococcosis. Identification of cryptococcal serotype and molecular type in clinical practice has the potential to guide treatment regimens and hence reduce morbidity and mortality in both sporadic cases and those associated with outbreaks. Our study significantly contributes to the understanding of the epidemiology, genetics and pathogenesis of Cryptococcus and cryptococcosis.
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Affiliation(s)
- Carolina Firacative
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School - Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Millennium Institute, Sydney, Australia
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - Chandler C. Roe
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Richard Malik
- Centre for Veterinary Education, The University of Sydney, Sydney, Australia
| | - Kennio Ferreira-Paim
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School - Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Millennium Institute, Sydney, Australia
- Infectious Disease Department, Triangulo Mineiro Federal University, Uberaba, Minas Gerais, Brazil
| | - Patricia Escandón
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - Jane E. Sykes
- Department of Medicine and Epidemiology, University of California, Davis, Davis, California, United States of America
| | - Laura Rocío Castañón-Olivares
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad National Autónoma de México, Mexico City, Mexico
| | | | | | - Tania C. Sorrell
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School - Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Millennium Institute, Sydney, Australia
| | | | - Shawn R. Lockhart
- Mycotic Diseases Branch, 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
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Sydney Medical School - Westmead Hospital, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Millennium Institute, Sydney, Australia
- * E-mail:
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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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Abstract
The effects of extension of myocardial infarction by reduction of regional myocardial blood flow (RMBF) to an ischemic region on serum CK activity was examined in 14 awake dogs. Initial infarction was effected by occlusion of the distal left circumflex coronary artery (LCCA) and subsequent extension was produced by occlusion of the proximal LCCA 6, 12 or 18 hours after distal occlusion. Extension was verified by serial measurements of RMBF using radioisotope-labeled microspheres before and after proximal occlusion. Serum CK activity increased initially 2-4 hours after distal coronary occlusion and then increased rapidly and reached peak values 12 hours after occlusion. When the infarction was extended at 6, 12 or 18 hours after initial occlusion, CK appearance was immediately reduced in the 6- and 12-hour experiments, but not in the 18-hour experiments. Extension of infarction at each interval caused delayed increases in CK activity beginning 2-5 hours after proximal occlusion, with peak values occurring 12 hours later. The immediate effects of extension of infarction by reducing blood flow on CK activity are a function of whether the infarcted myocardium continued to release CK, e.g., at 6 and 12 hours after occlusion, or CK release was completed, e.g., 18 hours. The immediate effects of extension of infarction were the result of perfusion on myocardium that is infarcted and continues to release CK, and do not necessarily indicate alterations in the extent of myocardial injury. The delayed effects of proximal and distal occlusion on CK activity were comparable, suggesting that delayed and not immediate alterations in CK activity represent extension of infarction.
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