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Szewc AM, Bell ME, Kelly AJ, Humrighouse BW, McQuiston JR. Using the BDFX40 Automated Continuous Blood Culture System to Isolate and Recover Streptobacillus moniliformis in the Presence of 0.05% SPS: A 55-Year, 56-Strain Retrospective Study. Lab Med 2021; 52:536-549. [PMID: 33693831 DOI: 10.1093/labmed/lmab009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Rat bite fever and Haverhill fever are often difficult to diagnose in a clinical setting. This difficulty results in part from clinicians and laboratory professionals not being able to reliably recover the causative agent Streptobacillus moniliformis using culture-based methods. After utilizing an automated continuous-monitoring blood culture bottle system, we showed that the organism can be reliably cultured when a blood volume inoculum of 10 mL is used. Further, we showed that when the above recommendation is followed, sodium polyanethole sulfonate (up to a concentration of 0.05% w/v) in commercially purchased blood culture bottle formulations seems to be inactivated, allowing for the growth and detection of S. moniliformis. Herein, we offer data and methods used to overcome these clinical limitations. This is a comprehensive study of the historical collection of S. moniliformis isolates maintained by our facility and believed to be the largest of its kind to date.
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Affiliation(s)
- Adam M Szewc
- Bacterial Special Pathogens Branch (BSPB), Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Melissa E Bell
- Bacterial Special Pathogens Branch (BSPB), Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Aubree J Kelly
- Bacterial Special Pathogens Branch (BSPB), Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ben W Humrighouse
- Bacterial Special Pathogens Branch (BSPB), Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - John R McQuiston
- Bacterial Special Pathogens Branch (BSPB), Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Kelly AJ, Ivey ML, Gulvik CA, Humrighouse BW, McQuiston JR. A real-time multiplex PCR assay for detection of the causative agents of rat bite fever, Streptobacillus moniliformis and zoonoticStreptobacillus species. Diagn Microbiol Infect Dis 2021; 100:115335. [PMID: 33618204 DOI: 10.1016/j.diagmicrobio.2021.115335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/24/2021] [Accepted: 01/28/2021] [Indexed: 12/17/2022]
Abstract
Rat bite fever (RBF) caused by Streptobacillus moniliformis has been described as a diagnostic challenge. While it has a favorable prognosis with treatment, timely diagnosis is hindered by the lack of culture-free identification methods. Here we present a multiplex real-time PCR assay that detects the zoonotic Streptobacillus spp. as well as differentiate the primary causative agent of RBF, Streptobacillus moniliformis. The performance of this assay was evaluated using mock clinical specimens for blood, serum, and urine. Analytical sensitivity was determined to be 3-4 genome equivalents (GE)/µl for the zoonotic Streptobacillus spp. target, and 1-2 GE/µl for the S. moniliformis specific target. The assay correctly detected only the intended targets with no cross-reactivity identified. The pathogen was detected in all spiked matrices and not detected in the negative non-spiked specimens. This rapid diagnostic assay may permit quicker diagnosis of RBF patients.
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Affiliation(s)
- Aubree J Kelly
- Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Melissa L Ivey
- Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Christopher A Gulvik
- Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ben W Humrighouse
- Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John R McQuiston
- Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
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3
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Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Bell ME, Holmes B, Steigerwalt AG, Villarma A, Sheth M, Batra D, Rowe LA, Burroughs M, Pryor JC, Bernardet JF, Hugo C, Kämpfer P, Newman JD, McQuiston JR. Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 2020; 70:4432-4450. [PMID: 32735208 PMCID: PMC7660247 DOI: 10.1099/ijsem.0.003935] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [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: 06/13/2019] [Revised: 10/28/2019] [Accepted: 12/02/2019] [Indexed: 01/10/2023] Open
Abstract
The genus Chryseobacterium in the family Weeksellaceae is known to be polyphyletic. Amino acid identity (AAI) values were calculated from whole-genome sequences of species of the genus Chryseobacterium, and their distribution was found to be multi-modal. These naturally-occurring non-continuities were leveraged to standardise genus assignment of these species. We speculate that this multi-modal distribution is a consequence of loss of biodiversity during major extinction events, leading to the concept that a bacterial genus corresponds to a set of species that diversified since the Permian extinction. Transfer of nine species (Chryseobacterium arachidiradicis, Chryseobacterium bovis, Chryseobacterium caeni, Chryseobacterium hispanicum, Chryseobacterium hominis, Chryseobacterium hungaricum,, Chryseobacterium pallidum and Chryseobacterium zeae) to the genus Epilithonimonas and eleven (Chryseobacterium anthropi, Chryseobacterium antarcticum, Chryseobacterium carnis, Chryseobacterium chaponense, Chryseobacterium haifense, Chryseobacterium jeonii, Chryseobacterium montanum, Chryseobacterium palustre, Chryseobacterium solincola, Chryseobacterium treverense and Chryseobacterium yonginense) to the genus Kaistella is proposed. Two novel species are described: Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. Evidence is presented to support the assignment of Planobacterium taklimakanense to a genus apart from Chryseobacterium, to which Planobacterium salipaludis comb nov. also belongs. The novel genus Halpernia is proposed, to contain the type species Halpernia frigidisoli comb. nov., along with Halpernia humi comb. nov., and Halpernia marina comb. nov.
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Affiliation(s)
- Ainsley C. Nicholson
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Christopher A. Gulvik
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Anne M. Whitney
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Ben W. Humrighouse
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Melissa E. Bell
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Barry Holmes
- National Collection of Type Cultures, Health Protection Agency, Colindale, London NW9 5EQ, UK
| | - Arnie G. Steigerwalt
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Aaron Villarma
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Mili Sheth
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Dhwani Batra
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Lori A. Rowe
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Mark Burroughs
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Jessica C. Pryor
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Jean-François Bernardet
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires, Domaine de Vilvert, Jouy-en-Josas, France
| | - Celia Hugo
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany
| | - Jeffrey D. Newman
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
- Biology Department, Lycoming College, Williamsport PA 17701, USA
| | - John R. McQuiston
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
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Shewmaker PL, Whitney AM, Gulvik CA, Humrighouse BW, Gartin J, Moura H, Barr JR, Moore ERB, Karlsson R, Pinto TCA, Teixeira LM. Vagococcus bubulae sp. nov., isolated from ground beef, and Vagococcus vulneris sp. nov., isolated from a human foot wound. Int J Syst Evol Microbiol 2019; 69:2268-2276. [PMID: 31125302 DOI: 10.1099/ijsem.0.003459] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 11/18/2022] Open
Abstract
Two unusual catalase-negative, Gram-stain-positive, Vagococcus-like isolates that were referred to the CDC Streptococcus Laboratory for identification are described. Strain SS1994T was isolated from ground beef and strain SS1995T was isolated from a human foot wound. Comparative 16S rRNA gene sequence analysis of isolates SS1994T and SS1995T against Vagococcus type strain sequences supported their inclusion in the genus Vagococcus. Strain SS1994T showed high sequence similarity (>97.0 %) to the two most recently proposed species, Vagococcus martis (99.2 %) and Vagococcus teuberi (99.0 %) followed by Vagococcus penaei (98.8 %), strain SS1995T (98.6 %), Vagococcus carniphilus (98.0 %), Vagococcus acidifermentans (98.0 %) and Vagococcus fluvialis (97.9 %). The 16S rRNA gene sequence of strain SS1995T was most similar to V. penaei (99.1 %), followed by SS1994T (98.6 %), V. martis (98.4 %), V. teuberi (98.1 %), V. acidifermentans (97.8 %), and both V. carniphilus and V. fluvialis (97.5 %). A polyphasic taxonomic study using conventional biochemical and the rapid ID 32 STREP system, MALDI-TOF MS, cell fatty acid analysis, pairwise sequence comparisons of the 16S rRNA, rpoA, rpoB, pheS and groL genes, and comparative core and whole genome sequence analyses revealed that strains SS1994T and SS1995T were two novel Vagococcus species. The novel taxonomic status of the two isolates was confirmed with core genome phylogeny, average nucleotide identity <84 % and in silico DNA-DNA hybridization <28 % to any other Vagococcus species. The names Vagococcusbubulae SS1994T=(CCUG 70831T=LMG 30164T) and Vagococcusvulneris SS1995T=(CCUG 70832T=LMG 30165T) are proposed.
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Affiliation(s)
- Patricia L Shewmaker
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Anne M Whitney
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Christopher A Gulvik
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Ben W Humrighouse
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Jarrett Gartin
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Hercules Moura
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - John R Barr
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Edward R B Moore
- Department of Clinical Microbiology, Sahlgrenska University Hospital, SE-41346 Region Västra Götaland, Sweden.,Culture Collection University of Gothenburg (CCUG), Gothenburg, Sweden.,Department of Infectious Disease, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-41346, Sweden
| | - Roger Karlsson
- Department of Clinical Microbiology, Sahlgrenska University Hospital, SE-41346 Region Västra Götaland, Sweden.,Department of Infectious Disease, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-41346, Sweden.,Nanoxis Consulting AB, SE-40016 Gothenburg, Sweden
| | - Tatiana C A Pinto
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucia M Teixeira
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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5
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Johnson WL, Ramachandran A, Torres NJ, Nicholson AC, Whitney AM, Bell M, Villarma A, Humrighouse BW, Sheth M, Dowd SE, McQuiston JR, Gustafson JE. The draft genomes of Elizabethkingia anophelis of equine origin are genetically similar to three isolates from human clinical specimens. PLoS One 2018; 13:e0200731. [PMID: 30024943 PMCID: PMC6053191 DOI: 10.1371/journal.pone.0200731] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 04/16/2018] [Accepted: 05/28/2018] [Indexed: 12/20/2022] Open
Abstract
We report the isolation and characterization of two Elizabethkingia anophelis strains (OSUVM-1 and OSUVM-2) isolated from sources associated with horses in Oklahoma. Both strains appeared susceptible to fluoroquinolones and demonstrated high MICs to all cell wall active antimicrobials including vancomycin, along with aminoglycosides, fusidic acid, chloramphenicol, and tetracycline. Typical of the Elizabethkingia, both draft genomes contained multiple copies of β-lactamase genes as well as genes predicted to function in antimicrobial efflux. Phylogenetic analysis of the draft genomes revealed that OSUVM-1 and OSUVM-2 differ by only 6 SNPs and are in a clade with 3 strains of Elizabethkingia anophelis that were responsible for human infections. These findings therefore raise the possibility that Elizabethkingia might have the potential to move between humans and animals in a manner similar to known zoonotic pathogens.
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Affiliation(s)
- William L. Johnson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Akhilesh Ramachandran
- Oklahoma Animal Disease Diagnostic Laboratory, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, Oklahoma, United States of America
- * E-mail: (AR); (JEG)
| | - Nathanial J. Torres
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Ainsley C. Nicholson
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Anne M. Whitney
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Melissa Bell
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Aaron Villarma
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Ben W. Humrighouse
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Mili Sheth
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Scot E. Dowd
- Molecular Research DNA Laboratory, Shallowater, Texas, United States of America
| | - John R. McQuiston
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - John E. Gustafson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, United States of America
- * E-mail: (AR); (JEG)
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Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Graziano J, Emery B, Bell M, Loparev V, Juieng P, Gartin J, Bizet C, Clermont D, Criscuolo A, Brisse S, McQuiston JR. Revisiting the taxonomy of the genus Elizabethkingia using whole-genome sequencing, optical mapping, and MALDI-TOF, along with proposal of three novel Elizabethkingia species: Elizabethkingia bruuniana sp. nov., Elizabethkingia ursingii sp. nov., and Elizabethkingia occulta sp. nov. Antonie Van Leeuwenhoek 2017; 111:55-72. [PMID: 28856455 DOI: 10.1007/s10482-017-0926-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 08/07/2017] [Indexed: 10/19/2022]
Abstract
The genus Elizabethkingia is genetically heterogeneous, and the phenotypic similarities between recognized species pose challenges in correct identification of clinically derived isolates. In addition to the type species Elizabethkingia meningoseptica, and more recently proposed Elizabethkingia miricola, Elizabethkingia anophelis and Elizabethkingia endophytica, four genomospecies have long been recognized. By comparing historic DNA-DNA hybridization results with whole genome sequences, optical maps, and MALDI-TOF mass spectra on a large and diverse set of strains, we propose a comprehensive taxonomic revision of this genus. Genomospecies 1 and 2 contain the type strains E. anophelis and E. miricola, respectively. Genomospecies 3 and 4 are herein proposed as novel species named as Elizabethkingia bruuniana sp. nov. (type strain, G0146T = DSM 2975T = CCUG 69503T = CIP 111191T) and Elizabethkingia ursingii sp. nov. (type strain, G4122T = DSM 2974T = CCUG 69496T = CIP 111192T), respectively. Finally, the new species Elizabethkingia occulta sp. nov. (type strain G4070T = DSM 2976T = CCUG 69505T = CIP 111193T), is proposed.
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Affiliation(s)
- Ainsley C Nicholson
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA.
| | - Christopher A Gulvik
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Anne M Whitney
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Ben W Humrighouse
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - James Graziano
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Brian Emery
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Melissa Bell
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Vladimir Loparev
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Phalasy Juieng
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Jarrett Gartin
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Chantal Bizet
- Microbiology Department, Institut Pasteur, Collection de L'Institut Pasteur (CIP), Paris, France
| | - Dominique Clermont
- Microbiology Department, Institut Pasteur, Collection de L'Institut Pasteur (CIP), Paris, France
| | - Alexis Criscuolo
- Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France
| | - Sylvain Brisse
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France.,CNRS, UMR 3525, Paris, France.,Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - John R McQuiston
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
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McLaughlin RW, Shewmaker PL, Whitney AM, Humrighouse BW, Lauer AC, Loparev VN, Gulvik CA, Cochran PA, Dowd SE. Enterococcus crotali sp. nov., isolated from faecal material of a timber rattlesnake. Int J Syst Evol Microbiol 2017. [PMID: 28632114 DOI: 10.1099/ijsem.0.001900] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A facultatively anaerobic, Gram-stain-positive bacterium, designated ETRF1T, was found in faecal material of a timber rattlesnake (Crotalus horridus). Based on a comparative 16S rRNA gene sequence analysis, the isolate was assigned to the genus Enterococcus. The 16S rRNA gene sequence of strain ETRF1T showed >97 % similarity to that of the type strains of Enterococcus rotai, E. caccae, E. silesiacus, E haemoperoxidus, E. ureasiticus, E. moraviensis, E. plantarum, E. quebecensis, E. ureilyticus, E. termitis, E. rivorum and E. faecalis. The organism could be distinguished from these 12 phylogenetically related enterococci using conventional biochemical testing, the Rapid ID32 Strep system, comparative pheS and rpoA gene sequence analysis, and comparative whole genome sequence analysis. The estimated in silico DNA-DNA hybridization values were <70 %, and average nucleotide identity values were <96 %, when compared to these 12 species, further validating that ETRF1T represents a unique species within the genus Enterococcus. On the basis of these analyses, strain ETRF1T (=CCUG 65857T=LMG 28312T) is proposed as the type strain of a novel species, Enterococcus crotali sp. nov.
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Affiliation(s)
- Richard W McLaughlin
- General Studies, Gateway Technical College, Kenosha, WI 53144, USA.,Biology Department, Saint Mary's University of Minnesota, Winona, MN 55987-1399, USA
| | | | - Anne M Whitney
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | | | - Ana C Lauer
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | | | | | - P A Cochran
- Biology Department, Saint Mary's University of Minnesota, Winona, MN 55987-1399, USA
| | - Scot E Dowd
- MR DNA (Molecular Research LP), Shallowater, TX, USA
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Humrighouse BW, Emery BD, Kelly AJ, Metcalfe MG, Mbizo J, McQuiston JR. Erratum to: Haematospirillum jordaniae gen. nov., sp. nov., isolated from human blood samples. Antonie Van Leeuwenhoek 2016; 109:895-896. [PMID: 27062531 DOI: 10.1007/s10482-016-0694-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- B W Humrighouse
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, USA.
| | - B D Emery
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, USA
| | - A J Kelly
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, USA
| | - M G Metcalfe
- Infectious Diseases Pathology Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, USA
| | - J Mbizo
- Department of Public Health, Clinical and Health Sciences, College of Science, Engineering and Health, University of West Florida, Pensacola, USA
| | - J R McQuiston
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, USA
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9
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Humrighouse BW, Emery BD, Kelly AJ, Metcalfe MG, Mbizo J, McQuiston JR. Haematospirillum jordaniae gen. nov., sp. nov., isolated from human blood samples. Antonie Van Leeuwenhoek 2016; 109:493-500. [PMID: 26857139 DOI: 10.1007/s10482-016-0654-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/15/2016] [Indexed: 10/22/2022]
Abstract
A Gram-negative, aerobic, motile, spiral-shaped bacterium, strain H5569(T), was isolated from a human blood sample. Phenotypic and molecular characteristics of the isolate were investigated. Optimal growth was found to occur at 35 °C under aerobic conditions on Heart Infusion Agar supplemented with 5 % rabbit blood. The major fatty acids present in the cells were identified as C16:0, C16:1ω7c and C18:1ω7c. The predominant respiratory quinone was found to be ubiquinone-Q10. The G+C content of genomic DNA for strain H5569(T) was found to be 49.9 %. Based on 16S rRNA gene sequence analysis results, 13 additional isolates were also analysed in this study. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism, represented by strain H5569(T), forms a distinct lineage within the family Rhodospirillaceae, closely related to two Novispirillum itersonii subspecies (93.9-94.1 %) and two Caenispirillum sp. (91.2-91.6 %). Based on these results, the isolate H5569(T) is concluded to represent a new genus and species for which the name Haematospirillum jordaniae gen. nov., sp. nov. is proposed. The type strain is H5569(T) (=DSM(T) 28903 = CCUG 66838(T)).
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Affiliation(s)
- B W Humrighouse
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, USA.
| | - B D Emery
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, USA
| | - A J Kelly
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, USA
| | - M G Metcalfe
- Infectious Diseases Pathology Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, USA
| | - J Mbizo
- Department of Public Health, Clinical and Health Sciences, College of Science, Engineering and Health, University of West Florida, Pensacola, USA
| | - J R McQuiston
- Special Bacteriology Reference Laboratory, Bacterial Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, USA
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10
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Mate SE, Kugelman JR, Nyenswah TG, Ladner JT, Wiley MR, Cordier-Lassalle T, Christie A, Schroth GP, Gross SM, Davies-Wayne GJ, Shinde SA, Murugan R, Sieh SB, Badio M, Fakoli L, Taweh F, de Wit E, van Doremalen N, Munster VJ, Pettitt J, Prieto K, Humrighouse BW, Ströher U, DiClaro JW, Hensley LE, Schoepp RJ, Safronetz D, Fair J, Kuhn JH, Blackley DJ, Laney AS, Williams DE, Lo T, Gasasira A, Nichol ST, Formenty P, Kateh FN, De Cock KM, Bolay F, Sanchez-Lockhart M, Palacios G. Molecular Evidence of Sexual Transmission of Ebola Virus. N Engl J Med 2015; 373:2448-54. [PMID: 26465384 PMCID: PMC4711355 DOI: 10.1056/nejmoa1509773] [Citation(s) in RCA: 307] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A suspected case of sexual transmission from a male survivor of Ebola virus disease (EVD) to his female partner (the patient in this report) occurred in Liberia in March 2015. Ebola virus (EBOV) genomes assembled from blood samples from the patient and a semen sample from the survivor were consistent with direct transmission. The genomes shared three substitutions that were absent from all other Western African EBOV sequences and that were distinct from the last documented transmission chain in Liberia before this case. Combined with epidemiologic data, the genomic analysis provides evidence of sexual transmission of EBOV and evidence of the persistence of infective EBOV in semen for 179 days or more after the onset of EVD. (Funded by the Defense Threat Reduction Agency and others.).
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Affiliation(s)
- Suzanne E Mate
- From the Center for Genome Sciences (S.E.M., J.R.K., J.T.L., M.R.W., K.P., M.S.-L., G.P.) and Diagnostic Systems Division (R.J.S.), U.S. Army Medical Research Institute of Infectious Diseases, and the Division of Clinical Research, Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH) (J.P., L.E.H., J.H.K.) - all in Frederick, MD; the Ministry of Health and Social Welfare (T.G.N., S.B.S., M.B., F.N.K.) and the World Health Organization (WHO) (G.J.D.-W., R.M.), Monrovia, and the Liberian Institute for Biomedical Research, Charlesville (L.F., F.T., F.B.) - all in Liberia; WHO, Geneva (T.C.-L., A.G., P.F.); the Centers for Disease Control and Prevention, Atlanta (A.C., B.W.H., U.S., D.J.B., A.S.L., D.E.W., T.L., S.T.N., K.M.D.C.); Illumina, San Diego, CA (G.P.S., S.M.G.); WHO, New Delhi, India (S.A.S); Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT (E.W., N.D., V.J.M., D.S.); Naval Medical Research Unit 3, Cairo (J.W.D.); and the Foundation Mérieux, Washington, DC (J.F.)
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11
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Gomez-Alvarez V, Humrighouse BW, Revetta RP, Santo Domingo JW. Bacterial composition in a metropolitan drinking water distribution system utilizing different source waters. J Water Health 2015; 13:140-151. [PMID: 25719474 DOI: 10.2166/wh.2014.057] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We investigated the bacterial composition of water samples from two service areas within a drinking water distribution system (DWDS), each associated with a different primary source of water (groundwater, GW; surface water, SW) and different treatment process. Community analysis based on 16S rRNA gene clone libraries indicated that Actinobacteria (Mycobacterium spp.) and α-Proteobacteria represented nearly 43 and 38% of the total sequences, respectively. Sequences closely related to Legionella, Pseudomonas, and Vibrio spp. were also identified. In spite of the high number of sequences (71%) shared in both areas, multivariable analysis revealed significant differences between the GW and SW areas. While the dominant phylotypes where not significantly contributing in the ordination of samples, the populations associated with the core of phylotypes (1-10% in each sample) significantly contributed to the differences between both service areas. Diversity indices indicate that the microbial community inhabiting the SW area is more diverse and contains more distantly related species coexisting with local assemblages as compared with the GW area. The bacterial community structure of SW and GW service areas were dissimilar, suggesting that their respective source water and/or water quality parameters shaped by the treatment processes may contribute to the differences in community structure observed.
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Affiliation(s)
| | - Ben W Humrighouse
- Department of Civil and Environmental Engineering, University of Cincinnati, Cincinnati, Ohio, USA and US Centers for Disease Control and Prevention, 1600 Clifton Road, Mail Stop D11, Atlanta, GA 30333, USA
| | - Randy P Revetta
- United States Environmental Protection Agency, Cincinnati, Ohio, USA E-mail:
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