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Yerlikaya Z, Miranda-CasoLuengo R, Ó Gaora P, Meijer WG. Complete genome sequence of the saprophytic actinomycete Prescottella soli DSD51W T, closely related to the multi-host pathogen Prescottella ( Rhodococcus) equi. Microbiol Resour Announc 2024:e0059724. [PMID: 39470233 DOI: 10.1128/mra.00597-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Accepted: 09/30/2024] [Indexed: 10/30/2024] Open
Abstract
Prescottella soli strain DSD51WT is an aerobic, non-spore-forming, non-motile actinomycete isolated previously from soil collected from Kyoto Park, Japan, using a resuscitative technique. Here, we report the complete, circular genome sequence of P. soli DSD51WT. We employed a hybrid approach using Illumina and Oxford Nanopore platforms.
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Affiliation(s)
- Zeynep Yerlikaya
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute, University College, Dublin, Ireland
- Department of Microbiology, School of Veterinary Medicine, Firat University, Elazığ, Türkiye
| | - Raúl Miranda-CasoLuengo
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute, University College, Dublin, Ireland
| | - Peadar Ó Gaora
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute, University College, Dublin, Ireland
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science and UCD Conway Institute, University College, Dublin, Ireland
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Arahal DR, Bull CT, Christensen H, Chuvochina M, Dunlap C, del Carmen Montero-Calasanz M, Parker CT, Vandamme P, Ventosa A, Ventura S, Young P, Göker M. Judicial Opinion 130. Int J Syst Evol Microbiol 2024; 74:006414. [PMID: 38841989 PMCID: PMC11261725 DOI: 10.1099/ijsem.0.006414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 05/26/2024] [Indexed: 06/07/2024] Open
Abstract
Opinion 130 deals with a Request for an Opinion asking the Judicial Commission to clarify whether the genus name Rhodococcus Zopf 1891 (Approved Lists 1980) is illegitimate. The Request is approved and an answer is given. The name Rhodococcus Zopf 1891 (Approved Lists 1980) is illegitimate because it is a later homonym of the validly published cyanobacterial name Rhodococcus Hansgirg 1884. The Judicial Commission also clarifies that it has the means to resolve such cases by conserving a name over an earlier homonym. It is concluded that the name Rhodococcus Zopf 1891 (Approved Lists 1980) is significantly more important than the name Rhodococcus Hansgirg 1884 and therefore the former is conserved over the latter. This makes the name Rhodococcus Zopf 1891 (Approved Lists 1980) legitimate.
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Affiliation(s)
- David R. Arahal
- Departamento de Microbiología y Ecología, Universitat de València, Valencia, Spain
| | - Carolee T. Bull
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, PA 16802, USA
| | - Henrik Christensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, QLD 4072, Australia
| | - Christopher Dunlap
- Crop Bioprotection Research Unit, USDA/ARS/NCAUR, 1815 N. University St, 61604 Peoria, Illinois, USA
| | - Maria del Carmen Montero-Calasanz
- IFAPA Las Torres - Andalusian Institute of Agricultural and Fisheries Research and Training, Cra. Sevilla-Cazalla de la Sierra, 41200, Alcalá del Río, Sevilla, Spain
| | - Charles T. Parker
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Peter Vandamme
- BCCM/LMG, Laboratorium voor Microbiologie, Universiteit Gent (UGent) K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, C/. Prof. Garcia Gonzalez 2, ES-41012 Sevilla, Spain
| | - Stefano Ventura
- IRET-CNR, Research Institute on Terrestrial Ecosystems, National Research Council, Via Madonna del Piano 10, 50019 Sesto Fiorentino, and NBCF, National Biodiversity Future Center, Palermo, Italy
| | - Peter Young
- Department of Biology, University of York, York YO10 5DD, UK
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
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Goodfellow M, Oren A, Sangal V, Sutcliffe IC. Is the bacterial genus name Rhodococcus Zopf 1891 illegitimate? Request for an Opinion. Int J Syst Evol Microbiol 2024; 74. [PMID: 38265282 DOI: 10.1099/ijsem.0.006251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024] Open
Abstract
In 2014, it was reported that the bacterial genus name Rhodococcus Zopf 1891 was illegitimate due to the priority of the cyanobacterial genus name Rhodococcus Hansgirg 1884. Since that time, the consequences of this conclusion have been largely ignored, whilst changes have been made to relevant Rules of the International Code of Nomenclature of Prokaryotes, including significant changes to the way in which the Code treats the names of members of Cyanobacteriota. Given the complexity of the nomenclatural issues, we request the opinion of the Judicial Commission of the International Committee on Systematics of Prokaryotes as to whether the genus name Rhodococcus Zopf 1891 (Approved Lists 1980) is illegitimate.
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Affiliation(s)
- Michael Goodfellow
- School of Natural and Environmental Sciences, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
| | - Vartul Sangal
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Iain C Sutcliffe
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
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Xu X, Liang H, Song Y, Wang D, Wei Q, Wang Y. HIV complicated with Rhodococcus equi infection: A case report. INFECTIOUS MEDICINE 2022; 1:281-284. [DOI: 10.1016/j.imj.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
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Sangal V, Goodfellow M, Jones AL, Sutcliffe IC. A stable home for an equine pathogen: valid publication of the binomial Prescottella equi gen. nov., comb. nov., and reclassification of four rhodococcal species into the genus Prescottella. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Opinion 106 of the Judicial Commission has clarified the nomenclature of the taxon variously named
Rhodococcus equi
, ‘Prescottella equi’ and
Rhodococcus hoagii
. As a consequence, we present here the genus name
Prescottella
and that of its nomenclatural type species,
Prescottella equi
comb. nov., for valid publication and propose the reclassification of four rhodococcal species as novel combinations in the genus, namely Prescottella agglutinans Guo et al. 2015 comb. nov., Prescottella defluvii Kämpfer et al. 2014 comb. nov., Prescottella soli Li et al. 2015 comb. nov. and Prescottella subtropica Lee et al. 2019 comb. nov. In addition, we note that a clinical isolate, strain 86–07 (=W8901), likely represents an additional species within the genus
Prescottella
. Nearly a century after the original description of the type strain of the type species as
Corynebacterium equi
, we provide a stable home for
Prescottella equi
and its relatives.
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Affiliation(s)
- Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Amanda L. Jones
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Iain C. Sutcliffe
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
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Fatal Infection in an Alpaca (Vicugna pacos) Caused by Pathogenic Rhodococcus equi. Animals (Basel) 2022; 12:ani12101303. [PMID: 35625149 PMCID: PMC9137691 DOI: 10.3390/ani12101303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/05/2022] [Accepted: 05/13/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Serious consequences of septicemic bacterial infections include the formation of purulent and pyogranulomatous inflammation resulting in abscesses in inner organs. Different bacteria are known to cause these infections in livestock. In this study, we report in detail on a case of a fatal Rhodococcus (R.) equi infection in an alpaca (Vicugna pacos), to our knowledge, for the first time. R. equi is a member of the actinomycetes, a bacterial group known to contain several pathogenic bacteria. R. equi primarily affects equine foals and other domestic animals, but also humans, which renders this bacterium a zoonotic agent. The rhodococcal infection of the alpaca reported herein caused septicemia, resulting in emaciation and severe lesions in the lungs and heart. The onset of infection was presumably caused by aspiration pneumonia, resulting in abscesses exclusively in the lungs. The R. equi isolate proved to be pathogenic, based on the virulence gene vapA encoding the virulence-associated protein A. Antibiotic susceptibility testing revealed a susceptibility to doxycycline, erythromycin, gentamycin, neomycin, rifampicin, trimethoprim/sulfamethoxazole, tetracycline and vancomycin. This report of an R. equi infection in an alpaca makes clear that we still have knowledge gaps about bacterial infectious diseases in alpacas and potential zoonotic impacts. Therefore, the determination of pathogenic, zoonotic bacteria in alpacas is essential for treatment and preventive measures with respect to sustaining the health, welfare and productivity of this camelid species. Abstract Rhodococcus (R.) equi is a pathogen primarily known for infections in equine foals, but is also present in numerous livestock species including New World camelids. Moreover, R. equi is considered an emerging zoonotic pathogen. In this report, we describe in detail a fatal rhodococcal infection in an alpaca (Vicugna pacos), to our best knowledge, for the first time. The alpaca died due to a septicemic course of an R. equi infection resulting in emaciation and severe lesions including pyogranulomas in the lungs and pericardial effusion. The onset of the infection was presumably caused by aspiration pneumonia. R. equi could be isolated from the pyogranulomas in the lung and unequivocally identified by MALDI-TOF MS analysis and partial sequencing of the 16S rRNA gene, the 16S-23S internal transcribed spacer (ITS) region and the rpoB gene. The isolate proved to possess the vapA gene in accordance with tested isolates originating from the lungs of infected horses. The R. equi isolates revealed low minimal inhibitory concentrations (MIC values) for doxycycline, erythromycin, gentamycin, neomycin, rifampicin, trimethoprim/sulfamethoxazole, tetracycline and vancomycin in antibiotic susceptibility testing. Investigations on the cause of bacterial, especially fatal, septicemic infections in alpacas are essential for adequately addressing the requirements for health and welfare issues of this New World camelid species. Furthermore, the zoonotic potential of R. equi has to be considered with regard to the One Health approach.
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Song Y, Xu X, Huang Z, Xiao Y, Yu K, Jiang M, Yin S, Zheng M, Meng H, Han Y, Wang Y, Wang D, Wei Q. Genomic Characteristics Revealed Plasmid-Mediated Pathogenicity and Ubiquitous Rifamycin Resistance of Rhodococcus equi. Front Cell Infect Microbiol 2022; 12:807610. [PMID: 35252029 PMCID: PMC8891757 DOI: 10.3389/fcimb.2022.807610] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/27/2022] [Indexed: 11/22/2022] Open
Abstract
Rhodococcus equi is a zoonotic pathogen that can cause fatal disease in patients who are immunocompromised. At present, the epidemiology and pathogenic mechanisms of R. equi infection are not clear. This study characterized the genomes of 53 R. equi strains from different sources. Pan-genome analysis showed that all R. equi strains contained 11481 pan genes, including 3690 core genes and 602 ~ 1079 accessory genes. Functional annotation of pan genome focused on the genes related to basic lifestyle, such as the storage and expression of metabolic and genetic information. Phylogenetic analysis based on pan-genome showed that the R. equi strains were clustered into six clades, which was not directly related to the isolation location and host source. Also, a total of 84 virulence genes were predicted in 53 R. equi strains. These virulence factors can be divided into 20 categories related to substance metabolism, secreted protein and immune escape. Meanwhile, six antibiotic resistance genes (RbpA, tetA (33), erm (46), sul1, qacEdelta 1 and aadA9) were detected, and all strains carried RbpA related to rifamycin resistance. In addition, 28 plasmids were found in the 53 R. equi strains, belonging to Type-A (n = 14), Type-B (n = 8) and Type-N (n = 6), respectively. The genetic structures of the same type of plasmid were highly similar. In conclusion, R. equi strains show different genomic characteristics, virulence-related genes, potential drug resistance and virulence plasmid structures, which may be conducive to the evolution of its pathogenesis.
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Affiliation(s)
- Yang Song
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Xinmin Xu
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Zhenzhou Huang
- Center for human Pathogenic Culture Collection, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - Yue Xiao
- Center for human Pathogenic Culture Collection, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - Keyi Yu
- Center for human Pathogenic Culture Collection, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
| | - Mengnan Jiang
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Shangqi Yin
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Mei Zheng
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Huan Meng
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Ying Han
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Yajie Wang
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- *Correspondence: Qiang Wei, ; Duochun Wang, ; Yajie Wang,
| | - Duochun Wang
- Center for human Pathogenic Culture Collection, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, China
- *Correspondence: Qiang Wei, ; Duochun Wang, ; Yajie Wang,
| | - Qiang Wei
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
- *Correspondence: Qiang Wei, ; Duochun Wang, ; Yajie Wang,
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Abstract
In Opinion 103, the request to place the name Spirillum volutans Ehrenberg 1832 (Approved Lists 1980) on the list of rejected names is denied because a neotype may be designated. Similarly, because a neotype may be designated, in Opinion 104 the request to place the name
Beijerinckia fluminensis
Döbereiner and Ruschel 1958 (Approved Lists 1980) on the list of rejected names is denied. In Opinion 105, it is emphasized that the name
Rhodoligotrophos
Fukuda et al. 2012 does not contravene the Code. The request to orthographically correct
Rhodoligotrophos
Fukuda et al. 2012 to Rhodoligotrophus corrig. Fukuda et al. 2012 is denied. Opinion 106 addresses two Requests for an Opinion and results in the placement of the epithet hoagii in
Corynebacterium hoagii
(Morse 1912) Eberson 1918 (Approved Lists 1980) and
Rhodococcus hoagii
(Morse 1912) Kämpfer et al. 2014 on the list of rejected specific and subspecific epithets. Since this removes all known available earlier synonyms of
Rhodococcus equi
(Magnusson 1923) Goodfellow and Alderson 1977 (Approved Lists 1980), the request to conserve the epithet equi in this name is denied. In Opinion 107,
Thermomicrobium fosteri
Phillips and Perry 1976 (Approved Lists 1980) is placed on the list of rejected names as a nomen dubium et confusum. Opinion 108 denies the request to place
Hyphomonas rosenbergii
Weiner et al. 2000 on the list of rejected names because the information provided to the Judicial Commission is not sufficient to draw a conclusion on this matter. In Opinion 109, which addresses three Requests for an Opinion, the Judicial Commission denies the requests to place the names
Bacillus aerius
Shivaji et al. 2006,
Bacillus aerophilus
Shivaji et al. 2006 and
Bacillus stratosphericus
Shivaji et al. 2006 on the list of rejected names. Instead, it is concluded that these three names had not met the requirements for valid publication. Likewise, the Judicial Commission concludes in Opinion 110 that the name
Actinobaculum massiliense
corrig. Greub and Raoult 2006 had not met the requirements for valid publication. The Judicial Commission reaffirms in Opinion 111 that
Methanocorpusculum parvum
Zellner et al. 1988 is the nomenclatural type of
Methanocorpusculum
Zellner et al. 1988 and further emphasizes that the species was not in danger of losing this status. These Opinions were ratified by the voting members of the International Committee on Systematics of Prokaryotes.
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Göker M. Judicial Commission of the International Committee on Systematics of Prokaryotes: Minutes of the Meeting of 4 August 2021. Int J Syst Evol Microbiol 2021; 71. [PMID: 34546866 DOI: 10.1099/ijsem.0.005045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The minutes of the online meeting of the Judicial Commission of the International Committee on Systematics of Prokaryotes that was held on 4 August 2021 by video conference are presented.
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Affiliation(s)
- Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Department of Bioinformatics and Databases, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
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Salazar-Rodríguez D, Aleaga-Santiesteban Y, Iglesias E, Plascencia-Hernández A, Pérez-Gómez HR, Calderón EJ, Vázquez-Boland JA, de Armas Y. Virulence Plasmids of Rhodococcus equi Isolates From Cuban Patients With AIDS. Front Vet Sci 2021; 8:628239. [PMID: 33718470 PMCID: PMC7947234 DOI: 10.3389/fvets.2021.628239] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/05/2021] [Indexed: 11/13/2022] Open
Abstract
Rhodococcus equi is an animal pathogen and zoonotic human opportunistic pathogen associated with immunosuppressive conditions. The pathogenicity of R. equi is linked to three animal host-associated virulence plasmids encoding a family of “Virulence Associated Proteins” (VAPs). Here, the PCR-based TRAVAP molecular typing system for the R. equi virulence plasmids was applied to 26 R. equi strains isolated between 2010 and 2016 at the Institute of Tropical Medicine “Pedro Kourí,” Cuba, from individuals living with HIV/AIDS. TRAVAP detects 4 gene markers, traA common to the three virulence plasmids, and vapA, vapB, and vapN specific to each of the host-associated plasmid types (equine pVAPA, porcine pVAPB, and ruminant pVAPN). Of the 26 isolates, six were positive to the vapB (porcine-type) marker, 4 (15.4%) to the vapA (equine-type) marker, and 1 (3.8%) to the vapN (ruminant-type) marker. Most of the isolates 14 (53.8%) were negative to all TRAVAP markers, suggesting they lacked a virulence plasmid. To our knowledge, this work is the first to report the molecular characterization of R. equi isolates from Cuba. Our findings provide insight into the zoonotic origin of R. equi infections in people and the potential dispensability of the virulence plasmid in immunosuppressed patients.
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Affiliation(s)
- Daniel Salazar-Rodríguez
- Department of Clinical Microbiology Diagnostic, Hospital Center of Institute of Tropical Medicine "Pedro Kourí," Havana, Cuba
| | - Yamilé Aleaga-Santiesteban
- Department of Clinical Microbiology Diagnostic, Hospital Center of Institute of Tropical Medicine "Pedro Kourí," Havana, Cuba
| | - Enrique Iglesias
- Departamento de Vacunas, Centro de Ingeniería Genética y Biotecnología, Havana, Cuba
| | | | - Héctor R Pérez-Gómez
- Centro Universitario de Ciencias de la Salud de la Universidad de Guadalajara, Guadalajara, Mexico
| | - Enrique J Calderón
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Seville, Spain
| | - José A Vázquez-Boland
- Microbial Pathogenesis Group, Edinburgh Medical School (Biomedical Sciences - Infection Medicine), University of Edinburgh, Edinburgh, United Kingdom
| | - Yaxsier de Armas
- Department of Clinical Microbiology Diagnostic, Hospital Center of Institute of Tropical Medicine "Pedro Kourí," Havana, Cuba.,Pathology Department, Hospital Center of Institute of Tropical Medicine "Pedro Kourí," Havana, Cuba
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