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Ngalimat MS, Mohd Hata E, Zulperi D, Ismail SI, Ismail MR, Mohd Zainudin NAI, Saidi NB, Yusof MT. A laudable strategy to manage bacterial panicle blight disease of rice using biocontrol agents. J Basic Microbiol 2023; 63:1180-1195. [PMID: 37348082 DOI: 10.1002/jobm.202300182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/25/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023]
Abstract
Bacterial panicle blight (BPB) disease is a dreadful disease in rice-producing countries. Burkholderia glumae, a Gram-negative, rod-shaped, and flagellated bacterium was identified as the primary culprit for BPB disease. In 2019, the disease was reported in 18 countries, and to date, it has been spotted in 26 countries. Rice yield has been reduced by up to 75% worldwide due to this disease. Interestingly, the biocontrol strategy offers a promising alternative to manage BPB disease. This review summarizes the management status of BPB disease using biological control agents (BCA). Bacteria from the genera Bacillus, Burkholderia, Enterobacter, Pantoea, Pseudomonas, and Streptomyces have been examined as BCA under in vitro, glasshouse, and field conditions. Besides bacteria, bacteriophages have also been reported to reduce BPB pathogens under in vitro and glasshouse conditions. Here, the overview of the mechanisms of bacteria and bacteriophages in controlling BPB pathogens is addressed. The applications of BCA using various delivery methods could effectively manage BPB disease to benefit the agroecosystems and food security.
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Affiliation(s)
- Mohamad S Ngalimat
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Erneeza Mohd Hata
- Sustainable Agronomy and Crop Protection, Institute of Plantation Studies, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Dzarifah Zulperi
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Siti I Ismail
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Mohd R Ismail
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Nur A I Mohd Zainudin
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Noor B Saidi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Mohd T Yusof
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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2
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Currie BJ, Meumann EM, Kaestli M. The Expanding Global Footprint of Burkholderia pseudomallei and Melioidosis. Am J Trop Med Hyg 2023; 108:1081-1083. [PMID: 37160279 PMCID: PMC10540122 DOI: 10.4269/ajtmh.23-0223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 04/14/2023] [Indexed: 05/11/2023] Open
Affiliation(s)
- Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Infectious Diseases Department, Royal Darwin Hospital and Northern Territory Medical Program, Darwin, Northern Territory, Australia
| | - Ella M. Meumann
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Infectious Diseases Department, Royal Darwin Hospital and Northern Territory Medical Program, Darwin, Northern Territory, Australia
- Sullivan Nicolaides Pathology, Brisbane, Queensland, Australia
| | - Mirjam Kaestli
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
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3
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Somprasong N, Hagen JP, Sahl JW, Webb JR, Hall CM, Currie BJ, Wagner DM, Keim P, Schweizer HP. A conserved active site PenA β-lactamase Ambler motif specific for Burkholderia pseudomallei/B. mallei is likely responsible for intrinsic amoxicillin-clavulanic acid sensitivity and facilitates a simple diagnostic PCR assay for melioidosis. Int J Antimicrob Agents 2023; 61:106714. [PMID: 36640845 DOI: 10.1016/j.ijantimicag.2023.106714] [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: 05/31/2022] [Revised: 11/23/2022] [Accepted: 12/31/2022] [Indexed: 01/13/2023]
Abstract
Burkholderia pseudomallei is a soil- and water-dwelling Gram-negative bacterium that causes melioidosis in humans and animals. Amoxicillin-clavulanic acid (AMC) susceptibility has been hailed as an integral part of the screening algorithm for identification of B. pseudomallei, but the molecular basis for the inherent AMC susceptibility of this bacterium remains undefined. This study showed that B. pseudomallei (and the closely-related B. mallei) wild-type strains are the only Burkholderia spp. that contain a 70STSK73 PenA Ambler motif. This motif was present in >99.5% of 1820 analysed B. pseudomallei strains and 100% of 83 analysed B. mallei strains, and is proposed as the likely cause for their inherent AMC sensitivity. The authors developed a polymerase chain reaction (PCR) assay that specifically amplifies the penA70ST(S/F)K73-containing region from B. pseudomallei and B. mallei, but not from the remaining B. pseudomallei complex species or the 70STFK73 region from the closely-related penB of B. cepacia complex species. The abundance and purity of the 193-bp PCR fragment from putative B. pseudomallei isolates from clinical and environmental samples is likely sufficient for reliable confirmation of the presence of B. pseudomallei. The PCR assay is designed to be especially suited for use in resource-constrained areas. While not further explored in this study, the assay may allow diagnosis of putative B. mallei in culture isolates from animal and human samples.
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Affiliation(s)
- Nawarat Somprasong
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA
| | - Johannah P Hagen
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jessica R Webb
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia; Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Carina M Hall
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia; Department of Infectious Diseases and Northern Territory Medical Programme, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - David M Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Herbert P Schweizer
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA.
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Hall CM, Stone NE, Martz M, Hutton SM, Santana-Propper E, Versluis L, Guidry K, Ortiz M, Busch JD, Maness T, Stewart J, Sidwa T, Gee JE, Elrod MG, Petras JK, Ty MC, Gulvik C, Weiner ZP, Salzer JS, Hoffmaster AR, Rivera-Garcia S, Keim P, Kieffer A, Sahl JW, Soltero F, Wagner DM. Burkholderia thailandensis Isolated from the Environment, United States. Emerg Infect Dis 2023; 29:618-621. [PMID: 36823515 PMCID: PMC9973702 DOI: 10.3201/eid2903.221245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Burkholderia thailandensis, an opportunistic pathogen found in the environment, is a bacterium closely related to B. pseudomallei, the cause of melioidosis. Human B. thailandensis infections are uncommon. We isolated B. thailandensis from water in Texas and Puerto Rico and soil in Mississippi in the United States, demonstrating a potential public health risk.
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Hall CM, Romero-Alvarez D, Martz M, Santana-Propper E, Versluis L, Jiménez L, Alkishe A, Busch JD, Maness T, Stewart J, Sidwa T, Gee JE, Elrod MG, Weiner Z, Hoffmaster AR, Sahl JW, Salzer JS, Peterson AT, Kieffer A, Wagner DM. Low risk of acquiring melioidosis from the environment in the continental United States. PLoS One 2022; 17:e0270997. [PMID: 35905049 PMCID: PMC9337633 DOI: 10.1371/journal.pone.0270997] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/21/2022] [Indexed: 11/29/2022] Open
Abstract
Melioidosis is an underreported human disease of tropical and sub-tropical regions caused by the saprophyte Burkholderia pseudomallei. Although most global melioidosis cases are reported from tropical regions in Southeast Asia and northern Australia, there are multiple occurrences from sub-tropical regions, including the United States (U.S.). Most melioidosis cases reported from the continental U.S. are the result of acquiring the disease during travel to endemic regions or from contaminated imported materials. Only two human melioidosis cases from the continental U.S. have likely acquired B. pseudomallei directly from local environments and these cases lived only ~7 km from each other in rural Texas. In this study, we assessed the risk of acquiring melioidosis from the environment within the continental U.S. by surveying for B. pseudomallei in the environment in Texas where these two human melioidosis cases likely acquired their infections. We sampled the environment near the homes of the two cases and at additional sampling locations in surrounding counties in Texas that were selected based on ecological niche modeling. B. pseudomallei was not detected at the residences of these two cases or in the surrounding region. These negative data are important to demonstrate that B. pseudomallei is rare in the environment in the U.S. even at locations where locally acquired human cases likely have occurred, documenting the low risk of acquiring B. pseudomallei infection from the environment in the continental U.S.
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Affiliation(s)
- Carina M. Hall
- Pathogen Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Daniel Romero-Alvarez
- University of Kansas, Lawrence, Kansas, United States of America
- OneHealth Research Group, Facultad de Medicina, Universidad de las Américas, Quito, Ecuador
| | - Madison Martz
- Pathogen Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Ella Santana-Propper
- Pathogen Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Lora Versluis
- Pathogen Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Laura Jiménez
- University of Kansas, Lawrence, Kansas, United States of America
| | | | - Joseph D. Busch
- Pathogen Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Trevor Maness
- Texas Department of State Health Services, San Antonio, Texas, United States of America
| | - Jonathan Stewart
- Texas Department of State Health Services, San Antonio, Texas, United States of America
| | - Tom Sidwa
- Texas Department of State Health Services, Austin, Texas, United States of America
| | - Jay E. Gee
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Mindy G. Elrod
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Zachary Weiner
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Alex R. Hoffmaster
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jason W. Sahl
- Pathogen Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Johanna S. Salzer
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | | | - Amanda Kieffer
- Texas Department of State Health Services, San Antonio, Texas, United States of America
| | - David M. Wagner
- Pathogen Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail:
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Oslan SNH, Yusoff AH, Mazlan M, Lim SJ, Khoo JJ, Oslan SN, Ismail A. Comprehensive approaches for the detection of Burkholderia pseudomallei and diagnosis of melioidosis in human and environmental samples. Microb Pathog 2022; 169:105637. [PMID: 35710088 DOI: 10.1016/j.micpath.2022.105637] [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] [Received: 09/11/2021] [Revised: 06/06/2022] [Accepted: 06/10/2022] [Indexed: 11/16/2022]
Abstract
Melioidosis is endemic in Southeast Asia and northern Australia. The causative agent of melioidosis is a Gram-negative bacterium, Burkholderia pseudomallei. Its invasion can be fatal if melioidosis is not treated promptly. It is intrinsically resistant to a variety of antibiotics. In this paper, we present a comprehensive overview of the current trends on melioidosis cases, treatments, B. pseudomallei virulence factors, and molecular techniques to detect the bacterium from different samples. The clinical and microbial diagnosis methods of identification and detection of B. pseudomallei are commonly used for the rapid diagnosis and typing of strains, such as polymerase chain reaction or multi-locus sequence typing. The genotyping strategies and techniques have been constantly evolving to identify genomic loci linked to or associated with this human disease. More research strategies for detecting and controlling melioidosis should be encouraged and conducted to understand the current situation. In conclusion, we review existing diagnostic methodologies for melioidosis detection and provide insights on prospective diagnostic methods for the bacterium.
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Affiliation(s)
- Siti Nur Hazwani Oslan
- Faculty of Food Science and Nutrition, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia.
| | - Abdul Hafidz Yusoff
- Gold Rare Earth and Material Technopreneurship Centre (GREAT), Faculty of Bioengineering and Technology, Universiti Malaysia Kelantan, Jeli Campus, Jeli, 17600, Kelantan, Malaysia.
| | - Mazlina Mazlan
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, 43400 UPM, Serdang, Selangor, Malaysia.
| | - Si Jie Lim
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Jing Jing Khoo
- Tropical Infectious Diseases Research and Education Centre (TIDREC), High Impact Research Building, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Siti Nurbaya Oslan
- Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Enzyme and Microbial Technology (EMTech) Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Aziah Ismail
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.
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Diverse lineages of pathogenic Leptospira species are widespread in the environment in Puerto Rico, USA. PLoS Negl Trop Dis 2022; 16:e0009959. [PMID: 35584143 PMCID: PMC9154103 DOI: 10.1371/journal.pntd.0009959] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 05/31/2022] [Accepted: 04/04/2022] [Indexed: 01/04/2023] Open
Abstract
Background
Leptospirosis, caused by Leptospira bacteria, is a common zoonosis worldwide, especially in the tropics. Reservoir species and risk factors have been identified but surveys for environmental sources are rare. Furthermore, understanding of environmental Leptospira containing virulence associated genes and possibly capable of causing disease is incomplete, which may convolute leptospirosis diagnosis, prevention, and epidemiology.
Methodology/Principal findings
We collected environmental samples from 22 sites in Puerto Rico during three sampling periods over 14-months (Dec 2018-Feb 2020); 10 water and 10 soil samples were collected at each site. Samples were screened for DNA from potentially pathogenic Leptospira using the lipL32 PCR assay and positive samples were sequenced to assess genetic diversity. One urban site in San Juan was sampled three times over 14 months to assess persistence in soil; live leptospires were obtained during the last sampling period. Isolates were whole genome sequenced and LipL32 expression was assessed in vitro.
We detected pathogenic Leptospira DNA at 15/22 sites; both soil and water were positive at 5/15 sites. We recovered lipL32 sequences from 83/86 positive samples (15/15 positive sites) and secY sequences from 32/86 (10/15 sites); multiple genotypes were identified at 12 sites. These sequences revealed significant diversity across samples, including four novel lipL32 phylogenetic clades within the pathogenic P1 group. Most samples from the serially sampled site were lipL32 positive at each time point. We sequenced the genomes of six saprophytic and two pathogenic Leptospira isolates; the latter represent a novel pathogenic Leptospira species likely belonging to a new serogroup.
Conclusions/Significance
Diverse and novel pathogenic Leptospira are widespread in the environment in Puerto Rico. The disease potential of these lineages is unknown but several were consistently detected for >1 year in soil, which could contaminate water. This work increases understanding of environmental Leptospira diversity and should improve leptospirosis surveillance and diagnostics.
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Morales-Ruíz LM, Rodríguez-Cisneros M, Kerber-Díaz JC, Rojas-Rojas FU, Ibarra JA, Estrada-de Los Santos P. Burkholderia orbicola sp. nov., a novel species within the Burkholderia cepacia complex. Arch Microbiol 2022; 204:178. [PMID: 35174425 DOI: 10.1007/s00203-022-02778-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 11/30/2022]
Abstract
Genome analysis of strains placed in the NCBI genome database as Burkholderia cenocepacia defined nine genomic species groups. The largest group (259 strains) corresponds to B. cenocepacia and the second largest group (58 strains) was identified as "Burkholderia servocepacia", a Burkholderia species classification which has not been validly published. The publication of "B. servocepacia" did not comply with Rule 27 and Recommendation 30 from the International Code of Nomenclature of Prokaryotes (ICNP) and have errors in the type strain name and the protologue describing the novel species. Here, we correct the position of this species by showing essential information that meets the criteria defined by ICNP. After additional analysis complying with taxonomic criteria, we propose that the invalid "B. servocepacia" be renamed as Burkholderia orbicola sp. nov. The original study proposing "B. servocepacia" was misleading, because this name derives from the Latin "servo" meaning "to protect/watch over", and the authors proposed this based on the beneficial biocontrol properties of several strains within the group. However, it is clear that "B. servocepacia" isolates are capable of opportunistic infection, and the proposed name Burkholderia orbicola sp. nov. takes into account these diverse phenotypic traits. The type strain is TAtl-371 T (= LMG 30279 T = CM-CNRG 715 T).
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Affiliation(s)
- Leslie-Mariana Morales-Ruíz
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Plan de Ayala s/n, Col. Santo Tomás, Alcaldía Miguel Hidalgo, C.P. 11340, Mexico City, México
| | - Mariana Rodríguez-Cisneros
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Plan de Ayala s/n, Col. Santo Tomás, Alcaldía Miguel Hidalgo, C.P. 11340, Mexico City, México
| | - Jeniffer-Chris Kerber-Díaz
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Plan de Ayala s/n, Col. Santo Tomás, Alcaldía Miguel Hidalgo, C.P. 11340, Mexico City, México
| | - Fernando-Uriel Rojas-Rojas
- Laboratorio de Ciencias AgroGenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (ENES-León UNAM), Blvd. UNAM 2011, 37684, León, Guanajuato, México.,Laboratorio Nacional PlanTECC, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (ENES-León), Blvd. UNAM 2011, 37684, León, Guanajuato, México
| | - J Antonio Ibarra
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Plan de Ayala s/n, Col. Santo Tomás, Alcaldía Miguel Hidalgo, C.P. 11340, Mexico City, México
| | - Paulina Estrada-de Los Santos
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Plan de Ayala s/n, Col. Santo Tomás, Alcaldía Miguel Hidalgo, C.P. 11340, Mexico City, México.
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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] [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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10
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Alenazi J, Mayclin S, Subramanian S, Myler PJ, Asojo OA. Crystal structure of a short-chain dehydrogenase/reductase from Burkholderia phymatum in complex with NAD. Acta Crystallogr F Struct Biol Commun 2022; 78:52-58. [PMID: 35102893 PMCID: PMC8805215 DOI: 10.1107/s2053230x22000218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/06/2022] [Indexed: 11/10/2022] Open
Abstract
Burkholderia phymatum is an important symbiotic nitrogen-fixing betaproteobacterium. B. phymatum is beneficial, unlike other Burkholderia species, which cause disease or are potential bioagents. Structural genomics studies at the SSGCID include characterization of the structures of short-chain dehydrogenases/reductases (SDRs) from multiple Burkholderia species. The crystal structure of a short-chain dehydrogenase from B. phymatum (BpSDR) was determined in space group C2221 at a resolution of 1.80 Å. BpSDR shares less than 38% sequence identity with any known structure. The monomer is a prototypical SDR with a well conserved cofactor-binding domain despite its low sequence identity. The substrate-binding cavity is unique and offers insights into possible functions and likely inhibitors of the enzymatic functions of BpSDR.
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Affiliation(s)
- Jawaher Alenazi
- Department of Chemistry and Biochemistry, Hampton University, 200 William R. Harvey Way, Hampton, VA 23668, USA
| | - Stephen Mayclin
- UCB Pharma, Bedford, Massachusetts, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, 307 Westlake Avenue North Suite 500, Seattle, Washington, USA
| | - Peter J. Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, 307 Westlake Avenue North Suite 500, Seattle, Washington, USA
| | - Oluwatoyin A. Asojo
- Department of Chemistry and Biochemistry, Hampton University, 200 William R. Harvey Way, Hampton, VA 23668, USA
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Roe C, Vazquez AJ, Phillips PD, Allender CJ, Bowen RA, Nottingham RD, Doyle A, Wongsuwan G, Wuthiekanun V, Limmathurotsakul D, Peacock S, Keim P, Tuanyok A, Wagner DM, Sahl JW. Multiple phylogenetically-diverse, differentially-virulent Burkholderia pseudomallei isolated from a single soil sample collected in Thailand. PLoS Negl Trop Dis 2022; 16:e0010172. [PMID: 35143500 PMCID: PMC8865643 DOI: 10.1371/journal.pntd.0010172] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 02/23/2022] [Accepted: 01/14/2022] [Indexed: 11/24/2022] Open
Abstract
Burkholderia pseudomallei is a soil-dwelling bacterium endemic to Southeast Asia and northern Australia that causes the disease, melioidosis. Although the global genomic diversity of clinical B. pseudomallei isolates has been investigated, there is limited understanding of its genomic diversity across small geographic scales, especially in soil. In this study, we obtained 288 B. pseudomallei isolates from a single soil sample (~100g; intensive site 2, INT2) collected at a depth of 30cm from a site in Ubon Ratchathani Province, Thailand. We sequenced the genomes of 169 of these isolates that represent 7 distinct sequence types (STs), including a new ST (ST1820), based on multi-locus sequence typing (MLST) analysis. A core genome SNP phylogeny demonstrated that all identified STs share a recent common ancestor that diverged an estimated 796-1260 years ago. A pan-genomics analysis demonstrated recombination between clades and intra-MLST phylogenetic and gene differences. To identify potential differential virulence between STs, groups of BALB/c mice (5 mice/isolate) were challenged via subcutaneous injection (500 CFUs) with 30 INT2 isolates representing 5 different STs; over the 21-day experiment, eight isolates killed all mice, 2 isolates killed an intermediate number of mice (1-2), and 20 isolates killed no mice. Although the virulence results were largely stratified by ST, one virulent isolate and six attenuated isolates were from the same ST (ST1005), suggesting that variably conserved genomic regions may contribute to virulence. Genomes from the animal-challenged isolates were subjected to a bacterial genome-wide association study to identify genomic regions associated with differential virulence. One associated region is a unique variant of Hcp1, a component of the type VI secretion system, which may result in attenuation. The results of this study have implications for comprehensive sampling strategies, environmental exposure risk assessment, and understanding recombination and differential virulence in B. pseudomallei.
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Affiliation(s)
- Chandler Roe
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Adam J. Vazquez
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul D. Phillips
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Chris J. Allender
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Richard A. Bowen
- Department of Biological Sciences, Colorado State University, Ft. Collins, Colorado, United States of America
| | - Roxanne D. Nottingham
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Adina Doyle
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Gumphol Wongsuwan
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | | | - Sharon Peacock
- Department of Medicine, University of Cambridge, Cambridge, England
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Apichai Tuanyok
- 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
| | - Jason W. Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
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12
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Beard DK, Subramanian S, Abendroth J, Dranow DM, Edwards TE, Myler PJ, Asojo OA. Crystal structure of betaine aldehyde dehydrogenase from Burkholderia pseudomallei. Acta Crystallogr F Struct Biol Commun 2022; 78:45-51. [PMID: 35102892 PMCID: PMC8805214 DOI: 10.1107/s2053230x21013455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/19/2021] [Indexed: 11/10/2022] Open
Abstract
Burkholderia pseudomallei infection causes melioidosis, which is often fatal if untreated. There is a need to develop new and more effective treatments for melioidosis. This study reports apo and cofactor-bound crystal structures of the potential drug target betaine aldehyde dehydrogenase (BADH) from B. pseudomallei. A structural comparison identified similarities to BADH from Pseudomonas aeruginosa which is inhibited by the drug disulfiram. This preliminary analysis could facilitate drug-repurposing studies for B. pseudomallei.
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Affiliation(s)
- Dylan K Beard
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Sandhya Subramanian
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | | | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Peter J Myler
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Oluwatoyin A Asojo
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
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13
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Jayasinghearachchi HS, Corea EM, Jayaratne KI, Fonseka RA, Muthugama TA, Masakorala J, Ramasinghe RYC, De Silva AD. Biogeography and genetic diversity of clinical isolates of Burkholderia pseudomallei in Sri Lanka. PLoS Negl Trop Dis 2021; 15:e0009917. [PMID: 34851950 PMCID: PMC8824316 DOI: 10.1371/journal.pntd.0009917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 02/08/2022] [Accepted: 10/16/2021] [Indexed: 11/19/2022] Open
Abstract
Background Melioidosis is a potentially fatal infectious disease caused by Burkholderia pseudomallei and the disease is endemic in Southeast Asia and Northern Australia. It has been confirmed as endemic in Sri Lanka. Genomic epidemiology of B. pseudomallei in Sri Lanka is largely unexplored. This study aims to determine the biogeography and genetic diversity of clinical isolates of B. pseudomallei and the phylogenetic and evolutionary relationship of Sri Lankan sequence types (STs) to those found in other endemic regions of Southeast Asia and Oceania. Methods The distribution of variably present genetic markers [Burkholderia intracellular motility A (bimA) gene variants bimABP/bimABM, filamentous hemagglutinin 3 (fhaB3), Yersinia-like fimbrial (YLF) and B. thailandensis-like flagellum and chemotaxis (BTFC) gene clusters and lipopolysaccharide O-antigen type A (LPS type A)] was examined among 310 strains. Multilocus sequence typing (MLST) was done for 84 clinical isolates. The phylogenetic and evolutionary relationship of Sri Lankan STs within Sri Lanka and in relation to those found in other endemic regions of Southeast Asia and Oceania were studied using e BURST, PHYLOViZ and minimum evolutionary analysis. Results The Sri Lankan B. pseudomallei population contained a large proportion of the rare BTFC clade (14.5%) and bimABM allele variant (18.5%) with differential geographic distribution. Genotypes fhaB3 and LPSA were found in 80% and 86% respectively. This study reported 43 STs (including 22 novel). e-BURST analysis which include all Sri Lankan STs (71) resulted in four groups, with a large clonal group (group 1) having 46 STs, and 17 singletons. ST1137 was the commonest ST. Several STs were shared with India, Bangladesh and Cambodia. Conclusion This study demonstrates the usefulness of high-resolution molecular typing to locate isolates within the broad geographical boundaries of B. pseudomallei at a global level and reveals that Sri Lankan isolates are intermediate between Southeast Asia and Oceania. Burkholderia pseudomallei is an important cause of community acquired pneumonia, septicemia and abscesses in Sri Lanka. The risk of infection is increased after flooding following heavy rainfall. Risk groups include rice farmers and rural populations engaged in subsistence cultivation in home gardens. Nationwide surveillance has been carried out since 2006 and the state public health system offers free diagnostics and free antibiotic therapy. The incidence of melioidosis in Sri Lanka has increased in tandem with increased awareness among clinicians. This study reports the genetic diversity among Sri Lankan B. pseudomallei clinical isolates and shows that some variably present genes are regionally distributed. The population is intermediate between Southeast Asia and Oceania. This may reflect its past geological history.
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Affiliation(s)
- Himali S. Jayasinghearachchi
- Institute for Combinatorial Advance Research and Education (KDU-CARE), General Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
- * E-mail: (ASJ); (ADDeS)
| | - Enoka M. Corea
- Department of Medical Microbiology and Immunology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Kumari I. Jayaratne
- Biomedical Laboratory 2, Faculty of Medicine, General Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
| | - Regina A. Fonseka
- Department of Medical Microbiology and Immunology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Thilini A. Muthugama
- Biomedical Laboratory 2, Faculty of Medicine, General Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
| | - Jayanthi Masakorala
- Department of Medical Microbiology and Immunology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Ravija YC. Ramasinghe
- Biomedical Laboratory 2, Faculty of Medicine, General Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
| | - Aruna D. De Silva
- Biomedical Laboratory 2, Faculty of Medicine, General Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
- Department of Para-Clinical Sciences, Faculty of Medicine, General Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
- * E-mail: (ASJ); (ADDeS)
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14
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Dawson P, Duwell MM, Elrod MG, Thompson RJ, Crum DA, Jacobs RM, Gee JE, Kolton CB, Liu L, Blaney DD, Thomas LG, Sockwell D, Weiner Z, Bower WA, Hoffmaster AR, Salzer JS. Human Melioidosis Caused by Novel Transmission of Burkholderia pseudomallei from Freshwater Home Aquarium, United States 1. Emerg Infect Dis 2021; 27:3030-3035. [PMID: 34570693 PMCID: PMC8632198 DOI: 10.3201/eid2712.211756] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Nearly all cases of melioidosis in the continental United States are related to international travel to areas to which Burkholderia pseudomallei, the bacterium that causes melioidosis, is endemic. We report the diagnosis and clinical course of melioidosis in a patient from the United States who had no international travel history and the public health investigation to determine the source of exposure. We tested environmental samples collected from the patient’s home for B. pseudomallei by PCR and culture. Whole-genome sequencing was conducted on PCR-positive environmental samples, and results were compared with sequences from the patient’s clinical specimen. Three PCR-positive environmental samples, all collected from a freshwater home aquarium that had contained imported tropical fish, were a genetic match to the clinical isolate from the patient. This finding suggests a novel route of exposure and a potential for importation of B. pseudomallei, a select agent, into the United States from disease-endemic areas.
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15
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Currie BJ, Mayo M, Ward LM, Kaestli M, Meumann EM, Webb JR, Woerle C, Baird RW, Price RN, Marshall CS, Ralph AP, Spencer E, Davies J, Huffam SE, Janson S, Lynar S, Markey P, Krause VL, Anstey NM. The Darwin Prospective Melioidosis Study: a 30-year prospective, observational investigation. THE LANCET. INFECTIOUS DISEASES 2021; 21:1737-1746. [PMID: 34303419 DOI: 10.1016/s1473-3099(21)00022-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 12/14/2020] [Accepted: 01/11/2021] [Indexed: 01/23/2023]
Abstract
BACKGROUND The global distribution of melioidosis is under considerable scrutiny, with both unmasking of endemic disease in African and Pacific nations and evidence of more recent dispersal in the Americas. Because of the high incidence of disease in tropical northern Australia, The Darwin Prospective Melioidosis Study commenced in October, 1989. We present epidemiology, clinical features, outcomes, and bacterial genomics from this 30-year study, highlighting changes in the past decade. METHODS The present study was a prospective analysis of epidemiological, clinical, and laboratory data for all culture-confirmed melioidosis cases from the tropical Northern Territory of Australia from Oct 1, 1989, until Sept 30, 2019. Cases were identified on the basis of culture-confirmed melioidosis, a laboratory-notifiable disease in the Northern Territory of Australia. Patients who were culture-positive were included in the study. Multivariable analysis determined predictors of clinical presentations and outcome. Incidence, survival, and cluster analyses were facilitated by population and rainfall data and genotyping of Burkholderia pseudomallei, including multilocus sequence typing and whole-genome sequencing. FINDINGS There were 1148 individuals with culture-confirmed melioidosis, of whom 133 (12%) died. Median age was 50 years (IQR 38-60), 48 (4%) study participants were children younger than 15 years of age, 721 (63%) were male individuals, and 600 (52%) Indigenous Australians. All but 186 (16%) had clinical risk factors, 513 (45%) had diabetes, and 455 (40%) hazardous alcohol use. Only three (2%) of 133 fatalities had no identified risk. Pneumonia was the most common presentation occurring in 595 (52%) patients. Bacteraemia occurred in 633 (56%) of 1135 patients, septic shock in 240 (21%) patients, and 180 (16%) patients required mechanical ventilation. Cases correlated with rainfall, with 80% of infections occurring during the wet season (November to April). Median annual incidence was 20·5 cases per 100 000 people; the highest annual incidence in Indigenous Australians was 103·6 per 100 000 in 2011-12. Over the 30 years, annual incidences increased, as did the proportion of patients with diabetes, although mortality decreased to 17 (6%) of 278 patients over the past 5 years. Genotyping of B pseudomallei confirmed case clusters linked to environmental sources and defined evolving and new sequence types. INTERPRETATION Melioidosis is an opportunistic infection with a diverse spectrum of clinical presentations and severity. With early diagnosis, specific antimicrobial therapy, and state-of-the-art intensive care, mortality can be reduced to less than 10%. However, mortality remains much higher in the many endemic regions where health resources remain scarce. Genotyping of B pseudomallei informs evolving local and global epidemiology. FUNDING The Australian National Health and Medical Research Council.
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Affiliation(s)
- Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Infectious Diseases Department, Royal Darwin Hospital and Northern Territory Medical Programme, Darwin, NT, Australia.
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Linda M Ward
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Mirjam Kaestli
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Ella M Meumann
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Infectious Diseases Department, Royal Darwin Hospital and Northern Territory Medical Programme, Darwin, NT, Australia
| | - Jessica R Webb
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Celeste Woerle
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Robert W Baird
- Infectious Diseases Department, Royal Darwin Hospital and Northern Territory Medical Programme, Darwin, NT, Australia; Pathology Department, Royal Darwin Hospital and Northern Territory Medical Programme, Darwin, NT, Australia
| | - Ric N Price
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Infectious Diseases Department, Royal Darwin Hospital and Northern Territory Medical Programme, Darwin, NT, Australia
| | - Catherine S Marshall
- Infectious Diseases Department, Royal Darwin Hospital and Northern Territory Medical Programme, Darwin, NT, Australia
| | - Anna P Ralph
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Infectious Diseases Department, Royal Darwin Hospital and Northern Territory Medical Programme, Darwin, NT, Australia
| | - Emma Spencer
- Infectious Diseases Department, Royal Darwin Hospital and Northern Territory Medical Programme, Darwin, NT, Australia
| | - Jane Davies
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Infectious Diseases Department, Royal Darwin Hospital and Northern Territory Medical Programme, Darwin, NT, Australia
| | - Sarah E Huffam
- Infectious Diseases Department, Royal Darwin Hospital and Northern Territory Medical Programme, Darwin, NT, Australia
| | - Sonja Janson
- Infectious Diseases Department, Royal Darwin Hospital and Northern Territory Medical Programme, Darwin, NT, Australia
| | - Sarah Lynar
- Infectious Diseases Department, Royal Darwin Hospital and Northern Territory Medical Programme, Darwin, NT, Australia
| | - Peter Markey
- Centre for Disease Control, Top End Health Services, Northern Territory Department of Health, Darwin, NT, Australia
| | - Vicki L Krause
- Centre for Disease Control, Top End Health Services, Northern Territory Department of Health, Darwin, NT, Australia
| | - Nicholas M Anstey
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Infectious Diseases Department, Royal Darwin Hospital and Northern Territory Medical Programme, Darwin, NT, Australia
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16
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Meumann EM, Kaestli M, Mayo M, Ward L, Rachlin A, Webb JR, Kleinecke M, Price EP, Currie BJ. Emergence of Burkholderia pseudomallei Sequence Type 562, Northern Australia. Emerg Infect Dis 2021; 27:1057-1067. [PMID: 33754984 PMCID: PMC8007296 DOI: 10.3201/eid2704.202716] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Since 2005, the range of Burkholderia pseudomallei sequence type 562 (ST562) has expanded in northern Australia. During 2005–2019, ST562 caused melioidosis in 61 humans and 3 animals. Cases initially occurred in suburbs surrounding a creek before spreading across urban Darwin, Australia and a nearby island community. In urban Darwin, ST562 caused 12% (53/440) of melioidosis cases, a proportion that increased during the study period. We analyzed 2 clusters of cases with epidemiologic links and used genomic analysis to identify previously unassociated cases. We found that ST562 isolates from Hainan Province, China, and Pingtung County, Taiwan, were distantly related to ST562 strains from Australia. Temporal genomic analysis suggested a single ST562 introduction into the Darwin region in ≈1988. The origin and transmission mode of ST562 into Australia remain uncertain.
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Melot B, Bastian S, Dournon N, Valade E, Gorgé O, Le Fleche A, Idier C, Vernier M, Fernandes E, Hoen B, Breurec S, Carles M. Three New Cases of Melioidosis, Guadeloupe, French West Indies. Emerg Infect Dis 2021; 26:617-619. [PMID: 32091384 PMCID: PMC7045835 DOI: 10.3201/eid2603.190718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Melioidosis has been detected in the Caribbean, and an increasing number of cases has been reported in the past few decades, but only 2 cases were reported in Guadeloupe during the past 20 years. We describe 3 more cases that occurred during 2016–2017 and examine arguments for increasing endemicity.
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Complete Genome Sequence of Peptacetobacter (Clostridium) hiranonis Strain DGF055142, Isolated from Dog Feces from Flagstaff, Arizona, USA, 2019. Microbiol Resour Announc 2021; 10:10/9/e00067-21. [PMID: 33664150 PMCID: PMC7936630 DOI: 10.1128/mra.00067-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
A single-chromosome closed genome of Peptacetobacter (Clostridium) hiranonis strain DGF055142 was generated using Illumina MiSeq short reads paired with Oxford Nanopore MinION long reads. This isolate was obtained from a canine in Flagstaff, Arizona, in 2019. Peptacetobacter (C.) hiranonis was hypothesized to contribute to canine Clostridium difficile infection resistance. A single-chromosome closed genome of Peptacetobacter (Clostridium) hiranonis strain DGF055142 was generated using Illumina MiSeq short reads paired with Oxford Nanopore MinION long reads. This isolate was obtained from a canine in Flagstaff, Arizona, in 2019. Peptacetobacter (C.) hiranonis was hypothesized to contribute to canine Clostridium difficile infection resistance.
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A Persisting Nontropical Focus of Burkholderia pseudomallei with Limited Genome Evolution over Five Decades. mSystems 2020; 5:5/6/e00726-20. [PMID: 33172968 PMCID: PMC7657595 DOI: 10.1128/msystems.00726-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Burkholderia pseudomallei is predominantly a tropical pathogen uncommonly found in the environment of temperate climatic regions. It is unclear if introduction into temperate regions is sporadic and temporary or if B. pseudomallei can persist in such environments. B. pseudomallei was identified in the environment of southwest Western Australia with melioidosis cases between 1966 and 1991. We report a new cluster with 23 animal fatalities in the same region from 2017, with B. pseudomallei again being recovered from the environment. Comparison of the isolates from the first and second clusters using genomics revealed a single sequence type, high clonality, and limited recombination, even though the time of recovery of the isolates spanned 51 years. This is a major contrast to the extensive genomic diversity seen in the tropics. Our data support the suggestion that B. pseudomallei has the ability to persist in nontropical environments, potentially in a latent state, and has the ability to activate following favorable conditions (rainfall) and then infect animals and humans. Burkholderia pseudomallei is the causative agent of the high-mortality disease melioidosis. Although melioidosis is classified as a tropical disease, rare autochthonous cases have been reported from temperate climatic regions, with uncertainty as to whether B. pseudomallei is persistent in the local environment and whether specific genetic mechanisms facilitate the survival of B. pseudomallei outside the tropics. Sporadic cases of melioidosis occurred in a valley region (latitude 31.6°S) in southwest Western Australia, Australia, between 1966 and 1992. We report a new melioidosis cluster in the same region following high rainfall in January 2017. More than 20 animals died, and B. pseudomallei was isolated from four alpacas, a parrot, and three environmental samples taken from the farm where the alpacas resided. Epidemiological data and genomics revealed that two locations on the farm were the probable sources of the alpaca infections. We determined that B. pseudomallei isolates from the 2017 cluster belonged to sequence type 284 (ST-284), as did all isolates recovered from 1966 to 1992. Genomic analysis confirmed that the ST-284 isolates were clonal and contained conserved genomic islands and limited evidence of recombination. We identified protein-coding regions unique to these isolates that might influence the persistence of B. pseudomallei in this temperate region. We demonstrate the environmental persistence of B. pseudomallei in a temperate region for over 50 years, with limited genetic changes suggesting a latent state and with activation, potential aerosolization, and local dispersal following unusually high rainfall. IMPORTANCEBurkholderia pseudomallei is predominantly a tropical pathogen uncommonly found in the environment of temperate climatic regions. It is unclear if introduction into temperate regions is sporadic and temporary or if B. pseudomallei can persist in such environments. B. pseudomallei was identified in the environment of southwest Western Australia with melioidosis cases between 1966 and 1991. We report a new cluster with 23 animal fatalities in the same region from 2017, with B. pseudomallei again being recovered from the environment. Comparison of the isolates from the first and second clusters using genomics revealed a single sequence type, high clonality, and limited recombination, even though the time of recovery of the isolates spanned 51 years. This is a major contrast to the extensive genomic diversity seen in the tropics. Our data support the suggestion that B. pseudomallei has the ability to persist in nontropical environments, potentially in a latent state, and has the ability to activate following favorable conditions (rainfall) and then infect animals and humans.
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Stone NE, Hall CM, Browne AS, Sahl JW, Hutton SM, Santana-Propper E, Celona KR, Guendel I, Harrison CJ, Gee JE, Elrod MG, Busch JD, Hoffmaster AR, Ellis EM, Wagner DM. Burkholderia pseudomallei in Soil, US Virgin Islands, 2019. Emerg Infect Dis 2020; 26:2773-2775. [PMID: 33079041 PMCID: PMC7588534 DOI: 10.3201/eid2611.191577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The distribution of Burkholderia pseudomallei in the Caribbean is poorly understood. We isolated B. pseudomallei from US Virgin Islands soil. The soil isolate was genetically similar to other isolates from the Caribbean, suggesting that B. pseudomallei might have been introduced to the islands multiple times through severe weather events.
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Webb JR, Win MM, Zin KN, Win KKN, Wah TT, Ashley EA, Smithuis F, Swe MMM, Mayo M, Currie BJ, Dance DAB. Myanmar Burkholderia pseudomallei strains are genetically diverse and originate from Asia with phylogenetic evidence of reintroductions from neighbouring countries. Sci Rep 2020; 10:16260. [PMID: 33004984 PMCID: PMC7530998 DOI: 10.1038/s41598-020-73545-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/11/2020] [Indexed: 02/08/2023] Open
Abstract
Melioidosis was first identified in Myanmar in 1911 but for the last century it has remained largely unreported there. Burkholderia pseudomallei was first isolated from the environment of Myanmar in 2016, confirming continuing endemicity. Recent genomic studies showed that B. pseudomallei originated in Australia and spread to Asia, with phylogenetic evidence of repeated reintroduction of B. pseudomallei across countries bordered by the Mekong River and the Malay Peninsula. We present the first whole-genome sequences of B. pseudomallei isolates from Myanmar: nine clinical and seven environmental isolates. We used large-scale comparative genomics to assess the genetic diversity, phylogeography and potential origins of B. pseudomallei in Myanmar. Global phylogenetics demonstrated that Myanmar isolates group in two distantly related clades that reside in a more ancestral Asian clade with high amounts of genetic diversity. The diversity of B. pseudomallei from Myanmar and divergence within our global phylogeny suggest that the original introduction of B. pseudomallei to Myanmar was not a recent event. Our study provides new insights into global patterns of B. pseudomallei dissemination, most notably the dynamic nature of movement of B. pseudomallei within densely populated Southeast Asia. The role of anthropogenic influences in both ancient and more recent dissemination of B. pseudomallei to Myanmar and elsewhere in Southeast Asia and globally requires further study.
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Affiliation(s)
- Jessica R Webb
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia.
| | - Mo Mo Win
- Department of Medical Research, Yangon, Myanmar
| | - Khwar Nyo Zin
- Microbiology Laboratory, Yangon General Hospital, Yangon, Myanmar
| | | | | | - Elizabeth A Ashley
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Myanmar-Oxford Clinical Research Unit, Yangon, Myanmar
| | - Frank Smithuis
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Myanmar-Oxford Clinical Research Unit, Yangon, Myanmar
| | - Myo Maung Maung Swe
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Department of Infectious Diseases and Northern Territory Medical Program, Royal Darwin Hospital, Darwin, NT, Australia
| | - David A B Dance
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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22
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Somprasong N, Hall CM, Webb JR, Sahl JW, Wagner DM, Keim P, Currie BJ, Schweizer HP. Burkholderia ubonensis Meropenem Resistance: Insights into Distinct Properties of Class A β-Lactamases in Burkholderia cepacia Complex and Burkholderia pseudomallei Complex Bacteria. mBio 2020; 11:e00592-20. [PMID: 32291300 PMCID: PMC7157819 DOI: 10.1128/mbio.00592-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/12/2022] Open
Abstract
Burkholderia pseudomallei, the founding member of the B. pseudomallei complex (Bpc), is a biothreat agent and causes melioidosis, a disease whose treatment mainly relies on ceftazidime and meropenem. The concern is that B. pseudomallei could enhance its drug resistance repertoire by the acquisition of DNA from resistant near-neighbor species. Burkholderia ubonensis, a member of the B. cepacia complex (Bcc), is commonly coisolated from environments where B. pseudomallei is present. Unlike B. pseudomallei, in which significant primary carbapenem resistance is rare, it is not uncommon in B. ubonensis, but the underlying mechanisms are unknown. We established that carbapenem resistance in B. ubonensis is due to an inducible class A PenB β-lactamase, as has been shown for other Bcc bacteria. Inducibility is not sufficient for high-level resistance but also requires other determinants, such as a PenB that is more robust than that present in susceptible isolates, as well as other resistance factors. Curiously and diagnostic for the two complexes, both Bpc and Bcc bacteria contain distinct annotated PenA class A β-lactamases. However, the protein from Bcc bacteria is missing its essential active-site serine and, therefore, is not a β-lactamase. Regulated expression of a transcriptional penB'-lacZ (β-galactosidase) fusion in the B. pseudomallei surrogate B. thailandensis confirms that although Bpc bacteria lack an inducible β-lactamase, they contain the components required for responding to aberrant peptidoglycan synthesis resulting from β-lactam challenge. Understanding the diversity of antimicrobial resistance in Burkholderia species is informative about how the challenges arising from potential resistance transfer between them can be met.IMPORTANCEBurkholderia pseudomallei causes melioidosis, a tropical disease that is highly fatal if not properly treated. Our data show that, in contrast to B. pseudomallei, B. ubonensis β-lactam resistance is fundamentally different because intrinsic resistance is mediated by an inducible class A β-lactamase. This includes resistance to carbapenems. Our work demonstrates that studies with near-neighbor species are informative about the diversity of antimicrobial resistance in Burkholderia and can also provide clues about the potential of resistance transfer between bacteria inhabiting the same environment. Knowledge about potential adverse challenges resulting from the horizontal transfer of resistance genes between members of the two complexes enables the design of effective countermeasures.
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Affiliation(s)
- Nawarat Somprasong
- Department of Molecular Genetics & Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Carina M Hall
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jessica R Webb
- Global and Tropical Heath Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - 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
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Bart J Currie
- Global and Tropical Heath Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Department of Infectious Diseases, Royal Darwin Hospital, Darwin, Northern Territory, Australia
- Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Herbert P Schweizer
- Department of Molecular Genetics & Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
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23
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Huggins LG, Koehler AV, Schunack B, Inpankaew T, Traub RJ. A Host-Specific Blocking Primer Combined with Optimal DNA Extraction Improves the Detection Capability of a Metabarcoding Protocol for Canine Vector-Borne Bacteria. Pathogens 2020; 9:E258. [PMID: 32244645 PMCID: PMC7238069 DOI: 10.3390/pathogens9040258] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 12/20/2022] Open
Abstract
Bacterial canine vector-borne diseases are responsible for some of the most life-threatening conditions of dogs in the tropics and are typically poorly researched with some presenting a zoonotic risk to cohabiting people. Next-generation sequencing based methodologies have been demonstrated to accurately characterise a diverse range of vector-borne bacteria in dogs, whilst also proving to be more sensitive than conventional PCR techniques. We report two improvements to a previously developed metabarcoding tool that increased the sensitivity and diversity of vector-borne bacteria detected from canine blood. Firstly, we developed and tested a canine-specific blocking primer that prevents cross-reactivity of bacterial primer amplification on abundant canine mitochondrial sequences. Use of our blocking primer increased the number of canine vector-borne infections detected (five more Ehrlichia canis and three more Anaplasma platys infections) and increased the diversity of bacterial sequences found. Secondly, the DNA extraction kit employed can have a significant effect on the bacterial community characterised. Therefore, we compared four different DNA extraction kits finding the Qiagen DNeasy Blood and Tissue Kit to be superior for detection of blood-borne bacteria, identifying nine more A. platys, two more E. canis, one more Mycoplasma haemocanis infection and more putative bacterial pathogens than the lowest performing kit.
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Affiliation(s)
- Lucas G. Huggins
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3050, Australia; (A.V.K.); (R.J.T.)
| | - Anson V. Koehler
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3050, Australia; (A.V.K.); (R.J.T.)
| | | | - Tawin Inpankaew
- Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand;
| | - Rebecca J. Traub
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3050, Australia; (A.V.K.); (R.J.T.)
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24
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French CT, Bulterys PL, Woodward CL, Tatters AO, Ng KR, Miller JF. Virulence from the rhizosphere: ecology and evolution of Burkholderia pseudomallei-complex species. Curr Opin Microbiol 2020; 54:18-32. [PMID: 32028234 DOI: 10.1016/j.mib.2019.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/30/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Christopher T French
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, 609 Charles E. Young Drive East, Los Angeles, CA 90095, United States; Northern Arizona University, Department of Biological Sciences, Pathogen and Microbiome Institute 1395 S Knoles Drive, Flagstaff, AZ 86011, United States.
| | - Philip L Bulterys
- Department of Pathology, Stanford University, Lane Building, L235, 300 Pasteur Drive, Stanford, CA, 94305, United States
| | - Cora L Woodward
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States
| | - Avery O Tatters
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States
| | - Ken R Ng
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States
| | - Jeff F Miller
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States; Molecular Biology Institute, UCLA, 611 Charles E. Young Drive East, Los Angeles, CA 90095, United States; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, 609 Charles E. Young Drive East, Los Angeles, CA 90095, United States
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