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Varshith MR, Ghosh Dastidar R, Shrilaxmi MS, Bhattacharya R, Jha S, Choudhary S, Varny E, Carvalho RA, John L, Sundaramoorthy V, Smith CM, Damerla RR, Herai RH, Biswas SR, Lal PB, Mukhopadhyay C, Ghosh Dastidar S. Virulome and phylogenomic profiling of a novel Burkholderia pseudomallei strain from an Indian clinical isolate. Mol Genet Genomics 2024; 299:98. [PMID: 39441253 DOI: 10.1007/s00438-024-02188-5] [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: 09/02/2023] [Accepted: 09/18/2024] [Indexed: 10/25/2024]
Abstract
Highly pathogenic Burkholderia pseudomallei is the causative agent of melioidosis, a neglected tropical disease endemic in Southeast Asian tropical region. This bacterium encompasses diverse virulence factors which further undergo dynamic gene-expression flux as it transits through distinct environmental niches within the host which may lead to manifestation of differential clinical symptoms. B. pseudomallei, is classified as a Tier 1 select agent in the United States and regarded as a risk group 3 organism in India with the potential to be used as bioweapon. Considering these facts, it is vital to uncover both physiological and genetic heterogeneity of B. pseudomallei, particularly to identify any novel virulence factors that may contribute to pathogenicity. B. pseudomallei strain CM000113 was isolated from a clinical case in India, characterized it for its physiological, biochemical, and prominently genetic traits through WGS. It has a type 2 morphotype with faster doubling time and high biofilm producing capacity as compared to Pseudomonas aeruginosa. The genome size is 7.3 Mbp and it is phylogenetically close to B. pseudomallei strain Mahidol 1106a and Burkholderia mallei Turkey 2. We observed genetic heterogeneity, as key virulence factors that were identified shows sequence dissimilarity with reference strains. Additionally, presence of genomic islands, harbouring two virulence factors, GmhA and GmhB2, associated with pathogenesis indicates possibility of horizontal gene transfer. These results emphasize the need for an extensive study focusing the genome of B. pseudomallei and its associated heterogeneity, to identify molecular biomarkers aiding to develop point-of-care diagnostic kits for early diagnosis of melioidosis.
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Affiliation(s)
- M R Varshith
- Centre for Molecular Neurosciences, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
- Center for Emerging and Tropical Diseases, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Ranita Ghosh Dastidar
- Center for Emerging and Tropical Diseases, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
- Department of Biochemistry, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - M S Shrilaxmi
- Centre for Molecular Neurosciences, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
- Center for Emerging and Tropical Diseases, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Rajarshi Bhattacharya
- Centre for Molecular Neurosciences, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
- Department of Botany, Visva Bharati University, Santiniketan, India
| | - S Jha
- Center for Emerging and Tropical Diseases, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - S Choudhary
- Center for Emerging and Tropical Diseases, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - E Varny
- Center for Emerging and Tropical Diseases, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - R A Carvalho
- Graduate Program in Health Sciences, School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Paraná, Brazil
| | - L John
- School of Medicine, Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geeelong, Australia
| | - V Sundaramoorthy
- School of Medicine, Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geeelong, Australia
| | - C M Smith
- School of Medicine, Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geeelong, Australia
| | - R R Damerla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - R H Herai
- Graduate Program in Health Sciences, School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Paraná, Brazil
| | - S R Biswas
- Department of Botany, Visva Bharati University, Santiniketan, India
| | - P B Lal
- Center for Emerging and Tropical Diseases, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Chiranjay Mukhopadhyay
- Center for Emerging and Tropical Diseases, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
| | - Somasish Ghosh Dastidar
- Centre for Molecular Neurosciences, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
- Center for Emerging and Tropical Diseases, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
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Fenske L, Jelonek L, Goesmann A, Schwengers O. BakRep - a searchable large-scale web repository for bacterial genomes, characterizations and metadata. Microb Genom 2024; 10:001305. [PMID: 39475723 PMCID: PMC11524574 DOI: 10.1099/mgen.0.001305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 09/19/2024] [Indexed: 11/02/2024] Open
Abstract
Bacteria are fascinating research objects in many disciplines for countless reasons, and whole-genome sequencing (WGS) has become the paramount methodology to advance our microbiological understanding. Meanwhile, access to cost-effective sequencing platforms has accelerated bacterial WGS to unprecedented levels, introducing new challenges in terms of data accessibility, computational demands, heterogeneity of analysis workflows and, thus, ultimately its scientific usability. To this end, a previous study released a uniformly processed set of 661 405 bacterial genome assemblies obtained from the European Nucleotide Archive as of November 2018. Building on these accomplishments, we conducted further genome-based analyses like taxonomic classification, multilocus sequence typing and annotation of all genomes. Here, we present BakRep, a searchable large-scale web repository of these genomes enriched with consistent genome characterizations and original metadata. The platform provides a flexible search engine combining taxonomic, genomic and metadata information, as well as interactive elements to visualize genomic features. Furthermore, all results can be downloaded for offline analyses via an accompanying command line tool. The web repository is accessible via https://bakrep.computational.bio.
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Affiliation(s)
- Linda Fenske
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Lukas Jelonek
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Oliver Schwengers
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
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3
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Ichikawa Y, Borjigin L, Enkhtuul B, Khurtsbaatar O, Aoshima K, Kobayashi A, Batbaatar V, Kimura T. First molecular characterization of Burkholderia mallei strains isolated from horses in Mongolia. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105616. [PMID: 38852916 DOI: 10.1016/j.meegid.2024.105616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/17/2024] [Accepted: 06/05/2024] [Indexed: 06/11/2024]
Abstract
Glanders, a highly contagious and often fatal disease affecting equids, is caused by Burkholderia mallei. Although sporadic cases of equine glanders have recently been documented in Mongolia, genome sequencing and molecular studies of the bacteria within this region are lacking. This study provided the first molecular characterization of B. mallei isolated from four native Mongolian horses from two different provinces in 2019 and 2022 by applying whole-genome sequencing with two SNP types (previously developed genotyping with 15 SNP markers that provide global coverage of the B. mallei population and the core genome coding SNP typing developed in this study). The Mongolian isolates were located within the L3B1 cluster, which was previously associated with the V-120 strain from Russia. Within the L3B1 cluster shared by neighboring countries, they were in a unique subbranch. In this study, specific SNP markers unique to the Mongolian strains were identified to track these strains using a high-resolution melting analysis (HRMA). This study revealed the unique phylogenetic background of Mongolian strains isolated from the eastern part of Mongolia. HRMA specific to the Mongolian subbranch may contribute to the molecular epidemiological monitoring of glanders in Mongolia and surrounding countries.
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Affiliation(s)
- Yoshiki Ichikawa
- Laboratory of Comparative Pathology, Department of Clinical Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Liushiqi Borjigin
- Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Japan
| | - Batchuluun Enkhtuul
- Laboratory of Infectious Disease and Immunology, Institute of Veterinary Medicine, Mongolian University of Life Sciences, Khan-Uul district, Zaisan, 17024 Ulaanbaatar, Mongolia
| | - Ochirbat Khurtsbaatar
- Laboratory of Infectious Disease and Immunology, Institute of Veterinary Medicine, Mongolian University of Life Sciences, Khan-Uul district, Zaisan, 17024 Ulaanbaatar, Mongolia
| | - Keisuke Aoshima
- Laboratory of Comparative Pathology, Department of Clinical Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Atsushi Kobayashi
- Department of Biomedical Models, Graduate School of Biomedical Sciences, Nagasaki University, Sakamoto, Nagasaki, Japan
| | - Vanaabaatar Batbaatar
- Laboratory of Infectious Disease and Immunology, Institute of Veterinary Medicine, Mongolian University of Life Sciences, Khan-Uul district, Zaisan, 17024 Ulaanbaatar, Mongolia
| | - Takashi Kimura
- Laboratory of Comparative Pathology, Department of Clinical Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan.
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Krisna MA, Jolley KA, Monteith W, Boubour A, Hamers RL, Brueggemann AB, Harrison OB, Maiden MCJ. Development and implementation of a core genome multilocus sequence typing scheme for Haemophilus influenzae. Microb Genom 2024; 10:001281. [PMID: 39120932 PMCID: PMC11315579 DOI: 10.1099/mgen.0.001281] [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: 04/22/2024] [Accepted: 07/18/2024] [Indexed: 08/10/2024] Open
Abstract
Haemophilus influenzae is part of the human nasopharyngeal microbiota and a pathogen causing invasive disease. The extensive genetic diversity observed in H. influenzae necessitates discriminatory analytical approaches to evaluate its population structure. This study developed a core genome multilocus sequence typing (cgMLST) scheme for H. influenzae using pangenome analysis tools and validated the cgMLST scheme using datasets consisting of complete reference genomes (N = 14) and high-quality draft H. influenzae genomes (N = 2297). The draft genome dataset was divided into a development dataset (N = 921) and a validation dataset (N = 1376). The development dataset was used to identify potential core genes, and the validation dataset was used to refine the final core gene list to ensure the reliability of the proposed cgMLST scheme. Functional classifications were made for all the resulting core genes. Phylogenetic analyses were performed using both allelic profiles and nucleotide sequence alignments of the core genome to test congruence, as assessed by Spearman's correlation and ordinary least square linear regression tests. Preliminary analyses using the development dataset identified 1067 core genes, which were refined to 1037 with the validation dataset. More than 70% of core genes were predicted to encode proteins essential for metabolism or genetic information processing. Phylogenetic and statistical analyses indicated that the core genome allelic profile accurately represented phylogenetic relatedness among the isolates (R 2 = 0.945). We used this cgMLST scheme to define a high-resolution population structure for H. influenzae, which enhances the genomic analysis of this clinically relevant human pathogen.
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Affiliation(s)
- Made Ananda Krisna
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Department of Biology, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit Indonesia, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | | | - William Monteith
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Alexandra Boubour
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Raph L. Hamers
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit Indonesia, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | | | - Odile B. Harrison
- Department of Biology, University of Oxford, Oxford, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
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Krone M, Rauschenberger V, Blaschke V, Claus H, Kurzai O, Kampmeier S. Ralstonia pickettii bloodstream infections with potential genomic link to internationally distributed contaminated saline solution, Germany, October 2023. Euro Surveill 2024; 29:2400010. [PMID: 38240062 PMCID: PMC10797661 DOI: 10.2807/1560-7917.es.2024.29.3.2400010] [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] [Received: 01/03/2024] [Accepted: 01/12/2024] [Indexed: 01/22/2024] Open
Abstract
Ralstonia pickettii is a Gram-negative rod which may cause invasive infections when they contaminate liquid medical products. After R. pickettii was detected in blood cultures and a stem cell product from three patients in a tertiary care hospital in Germany, whole genome sequencing of these three isolates and two water isolates from the environment was performed. Core genome multilocus sequence typing analysis showed that the three patient isolates were closely related and there was a large distance to the environmental isolates. In a genomic comparison, the patients' isolates were distantly related to an R. pickettii strain from a cluster in Australia suspected to be caused by contaminated saline produced in India, while all liquid medical products with a link to all patients were produced in Europe or the United States. Our data point towards an ongoing risk by an unknown common source that could be traced back to medical products contaminated with R. pickettii and potentially distributed worldwide. Investigating invasive R. pickettii infections, identifying and testing medical products administered to the patients and timely whole genome sequencing may help identify the exact source of this potentially global outbreak.
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Affiliation(s)
- Manuel Krone
- University Hospital Würzburg, Infection Control and Antimicrobial Stewardship Unit, Würzburg, Germany
- University of Würzburg, Institute for Hygiene and Microbiology, Würzburg, Germany
| | - Vera Rauschenberger
- University Hospital Würzburg, Infection Control and Antimicrobial Stewardship Unit, Würzburg, Germany
- University of Würzburg, Institute for Hygiene and Microbiology, Würzburg, Germany
| | - Vera Blaschke
- University Hospital Würzburg, Infection Control and Antimicrobial Stewardship Unit, Würzburg, Germany
- University of Würzburg, Institute for Hygiene and Microbiology, Würzburg, Germany
| | - Heike Claus
- University of Würzburg, Institute for Hygiene and Microbiology, Würzburg, Germany
| | - Oliver Kurzai
- University of Würzburg, Institute for Hygiene and Microbiology, Würzburg, Germany
- Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knoell-Institute, Jena, Germany
| | - Stefanie Kampmeier
- University Hospital Würzburg, Infection Control and Antimicrobial Stewardship Unit, Würzburg, Germany
- University of Würzburg, Institute for Hygiene and Microbiology, Würzburg, Germany
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Charron P, Gao R, Chmara J, Hoover E, Nadin-Davis S, Chauvin D, Hazelwood J, Makondo K, Duceppe MO, Kang M. Influence of genomic variations on glanders serodiagnostic antigens using integrative genomic and transcriptomic approaches. Front Vet Sci 2023; 10:1217135. [PMID: 38125681 PMCID: PMC10730941 DOI: 10.3389/fvets.2023.1217135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
Glanders is a highly contagious and life-threatening zoonotic disease caused by Burkholderia mallei (B. mallei). Without an effective vaccine or treatment, early diagnosis has been regarded as the most effective method to prevent glanders transmission. Currently, the diagnosis of glanders is heavily reliant on serological tests. However, given that markedly different host immune responses can be elicited by genetically different strains of the same bacterial species, infection by B. mallei, whose genome is unstable and plastic, may result in various immune responses. This variability can make the serodiagnosis of glanders challenging. Therefore, there is a need for a comprehensive understanding and assessment of how B. mallei genomic variations impact the appropriateness of specific target antigens for glanders serodiagnosis. In this study, we investigated how genomic variations in the B. mallei genome affect gene content (gene presence/absence) and expression, with a special focus on antigens used or potentially used in serodiagnosis. In all the genome sequences of B. mallei isolates available in NCBI's RefSeq database (accessed in July 2023) and in-house sequenced samples, extensive small and large variations were observed when compared to the type strain ATCC 23344. Further pan-genome analysis of those assemblies revealed variations of gene content among all available genomes of B. mallei. Specifically, differences in gene content ranging from 31 to 715 genes with an average of 334 gene presence-absence variations were found in strains with complete or chromosome-level genome assemblies, using the ATCC 23344 strain as a reference. The affected genes included some encoded proteins used as serodiagnostic antigens, which were lost due mainly to structural variations. Additionally, a transcriptomic analysis was performed using the type strain ATCC 23344 and strain Zagreb which has been widely utilized to produce glanders antigens. In total, 388 significant differentially expressed genes were identified between these two strains, including genes related to bacterial pathogenesis and virulence, some of which were associated with genomic variations, particularly structural variations. To our knowledge, this is the first comprehensive study to uncover the impacts of genetic variations of B. mallei on its gene content and expression. These differences would have significant impacts on host innate and adaptive immunity, including antibody production, during infection. This study provides novel insights into B. mallei genetic variants, knowledge which will help to improve glanders serodiagnosis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Mingsong Kang
- Ottawa Laboratory-Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
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Schmidt K, Scholz HC, Appelt S, Michel J, Jacob D, Dupke S. Virulence and resistance patterns of Vibrio cholerae non-O1/non-O139 acquired in Germany and other European countries. Front Microbiol 2023; 14:1282135. [PMID: 38075873 PMCID: PMC10703170 DOI: 10.3389/fmicb.2023.1282135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/30/2023] [Indexed: 01/25/2025] Open
Abstract
Global warming has caused an increase in the emergence of Vibrio species in marine and estuarine environments as well as fresh water bodies. Over the past decades, antimicrobial resistance (AMR) has evolved among Vibrio species toward various antibiotics commonly used for the treatment of Vibrio infections. In this study, we assessed virulence and resistance patterns of Vibrio cholerae non-O1/non-O139 strains derived from Germany and other European countries. A total of 63 clinical and 24 environmental Vibrio cholerae non-O1/non-O139 strains, collected between 2011 and 2021, were analyzed. In silico antibiotic resistances were compared with resistance phenotypes according to EUCAST breakpoints. Additionally, genetic relatedness between isolates was assessed by two cgMLST schemes (SeqSphere +, pubMLST). Both cgMLST schemes yielded similar results, indicating high genetic diversity among V. cholerae non-O1/non-O139 isolates. Some isolates were found to be genetically closely related (allelic distance < 20), which suggests an epidemiological link. Thirty-seven virulence genes (VGs) were identified among 87 V. cholerae non-O1/non-O139 isolates, which resulted in 38 virulence profiles (VPs). VPs were similar between clinical and environmental isolates, with the exception of one clinical isolate that displayed a higher abundance of VGs. Also, a cluster of 11 environmental isolates was identified to have the lowest number of VGs. Among all strains, the predominant virulence factors were quorum sensing protein (luxS), repeats-in-toxins (rtxC/rtxD), hemolysin (hlyA) and different type VI secretion systems (T6SS) genes. The genotypic profiles revealed antibiotic resistance genes (ARGs) associated with resistance to beta-lactams, quinolones, macrolides, tetracycline, antifolate, aminoglycosides, fosfomycin, phenicols and sulfonamide. Carbapenemase gene VCC-1 was detected in 10 meropenem-resistant V. cholerae non-O1/non-O139 isolates derived from surface water in Germany. The proportion of resistance among V. cholerae non-O1/non-O139 species isolates against first line treatment (3rd generation cephalosporin, tetracycline and fluoroquinolone) was low. Empirical treatment would likely have been effective for all of the clinical V. cholerae non-O1/non-O139 isolates examined. Nevertheless, carbapenem-resistant isolates have been present in fresh water in Germany and might represent a reservoir for ARGs. Monitoring antimicrobial resistance is crucial for public health authorities to minimize the risks for the human population.
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Affiliation(s)
- Katarzyna Schmidt
- Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
- ECDC Fellowship Programme, Public Health Microbiology Path (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Holger C Scholz
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Microorganisms (ZBS 2), Robert Koch Institute, Berlin, Germany
| | - Sandra Appelt
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Microorganisms (ZBS 2), Robert Koch Institute, Berlin, Germany
| | - Jana Michel
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Microorganisms (ZBS 2), Robert Koch Institute, Berlin, Germany
| | - Daniela Jacob
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Microorganisms (ZBS 2), Robert Koch Institute, Berlin, Germany
| | - Susann Dupke
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Microorganisms (ZBS 2), Robert Koch Institute, Berlin, Germany
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Gaspar EB, dos Santos LR, do Egito AA, dos Santos MG, Mantovani C, Rieger JDSG, Abrantes GADS, Suniga PAP, Favacho JDM, Pinto IB, Nassar AFDC, dos Santos FL, de Araújo FR. Assessment of the Virulence of the Burkholderia mallei Strain BAC 86/19 in BALB/c Mice. Microorganisms 2023; 11:2597. [PMID: 37894255 PMCID: PMC10609534 DOI: 10.3390/microorganisms11102597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Burkholderia mallei is an aerobic, Gram-negative, non-motile bacillus. As an obligate mammalian pathogen, it primarily affects solipeds. Although rarely transmitted to humans, the disease it causes, glanders, is classified as a zoonosis. The bacterium was officially eradicated in Brazil in 1969; however, it reemerged after three decades. This study aims to assess the virulence of a specific B. mallei strain, isolated in Brazil, in BALB/c mice through intranasal infection. The strain, B. mallei BAC 86/19, was obtained from the tracheal secretion of a young mare displaying positive serology but no clinical signs of glanders. Post-mortem examinations revealed macroscopic lesions consistent with the disease, however. In mice, the LD50 was determined to be approximately 1.59 × 105 colony-forming units (CFU)/animal. Mice exposed to either 0.1 × LD50 or 1 × LD50 displayed transient weight loss, which resolved after three or five days, respectively. B. mallei persisted within the liver and lung for five days post-infection and in the spleen for seven days. These findings underscore the detectable virulence of the Brazilian B. mallei BAC 86/19 strain in mice, which are relatively resilient hosts. This research points to the importance of the continued investigation of the virulence mechanisms and potential countermeasures associated with B. mallei infections, including their Brazilian isolates.
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Affiliation(s)
- Emanuelle Baldo Gaspar
- Embrapa South Livestock, BR-153, Km 632, 9 Vila Industrial, Rural Area, Mailbox 242, Bagé 96401-970, RS, Brazil
| | - Lenita Ramires dos Santos
- Embrapa Beef Cattle, Rádio Maia Ave., 830, Campo Grande 79106-550, MS, Brazil; (L.R.d.S.); (A.A.d.E.); (M.G.d.S.); (F.R.d.A.)
| | - Andréa Alves do Egito
- Embrapa Beef Cattle, Rádio Maia Ave., 830, Campo Grande 79106-550, MS, Brazil; (L.R.d.S.); (A.A.d.E.); (M.G.d.S.); (F.R.d.A.)
| | - Maria Goretti dos Santos
- Embrapa Beef Cattle, Rádio Maia Ave., 830, Campo Grande 79106-550, MS, Brazil; (L.R.d.S.); (A.A.d.E.); (M.G.d.S.); (F.R.d.A.)
| | - Cynthia Mantovani
- Embrapa Beef Cattle/Ministry of Agriculture, Livestock and Food Supply Scholarship, Embrapa Beef Cattle, Rádio Maia Ave., 830, Campo Grande 79106-550, MS, Brazil; (C.M.); (J.d.S.G.R.); (G.A.d.S.A.); (I.B.P.)
| | - Juliana da Silva Gomes Rieger
- Embrapa Beef Cattle/Ministry of Agriculture, Livestock and Food Supply Scholarship, Embrapa Beef Cattle, Rádio Maia Ave., 830, Campo Grande 79106-550, MS, Brazil; (C.M.); (J.d.S.G.R.); (G.A.d.S.A.); (I.B.P.)
| | - Guilherme Augusto de Sousa Abrantes
- Embrapa Beef Cattle/Ministry of Agriculture, Livestock and Food Supply Scholarship, Embrapa Beef Cattle, Rádio Maia Ave., 830, Campo Grande 79106-550, MS, Brazil; (C.M.); (J.d.S.G.R.); (G.A.d.S.A.); (I.B.P.)
| | - Paula Adas Pereira Suniga
- MAI/DAI Scholarship, Federal University of Mato Grosso do Sul, Cidade Universitária, Costa e Silva Ave., Campo Grande 79070-900, MS, Brazil;
- Postgraduate Program in Animal Science, Faculty of Veterinary Medicine and Animal Science-FAMEZ/UFMS, Federal University of Mato Grosso do Sul, Senador Filinto Muller Ave., 2443, Campo Grande 79074-460, MS, Brazil
| | | | - Ingrid Batista Pinto
- Embrapa Beef Cattle/Ministry of Agriculture, Livestock and Food Supply Scholarship, Embrapa Beef Cattle, Rádio Maia Ave., 830, Campo Grande 79106-550, MS, Brazil; (C.M.); (J.d.S.G.R.); (G.A.d.S.A.); (I.B.P.)
| | | | - Fernando Leandro dos Santos
- UFPE Department of Veterinary Medicine, Federal Rural University of Pernambuco, Recife 52171-900, PE, Brazil;
| | - Flábio Ribeiro de Araújo
- Embrapa Beef Cattle, Rádio Maia Ave., 830, Campo Grande 79106-550, MS, Brazil; (L.R.d.S.); (A.A.d.E.); (M.G.d.S.); (F.R.d.A.)
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Suniga PAP, Mantovani C, dos Santos MG, do Egito AA, Verbisck NV, dos Santos LR, Dávila AMR, Zimpel CK, Zerpa MCS, Chiebao DP, de Sá Guimarães AM, de Castro Nassar AF, de Araújo FR. Glanders Diagnosis in an Asymptomatic Mare from Brazil: Insights from Serology, Microbiological Culture, Mass Spectrometry, and Genome Sequencing. Pathogens 2023; 12:1250. [PMID: 37887766 PMCID: PMC10609850 DOI: 10.3390/pathogens12101250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/21/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023] Open
Abstract
This manuscript elucidates the occurrence of glanders in an asymptomatic mare from Brazil presenting positive Burkholderia mallei antibody titers. The diagnosis was established through a multi-pronged approach encompassing microbiological culture, mass spectrometry, and genome sequencing. The outbreak occurred in 2019 in Tatuí, São Paulo, Brazil, and the infected mare, despite displaying no clinical symptoms, had multiple miliary lesions in the liver, as well as intense catarrhal discharge in the trachea. Samples were collected from various organs and subjected to bacterial isolation, molecular detection, and identification. The strain was identified as B. mallei using PCR and confirmed by MALDI-TOF mass spectrometry. Whole-genome sequencing revealed a genome size of 5.51 Mb with a GC content of 65.8%, 5871 genes (including 4 rRNA and 53 tRNA genes), and 5583 coding DNA sequences (CDSs). Additionally, 227 predicted pseudogenes were detected. In silico analysis of different genomic loci that allow for differentiation with Burkholderia pseudomallei confirmed the identity of the isolate as B. mallei, in addition to the characteristic genome size. The BAC 86/19 strain was identified as lineage 3, sublineage 2, which includes other strains from Brazil, India, and Iran. The genome sequencing of this strain provides valuable information that can be used to better understand the pathogen and its epidemiology, as well as to develop diagnostic tools for glanders.
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Affiliation(s)
- Paula Adas Pereira Suniga
- Postgraduate Program in Animal Science, Faculty of Veterinary Medicine and Animal Science-FAMEZ/UFMS, Federal University of Mato Grosso Do Sul, Av. Senador Filinto Muller, 2443, Campo Grande 79074-460, MS, Brazil; (P.A.P.S.); (A.A.d.E.)
- MAI/DAI Scholarship, Federal University of Mato Grosso Do Sul, Cidade Universitária, Av. Costa E Silva, Campo Grande 79070-900, MS, Brazil
| | - Cynthia Mantovani
- Embrapa Beef Cattle/Ministry of Agriculture and Livestock Scholarship, Embrapa Beef Cattle, Av. Rádio Maia, 830, Campo Grande 79106-550, MS, Brazil;
| | | | - Andréa Alves do Egito
- Postgraduate Program in Animal Science, Faculty of Veterinary Medicine and Animal Science-FAMEZ/UFMS, Federal University of Mato Grosso Do Sul, Av. Senador Filinto Muller, 2443, Campo Grande 79074-460, MS, Brazil; (P.A.P.S.); (A.A.d.E.)
- Embrapa Beef Cattle, Campo Grande 79106-550, MS, Brazil; (M.G.d.S.); (N.V.V.); (F.R.d.A.)
| | | | | | - Alberto Martín Rivera Dávila
- Computational and Systems Biology Laboratory, Graduate Program in Biodiversity and Health, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil;
| | - Cristina Kraemer Zimpel
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA;
| | - Maria Carolina Sisco Zerpa
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil; (M.C.S.Z.); (A.M.d.S.G.)
| | - Daniela Pontes Chiebao
- Animal Health Research Center, Biological Institute, Av. Conselheiro Rodrigues Alves, 1252, São Paulo 04014-002, SP, Brazil; (D.P.C.); (A.F.d.C.N.)
| | - Ana Márcia de Sá Guimarães
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil; (M.C.S.Z.); (A.M.d.S.G.)
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Suniga PAP, Mantovani C, Santos MG, Rieger JSG, Gaspar EB, Dos Santos FL, Mota RA, Chaves KP, Egito AA, Filho JCO, Nassar AFC, Dos Santos LR, Araújo FR. Molecular detection of Burkholderia mallei in different geographic regions of Brazil. Braz J Microbiol 2023; 54:1275-1285. [PMID: 37074557 PMCID: PMC10235260 DOI: 10.1007/s42770-023-00965-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/03/2023] [Indexed: 04/20/2023] Open
Abstract
Glanders is a contagious disease of equids caused by the Gram-negative bacterium Burkholderia mallei. In Brazil, the disease is considered to be reemerging and has been expanding, with records of equids with positive serology in most of the federative units. However, there are few reports describing the genotypic detection of the agent. This study demonstrated the detection of B. mallei by species-specific PCR directly from tissues or from bacterial cultures, followed by amplicon sequencing in equids (equines, mules, and asinines) with positive serology for glanders in all five geographic regions of Brazil. The molecular evidence of B. mallei infection in serologically positive equids in this study expands the possibility of strain isolation and the conduction of epidemiological characterizations based on molecular information. The microbiological detection of B. mallei in cultures from nasal and palate swabs, even in equids without clinical manifestations, raises the possibility of environmental elimination of the agent.
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Affiliation(s)
- Paula A Pereira Suniga
- MAI/DAI Scholarship, Federal University of Mato Grosso Do Sul, Cidade Universitária, Av. Costa E Silva, Campo Grande, MS, 79070-900, Brazil
- Postgraduate Program in Animal Science, Federal University of Mato Grosso Do Sul, Faculty of Veterinary Medicine and Animal Science-FAMEZ/UFMS, Av. Senador Filinto Muller, 2443, Campo Grande, MS, 79074-460, Brazil
| | - Cynthia Mantovani
- Embrapa Beef Cattle/Ministry of Agriculture, Livestock and Food Supply Scholarship, Embrapa Beef Cattle, Av. Rádio Maia, 830, Campo Grande, MS, 79106-550, Brazil
| | - Maria G Santos
- Embrapa Beef Cattle, Av. Rádio Maia, 830, Campo Grande, MS, 79106-550, Brazil
| | - Juliana S Gomes Rieger
- Embrapa Beef Cattle/Ministry of Agriculture, Livestock and Food Supply Scholarship, Embrapa Beef Cattle, Av. Rádio Maia, 830, Campo Grande, MS, 79106-550, Brazil
| | - Emanuelle B Gaspar
- Embrapa South Livestock, Rodovia BR-153, Km 632,9 Vila Industrial, Zona Rural, Caixa Postal 242, Bagé, RS, 96401-970, Brazil
| | | | - Rinaldo A Mota
- Department of Veterinary Medicine, Federal Rural University of Pernambuco, Recife, Pernambuco, Brazil
| | - Karla P Chaves
- Department of Veterinary Medicine, Federal University of Alagoas, Maceió, Alagoas, Brazil
| | - Andréa A Egito
- Postgraduate Program in Animal Science, Federal University of Mato Grosso Do Sul, Faculty of Veterinary Medicine and Animal Science-FAMEZ/UFMS, Av. Senador Filinto Muller, 2443, Campo Grande, MS, 79074-460, Brazil
- Embrapa Beef Cattle, Av. Rádio Maia, 830, Campo Grande, MS, 79106-550, Brazil
| | - José Carlos O Filho
- Veterinary Pathology Sector, Universidade Federal Do Recôncavo da Bahia (UFRB), Rua Rui Barbosa 710, Cruz Das Almas, BA, 44380-000, Brazil
| | - Alessandra F Castro Nassar
- Centro de Pesquisa Em Sanidade Animal, Instituto Biológico, Av. Conselheiro Rodrigues Alves, 1252, São Paulo, SP, 04014-002, Brazil
| | | | - Flábio R Araújo
- Embrapa Beef Cattle, Av. Rádio Maia, 830, Campo Grande, MS, 79106-550, Brazil
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Paauw A, Scholz HC, Mars-Groenendijk RH, Dekker LJM, Luider TM, van Leeuwen HC. Expression of virulence and antimicrobial related proteins in Burkholderia mallei and Burkholderia pseudomallei. PLoS Negl Trop Dis 2023; 17:e0011006. [PMID: 36607891 PMCID: PMC9821509 DOI: 10.1371/journal.pntd.0011006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/06/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Burkholderia mallei and Burkholderia pseudomallei are both potential biological threat agents. Melioidosis caused by B. pseudomallei is endemic in Southeast Asia and Northern Australia, while glanders caused by B. mallei infections are rare. Here we studied the proteomes of different B. mallei and B. pseudomallei isolates to determine species specific characteristics. METHODS The expressed proteins of 5 B. mallei and 6 B. pseudomallei strains were characterized using liquid chromatography high-resolution tandem mass spectrometry (LC-HRMS/MS). Subsequently, expression of potential resistance and virulence related characteristics were analyzed and compared. RESULTS Proteome analysis can be used for the identification of B. mallei and B. pseudomallei. Both species were identified based on >60 discriminative peptides. Expression of proteins potentially involved in antimicrobial resistance, AmrAB-OprA, BpeAB-OprB, BpeEF-OprC, PenA as well as several other efflux pump related proteins and putative β-lactamases was demonstrated. Despite, the fact that efflux pump BpeAB-OprB was expressed in all isolates, no clear correlation with an antimicrobial phenotype and the efflux-pump could be established. Also consistent with the phenotypes, no amino acid mutations in PenA known to result in β-lactam resistance could be identified. In all studied isolates, the expression of virulence (related) factors Capsule-1 and T2SS was demonstrated. The expression of T6SS-1 was demonstrated in all 6 B. pseudomallei isolates and in 2 of the 5 B. mallei isolates. In all, except one B. pseudomallei isolate, poly-beta-1,6 N-acetyl-D-glucosamine export porin (Pga), important for biofilm formation, was detected, which were absent in the proteomes of B. mallei. Siderophores, iron binding proteins, malleobactin and malleilactone are possibly expressed in both species under standard laboratory growth conditions. Expression of multiple proteins from both the malleobactin and malleilactone polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) clusters was demonstrated in both species. All B. pseudomallei expressed at least seven of the nine proteins of the bactobolin synthase cluster (bactobolin, is a ribosome targeting antibiotic), while only in one B. mallei isolate expression of two proteins of this synthase cluster was identified. CONCLUSIONS Analyzing the expressed proteomes revealed differences between B. mallei and B. pseudomallei but also between isolates from the same species. Proteome analysis can be used not only to identify B. mallei and B. pseudomallei but also to characterize the presence of important factors that putatively contribute to the pathogenesis of B. mallei and B. pseudomallei.
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Affiliation(s)
- Armand Paauw
- Netherlands Organization for Applied Scientific Research TNO, Department of CBRN Protection, Rijswijk, The Netherlands
| | - Holger C. Scholz
- Centre for Biological Threats and Special Pathogens, Highly Pathogenic Microorganisms (ZBS 2), Robert Koch Institute, Berlin, Germany
| | - Roos H. Mars-Groenendijk
- Netherlands Organization for Applied Scientific Research TNO, Department of CBRN Protection, Rijswijk, The Netherlands
| | | | - Theo M. Luider
- Department of Neurology, Erasmus MC, Rotterdam, The Netherlands
| | - Hans C. van Leeuwen
- Netherlands Organization for Applied Scientific Research TNO, Department of CBRN Protection, Rijswijk, The Netherlands
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Brangsch H, Singha H, Laroucau K, Elschner M. Sequence-based detection and typing procedures for Burkholderia mallei: Assessment and prospects. Front Vet Sci 2022; 9:1056996. [PMID: 36452150 PMCID: PMC9703372 DOI: 10.3389/fvets.2022.1056996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 10/26/2022] [Indexed: 10/28/2023] Open
Abstract
Although glanders has been eradicated in most of the developed world, the disease still persists in various countries such as Brazil, India, Pakistan, Bangladesh, Nepal, Iran, Bahrain, UAE and Turkey. It is one of the notifiable diseases listed by the World Organization for Animal Health. Occurrence of glanders imposes restriction on equestrian events and restricts equine movement, thus causing economic losses to equine industry. The genetic diversity and global distribution of the causing agent, Burkholderia (B.) mallei, have not been assessed in detail and are complicated by the high clonality of this organism. Among the identification and typing methods, PCR-based methods for distinguishing B. mallei from its close relative B. pseudomallei as well as genotyping using tandem repeat regions (MLVA) are established. The advent and continuous advancement of the sequencing techniques and the reconstruction of closed genomes enable the development of genome guided epidemiological tools. For achieving a higher genomic resolution, genotyping methods based on whole genome sequencing data can be employed, like genome-wide single nucleotide polymorphisms. One of the limitations in obtaining complete genomic sequences for further molecular characterization of B. mallei is its high GC content. In this review, we aim to provide an overview of the widely used detection and typing methods for B. mallei and illustrate gaps that still require development. The genomic features of Burkholderia, their high homology and clonality will be first described from a comparative genomics perspective. Then, the commonly used molecular detection (PCR systems) and typing systems (e.g., multilocus sequence typing, variable number of tandem repeat analysis) will be presented and put in perspective with recently developed genomic methods. Also, the increasing availability of B. mallei genomic sequences and evolution of the sequencing methods offers exciting prospects for further refinement of B. mallei typing, that could overcome the difficulties presently encountered with this particular bacterium.
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Affiliation(s)
- Hanka Brangsch
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut – Federal Research Institute for Animal Health, Jena, Germany
| | | | - Karine Laroucau
- Bacterial Zoonosis Unit, Animal Health Laboratory, French Food Agency (Anses), Maisons-Alfort, France
| | - Mandy Elschner
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut – Federal Research Institute for Animal Health, Jena, Germany
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