1
|
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] [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.
Collapse
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.
| |
Collapse
|
2
|
DÜLGER D, EKİCİ S, DEMİRCİ M, YİĞİN A, BABACAN O. Tracking the footsteps of Burkholderia mallei: determination of the molecular differences and potential resistance genes. Turk J Med Sci 2023; 54:16-25. [PMID: 38812620 PMCID: PMC11031151 DOI: 10.55730/1300-0144.5761] [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: 11/21/2023] [Revised: 02/15/2024] [Accepted: 12/21/2023] [Indexed: 05/31/2024] Open
Abstract
Background/aim Chemical biological radiological nuclear threats are at an important point in the agenda of world health today, as they can cause mass deaths. B. mallei attracts attention as a potential biological warfare agent due to its features such as multidrug resistance, a rapid transmission mechanism via aerosol, the absence of a complete treatment protocol for the infection it causes, and the absence of an approved vaccine for protection against the bacteria. B. mallei suspect samples must be studied by experienced personnel in biosafety level III laboratories. B mallei is a difficult and troublesome pathogen to diagnose and many unknowns about B. mallei today. Therefore, the aim of the study was to determine the molecular differences and potential resistance genes of B mallei strains. Materials and methods Determination of the molecular differences and potential resistance genes of B mallei strains with new bioinformatics approaches by comparatively examining the data of 29 B mallei strains, 10 of which were isolated from Türkiye, on the genome list of the National Biotechnology Information Center (NCBI). Results According to the genome annotations of the origins, the origin containing the highest number of CDS which is 5172 was found as the 11th strain obtained in Türkiye in 1949. The origin with the highest number of pseudogenes was determined as 23,344 (China 7) origin. Two hundred and eighty-five pseudogenes found in this strain were obtained from a knee effusion in Myanmar. According to chromosome 2 data, B. mallei strain was determined as the most similar strain to ATCC 23344, line 11 with NCTC 10229 strain, and SAVP1 strain was determined as the least similar strain. When the antimicrobial resistance gene markers of the isolates included in the study were examined, amrA and amrB, qacG ade, Burkholderia pseudomallei Omp38 were found to be carrying. Conclusion In terms of public health, it was thought that the data obtained as a result of our study about B mallei, which is defined as a biological weapon, is very valuable for creating treatment protocols to be applied to possible epidemics in the future. In addition, the available genetic epidemiological data of these strains belonging to a category that is dangerous to work with in a laboratory environment were reviewed.
Collapse
Affiliation(s)
- Dilek DÜLGER
- Department of Medical Microbiology, Faculty of Medicine, Karabük University, Karabük,
Turkiye
| | - Seda EKİCİ
- Republic of Türkiye, the Ministry of Agriculture and Forestry, Veterinary Control Central Research Institute, Ankara,
Turkiye
| | - Mehmet DEMİRCİ
- Department of Medical Microbiology, Faculty of Medicine, Kırklareli University, Kırklareli,
Turkiye
| | - Akın YİĞİN
- Department of Genetics, Faculty of Veterinary, Harran University, Şanlıurfa,
Turkiye
| | - Orkun BABACAN
- Department of Veterinary, Kepsut Vocational School, Balıkesir University, Balıkesir,
Turkiye
| |
Collapse
|
3
|
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.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Mingsong Kang
- Ottawa Laboratory-Fallowfield, Canadian Food Inspection Agency, Ottawa, ON, Canada
| |
Collapse
|
4
|
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.
Collapse
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.)
| |
Collapse
|
5
|
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: 3.0] [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.
Collapse
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
| |
Collapse
|
6
|
Linde J, Brangsch H, Hölzer M, Thomas C, Elschner MC, Melzer F, Tomaso H. Comparison of Illumina and Oxford Nanopore Technology for genome analysis of Francisella tularensis, Bacillus anthracis, and Brucella suis. BMC Genomics 2023; 24:258. [PMID: 37173617 PMCID: PMC10182678 DOI: 10.1186/s12864-023-09343-z] [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: 03/02/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Bacterial epidemiology needs to understand the spread and dissemination of strains in a One Health context. This is important for highly pathogenic bacteria such as Bacillus anthracis, Brucella species, and Francisella tularensis. Whole genome sequencing (WGS) has paved the way for genetic marker detection and high-resolution genotyping. While such tasks are established for Illumina short-read sequencing, Oxford Nanopore Technology (ONT) long-read sequencing has yet to be evaluated for such highly pathogenic bacteria with little genomic variations between strains. In this study, three independent sequencing runs were performed using Illumina, ONT flow cell version 9.4.1, and 10.4 for six strains of each of Ba. anthracis, Br. suis and F. tularensis. Data from ONT sequencing alone, Illumina sequencing alone and two hybrid assembly approaches were compared. RESULTS As previously shown, ONT produces ultra-long reads, while Illumina produces short reads with higher sequencing accuracy. Flow cell version 10.4 improved sequencing accuracy over version 9.4.1. The correct (sub-)species were inferred from all tested technologies, individually. Moreover, the sets of genetic markers for virulence, were almost identical for the respective species. The long reads of ONT allowed to assemble not only chromosomes of all species to near closure, but also virulence plasmids of Ba. anthracis. Assemblies based on nanopore data alone, Illumina data alone, and both hybrid assemblies correctly detected canonical (sub-)clades for Ba. anthracis and F. tularensis as well as multilocus sequence types for Br. suis. For F. tularensis, high-resolution genotyping using core-genome MLST (cgMLST) and core-genome Single-Nucleotide-Polymorphism (cgSNP) typing produced highly comparable results between data from Illumina and both ONT flow cell versions. For Ba. anthracis, only data from flow cell version 10.4 produced similar results to Illumina for both high-resolution typing methods. However, for Br. suis, high-resolution genotyping yielded larger differences comparing Illumina data to data from both ONT flow cell versions. CONCLUSIONS In summary, combining data from ONT and Illumina for high-resolution genotyping might be feasible for F. tularensis and Ba. anthracis, but not yet for Br. suis. The ongoing improvement of nanopore technology and subsequent data analysis may facilitate high-resolution genotyping for all bacteria with highly stable genomes in future.
Collapse
Affiliation(s)
- Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany.
| | - Hanka Brangsch
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| | - Martin Hölzer
- Genome Competence Center (MF1), Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Christine Thomas
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Mandy C Elschner
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| | - Falk Melzer
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| |
Collapse
|
7
|
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: 1.0] [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.
Collapse
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
| |
Collapse
|