The use of multilocus sequence typing (MLST) and randomly amplified polymorphic DNA (RAPD) to differentiate among strains of the glanders pathogen Burkholderia mallei

Антонов, В. А.; Altukhova, V. V.; Савченко, С. С.; Замараев, В. С.; Ilyukhin, V. I.; Алексеев, В. В.

doi:10.3103/s0891416807030019

Cited by 6 publications

(5 citation statements)

References 20 publications

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“…However, other typing methods have revealed greater diversity between B. mallei strains. Indeed, RAPD analysis, which is based on random amplification of genomic fragments by PCR and comparison of amplified bands on agarose gels ( 32 , 33 ), proved to have a higher discriminatory power than MLST-7 as it enabled the identification of B. mallei clusters. However, clustering, and thus also the conclusions drawn on the basis of this method, heavily depends on the primers used for the initial amplification ( 33 ).…”

Section: B Mallei Diversitymentioning

confidence: 99%

“…Indeed, RAPD analysis, which is based on random amplification of genomic fragments by PCR and comparison of amplified bands on agarose gels ( 32 , 33 ), proved to have a higher discriminatory power than MLST-7 as it enabled the identification of B. mallei clusters. However, clustering, and thus also the conclusions drawn on the basis of this method, heavily depends on the primers used for the initial amplification ( 33 ). Genotyping by different region (DFR) PCR targeting species-specific DNA sequences segregated 18 B. mallei strains into 11 types, which could be further clustered into two groups ( 34 ).…”

Section: B Mallei Diversitymentioning

confidence: 99%

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Sequence-based detection and typing procedures for Burkholderia mallei: Assessment and prospects

Brangsch

Singha²,

Laroucau³

et al. 2022

Front. Vet. Sci.

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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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Section: B Mallei Diversitymentioning

confidence: 99%

Section: B Mallei Diversitymentioning

confidence: 99%

Sequence-based detection and typing procedures for Burkholderia mallei: Assessment and prospects

Brangsch

Singha²,

Laroucau³

et al. 2022

Front. Vet. Sci.

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“…Molecular methods viz. randomly amplified polymorphic DNA (RAPD), MLST, BurkDiff, pulse‐field gel electrophoresis, multiple locus variable number of tandem repeats, MLVA and one gene pyrosequencing have also been developed for identification and differentiation of B. mallei and B. pseudomallei (Antonov et al., ; Bowers et al., ; Chantratita et al., ; Gilling, Luna, & Pflugradt, ; Scholz et al., ). Polymerase chain reaction and other molecular assays are laboratory based, time consuming, labour intensive and require complicated instrumentation and technical expertise.…”

Section: Discussionmentioning

confidence: 99%

“…The fliP-IS407A genomic region has earlier been used for the development of PCR and real-time PCR assays for direct and specific detection of B. mallei Tomaso et al, 2006). Polymerase chain reaction-based assays reported prior to the year 2006 provided indirect proof of B. mallei detection based on the absence of B. pseudomallei-specific DNA sequences in B. mallei (Lee, Wang, & Yap, 2005;Thibault, Valade, & Vidal, 2004 pseudomallei (Antonov et al, 2007;Bowers et al, 2010;Chantratita et al, 2006;Gilling, Luna, & Pflugradt, 2014;Scholz et al, 2014 (Mirzai, Safi, Mossavari, Afshar, & Bolourchian, 2016;Pal et al, 2018). One LAMP assay has limitation regarding specificity (Mirzai et al, 2016) and the other has a detection limit of 1 pg genomic DNA of B. mallei (Pal et al, 2018).…”

Section: B Malleimentioning

confidence: 99%

Development of a rapid and sensitive recombinase polymerase amplification‐lateral flow assay for detection ofBurkholderia mallei

Saxena

Pal

Tripathi

et al. 2019

Transbound Emerg Dis

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Summary Burkholderia mallei, a potential biothreat agent is the aetiological agent of glanders, a zoonotic disease primarily affecting equines. B. mallei shares close genetic proximity with B. pseudomallei, the aetiological agent of melioidosis. Hence, molecular detection of B. mallei and its differentiation from B. pseudomallei has always been challenging. Early diagnosis of glanders is critical for timely treatment in humans and disease containment in animals. In this study a recombinase polymerase amplification‐lateral flow (RPA‐LF) assay has been developed for early and accurate detection of B. mallei. RPA‐LF assay was found to be highly sensitive and detected as low as 10 fg genomic DNA of B. mallei. The assay was highly specific and could differentiate B. mallei and B. pseudomallei. The assay also detected B. mallei in artificially spiked blood, tap water and garden soil. The established assay is simple, rapid and does not require complex instrumentation. The field deployable assay can have better implications in rapid glanders diagnosis and environmental detection of B. mallei over PCR‐based detection tools in glanders endemic areas with limited laboratory resources.

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“…In year 2006, A PCR assay and a 5ʹ nuclease real‐time PCR test targeting flagellar biosynthesis protein‐insertion sequence ( fliP‐ IS 407 A) were reported for specific and direct identification of B. mallei (Scholz et al., ; Tomaso et al., ). Other molecular methods for identification and differentiation of B. mallei from B. pseudomallei include pulse‐field gel electrophoresis, 16S rRNA sequencing, MLVA, PCR‐restriction fragment length polymorphism, randomly amplified polymorphic DNA (RAPD), MLST, BurkDiff and one gene pyrosequencing (Antonov et al., , ; Bowers et al., ; Chantratita et al., ; Gilling, Luna, & Pflugradt, ; Harvey & Minter, ; Scholz et al., ; Tanpiboonsak, Paemanee, Bunyarataphan, & Tungpradabkul, ). The described molecular methods are expensive, time‐consuming and labour intensive and require technical expertise, making them non‐viable for many laboratories with resource‐poor settings.…”

Section: Discussionmentioning

confidence: 99%

Development of a real-time loop-mediated isothermal amplification assay for detection ofBurkholderia mallei

Pal

Saxena

Singh

et al. 2017

Transbound Emerg Dis

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SummaryBurkholderia mallei is the aetiological agent of glanders, a highly contagious and reemerging zoonotic disease. Early diagnosis of glanders is critically important to ensure timely treatment with appropriate antibiotics in humans, and to prevent spread of infection in animals. Molecular detection of B. mallei has always been troublesome because of its genetic similarity with Burkholderia pseudomallei, the causative agent of melioidosis. In present investigation, a set of six B. mallei-specific primers were designed and a simple, rapid, specific and sensitive real-time loopmediated isothermal amplification (LAMP) assay was developed for detection of B. mallei. The LAMP assay could detect as low as 1 pg of B. mallei genomic DNA and 5.5 9 10 3 CFU/ml of B. mallei in spiked human blood. The assay was highly specific for B. mallei as it did not cross-react with other bacterial strains used in the study. The established LAMP assay is field adaptable and can be a better and viable alternative to PCR-based techniques for detection of B. mallei in glanders endemic areas with resource-limited settings.

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The use of multilocus sequence typing (MLST) and randomly amplified polymorphic DNA (RAPD) to differentiate among strains of the glanders pathogen Burkholderia mallei

Cited by 6 publications

References 20 publications

Sequence-based detection and typing procedures for Burkholderia mallei: Assessment and prospects

Sequence-based detection and typing procedures for Burkholderia mallei: Assessment and prospects

Development of a rapid and sensitive recombinase polymerase amplification‐lateral flow assay for detection ofBurkholderia mallei

Development of a real-time loop-mediated isothermal amplification assay for detection ofBurkholderia mallei

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