Bacterial Genotyping Methods: From the Basics to Modern

Ochoa-Díaz, Margarita M.; Daza-Giovannetty, Silvana; Gómez‐Camargo, Doris

doi:10.1007/978-1-4939-7604-1_2

Cited by 9 publications

(6 citation statements)

References 13 publications

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“…The effective multilocus sequence analysis (MLSA) scheme has been used in the phylogenetic and taxonomic analyses of several bacterial taxa (19,27). Nevertheless, rare information is delineated among the genus Shewanella.…”

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confidence: 99%

Multilocus Sequence Analysis, a Rapid and Accurate Tool for Taxonomic Classification, Evolutionary Relationship Determination, and Population Biology Studies of the Genus Shewanella

Fang

Wang²,

Liu³

et al. 2019

Appl Environ Microbiol

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The genus Shewanella comprises a group of marine-dwelling species with worldwide distribution. Several species are regarded as causative agents of food spoilage and opportunistic pathogens of human diseases. In this study, a standard multilocus sequence analysis (MLSA) based on six protein-coding genes (gyrA, gyrB, infB, recN, rpoA, and topA) was established as a rapid and accurate identification tool in 59 Shewanella type strains. This method yielded sufficient resolving power in regard to enough informative sites, adequate sequence divergences, and distinct interspecies branches. The stability of phylogenetic topology was supported by high bootstrap values and concordance with different methods. The reliability of the MLSA scheme was further validated by identical phylogenies and high correlations of genomes. The MLSA approach provided a robust system to exhibit evolutionary relationships in the Shewanella genus. The split network tree proposed twelve distinct monophyletic clades with identical GϩC contents and high genetic similarities. A total of 86 tested strains were investigated to explore the population biology of the Shewanella genus in China. The most prevalent Shewanella species was Shewanella algae, followed by Shewanella xiamenensis, Shewanella chilikensis, Shewanella indica, Shewanella seohaensis, and Shewanella carassii. The strains frequently isolated from clinical and food samples highlighted the importance of increasing the surveillance of Shewanella species. Based on the combined genetic, genomic, and phenotypic analyses, Shewanella upenei should be considered a synonym of S. algae, and Shewanella pacifica should be reclassified as a synonym of Shewanella japonica. IMPORTANCE The MLSA scheme based on six housekeeping genes (HKGs) (gyrA, gyrB, infB, recN, rpoA, and topA) is well established as a reliable tool for taxonomic, evolutionary, and population diversity analyses of the genus Shewanella in this study. The standard MLSA method allows researchers to make rapid, economical, and precise identification of Shewanella strains. The robust phylogenetic network of MLSA provides profound insight into the evolutionary structure of the genus Shewanella. The population genetics of Shewanella species determined by the MLSA approach plays a pivotal role in clinical diagnosis and routine monitoring. Further stud-2019. Multilocus sequence analysis, a rapid and accurate tool for taxonomic classification, evolutionary relationship determination, and population biology studies of the genus Shewanella. Appl Environ Microbiol 85:e03126-18. https://doi. Downloaded fromies on remaining species and genomic analysis will enhance a more comprehensive understanding of the microbial systematics, phylogenetic relationships, and ecological status of the genus Shewanella.

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confidence: 99%

Multilocus Sequence Analysis, a Rapid and Accurate Tool for Taxonomic Classification, Evolutionary Relationship Determination, and Population Biology Studies of the Genus Shewanella

Fang

Wang²,

Liu³

et al. 2019

Appl Environ Microbiol

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“…Given that the number of described Psa populations continues to increase, there may be vast bacterial diversity still to be identified. This increase is mostly a result of the extensive survey campaigns implemented in several countries as part of local disease mitigation programs and the development of novel genotyping technologies [110]. However, the missing pieces regarding the genomes of bacterial pathogens greatly limit the full understanding of their origin and temporal development, hindering the knowledge of the evolutionary processes that lead to the appearance of current bacterial populations and the prediction of future evolutionary events.…”

Section: Bacterial Strainmentioning

confidence: 99%

Mitigation of Emergent Bacterial Pathogens Using Pseudomonas syringae pv. actinidiae as a Case Study—From Orchard to Gene and Everything in Between

Silva

Santos

Vasconcelos

et al. 2022

Crops

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Globalization propelled human migration and commercial exchanges at the global level, but woefully led to the introduction of non-indigenous organisms into several agroecological systems. These include pathogenic bacteria with devastating consequences for numerous crops of agronomical importance for food production worldwide. In the last decade, research efforts have focused on these noxious organisms, aiming to understand their evolutionary processes, degree of pathogenicity, and mitigation strategies, which have allowed stakeholders and policymakers to develop evidence-based regulatory norms to improve management practices and minimize production losses. One of these cases is the bacterium Pseudomonas syringae pv. actinidiae (Psa), the causal agent of the kiwifruit bacterial canker, which has been causing drastic production losses and added costs related to orchard management in the kiwifruit industry. Although Psa is presently considered a pandemic pathogen and far from being eradicated, the implementation of strict regulatory norms and the efforts employed by the scientific community allowed the mitigation, to some extent, of its negative impacts through an integrated pest management approach. This included implementing directive guidelines, modifying cultural practices, and searching for sources of plant resistance. However, bacterial pathogens often have high spatial and temporal variability, with new strains constantly arising through mutation, recombination, and gene flow, posing constant pressure to agroecosystems. This review aims to critically appraise the efforts developed to mitigate bacterial pathogens of agronomical impact, from orchard management to genome analysis, using Psa as a case study, which could allow a prompter response against emerging pathogens in agroecosystems worldwide.

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“…The typing of bacterial strains is fundamental in microbiology because it makes possible links between genetic and phenotypic diversity and other characteristics, for example, epidemiology. Given the importance of this field of study, many microbiological and molecular methods have been developed 43,44 . Relatively early in the history of A. salmonicida research, studies evaluated the potential of plasmids as epidemiological markers for this bacterium.…”

Section: The First Plasmid Descriptions In a Salmonicidamentioning

confidence: 99%

“…Given the importance of this field of study, many microbiological and molecular methods have been developed. 43,44 Relatively early in the history of A. salmonicida research, studies evaluated the potential of plasmids as epidemiological markers for this bacterium. Many of these studies stated that the plasmidome of typical A. salmonicida was too conserved and without enough variation to be used as a marker in an epidemiological context.…”

Section: The First Plasmid Descriptions In a Salmonicidamentioning

confidence: 99%

The Aeromonas salmonicida plasmidome: a model of modular evolution and genetic diversity

Vincent

Hosseini

Charette

2020

Annals of the New York Academy of Sciences

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High‐throughput genomic sequencing has helped to reveal the plasmidome of Aeromonas salmonicida. This literature review provides an overview of A. salmonicida’s rich plasmidome by presenting all the plasmids identified so far, addressing their biological importance and the functional links between them. The plasmids of A. salmonicida, especially those bearing antibiotic resistance genes, can provide clues about interactions of this species with other pathogens (animals and humans), as is the case for pRAS3‐3432 and Chlamydia suis or pSN254b and Salmonella enterica. In addition to antibiotic resistance, plasmids play an important role in the virulence of A. salmonicida, particularly for the subspecies salmonicida and the plasmid pAsa5, which carries genes for the type‐three secretion system, a virulence factor essential for the bacterium. The A. salmonicida plasmidome also has many cryptic plasmids with no known biological function, but which can be used for the acquisition of new genetic elements. Striking examples are pAsa7 and pAsaXII that provide, respectively, resistance to chloramphenicol and formaldehyde and are derivatives of cryptic pAsa2.

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Bacterial Genotyping Methods: From the Basics to Modern

Cited by 9 publications

References 13 publications

Multilocus Sequence Analysis, a Rapid and Accurate Tool for Taxonomic Classification, Evolutionary Relationship Determination, and Population Biology Studies of the Genus Shewanella

Multilocus Sequence Analysis, a Rapid and Accurate Tool for Taxonomic Classification, Evolutionary Relationship Determination, and Population Biology Studies of the Genus Shewanella

Mitigation of Emergent Bacterial Pathogens Using Pseudomonas syringae pv. actinidiae as a Case Study—From Orchard to Gene and Everything in Between

The Aeromonas salmonicida plasmidome: a model of modular evolution and genetic diversity

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