Multilocus Sequence Analysis of Housekeeping Genes and Antigenic Determinant Genes in Bordetella pertussis Strains Isolated in Korea

Walnut bacterial blight caused by Xanthomonas arboricola pv. juglandis (Xaj) has serious repercussions for walnut production around the world. Between 2015 and 2017, disease samples were collected from six counties (Danjiangkou, Baokang, Suizhou, Shennongjia, Zigui, and Xingshan) in Hubei province, China. Fifty-nine Xaj strains were identified by morphology and specific PCR primers from 206 isolates. The genetic diversity of 60 Xaj strains (59 from Hubei plus one from Beijing) was evaluated by Multilocus Sequence Analysis (MLST), and their resistance to copper ion (Cu2+) treatment was determined. A Neighbor Joining phylogenetic dendrogram was constructed based on four sequences of housekeeping genes (atpD-dnaK-glnA-gyrB). Two groups of strains were identified whose clustering was consistent with that of glnA. The minimal inhibitory concentration of copper ion on representative Xaj strain DW3F3 (the first genome sequenced Xaj from China) was 115 μg/ml. Setting the copper resistant threshold value to 125 μg/ml, 47 and 13 strains were considered sensitive and resistant to Cu2+, respectively. Furthermore, five strains showed Cu2+ resistance at 270 μg/ml. Compared to the copB from sensitive strains, the copB gene in resistant strains had a 15-bp insertion and eight scattered single nucleotide polymorphisms. Interestingly, the clustering based on MLSA was distinct between Xaj copper ion resistant and sensitive strains.

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Multilocus sequence analysis of Ensifer and related taxa

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64344-0 ◽

2007 ◽

Vol 57 (3) ◽

pp. 489-503 ◽

Cited By ~ 180

Author(s):

Miet Martens ◽

Manuel Delaere ◽

Renata Coopman ◽

Paul De Vos ◽

Monique Gillis ◽

...

Keyword(s):

Sequence Analysis ◽

16S Rrna ◽

Housekeeping Genes ◽

16S Rrna Genes ◽

New Combination ◽

Rrna Genes ◽

Multilocus Sequence Analysis ◽

Bootstrap Support ◽

Rrna Gene ◽

Separate Species

Multilocus sequence analysis (MLSA) was performed on representatives of Ensifer (including species previously assigned to the genus Sinorhizobium) and related taxa. Neighbour-joining (NJ), maximum-parsimony (MP) and maximum-likelihood (ML) phylogenies of dnaK, gltA, glnA, recA, thrC and 16S rRNA genes were compared. The data confirm that the potential for discrimination of Ensifer species is greater using MLSA of housekeeping genes than 16S rRNA genes. In incongruence-length difference tests, the 16S rRNA gene was found to be significantly incongruent with the other genes, indicating that this gene should not be used as a single indicator of relatedness in this group. Significant congruence was detected for dnaK, glnA and thrC. Analyses of concatenated sequences of dnaK, glnA and thrC genes yielded very similar NJ, MP and ML trees, with high bootstrap support. In addition, analysis of a concatenation of all six genes essentially produced the same result, levelling out potentially conflicting phylogenetic signals. This new evidence supports the proposal to unite Ensifer and Sinorhizobium in a single genus. Support for an alternative solution preserving the two genera is less strong. In view of the opinions expressed by the Judicial Commission, the name of the genus should be Ensifer, as proposed by Young [Young, J. M. (2003). Int J Syst Evol Microbiol 53, 2107–2110]. Data obtained previously and these new data indicate that Ensifer adhaerens and ‘Sinorhizobium morelense’ are not heterotypic synonyms, but represent separate species. However, transfer to the genus Ensifer is not possible at present because the species name is the subject of a pending Request for an Opinion, which would affect whether a novel species in the genus Ensifer or a new combination based on a basonym would be created.

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A New Borrelia Species Defined by Multilocus Sequence Analysis of Housekeeping Genes

Applied and Environmental Microbiology ◽

10.1128/aem.00116-09 ◽

2009 ◽

Vol 75 (16) ◽

pp. 5410-5416 ◽

Cited By ~ 184

Author(s):

Gabriele Margos ◽

Stephanie A. Vollmer ◽

Muriel Cornet ◽

Martine Garnier ◽

Volker Fingerle ◽

...

Keyword(s):

Sequence Analysis ◽

Lyme Borreliosis ◽

Phylogenetic Trees ◽

Evolutionary History ◽

Housekeeping Genes ◽

Multilocus Sequence Analysis ◽

Species Status ◽

Borrelia Garinii ◽

Analysis Scheme ◽

History Of

ABSTRACT Analysis of Lyme borreliosis (LB) spirochetes, using a novel multilocus sequence analysis scheme, revealed that OspA serotype 4 strains (a rodent-associated ecotype) of Borrelia garinii were sufficiently genetically distinct from bird-associated B. garinii strains to deserve species status. We suggest that OspA serotype 4 strains be raised to species status and named Borrelia bavariensis sp. nov. The rooted phylogenetic trees provide novel insights into the evolutionary history of LB spirochetes.

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Multilocus Sequence Analysis Reveals Genetic Diversity in Xanthomonads Associated With Poinsettia Production

Plant Disease ◽

10.1094/pdis-08-14-0867-re ◽

2015 ◽

Vol 99 (6) ◽

pp. 874-882 ◽

Cited By ~ 8

Author(s):

W. Rockey ◽

N. Potnis ◽

S. Timilsina ◽

J. C. Hong ◽

G. E. Vallad ◽

...

Keyword(s):

Sequence Analysis ◽

Leaf Spot ◽

Reference Strain ◽

Housekeeping Genes ◽

Causal Agent ◽

Multilocus Sequence Analysis ◽

Bacterial Leaf Spot ◽

The Family ◽

Systemic Infections ◽

Spot Formation

Xanthomonas axonopodis pv. poinsettiicola is traditionally identified as the primary causal agent of bacterial leaf spot on poinsettia (family Euphorbiaceae). Sixty-seven strains of xanthomonads isolated from lesions associated with several species within the family Euphorbiaceae were collected over a 64-year period. The pathogenicity of these strains was compared on several potential hosts and they were analyzed by multilocus sequence analysis (MLSA) using six housekeeping genes. The 67 Xanthomonas strains associated with poinsettia production were separated into three distinct clades based on MLSA. The first clade identified contained the X. axonopodis pv. poinsettiicola reference strain (LMG849PT). A second clade was more closely related to X. hortorum pv. pelargonii (LMG7314PT) and the third clade contained the X. codiaei type strain (LMG8678T). This analysis indicated that there may also be other closely related pathovars or species of Xanthomonas that can infect poinsettia. Strains from the three clades could not be distinguished by symptoms or virulence on poinsettia plants. Strains capable of infecting geranium were found in all three clades, although the extent of leaf spot formation and number of systemic infections were significantly less than those produced by X. hortorum pv. pelargonii strains, typically the main causal agent of bacterial leaf spot on geranium. Clade III also contained strains isolated from zebra plant (Aphelandra squarrosa, family Acanthaceae), which is a newly recognized host for X. codiaei and X. axonopodis pv. poinsettiicola. Xanthomonas leaf spot is a serious threat to poinsettia production that can be caused by several Xanthomonas spp. that can infect different ornamental plant hosts. It is imperative that growers maintain a strict sanitation program because reservoirs of inoculum can occur on a number of ornamental hosts.

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Characterization of Rhizobium naphthalenivorans sp. nov. with special emphasis on aromatic compound degradation and multilocus sequence analysis of housekeeping genes

The Journal of General and Applied Microbiology ◽

10.2323/jgam.58.211 ◽

2012 ◽

Vol 58 (3) ◽

pp. 211-224 ◽

Cited By ~ 25

Author(s):

Shinichi Kaiya ◽

Owen Rubaba ◽

Naoko Yoshida ◽

Takeshi Yamada ◽

Akira Hiraishi

Keyword(s):

Sequence Analysis ◽

Aromatic Compound ◽

Housekeeping Genes ◽

Multilocus Sequence Analysis ◽

Aromatic Compound Degradation

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Molecular Epidemiology of Bordetella pertussis Strains Isolated in Vietnam During 2015–2017

Infection Control and Hospital Epidemiology ◽

10.1017/ice.2020.916 ◽

2020 ◽

Vol 41 (S1) ◽

pp. s319-s320

Author(s):

Anh H. V. Nguyen ◽

Hoan T. Pham ◽

Cao Huu Nghia

Keyword(s):

Molecular Epidemiology ◽

Bordetella Pertussis ◽

Antigenic Determinant ◽

Phylogenetic Trees ◽

Minimum Spanning Tree ◽

Whooping Cough ◽

Evolutionary Relationship ◽

Housekeeping Genes ◽

Southern Vietnam ◽

Reference Sequences

Background: Whooping cough is a serious respiratory illness in infants caused by Bordetella pertussis. In spite of the vaccination program, the incidence rates of whooping cough per 100,000 population in Vietnam increased from 0.33 in 2015 to 0.58 in 2017. If this represents a pertussis resurgence, contributors may include pathogen adaptation, the spread of specific variants, vaccine failure, and failure to effectively treat cases and contacts. There has been little research in Vietnam on B. pertussis strains. Therefore, we investigated the molecular epidemiology of circulating B. pertussis strains in Southern Vietnam by applying multilocus sequence typing (MLST) for 7 housekeeping genes and 4 antigenic determinant genes as components in the acellular vaccine including prn, ptxP, ptxS1, and fim3. Methods: DNA was extracted from 15 isolates collected from 263 case patients during 2015–2017 and was subject to MLST using primers and cycling conditions from the Bordetella pubMLST website (www.Pubmlst.org/Bordetella/). The products were analyzed using BioEdit version 7.2.5 software and then were aligned and compared to reference sequences of each genotype in the database. The evolutionary relationship among sequence types (STs) from housekeeping genes was performed as a minimum spanning tree via the goeBURST algorithm, whereas the correlation of different variants from 4 antigenic determinant genes was built up and clarified with phylogenetic trees based on the UPGMA method by MEGA 7 program. Results: The 15 isolates were all classified as ST2 (100%) by MLST of housekeeping genes, and they belonged to a common global clonal group (Fig. 1). Sequencing of antigenic determinant genes prn2 – ptxP3 – ptxS1-1 – fim3-1 determined that all were identical to each another and the reference sequences (Fig. 2). Conclusions:B. pertussis isolates circulating in Southern Vietnam appeared to be the same as the common global strain. Few isolates were available for testing; therefore, continued surveillance is important to confirm these findings and to monitor population changes over time.Funding: NoneDisclosures: None

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Multilocus Sequence Analysis of Xanthomonads Causing Bacterial Spot of Tomato and Pepper Plants Reveals Strains Generated by Recombination among Species and Recent Global Spread of Xanthomonas gardneri

Applied and Environmental Microbiology ◽

10.1128/aem.03000-14 ◽

2014 ◽

Vol 81 (4) ◽

pp. 1520-1529 ◽

Cited By ~ 38

Author(s):

Sujan Timilsina ◽

Mustafa O. Jibrin ◽

Neha Potnis ◽

Gerald V. Minsavage ◽

Misrak Kebede ◽

...

Keyword(s):

Genetic Diversity ◽

Sequence Analysis ◽

Housekeeping Genes ◽

Global Distribution ◽

Multilocus Sequence Analysis ◽

Regional Differentiation ◽

Bacterial Spot ◽

Content Type ◽

Global Spread ◽

Pathogen Populations

ABSTRACTFourXanthomonasspecies are known to cause bacterial spot of tomato and pepper, but the global distribution and genetic diversity of these species are not well understood. A collection of bacterial spot-causing strains from the Americas, Africa, Southeast Asia, and New Zealand were characterized for genetic diversity and phylogenetic relationships using multilocus sequence analysis of six housekeeping genes. By examining strains from different continents, we found unexpected phylogeographic patterns, including the global distribution of a single multilocus haplotype ofX. gardneri, possible regional differentiation inX. vesicatoria, and high species diversity on tomato in Africa. In addition, we found evidence of multiple recombination events betweenX. euvesicatoriaandX. perforans.Our results indicate that there have been shifts in the species composition of bacterial spot pathogen populations due to the global spread of dominant genotypes and that recombination between species has generated genetic diversity in these populations.

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Assessment of Multilocus Sequence Analysis (MLSA) for Identification of Candidatus Liberibacter Solanacearum from Different Host Plants in Spain

Microorganisms ◽

10.3390/microorganisms8091446 ◽

2020 ◽

Vol 8 (9) ◽

pp. 1446

Author(s):

Ana Ruiz-Padilla ◽

Cristina Redondo ◽

Adrián Asensio ◽

Jerson Garita-Cambronero ◽

Carmen Martínez ◽

...

Keyword(s):

Sequence Analysis ◽

Disease Outbreaks ◽

Housekeeping Genes ◽

Multilocus Sequence Analysis ◽

Complete Analysis ◽

Evolutionary Divergence ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Candidatus Liberibacter ◽

Potato Crops

Liberibacter is a bacterial group causing different diseases and disorders in plants. Among liberibacters, Candidatus Liberibacter solanaceraum (CLso) produces disorders in several species mainly within Apiaceae and Solanaceae families. CLso isolates are usually grouped in defined haplotypes according to single nucleotide polymorphisms in genes associated with ribosomal elements. In order to characterize more precisely isolates of CLso identified in potato in Spain, a Multilocus Sequence Analysis (MLSA) was applied. This methodology was validated by a complete analysis of ten housekeeping genes that showed an absence of positive selection and a nearly neutral mechanism for their evolution. Most of the analysis performed with single housekeeping genes, as well as MLSA, grouped together isolates of CLso detected in potato crops in Spain within the haplotype E, undistinguishable from those infecting carrots, parsnips or celery. Moreover, the information from these housekeeping genes was used to estimate the evolutionary divergence among the different CLso by using the concatenated sequences of the genes assayed. Data obtained on the divergence among CLso haplotypes support the hypothesis of evolutionary events connected with different hosts, in different geographic areas, and possibly associated with different vectors. Our results demonstrate the absence in Spain of CLso isolates molecularly classified as haplotypes A and B, traditionally considered causal agents of zebra chip in potato, as well as the uncertain possibility of the present haplotype to produce major disease outbreaks in potato that may depend on many factors that should be further evaluated in future works.

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Inferring the Evolutionary History of Vibrios by Means of Multilocus Sequence Analysis

Journal of Bacteriology ◽

10.1128/jb.00693-07 ◽

2007 ◽

Vol 189 (21) ◽

pp. 7932-7936 ◽

Cited By ~ 230

Author(s):

Tomoo Sawabe ◽

Kumiko Kita-Tsukamoto ◽

Fabiano L. Thompson

Keyword(s):

Sequence Analysis ◽

Evolutionary History ◽

Gene Sequence ◽

Sequence Data ◽

Sequence Similarity ◽

Housekeeping Genes ◽

Amino Acid Identity ◽

Multilocus Sequence Analysis ◽

Protein Coding ◽

History Of

ABSTRACT We performed the first broad study aiming at the reconstruction of the evolutionary history of vibrios by means of multilocus sequence analysis of nine genes. Overall, 14 distinct clades were recognized using the SplitsTree decomposition method. Some of these clades may correspond to families, e.g., the clades Salinivibrio and Photobacteria, while other clades, e.g., Splendidus and Harveyi, correspond to genera. The common ancestor of all vibrios was estimated to have been present 600 million years ago. We can define species of vibrios as groups of strains that share >95% gene sequence similarity and >99.4% amino acid identity based on the eight protein-coding housekeeping genes. The gene sequence data were used to refine the standard online electronic taxonomic scheme for vibrios (http://www.taxvibrio.lncc.br ).

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Identification and classification of the genus Bacteroides by multilocus sequence analysis

Microbiology ◽

10.1099/mic.0.052332-0 ◽

2011 ◽

Vol 157 (12) ◽

pp. 3388-3397 ◽

Cited By ~ 22

Author(s):

Mitsuo Sakamoto ◽

Moriya Ohkuma

Keyword(s):

Sequence Analysis ◽

16S Rrna ◽

Sequence Similarity ◽

Single Gene ◽

Housekeeping Genes ◽

16S Rrna Genes ◽

Rrna Genes ◽

Multilocus Sequence Analysis ◽

Rrna Gene

Multilocus sequence analysis (MLSA) was performed on representative species of the genus Bacteroides. Internal fragments of the genes selected, dnaJ, gyrB, hsp60, recA, rpoB and 16S rRNA, were amplified by direct PCR and then sequenced from 38 Bacteroides strains representing 35 species. Neighbour-joining (NJ), maximum-likelihood (ML) and maximum-parsimony (MP) phylogenies of the individual genes were compared. The data confirm that the potential for discrimination of Bacteroides species is greater using MLSA of housekeeping genes than 16S rRNA genes. Among the housekeeping genes analysed, gyrB was the most informative, followed by dnaJ. Analyses of concatenated sequences (4816 bp) of all six genes revealed robust phylogenetic relationships among different Bacteroides species when compared with the single-gene trees. The NJ, ML and MP trees were very similar, and almost fully resolved relationships of Bacteroides species were obtained, to our knowledge for the first time. In addition, analysis of a concatenation (2457 bp) of the dnaJ, gyrB and hsp60 genes produced essentially the same result. Ten distinct clades were recognized using the SplitsTree4 program. For the genus Bacteroides, we can define species as a group of strains that share at least 97.5 % gene sequence similarity based on the fragments of five protein-coding housekeeping genes and the 16S rRNA gene. This study demonstrates that MLSA of housekeeping genes is a valuable alternative technique for the identification and classification of species of the genus Bacteroides.

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