scholarly journals Roles of Different Forms of Lipopolysaccharides in Ralstonia solanacearum Pathogenesis

2014 ◽  
Vol 27 (5) ◽  
pp. 471-478 ◽  
Author(s):  
Chien-Hui Li ◽  
Kuan-Chung Wang ◽  
Yu-Hau Hong ◽  
Tai-Hsiang Chu ◽  
Yu-Ju Chu ◽  
...  
Keyword(s):  
Ralstonia Solanacearum ◽  
Nicotiana Benthamiana ◽  
Genomic Sequence ◽  
Structural Defects ◽  
Gram Negative Bacteria ◽  
Genome Sequences ◽  
Bacterial Proliferation ◽  
Resistant Mutants ◽  
Critical Components ◽  
Key Steps

Lipopolysaccharides (LPS) are critical components for the fitness of most gram-negative bacteria. Ralstonia solanacearum causes a deadly wilting disease in many crops; however, the pathogenic roles of different forms of LPS and their pathways of biogenesis remain unknown. By screening for phage-resistant mutants of R. solanacearum Pss4, whose genome sequence is unavailable, mutants with various types of structural defects in LPS were isolated. Pathogenesis assays of the mutants revealed that production of rough LPS (R-LPS), which does not contain O-polysaccharides, was sufficient to cause necrosis on Nicotiana benthamiana and induce the hypersensitive response on N. tabacum. However, biosynthesis of smooth LPS (S-LPS), which contains O-polysaccharides, was required for bacterial proliferation at infection sites on N. benthamiana leaves and for proliferation and causing wilt on tomato. Complementation tests confirmed the involvement of the previously unidentified cluster RSc2201 to RSc2204 in the formation of R. solanacearum S-LPS. With these data and the availability of the annotated genomic sequence of strain GMI1000, certain loci involved in key steps of R. solanacearum LPS biosynthesis were identified. The strategy of this work could be useful for similar studies in other bacteria without available genome sequences.

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 316-324 ◽  
Author(s):  
Jongsik Chun ◽  
Fred A. Rainey
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Original Research ◽  
Rrna Gene ◽  
New Taxon ◽  
Genome Sequences ◽  
Microbial World ◽  
Content Type ◽  
Link Type ◽  
Type Strains

The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the Bacteria and Archaea coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.

scholarly journals Whole genome characterization of strains belonging to the Ralstonia solanacearum species complex and in silico analysis of TaqMan assays for detection in this heterogenous species complex

2021 ◽  
Author(s):  
Viola Kurm ◽  
Ilse Houwers ◽  
Claudia E. Coipan ◽  
Peter Bonants ◽  
Cees Waalwijk ◽  
...  
Keyword(s):  
Ralstonia Solanacearum ◽  
In Silico ◽  
Species Complex ◽  
Sequence Data ◽  
In Silico Analysis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
Pcr Assays

AbstractIdentification and classification of members of the Ralstonia solanacearum species complex (RSSC) is challenging due to the heterogeneity of this complex. Whole genome sequence data of 225 strains were used to classify strains based on average nucleotide identity (ANI) and multilocus sequence analysis (MLSA). Based on the ANI score (>95%), 191 out of 192(99.5%) RSSC strains could be grouped into the three species R. solanacearum, R. pseudosolanacearum, and R. syzygii, and into the four phylotypes within the RSSC (I,II, III, and IV). R. solanacearum phylotype II could be split in two groups (IIA and IIB), from which IIB clustered in three subgroups (IIBa, IIBb and IIBc). This division by ANI was in accordance with MLSA. The IIB subgroups found by ANI and MLSA also differed in the number of SNPs in the primer and probe sites of various assays. An in-silico analysis of eight TaqMan and 11 conventional PCR assays was performed using the whole genome sequences. Based on this analysis several cases of potential false positives or false negatives can be expected upon the use of these assays for their intended target organisms. Two TaqMan assays and two PCR assays targeting the 16S rDNA sequence should be able to detect all phylotypes of the RSSC. We conclude that the increasing availability of whole genome sequences is not only useful for classification of strains, but also shows potential for selection and evaluation of clade specific nucleic acid-based amplification methods within the RSSC.

scholarly journals Implication of the Identification of an Earlier Pseudorabies Virus (PRV) Strain HLJ-2013 to the Evolution of Chinese PRVs

2020 ◽  
Vol 11 ◽  
Author(s):  
Huimin Liu ◽  
Zhibin Shi ◽  
Chunguo Liu ◽  
Pengfei Wang ◽  
Ming Wang ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Pseudorabies Virus ◽  
High Throughput Sequencing ◽  
Genomic Sequence ◽  
Full Genome Sequence ◽  
Genome Sequences ◽  
Protein Coding ◽  
One Step ◽  
Human Infections ◽  
Full Length Genome

Pseudorabies viruses (PRVs) pose a great threat to the pig industry of many countries around the world. Human infections with PRV have also been reported occasionally in China. Therefore, understanding the epidemiology and evolution of PRVs is of great importance for disease control in the pig populations and humans as well. In this study, we isolated a PRV designated HLJ-2013 from PRV-positive samples that had been collected in Heilongjiang, China, in 2013. The full genome sequence of the virus was determined to be ∼143 kbp in length using high-throughput sequencing. The genomic sequence identities between this isolate and 21 other previous PRV isolates ranged from 92.4% (with Bartha) to 97.3% (with SC). Phylogenetic analysis based on the full-length genome sequences revealed that PRV HLJ-2013 clustered together with all the Chinese strains in one group belonging to Genotype II, but this virus occurred phylogenetically earlier than all the other Chinese PRV strains. Phylogenetic trees based on both protein-coding genes and non-coding regions revealed that HLJ-2013 probably obtained its genome sequences from three origins: a yet unknown parent virus, the European viruses, and the same ancestor of all Chinese PRVs. Recombination analysis showed that HLJ-2013-like virus possibly donated the main framework of the genome of the Chinese PRVs. HLJ-2013 exhibited cytopathic and growth characteristics similar to that of the Chinese PRV strains SC and HeN1, but its pathogenicity in mice was higher than that of SC and lower than that of HeN1. The identification of HLJ-2013 takes us one step closer to understanding the origin of PRVs in China and provides new knowledge about the evolution of PRVs worldwide.

scholarly journals Formation in vitro of colistin resistance in carbapenem-resistant Gram-negative bacteria and its biological cost

2021 ◽  
Author(s):  
D. V. Tapalski ◽  
T. A. Petrovskaya ◽  
A. E. Kozlov
Keyword(s):  
Broth Culture ◽  
Exponential Growth Phase ◽  
Lag Phase ◽  
Gram Negative Bacteria ◽  
Colistin Resistance ◽  
Gram Negative ◽  
Broth Microdilution Method ◽  
Resistant Mutants ◽  
Biological Cost

Introduction. The spread of resistance to carbapenems among gram-negative bacteria have led to an increase in the consumption of polymyxins and the emergence of certain strains resistant to them. Polymyxin resistance is mainly associated with mutations in chromosomal genes. The development of mutational resistance to antibiotics can lead to a decrease in the viability of bacteria, which is manifested by an increase in the duration of the cell cycle, a decrease in virulence and competitive fitness. The purpose of the study was to assess in vitro the intensity of the formation of colistin resistance in carbapenemresistant clinical isolates of gram-negative bacteria, the stability of the formed emerged resistance and its biological cost.Materials and methods. For 46 strains of Klebsiella pneumoniae, 77 strains of Pseudomonas aeruginosa and 42 strains of Acinetobacter baumannii, real time polymerase chain reaction (PCR) was used to detect the genes of carbapenemases, the minimum inhibitory concentrations (MIC) of meropenem and colistin were determined by broth microdilution method. The selection of resistant subpopulations on Muller–Hinton agar with the addition of 16 mg/l colistin was carried out. For colistin-resistant mutants and their isogenic sensitive strains, the kinetic parameters of growth in broth culture were determined. Incubation and result recording were performed on an Infinite M200 microplate reader for 18.5 hours at 35°C with measurement of light scatter in the wells every 15 minutes.Results. The production of carbapenemases MBL VIM in P. aeruginosa, MBL NDM, KPC and OXA-48 in K. pneumoniae, OXA-23 and OXA-40 in A. baumannii was observed. All strains were sensitive to colistin (MIC varied from 0.062 to 2 mg/l). The colony growth on a selective medium with16 mg/l colistin was observed for 97.8% of K. pneumoniae strains, 16.9% of P. aeruginosa strains, and 61.9% of A. baumannii strains. The mutational nature of colistin resistance was confirmed for 21.7% of K. pneumoniae strains. For colistin-resistant mutants of K. pneumoniae, a significant increase in the duration of the lag phase (Tlag) was observed: 225.6 ± 7.037 min in the wild-type susceptible strains and 245.5 ± 8.726 in resistant mutants, p = 0.037. The indicators of the doubling time of the number of microbial cells in the exponential growth phase (Tdoubling) and the area under the bacterial growth curve did not differ significantly.Conclusion. A high frequency of formation of colistin resistance in vitro in carbapenemase-producing strains of K. pneumoniae was observed. The absence of significant changes in the kinetics of microbial growth in resistant strains makes it possible to predict the further spread of mutational resistance to colistin, as well as its preservation in microbial populations of K. pneumoniae even in the case of limiting the use of this antibiotic. 

scholarly journals Patterns of Genomic Sequence Diversity among Their Simian Immunodeficiency Viruses Suggest that L'Hoest Monkeys (Cercopithecus lhoesti) Are a Natural Lentivirus Reservoir

2000 ◽  
Vol 74 (8) ◽  
pp. 3892-3898 ◽  
Author(s):  
Brigitte E. Beer ◽  
Elizabeth Bailes ◽  
George Dapolito ◽  
Barbara J. Campbell ◽  
Robert M. Goeken ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Democratic Republic ◽  
Genomic Sequence ◽  
Democratic Republic Of Congo ◽  
Vervet Monkeys ◽  
Genome Sequences ◽  
Distinct Cluster ◽  
Immunodeficiency Virus ◽  
Genomic Regions ◽  
Full Length Genome

ABSTRACT Recently, we described a novel simian immunodeficiency virus (SIVlhoest) from a wild-caught L'Hoest monkey (Cercopithecus lhoesti) from a North American zoo. To investigate whether L'Hoest monkeys are the natural host for these viruses, we have screened blood samples from 14 wild animals from the Democratic Republic of Congo. Eight (57%) were found to be seropositive for SIV. Nearly full-length genome sequences were obtained for SIV isolates from three of these monkeys and compared to the original isolate and to other SIVs. The four samples of SIVlhoest formed a distinct cluster in phylogenetic trees. Two of these isolates differed on average at only about 5% of nucleotides, suggesting that they were epidemiologically linked; otherwise, the SIVlhoest isolates differed on average by 18%. Both the level of diversity and the pattern of its variation along the genome were very similar to those seen among isolates of SIVagm from vervet monkeys, pointing to similarities in the nature of, and constraints on, SIV evolution in these two species. Discordant phylogenetic relationships among the SIVlhoest isolates for different genomic regions indicated that mosaic viruses have been generated by recombination, implying that individual monkeys have been coinfected by more than one strain of SIV. Taken together, these observations provide strong evidence that L'Hoest monkeys constitute a natural reservoir for SIV.

scholarly journals Genome Resource of Two Potato Strains of Ralstonia solanacearum Biovar 2 (Phylotype IIB Sequevar 1) and Biovar 2T (Phylotype IIB Sequevar 25) Isolated from Lowlands in Iran

2020 ◽  
Vol 33 (7) ◽  
pp. 872-875 ◽  
Author(s):  
Nasim Sedighian ◽  
Marjon Krijger ◽  
Tanvi Taparia ◽  
S. Mohsen Taghavi ◽  
Emmanuel Wicker ◽  
...  
Keyword(s):  
South America ◽  
Bacterial Wilt ◽  
Ralstonia Solanacearum ◽  
Complete Genome ◽  
Genomic Data ◽  
Brown Rot ◽  
Genome Sequences ◽  
Rot Disease ◽  
Tropical Lowlands ◽  
Major Pathogens

Ralstonia solanacearum, the causal agent of bacterial wilt and brown rot disease, is one of the major pathogens of solanaceous crops, including potato, around the globe. Biovar 2T (phylotype II/sequevar 25) of R. solanacearum is adapted to tropical lowlands and is only reported in South America and Iran. Thus far, no genome resource of the biovar 2T of the pathogen has been available. Here, we present the near-complete genome sequences of the biovar 2T strain CFBP 8697 as well as strain CFBP 8695 belonging to biovar 2 race 3, both isolated from potato in Iran. The genomic data of biovar 2T will extend our understanding of the virulence features of R. solanacearum and pave the way for research on biovar 2T functional and interaction genetics.

scholarly journals Three Draft Genome Sequences of the Bacterial Plant Pathogen Ralstonia solanacearum, Isolated in Georgia

2017 ◽  
Vol 5 (23) ◽  
Author(s):  
Adam Kotorashvili ◽  
Galina Meparishvili ◽  
Giorgi Gogoladze ◽  
Nato Kotaria ◽  
Maka Muradashvili ◽  
...  
Keyword(s):  
Causative Agent ◽  
Plant Pathogen ◽  
Bacterial Wilt ◽  
Ralstonia Solanacearum ◽  
Draft Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Wide Range ◽  
Bacterial Plant Pathogen ◽  
Pepper Plants

ABSTRACT Ralstonia solanacearum, the causative agent of bacterial wilt, is a devastating bacterial plant pathogen with a wide range of hosts. We report here the first draft genome sequences for three strains of Ralstonia solanacearum isolated from infected potato, tomato, and pepper plants in Georgia.

scholarly journals Optimizing RNAi-Target by Nicotiana benthamiana-Soybean Mosaic Virus System Drives Broad Resistance to Soybean Mosaic Virus in Soybean

2021 ◽  
Vol 12 ◽  
Author(s):  
Hua Jiang ◽  
Kai Li ◽  
Junyi Gai
Keyword(s):  
Mosaic Virus ◽  
Nicotiana Benthamiana ◽  
Soybean Mosaic Virus ◽  
Multiple Resistance ◽  
Genome Sequences ◽  
Multiple Sequence ◽  
Detached Leaf ◽  
Broad Spectrum Resistance ◽  
Inoculation Assay ◽  
Virus System

Soybean mosaic virus (SMV) is a prevalent pathogen of soybean (Glycine max). Pyramiding multiple SMV-resistance genes into one individual is tedious and difficult, and even if successful, the obtained multiple resistance might be broken by pathogen mutation, while targeting viral genome via host-induced gene silencing (HIGS) has potential to explore broad-spectrum resistance (BSR) to SMV. We identified five conserved target fragments (CTFs) from S1 to S5 using multiple sequence alignment of 30 SMV genome sequences and assembled the corresponding target-inverted-repeat constructs (TIRs) from S1-TIR to S5-TIR. Since the inefficiency of soybean genetic transformation hinders the function verification of batch TIRs in SMV-resistance, the Nicotiana benthamiana-chimeric-SMV and N. benthamiana-pSMV-GUS pathosystems combined with Agrobacterium-mediated transient expression assays were invented and used to test the efficacy of these TIRs. From that, S1-TIR assembled from 462 bp CTF-S1 with 92% conservation rate performed its best on inhibiting SMV multiplication. Accordingly, S1-TIR was transformed into SMV-susceptible soybean NN1138-2, the resistant-healthy transgenic T1-plants were then picked out via detached-leaf inoculation assay with the stock-plants continued for progeny reproduction (T1 dual-utilization). All the four T3 transgenic progenies showed immunity to all the inoculated 11 SMV strains under individual or mixed inoculation, achieving a strong BSR. Thus, optimizing target for HIGS via transient N. benthamiana-chimeric-SMV and N. benthamiana-pSMV-GUS assays is crucial to drive robust resistance to SMV in soybean and the transgenic S1-TIR-lines will be a potential breeding source for SMV control in field.

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