Comparative genomic analysis of wide and narrow host range strains of Xanthomonas citri subsp. citri, showing differences in the genetic content of their pathogenicity and virulence factors

2017 ◽  
Vol 46 (1) ◽  
pp. 49-61 ◽  
Author(s):  
Amir Jalali ◽  
Seyed Mehdi Alavi ◽  
Mohammad Hossein Sangtarash
Keyword(s):  
Host Range ◽  
Virulence Factors ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Xanthomonas Citri ◽  
Narrow Host Range

scholarly journals Prevalence, Host Range, and Comparative Genomic Analysis of Temperate Ochrobactrum Phages

2017 ◽  
Vol 8 ◽  
Author(s):  
Claudia Jäckel ◽  
Stefan Hertwig ◽  
Holger C. Scholz ◽  
Karsten Nöckler ◽  
Jochen Reetz ◽  
...  
Keyword(s):  
Host Range ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic

scholarly journals Identification of Genetic Bases ofVibrio fluvialisSpecies-Specific Biochemical Pathways and Potential Virulence Factors by Comparative Genomic Analysis

2014 ◽  
Vol 80 (6) ◽  
pp. 2029-2037 ◽  
Author(s):  
Xin Lu ◽  
Weili Liang ◽  
Yunduan Wang ◽  
Jialiang Xu ◽  
Jun Zhu ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Type Vi Secretion System ◽  
Biochemical Tests ◽  
Regulatory Pathways ◽  
Vibrio Fluvialis ◽  
Genes Encoding ◽  
Genetic Mechanisms

ABSTRACTVibrio fluvialisis an important food-borne pathogen that causes diarrheal illness and sometimes extraintestinal infections in humans. In this study, we sequenced the genome of a clinicalV. fluvialisstrain and determined its phylogenetic relationships with otherVibriospecies by comparative genomic analysis. We found that the closest relationship was betweenV. fluvialisandV. furnissii, followed by those withV. choleraeandV. mimicus. Moreover, based on genome comparisons and gene complementation experiments, we revealed genetic mechanisms of the biochemical tests that differentiateV. fluvialisfrom closely related species. Importantly, we identified a variety of genes encoding potential virulence factors, including multiple hemolysins, transcriptional regulators, and environmental survival and adaptation apparatuses, and the type VI secretion system, which is indicative of complex regulatory pathways modulating pathogenesis in this organism. The availability ofV. fluvialisgenome sequences may promote our understanding of pathogenic mechanisms for this emerging pathogen.

scholarly journals Comparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity

2019 ◽  
Author(s):  
Liu Bin ◽  
Zhiqiu Yin ◽  
Chao Yuan ◽  
Yuhui Du ◽  
Pan Yang ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Resistance Genes ◽  
Efflux Pump ◽  
Draft Genome ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Secretion Systems ◽  
Species Specific

Abstract Background The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of Hafnia, identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis. Results One complete genome sequence and 19 draft genome sequences for Hafnia strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant Hafnia species (alvei and paralvei) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that Hafnia has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between alvei and paralvei. We also identified possession of diverse virulence-related profiles in both Hafnia species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in Hafnia, whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in Hafnia are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with beta-lactamases and tetracycline. These virulence-related profiles identified at the genomic level provide insights into Hafnia pathogenesis and the differentiation between alvei and paralvei. Conclusions Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between Hafnia species. Deciphering the genome of Hafnia strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.

scholarly journals Comparative Genomic Analysis of Xanthomonas axonopodis pv. citrumelo F1, Which Causes Citrus Bacterial Spot Disease, and Related Strains Provides Insights into Virulence and Host Specificity

2011 ◽  
Vol 193 (22) ◽  
pp. 6342-6357 ◽  
Author(s):  
Neha Jalan ◽  
Valente Aritua ◽  
Dibyendu Kumar ◽  
Fahong Yu ◽  
Jeffrey B. Jones ◽  
...  
Keyword(s):  
Host Range ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Bacterial Spot ◽  
Content Type ◽  
Xanthomonas Axonopodis ◽  
Bacterial Spot Disease

Xanthomonas axonopodispv. citrumelo is a citrus pathogen causing citrus bacterial spot disease that is geographically restricted within the state of Florida. Illumina, 454 sequencing, and optical mapping were used to obtain a complete genome sequence ofX. axonopodispv. citrumelo strain F1, 4.9 Mb in size. The strain lacks plasmids, in contrast to other citrusXanthomonaspathogens. Phylogenetic analysis revealed that this pathogen is very close to the tomato bacterial spot pathogenX. campestrispv. vesicatoria 85-10, with a completely different host range. We also comparedX. axonopodispv. citrumelo to the genome of citrus canker pathogenX. axonopodispv. citri 306. Comparative genomic analysis showed differences in several gene clusters, like those for type III effectors, the type IV secretion system, lipopolysaccharide synthesis, and others. In addition topthA, effectors such asxopE3, xopAI, andhrpWwere absent fromX. axonopodispv. citrumelo while present inX. axonopodispv. citri. These effectors might be responsible for survival and the low virulence of this pathogen on citrus compared to that ofX. axonopodispv. citri. We also identified unique effectors inX. axonopodispv. citrumelo that may be related to the different host range as compared to that ofX. axonopodispv. citri.X. axonopodispv. citrumelo also lacks various genes, such assyrE1, syrE2, and RTX toxin family genes, which were present inX. axonopodispv. citri. These may be associated with the distinct virulences ofX. axonopodispv. citrumelo andX. axonopodispv. citri. Comparison of the complete genome sequence ofX. axonopodispv. citrumelo to those ofX. axonopodispv. citri andX. campestrispv. vesicatoria provides valuable insights into the mechanism of bacterial virulence and host specificity.

scholarly journals Comparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity

2019 ◽  
Author(s):  
Liu Bin ◽  
Zhiqiu Yin ◽  
Chao Yuan ◽  
Yuhui Du ◽  
Pan Yang ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Resistance Genes ◽  
Efflux Pump ◽  
Draft Genome ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Secretion Systems ◽  
Species Specific

Abstract Background The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of Hafnia, identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis. Results One complete genome sequence and 19 draft genome sequences for Hafnia strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant Hafnia species (alvei and paralvei) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that Hafnia has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between alvei and paralvei. We also identified possession of diverse virulence-related profiles in both Hafnia species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in Hafnia, whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in Hafnia are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with beta-lactamases and tetracycline. These virulence-related profiles identified at the genomic level provide insights into Hafnia pathogenesis and the differentiation between alvei and paralvei. Conclusions Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between Hafnia species. Deciphering the genome of Hafnia strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.

scholarly journals Comparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Zhiqiu Yin ◽  
Chao Yuan ◽  
Yuhui Du ◽  
Pan Yang ◽  
Chengqian Qian ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Resistance Genes ◽  
Draft Genome ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Secretion Systems ◽  
Cationic Antimicrobial Peptide ◽  
Species Specific

Abstract Background The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of Hafnia, identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis. Results One complete genome sequence and 19 draft genome sequences for Hafnia strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant Hafnia species (alvei and paralvei) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that Hafnia has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between alvei and paralvei. We also identified possession of diverse virulence-related profiles in both Hafnia species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in Hafnia, whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in Hafnia are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with aminoglycoside, beta-lactam, bacitracin, cationic antimicrobial peptide, fluoroquinolone, and rifampin. These virulence-related profiles identified at the genomic level provide insights into Hafnia pathogenesis and the differentiation between alvei and paralvei. Conclusions Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between Hafnia species. Deciphering the genome of Hafnia strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.

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