Comparative genomic analysis of Mycobacterium intracellulare: implications for clinical taxonomic classification in pulmonary Mycobacterium avium-intracellulare complex disease

Abstract Background Mycobacterium intracellulare is a representative etiological agent of emerging pulmonary M. avium-intracellulare complex disease in the industrialized countries worldwide. The recent genome sequencing of clinical strains isolated from pulmonary M. avium-intracellulare complex disease has provided insight into the genomic characteristics of pathogenic mycobacteria, especially for M. avium; however, the genomic characteristics of M. intracellulare remain to be elucidated. Results In this study, we performed comparative genomic analysis of 55 M. intracellulare and related strains such as M. paraintracellulare (MP), M. indicus pranii (MIP) and M. yonogonense. Based on the average nucleotide identity, the clinical M. intracellulare strains were phylogenetically grouped in two clusters: (1) the typical M. intracellulare (TMI) group, including ATCC13950 and virulent M.i.27 and M.i.198 that we previously reported, and (2) the MP-MIP group. The alignment of the genomic regions was mostly preserved between groups. Plasmids were identified between groups and subgroups, including a plasmid common among some strains of the M.i.27 subgroup. Several genomic regions including those encoding factors involved in lipid metabolism (e.g., fadE3, fadE33), transporters (e.g., mce3), and type VII secretion system (genes of ESX-2 system) were shown to be hypermutated in the clinical strains. M. intracellulare was shown to be pan-genomic at the species and subspecies levels. The mce genes were specific to particular subspecies, suggesting that these genes may be helpful in discriminating virulence phenotypes between subspecies. Conclusions Our data suggest that genomic diversity among M. intracellulare, M. paraintracellulare, M. indicus pranii and M. yonogonense remains at the subspecies or genovar levels and does not reach the species level. Genetic components such as mce genes revealed by the comparative genomic analysis could be the novel focus for further insight into the mechanism of human pathogenesis for M. intracellulare and related strains.

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Comparative Genomic Analysis of Rhodococcus equi: An Insight into Genomic Diversity and Genome Evolution

International Journal of Genomics ◽

10.1155/2019/8987436 ◽

2019 ◽

Vol 2019 ◽

pp. 1-14

Author(s):

Jianchao Ying ◽

Jun Ye ◽

Teng Xu ◽

Qian Wang ◽

Qiyu Bao ◽

...

Keyword(s):

Core Genome ◽

Genomic Analysis ◽

Rhodococcus Equi ◽

Comparative Genomic Analysis ◽

Genomic Islands ◽

Genomic Diversity ◽

Comparative Genomic ◽

Niche Adaptation ◽

Genomic Studies ◽

Insight Into

Rhodococcus equi, a member of the Rhodococcus genus, is a gram-positive pathogenic bacterium. Rhodococcus possesses an open pan-genome that constitutes the basis of its high genomic diversity and allows for adaptation to specific niche conditions and the changing host environments. Our analysis further showed that the core genome of R. equi contributes to the pathogenicity and niche adaptation of R. equi. Comparative genomic analysis revealed that the genomes of R. equi shared identical collinearity relationship, and heterogeneity was mainly acquired by means of genomic islands and prophages. Moreover, genomic islands in R. equi were always involved in virulence, resistance, or niche adaptation and possibly working with prophages to cause the majority of genome expansion. These findings provide an insight into the genomic diversity, evolution, and structural variation of R. equi and a valuable resource for functional genomic studies.

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Metabolic Diversity within the Globally Abundant Marine Group IIEuryarchaeaOffers Insight into Ecological Patterns

10.1101/349548 ◽

2018 ◽

Author(s):

Benjamin J Tully

Keyword(s):

Organic Matter ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Metabolic Diversity ◽

Metabolic Potential ◽

Surface Ocean ◽

Ecological Patterns ◽

Reference Genomes ◽

Insight Into

AbstractDespite their discovery over 25 years ago, the Marine Group IIEuryarchaea(MGII) have remained a difficult group of organisms to study, lacking cultured isolates and genome references. The MGII have been identified in marine samples from around the world and evidence supports a photoheterotrophic lifestyle combining phototrophy via proteorhodopsins with the remineralization of high molecular weight organic matter. Divided between two clades, the MGII have distinct ecological patterns that are not understood based on the limited number of available genomes. Here, I present the comparative genomic analysis of 250 MGII genomes, providing the most detailed view of these mesophilic archaea to-date. This analysis identified 17 distinct subclades including nine subclades that previously lacked reference genomes. The metabolic potential and distribution of the MGII genera revealed distinct roles in the environment, identifying algal-saccharide-degrading coastal subclades, protein-degrading oligotrophic surface ocean subclades, and mesopelagic subclades lacking proteorhodopsins common in all other subclades. This study redefines the MGII and provides an avenue for understanding the role these organisms play in the cycling of organic matter throughout the water column.

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Comparative genomic analysis provides insight into the phylogeny and virulence of atypical enteropathogenic Escherichia coli strains from Brazil

PLoS Neglected Tropical Diseases ◽

10.1371/journal.pntd.0008373 ◽

2020 ◽

Vol 14 (6) ◽

pp. e0008373 ◽

Cited By ~ 1

Author(s):

Rodrigo T. Hernandes ◽

Tracy H. Hazen ◽

Luís F. dos Santos ◽

Taylor K. S. Richter ◽

Jane M. Michalski ◽

...

Keyword(s):

Escherichia Coli ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Enteropathogenic Escherichia Coli ◽

Insight Into

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The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

Journal of Bacteriology ◽

10.1128/jb.00619-08 ◽

2008 ◽

Vol 190 (20) ◽

pp. 6881-6893 ◽

Cited By ~ 499

Author(s):

David A. Rasko ◽

M. J. Rosovitz ◽

Garry S. A. Myers ◽

Emmanuel F. Mongodin ◽

W. Florian Fricke ◽

...

Keyword(s):

Escherichia Coli ◽

Genome Sequencing ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Genomic Diversity ◽

Comparative Genomic ◽

Whole Genome ◽

E Coli ◽

Important Group ◽

Commensal Species

ABSTRACT Whole-genome sequencing has been skewed toward bacterial pathogens as a consequence of the prioritization of medical and veterinary diseases. However, it is becoming clear that in order to accurately measure genetic variation within and between pathogenic groups, multiple isolates, as well as commensal species, must be sequenced. This study examined the pangenomic content of Escherichia coli. Six distinct E. coli pathovars can be distinguished using molecular or phenotypic markers, but only two of the six pathovars have been subjected to any genome sequencing previously. Thus, this report provides a seminal description of the genomic contents and unique features of three unsequenced pathovars, enterotoxigenic E. coli, enteropathogenic E. coli, and enteroaggregative E. coli. We also determined the first genome sequence of a human commensal E. coli isolate, E. coli HS, which will undoubtedly provide a new baseline from which workers can examine the evolution of pathogenic E. coli. Comparison of 17 E. coli genomes, 8 of which are new, resulted in identification of ∼2,200 genes conserved in all isolates. We were also able to identify genes that were isolate and pathovar specific. Fewer pathovar-specific genes were identified than anticipated, suggesting that each isolate may have independently developed virulence capabilities. Pangenome calculations indicate that E. coli genomic diversity represents an open pangenome model containing a reservoir of more than 13,000 genes, many of which may be uncharacterized but important virulence factors. This comparative study of the species E. coli, while descriptive, should provide the basis for future functional work on this important group of pathogens.

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Comparative genomic analysis of Streptococcus suis reveals significant genomic diversity among different serotypes

BMC Genomics ◽

10.1186/1471-2164-12-523 ◽

2011 ◽

Vol 12 (1) ◽

Cited By ~ 49

Author(s):

Anding Zhang ◽

Ming Yang ◽

Pan Hu ◽

Jiayan Wu ◽

Bo Chen ◽

...

Keyword(s):

Genomic Analysis ◽

Streptococcus Suis ◽

Comparative Genomic Analysis ◽

Genomic Diversity ◽

Comparative Genomic

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Insight into Evolution of Bordetella pertussis from Comparative Genomic Analysis: Evidence of Vaccine-Driven Selection

Molecular Biology and Evolution ◽

10.1093/molbev/msq245 ◽

2010 ◽

Vol 28 (1) ◽

pp. 707-715 ◽

Cited By ~ 46

Author(s):

Sophie Octavia ◽

Ram P. Maharjan ◽

Vitali Sintchenko ◽

Gordon Stevenson ◽

Peter R. Reeves ◽

...

Keyword(s):

Bordetella Pertussis ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Insight Into

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A Comparative Genomic Analysis of Diverse Clonal Types of EnterotoxigenicEscherichia coliReveals Pathovar-Specific Conservation

Infection and Immunity ◽

10.1128/iai.00932-10 ◽

2010 ◽

Vol 79 (2) ◽

pp. 950-960 ◽

Cited By ~ 98

Author(s):

Jason W. Sahl ◽

Hans Steinsland ◽

Julia C. Redman ◽

Samuel V. Angiuoli ◽

James P. Nataro ◽

...

Keyword(s):

Vaccine Development ◽

Genomic Sequence ◽

Genomic Analysis ◽

Genomic Diversity ◽

Comparative Genomic ◽

Middle Income ◽

E Coli ◽

Colonization Factor ◽

Genomic Core ◽

Genomic Regions

ABSTRACTEnterotoxigenicEscherichia coli(ETEC) is a major cause of diarrheal illness in children less than 5 years of age in low- and middle-income nations, whereas it is an emerging enteric pathogen in industrialized nations. Despite being an important cause of diarrhea, little is known about the genomic composition of ETEC. To address this, we sequenced the genomes of five ETEC isolates obtained from children in Guinea-Bissau with diarrhea. These five isolates represent distinct and globally dominant ETEC clonal groups. Comparative genomic analyses utilizing a gene-independent whole-genome alignment method demonstrated that sequenced ETEC strains share approximately 2.7 million bases of genomic sequence. Phylogenetic analysis of this “core genome” confirmed the diverse history of the ETEC pathovar and provides a finer resolution of theE. colirelationships than multilocus sequence typing. No identified genomic regions were conserved exclusively in all ETEC genomes; however, we identified more genomic content conserved among ETEC genomes than among non-ETECE. coligenomes, suggesting that ETEC isolates share a genomic core. Comparisons of known virulence and of surface-exposed and colonization factor genes across all sequenced ETEC genomes not only identified variability but also indicated that some antigens are restricted to the ETEC pathovar. Overall, the generation of these five genome sequences, in addition to the two previously generated ETEC genomes, highlights the genomic diversity of ETEC. These studies increase our understanding of ETEC evolution, as well as provide insight into virulence factors and conserved proteins, which may be targets for vaccine development.

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