scholarly journals A Novel Approach to Helicobacter pylori Pan-Genome Analysis for Identification of Genomic Islands

PLoS ONE ◽  
2016 ◽  
Vol 11 (8) ◽  
pp. e0159419 ◽  
Author(s):  
Ikuo Uchiyama ◽  
Jacob Albritton ◽  
Masaki Fukuyo ◽  
Kenji K. Kojima ◽  
Koji Yahara ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Genome Analysis ◽  
Genomic Islands ◽  
Pan Genome ◽  
Novel Approach

scholarly journals Co-existence of multiple distinct lineages in Vibrio parahaemolyticus serotype O4:K12

2020 ◽  
Vol 6 (12) ◽  
Author(s):  
Lin Zhao ◽  
Hongyou Chen ◽  
Xavier Didelot ◽  
Zhenpeng Li ◽  
Yinghui Li ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Vibrio Parahaemolyticus ◽  
Type Species ◽  
Genomic Islands ◽  
Content Type ◽  
Pan Genome ◽  
Link Type ◽  
Gene Segregation ◽  
Strain Collection ◽  
The Usa

Vibrio parahaemolyticus is an important cause of foodborne gastroenteritis globally. Thermostable direct haemolysin (TDH) and the TDH-related haemolysin are the two key virulence factors in V. parahaemolyticus. Vibrio pathogenicity islands harbour the genes encoding these two haemolysins. The serotyping of V. parahaemolyticus is based on the combination of O and K antigens. Frequent recombination has been observed in V. parahaemolyticus , including in the genomic regions encoding the O and K antigens. V. parahaemolyticus serotype O4:K12 has caused gastroenteritis outbreaks in the USA and Spain. Recently, outbreaks caused by this serotype of V. parahaemolyticus have been reported in China. However, the relationships among this serotype of V. parahaemolyticus strains isolated in different regions have not been addressed. Here, we investigated the genome variation of the V. parahaemolyticus serotype O4:K12 using the whole-genome sequences of 29 isolates. We determined five distinct lineages in this strain collection. We observed frequent recombination among different lineages. In contrast, little recombination was observed within each individual lineage. We showed that the lineage of this serotype of V. parahaemolyticus isolated in America was different from those isolated in Asia and identified genes that exclusively existed in the strains isolated in America. Pan-genome analysis showed that strain-specific and cluster-specific genes were mostly located in the genomic islands. Pan-genome analysis also showed that the vast majority of the accessory genes in the O4:K12 serotype of V. parahaemolyticus were acquired from within the genus Vibrio . Hence, we have shown that multiple distinct lineages exist in V. parahaemolyticus serotype O4:K12 and have provided more evidence about the gene segregation found in V. parahaemolyticus isolated in different continents.

From Pan-genome to the Genomic Context of the Two Integrons of ST-111 Pseudomonas Aeruginosa AG1: A VIM-2-carrying Old-acquaintance and a Novel Imp-18-carrying Integron

2020 ◽  
Author(s):  
Jose Arturo Molina-Mora ◽  
Raquel García Batán ◽  
Fernando García
Keyword(s):  
Pseudomonas Aeruginosa ◽  
High Risk ◽  
Genome Analysis ◽  
Genomic Region ◽  
Genomic Islands ◽  
Comparative Genomic ◽  
Genomic Context ◽  
Intrinsic Resistance ◽  
Pan Genome ◽  
Genomic Regions

Abstract Background Pseudomonas aeruginosa is an opportunist and versatile organism responsible for infections among immunocompromised hosts. This pathogen has high intrinsic resistance to most antimicrobials, including critical strains due to resistance to carbapenems, a last-resort antibiotic. P. aeruginosa AG1 (PaeAG1) is a Costa Rican high-risk ST-111 strain with resistance to multiple antibiotics, including carbapenems due to the activity of both VIM-2 and IMP-18 metallo-β-lactamases (MBLs). These genes are harbored in two class 1 integrons, belonging to one out of the 57 PaeAG1 genomic islands. However, the genomic context related to these determinants in PaeAG1 and other P. aeruginosa strains is unclear. Thus, we implemented a comparative genomic approach to define and up-date the phylogenetic relationship among complete P. aeruginosa genomes using a pan-genome analysis. We also studied the PaeAG1 genomic islands content in other strains and the architecture of genomic regions around the VIM-2- and IMP-18-carrying integrons. Results With 211 strains, the up-dated P. aeruginosa pan-genome revealed that complete genome sequences are able to separate clones by MLST profile (ST), including a clear ST-111 cluster with PaeAG1. The PaeAG1 genomic islands were found to define a diverse presence/absence pattern among related genomes, but content was related to phylogenetic relationships. Finally, landscape reconstruction of specific genomic regions showed that VIM-2-carrying integron (In59-like) is an old-acquaintance element harbored in a known genomic region completely found in other two ST-111 strains. In addition, PaeAG1 has an exclusive genomic region containing a novel IMP-18-carrying integron (registered as In1666), with an arrangement never reported before. Conclusions We provide new insights about the genomic determinants associated with the resistance to carbapenems in the high-risk PaeAG1 using comparative genomics. With the pan-genome analysis and the comparison of PaeAG1 genomic islands in other strains, it was possible to describe the genomic landscape of the two MBLs-carrying integrons, including an old-acquaintance element carrying VIM-2 and a new IMP-18-carrying integron.

scholarly journals Newly Named Klebsiella aerogenes (formerly Enterobacter aerogenes) Is Associated with Poor Clinical Outcomes Relative to Other Enterobacter Species in Patients with Bloodstream Infection

2020 ◽  
Vol 58 (9) ◽  
Author(s):  
Austin Wesevich ◽  
Granger Sutton ◽  
Felicia Ruffin ◽  
Lawrence P. Park ◽  
Derrick E. Fouts ◽  
...  
Keyword(s):  
Clinical Outcome ◽  
Hospital Mortality ◽  
Clinical Outcomes ◽  
Genome Analysis ◽  
Enterobacter Aerogenes ◽  
Genomic Islands ◽  
Klebsiella Aerogenes ◽  
Poor Clinical Outcome ◽  
Content Type ◽  
Pan Genome

ABSTRACT Enterobacter aerogenes was recently renamed Klebsiella aerogenes. This study aimed to identify differences in clinical characteristics, outcomes, and bacterial genetics among patients with K. aerogenes versus Enterobacter species bloodstream infections (BSI). We prospectively enrolled patients with K. aerogenes or Enterobacter cloacae complex (Ecc) BSI from 2002 to 2015. We performed whole-genome sequencing (WGS) and pan-genome analysis on all bacteria. Overall, 150 patients with K. aerogenes (46/150 [31%]) or Ecc (104/150 [69%]) BSI were enrolled. The two groups had similar baseline characteristics. Neither total in-hospital mortality (13/46 [28%] versus 22/104 [21%]; P = 0.3) nor attributable in-hospital mortality (9/46 [20%] versus 13/104 [12%]; P = 0.3) differed between patients with K. aerogenes versus Ecc BSI, respectively. However, poor clinical outcome (death before discharge, recurrent BSI, and/or BSI complication) was higher for K. aerogenes than Ecc BSI (32/46 [70%] versus 42/104 [40%]; P = 0.001). In a multivariable regression model, K. aerogenes BSI, relative to Ecc BSI, was predictive of poor clinical outcome (odds ratio 3.3; 95% confidence interval 1.4 to 8.1; P = 0.008). Pan-genome analysis revealed 983 genes in 323 genomic islands unique to K. aerogenes isolates, including putative virulence genes involved in iron acquisition (n = 67), fimbriae/pili/flagella production (n = 117), and metal homeostasis (n = 34). Antibiotic resistance was largely found in Ecc lineage 1, which had a higher rate of multidrug resistant phenotype (23/54 [43%]) relative to all other bacterial isolates (23/96 [24%]; P = 0.03). K. aerogenes BSI was associated with poor clinical outcomes relative to Ecc BSI. Putative virulence factors in K. aerogenes may account for these differences.

scholarly journals Insights on genomic diversity of Vibrio spp. through Pan-genome analysis

2019 ◽  
Vol 69 (13) ◽  
pp. 1547-1555
Author(s):  
Suganya Nathamuni ◽  
Ashok Kumar Jangam ◽  
Vinaya Kumar Katneni ◽  
Ashok Selvaraj ◽  
Karthic Krishnan ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Genome Analysis ◽  
Antibiotic Resistance Genes ◽  
Economic Loss ◽  
Genomic Islands ◽  
Genomic Diversity ◽  
Pan Genome ◽  
Gene Sets ◽  
Downstream Analysis ◽  
Unique Genes

Abstract Purpose The aquaculture sector is a major contributor to the economic and nutritional security for a number of countries. India’s total seafood exports for the year 2017–2018 accounted for US$ Million 7082. One of the major setbacks in this sector is the frequent outbreaks of diseases often due to bacterial pathogens. Vibriosis is one of the major diseases caused by bacteria of Vibrio spp., causing significant economic loss to the aquaculture sector. The objective of this study was to understand the genetic composition of Vibrio spp. Methods Thirty-five complete genomes were downloaded from GenBank comprising seven vibrio species, namely, Vibrio alginolyticus, V. anguillarum, V. campbellii, V. harveyi, V. furnissii, V. parahaemolyticus, and V. vulnificus. Pan-genome analysis was carried out with coding sequences (CDS) generated from all the Vibrio genomes. In addition, genomes were mined for genes coding for toxin-antitoxin systems, antibiotic resistance, genomic islands, and virulence factors. Results Results revealed an open pan-genome comprising of 2004 core, 8249 accessory, and 6780 unique genes. Downstream analysis of genomes and the identified unique genes resulted in 312 antibiotic resistance genes, 430 genes coding for toxin and antitoxin systems along with 4802, and 4825 putative virulent genes from genomic island regions and unique gene sets, respectively. Conclusion Pan-genome and other downstream analytical procedures followed in this study have the potential to predict strain-specific genes and their association with habitat and pathogenicity.

scholarly journals Pan-Genome Analysis of Mycobacterium Africanum: Insights to Dynamics and Evolution.

2020 ◽  
Author(s):  
Idowu Olawoye ◽  
Simon D.W. Frost ◽  
Christian T. Happi
Keyword(s):  
West Africa ◽  
Genome Analysis ◽  
West African ◽  
Multiple Copy ◽  
Genome Sequences ◽  
Animal Reservoir ◽  
Pan Genome ◽  
Lineage Specificity ◽  
Mycobacterium Africanum ◽  
Core Genes

Abstract Background: Mycobacterium tuberculosis complex (MTBC) consists of seven major lineages with three of them reported to circulate within West Africa: lineage 5 (West African 1) and lineage 6 (West African 2) which are geographically restricted to West Africa and lineage 4 (Euro-American lineage) which is found globally. It is unclear why the West African lineages are not found elsewhere; some hypotheses suggest that it could either be harboured by an animal reservoir which is restricted to West Africa, or strain preference for hosts of West African ethnicity, or inability to compete with other lineages in other locations.We tested the hypothesis that M. africanum West African 2 (lineage 6) might have emigrated out of West Africa but was outcompeted by more virulent modern strains of M. tuberculosis (MTB).Whole genome sequences of M. tuberculosis from Nigeria (n=21), South Africa (n=24) and M. africanum West African 2 from Mali (n=22) were retrieved, and a pan-genome analysis was performed after fully annotating these genomes. Results: The outcome of this analysis shows that Lineages 2, 4 and 6 all have a close pan-genome. We also see a correlation in numbers of some multiple copy core genes and amino acid substitution with lineage specificity that may have contributed to geographical distribution of these lineages.Conclusions: The findings in this study provides a perspective to one of the hypotheses that M. africanum West African 2 might find it difficult to compete against the more modern lineages outside West Africa hence its localization to the geographical region.

scholarly journals Identity and compatibility of reference genome resources

2021 ◽  
Author(s):  
Michał Stolarczyk ◽  
Bingjie Xue ◽  
Nathan C. Sheffield
Keyword(s):  
Coordinate System ◽  
Genome Analysis ◽  
Reference Genome ◽  
Reference Data ◽  
Coordinate Systems ◽  
Link Type ◽  
Novel Approach ◽  
Many Sources ◽  
Parent Child Relationships ◽  
Parent Child

Genome analysis relies on reference data like sequences, feature annotations, and aligner indexes. These data can be found in many versions from many sources, making it challenging to identify and assess compatibility among them. For example, how can you determine which indexes are derived from identical raw sequence files, or which annotations share a compatible coordinate system? Here, we describe a novel approach to establish identity and compatibility of reference genome resources. We approach this with three advances: First, we derive unique identifiers for each resource; second, we record parent-child relationships among resources; and third, we describe recursive identifiers that determine identity as well as compatibility of coordinate systems and sequence names. These advances facilitate portability, reproducibility, and re-use of genome reference data.Availabilityhttps://refgenie.databio.org

scholarly journals Mycobacterial Pan-Genome Analysis Suggests Important Role of Plasmids in the Radiation of Type VII Secretion Systems

2016 ◽  
Vol 8 (2) ◽  
pp. 387-402 ◽  
Author(s):  
Emilie Dumas ◽  
Eva Christina Boritsch ◽  
Mathias Vandenbogaert ◽  
Ricardo C. Rodríguez de la Vega ◽  
Jean-Michel Thiberge ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Secretion Systems ◽  
Pan Genome ◽  
Type Vii Secretion
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