This may be because the snippet appears in a figure legend, contains special characters or spans different sections of the article. Nucleic Acids Res. Published online Nov 4. PMID: The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
Looking for other ways to read this?
This article has been cited by other articles in PMC. Abstract Virulence factor database VFDB was set up in dedicated for providing current knowledge of virulence factors VFs from various medical significant bacterial pathogens to facilitate pathogenomic research. Full tabular comparison of the pathogenomic composition Tabular style was commonly used in scientific literatures for comparative analysis. Open in a separate window. Figure 1. Multiple alignments of homologous virulence genes Analysis of homologous genes is a powerful approach for elucidating gene structure, function and evolution.
Concise graphical comparison of pathogenomic organization Bacterial genome evolution has been driven by nucleotide substitutions and indels, as well as the changes of the genome architecture by genetic rearrangements including translocations and inversions 8.
- SMBE Satellite Workshop: Pathogen Transmission and Disease.
- Low-Fat Love: Expanded Anniversary Edition;
- The Modern World-System, volume 1: Capitalist Agriculture and the Origins of the European World-Economy in the Sixteenth Century, With a New Prologue.
- ABC of Sports and Exercise Medicine (ABC Series)?
- The Rough Guide to Czech Dictionary Phrasebook (Rough Guide Phrasebooks)?
Conflict of interest statement. None declared. Infectious diseases- a global challenge. VFDB: a reference database for bacterial virulence factors. NCBI reference sequences RefSeq : a curated non-redundant sequence database of genomes, transcripts and proteins. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Haemophilus influenzae: genetic variability and natural selection to identify virulence factors.
Microbial genome evolution: sources of variability. Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Pathogenomics of Listeria spp.
How does Europe PMC derive its citations network? Protein Interactions. Protein Families. Nucleotide Sequences. Functional Genomics Experiments. Protein Structures. Gene Ontology GO Terms. Data Citations.
Proteomics Data. S almonella are enteric bacteria that can infect a broad range of host species causing various infectious diseases. Presently, there are two well recognized species of Salmonella - S. Further, based on Kauffman-White classification scheme, S. However, serovar S. Typhi of Salmonella enterica subspecies enterica infects only humans resulting in a systemic infection, typhoid fever 2. This infection is of immense concern to public health worldwide as it is responsible for about The control and prevention strategies are also severely hampered due to the emergence of antibiotic resistant strains in these regions, which are responsible for periodic outbreaks and sporadic cases causing severe complications and mortality 5.
Further, the presence of these antimicrobial resistance genes carried on mobile elements such as integrons and self-transmissible plasmids like that of IncH1, which was reported to be associated with many strains from endemic zones such as Vietnam, pose a constant threat to public health world-wide 6 , 7. For a host adapted strain like S. Typhi, survival in the host and dissemination are vital for establishing persistent infections. Some infected individuals even serve as asymptomatic reservoirs who continue to shed the bacterium in stools for a long period of time 8 , 9. The studies on transmission dynamics of salmonellae have emphasized on monitoring of the carrier isolates for effective epidemiological tracking and surveillance The carrier isolates have also been shown to exhibit similar pulsed field gel electrophoresis PFGE profiles with other S.
Typhi isolates from various regions of Southeast Asia. Therefore, it appears that the spread of S.
Typhi occurs mostly through carrier individuals In the past, various genomic studies have attributed signatures like pseudogenisation loss of gene function or gene deletion for host restriction in pathogenic bacteria It was also reported that in human-restricted serovar S. Typhi, pseudogenisation is an active process compared to other generalist serovars like S. Typhimurium Further, the extent of this pseudogenisation also varies considerably even among host restricted serovars 14 , 15 , Pseudogenes constitute up to 4.
Typhi gene pool, making them an important driver of genome re-assortment over time However the potential role of pseudogenisation in persistence and adaptation of S. Typhi still remains elusive. Given this, it is important to characterize S. Typhi's pan-genome, more importantly with respect to functional and pseudogene complements and investigate their gene-frequency distributions among various strains.
The pan-genome of a species is the complete inventory of genes in the population and is always significantly greater than the gene content of an individual This accessory or dispensable part confers various selective advantages such as antibiotic resistance, niche adaptation, pathogenicity and host specificity 19 , Thus, the pan-genome analysis helps us to better understand the population genetic structure and provides cues about the mechanisms underlying adaptation and evolution of bacteria.
Studies based on whole genome comparative analyses carried out at the population level involving other S. The whole genome sequences corresponding to eight strains previously isolated from different endemic regions of Southeast Asia and Oceania were extensively analyzed in this study. These strains were associated with different clinical manifestations - outbreaks, sporadic cases, carrier strains and fatal episodes. The strain BL was associated with a large outbreak in Kelantan, Malaysia in Genomes of multi-drug resistant strains, CT18 from Vietnam, and P-stx strain isolated from a carrier individual in India 28 , 29 , were also analyzed.
Some of the earlier studies based on PFGE observed minimal to moderate diversity among the isolates from Papua New Guinea and elsewhere in Asia 30 , 31 , thus verifying the limited observed diversity if not a clonal nature of this organism. Herein, we analyzed genomes of the strains described in some of the above pioneering studies. These genomes, although limited in number, were chosen owing to their being most authentic available representatives of geographically distinct populations from different endemic countries such as India, Vietnam, Papua New Guinea and Malaysia and thus were used for extensive genomic analyses hitherto unreported for these unique strains.
Our comprehensive genomic analyses reported herein highlight the possible evolutionary mechanisms and in particular, the impact of pseudogenes on the evolution of S. Typhi in different patient types from the typhoid-endemic countries of the east.
The Engel Lab: Microbial symbiosis
The whole genome based phylogenetic tree allowed us to understand the close genetic relationship among various strains as shown in Figure 1. The strain BL isolated during the outbreak, and the carrier strain CR isolated a year later, co-clustered revealing close similarity. This suggests that the strain CR could have emerged due to clonal expansion of BL, whereas another carrier strain CR might have accumulated enough variations allowing it to cluster separately. As typhoid cases were rarely detected in Papua New Guinea before , the limited observed diversity might be due to clonal expansion of a single ancestral strain The close similarity of these genomes is also reflected in whole genome alignment as depicted Figure 2.
This analysis once again reinforces the genetically monomorphic nature of this pathogen and our observations are in concurrence with the previous findings based on Multilocus sequence typing and other techniques 17 , A similar co-clustering pattern was also observed with Maximum Likelihood based phylogenetic tree constructed using core gene clusters without paralogs Supplementary Figure S1. The whole genome information was used to build the distance matrix using Gegenees. The phylogenetic tree was developed using SplitsTree by NJ method.
This revealed close similarity among genomes and also co-clustering of strains isolated from the same regions. The whole genome alignment of all eight genomes was generated using progressiveMauve Each colored block represents similar sequences in the respective genomes.
- Pathogenomics | Plant Pathology and Plant-Microbe Biology Section?
- Microaggressions in Everyday Life: Race, Gender, and Sexual Orientation!
- The Fall of the Faculty: The Rise of the All-Administrative University and Why It Matters.
- Encyclopedia of Clinical Neuropsychology.
- The Renaissance of American Steel: Lessons for Managers in Competitive Industries?
- Bacterial pathogenomics.
- Citation metadata!
The phages and insertion sequence IS elements of the two complete genomes, CT18 and P-stx have been already reported 28 , However, the strain CR also contained copies that belonged to IS1 family. The determination of exact copy number of these IS elements was difficult because of the draft status of the genomes. Further search for putative phage elements revealed presence of 4 intact phage sequences together with various phage remnants in each of the genomes Supplementary table S1.
Gifsy-2 and fels-2 phage sequences were common in most of the genomes. The atypical regions which encode genes mostly associated with virulence are designated as Salmonella pathogenicity islands SPI. BRIG 33 was used to represent the status of major pathogenicity islands in these genomes as shown in Supplementary Figure S2. A list of genomic islands detected in these genomes as well as of the genes encoded by them is provided Supplementary table S2. The plasmid related genes were not found in any strains other than CT18 and P-stx The characteristics of the plasmids present in these strains along with the orthologous genes shared by them have already been discussed previously 28 , The pan-genome content measured up to a total of genes, 1.
The pan-genome extrapolation was carried out in accordance with Heap's law The Heap's law can be represented by the following equation:. The pan-genome analysis of S. Pan and core genome developments using median values of the combinations of all eight genomes. Pan and core genome developments of functional genes of these eight isolates.
Enfermedades Infecciosas y Microbiología Clínica
Here it can be observed that core genome is decreasing sharply. Pan and core genome developments of pseudogenes of these eight isolates. It can be seen that pan genome of pseudogenes is highly non conservative with a steep increase in accessory content while the core genome reached convergence.
Further, to investigate the effect of pseudogenisation on gene frequency distributions of functional and pseudogenes, their pan and core genome components were determined separately. The pan-genome of functional genes contained a total of genes which was 1. This increased proportion of pseudogene content compared to functional pan-genome suggests that pseudogenisation is an active process in S.
Typhi and this increase is also reflected in the pan-genome curve of pseudogenes Figure 3c.