Whole-Genome Sequences and Comparative Genomics of Salmonella enterica Serovar Typhi Isolates from Patients with Fatal and Nonfatal Typhoid Fever in Papua New Guinea

Baddam, Ramani; Thong, Kwai Lin; Tiruvayipati, Suma; Shaik, Sabiha; Yap, Kien-Pong; Teh, Cindy Shuan Ju; Chai, Lay Ching; Kumar, Narender; Ahmed, Niyaz

doi:10.1128/jb.01051-12

Cited by 12 publications

(11 citation statements)

References 21 publications

(13 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It is reasonable to speculate that these successful STs may have predisposed to advantageous genetic variations that drive evolutions, allowing the pathogens to be more adapted in the host as observed hitherto in several genomic studies of S . Typhi ( Parkhill et al, 2001 ; Deng et al, 2004 ; Baddam et al, 2012a , b ; Ong et al, 2012 ; Yap et al, 2014 ; Hendriksen et al, 2015 ). Thus, extensive genomic studies of the S .…”

Section: Discussionmentioning

confidence: 99%

Global MLST of Salmonella Typhi Revisited in Post-genomic Era: Genetic Conservation, Population Structure, and Comparative Genomics of Rare Sequence Types

Yap

Gan

et al. 2016

Front. Microbiol.

Self Cite

View full text Add to dashboard Cite

Typhoid fever, caused by Salmonella enterica serovar Typhi, remains an important public health burden in Southeast Asia and other endemic countries. Various genotyping methods have been applied to study the genetic variations of this human-restricted pathogen. Multilocus sequence typing (MLST) is one of the widely accepted methods, and recently, there is a growing interest in the re-application of MLST in the post-genomic era. In this study, we provide the global MLST distribution of S. Typhi utilizing both publicly available 1,826 S. Typhi genome sequences in addition to performing conventional MLST on S. Typhi strains isolated from various endemic regions spanning over a century. Our global MLST analysis confirms the predominance of two sequence types (ST1 and ST2) co-existing in the endemic regions. Interestingly, S. Typhi strains with ST8 are currently confined within the African continent. Comparative genomic analyses of ST8 and other rare STs with genomes of ST1/ST2 revealed unique mutations in important virulence genes such as flhB, sipC, and tviD that may explain the variations that differentiate between seemingly successful (widespread) and unsuccessful (poor dissemination) S. Typhi populations. Large scale whole-genome phylogeny demonstrated evidence of phylogeographical structuring and showed that ST8 may have diverged from the earlier ancestral population of ST1 and ST2, which later lost some of its fitness advantages, leading to poor worldwide dissemination. In response to the unprecedented increase in genomic data, this study demonstrates and highlights the utility of large-scale genome-based MLST as a quick and effective approach to narrow the scope of in-depth comparative genomic analysis and consequently provide new insights into the fine scale of pathogen evolution and population structure.

show abstract

Section: Discussionmentioning

confidence: 99%

Global MLST of Salmonella Typhi Revisited in Post-genomic Era: Genetic Conservation, Population Structure, and Comparative Genomics of Rare Sequence Types

Yap

Gan

et al. 2016

Front. Microbiol.

Self Cite

View full text Add to dashboard Cite

show abstract

“…These genomes were from Asia (India, Vietnam, Bangladesh, Indonesia, Nepal), Africa (Kenya, Senegal, Morocco, Central Africa) and North America (Mexico) . In 2012, another six genomes isolated from the endemic regions of Malaysia and Papua New Guinea were deposited , followed by the deposition of a Chilean S. Typhi genome (STH2370) isolated in 1991 from a female typhoid patient . Subsequently, a large number of genomes have been deposited in the public domain and it is growing rapidly.…”

Section: Introductionmentioning

confidence: 99%

Salmonella Typhi genomics: envisaging the future of typhoid eradication

Yap

Thong

2017

Tropical Med Int Health

Self Cite

View full text Add to dashboard Cite

SummaryNext-generation whole-genome sequencing has revolutionised the study of infectious diseases in recent years. The availability of genome sequences and its understanding have transformed the field of molecular microbiology, epidemiology, infection treatments and vaccine developments. We review the key findings of the publicly accessible genomes of Salmonella enterica serovar Typhi since the first complete genome to the most recent release of thousands of Salmonella Typhi genomes, which remarkably shape the genomic research of S. Typhi and other pathogens. Important new insights acquired from the genome sequencing of S. Typhi, pertaining to genomic variations, evolution, population structure, antibiotic resistance, virulence, pathogenesis, disease surveillance/investigation and disease control are discussed. As the numbers of sequenced genomes are increasing at an unprecedented rate, fine variations in the gene pool of S. Typhi are captured in high resolution, allowing deeper understanding of the pathogen's evolutionary trends and its pathogenesis, paving the way to bringing us closer to eradication of typhoid through effective vaccine/treatment development.

show abstract

“…The previous findings have also recorded shared PFGE patterns among the isolates from Southeast Asia 11 . Strains UJ308A and UJ816A were isolated in Papua New Guinea from fatal and non-fatal cases, respectively, in 1998 27 . Genomes of multi-drug resistant strains, CT18 from Vietnam, and P-stx-12 strain isolated from a carrier individual in India 28 29 , were also analyzed.…”

mentioning

confidence: 99%

Genome dynamics and evolution of Salmonella Typhi strains from the typhoid-endemic zones

Baddam

Kumar

Shaik

et al. 2014

Sci Rep

Self Cite

View full text Add to dashboard Cite

Typhoid fever poses significant burden on healthcare systems in Southeast Asia and other endemic countries. Several epidemiological and genomic studies have attributed pseudogenisation to be the major driving force for the evolution of Salmonella Typhi although its real potential remains elusive. In the present study, we analyzed genomes of S. Typhi from different parts of Southeast Asia and Oceania, comprising of isolates from outbreak, sporadic and carrier cases. The genomes showed high genetic relatedness with limited opportunity for gene acquisition as evident from pan-genome structure. Given that pseudogenisation is an active process in S. Typhi, we further investigated core and pan-genome profiles of functional and pseudogenes separately. We observed a decline in core functional gene content and a significant increase in accessory pseudogene content. Upon functional classification, genes encoding metabolic functions formed a major constituent of pseudogenes as well as core functional gene clusters with SNPs. Further, an in-depth analysis of accessory pseudogene content revealed the existence of heterogeneous complements of functional and pseudogenes among the strains. In addition, these polymorphic genes were also enriched in metabolism related functions. Thus, the study highlights the existence of heterogeneous strains in a population with varying metabolic potential and that S. Typhi possibly resorts to metabolic fine tuning for its adaptation.

show abstract

Whole-Genome Sequences and Comparative Genomics of Salmonella enterica Serovar Typhi Isolates from Patients with Fatal and Nonfatal Typhoid Fever in Papua New Guinea

Cited by 12 publications

References 21 publications

Global MLST of Salmonella Typhi Revisited in Post-genomic Era: Genetic Conservation, Population Structure, and Comparative Genomics of Rare Sequence Types

Global MLST of Salmonella Typhi Revisited in Post-genomic Era: Genetic Conservation, Population Structure, and Comparative Genomics of Rare Sequence Types

Salmonella Typhi genomics: envisaging the future of typhoid eradication

Genome dynamics and evolution of Salmonella Typhi strains from the typhoid-endemic zones

Contact Info

Product

Resources

About