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Analysis of mutations in pncA reveals non-overlapping patterns among various lineages of Mycobacterium tuberculosis

Baddam, Ramani ; Kumar, Narender ; Wieler, Lothar H. ; [et al.]

Springer Science and Business Media LLC ; 2018

In: Scientific Reports Vol. 8, No. 1 ( 2018-03-15)

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In: Scientific Reports, Springer Science and Business Media LLC, Vol. 8, No. 1 ( 2018-03-15)

Abstract: Pyrazinamide (PZA) is an important first-line anti-tuberculosis drug, resistance to which occurs primarily due to mutations in pncA ( Rv2043c ) that encodes the pyrazinamidase enzyme responsible for conversion of pro-drug PZA into its active form. Previous studies have reported numerous resistance-conferring mutations distributed across the entire length of pncA without any hotspot regions. As different lineages of Mycobacterium tuberculosis display a strong geographic association, we sought to understand whether the genetic background influenced the distribution of mutations in pncA . We analyzed the whole genome sequence data of 1,480 clinical isolates representing four major M. tuberculosis lineages to identify the distribution of mutations in the complete operon ( Rv2044c-pncA-Rv2042c) and its upstream promoter region. We observed a non-overlapping pattern of mutations among various lineages and identified a lineage 3-specific frame-shift deletion in gene Rv2044c upstream of pncA that disrupted the stop codon and led to its fusion with pncA . This resulted in the addition of a novel domain of unknown function (DUF2784) to the pyrazinamidase enzyme. The variant molecule was computationally modelled and physico-chemical parameters determined to ascertain stability. Although the functional impact of this mutation remains unknown, its lineage specific nature highlights the importance of genetic background and warrants further study.

Type of Medium: Online Resource

ISSN: 2045-2322

URL: Article

DOI: 10.1038/s41598-018-22883-9

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2018

detail.hit.zdb_id: 2615211-3

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Author Correction: Analysis of mutations in pncA reveals non-overlapping patterns among various lineages of Mycobacterium tuberculosis

Baddam, Ramani ; Kumar, Narender ; Wieler, Lothar H. ; [et al.]

Springer Science and Business Media LLC ; 2018

In: Scientific Reports Vol. 8, No. 1 ( 2018-05-15)

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In: Scientific Reports, Springer Science and Business Media LLC, Vol. 8, No. 1 ( 2018-05-15)

Abstract: A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

Type of Medium: Online Resource

ISSN: 2045-2322

URL: Article

DOI: 10.1038/s41598-018-25809-7

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2018

detail.hit.zdb_id: 2615211-3

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

Baddam, Ramani ; Kumar, Narender ; Shaik, Sabiha ; [et al.]

Springer Science and Business Media LLC ; 2014

In: Scientific Reports Vol. 4, No. 1 ( 2014-12-12)

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In: Scientific Reports, Springer Science and Business Media LLC, Vol. 4, No. 1 ( 2014-12-12)

Type of Medium: Online Resource

ISSN: 2045-2322

URL: Article

DOI: 10.1038/srep07457

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2014

detail.hit.zdb_id: 2615211-3

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A treponemal genome from an historic plague victim supports a recent emergence of yaws and its presence in 15th century Europe

Giffin, Karen ; Lankapalli, Aditya Kumar ; Sabin, Susanna ; [et al.]

Springer Science and Business Media LLC ; 2020

In: Scientific Reports Vol. 10, No. 1 ( 2020-06-11)

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In: Scientific Reports, Springer Science and Business Media LLC, Vol. 10, No. 1 ( 2020-06-11)

Abstract: Developments in techniques for identification of pathogen DNA in archaeological samples can expand our resolution of disease detection. Our application of a non-targeted molecular screening tool for the parallel detection of pathogens in historical plague victims from post-medieval Lithuania revealed the presence of more than one active disease in one individual. In addition to Yersinia pestis , we detected and genomically characterized a septic infection of Treponema pallidum pertenue , a subtype of the treponemal disease family recognised as the cause of the tropical disease yaws. Our finding in northern Europe of a disease that is currently restricted to equatorial regions is interpreted within an historical framework of intercontinental trade and potential disease movements. Through this we offer an alternative hypothesis for the history and evolution of the treponemal diseases, and posit that yaws be considered an important contributor to the sudden epidemic of late 15 th century Europe that is widely ascribed to syphilis.

Type of Medium: Online Resource

ISSN: 2045-2322

URL: Article

DOI: 10.1038/s41598-020-66012-x

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2020

detail.hit.zdb_id: 2615211-3

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Emergence of human-adapted Salmonella enterica is linked to the Neolithization process

Key, Felix M. ; Posth, Cosimo ; Esquivel-Gomez, Luis R. ; [et al.]

Springer Science and Business Media LLC ; 2020

In: Nature Ecology & Evolution Vol. 4, No. 3 ( 2020-02-24), p. 324-333

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In: Nature Ecology & Evolution, Springer Science and Business Media LLC, Vol. 4, No. 3 ( 2020-02-24), p. 324-333

Type of Medium: Online Resource

ISSN: 2397-334X

URL: Article

DOI: 10.1038/s41559-020-1106-9

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2020

detail.hit.zdb_id: 2879715-2

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A 3,000-year-old, basal S. enterica lineage from Bronze Age Xinjiang suggests spread along the Proto-Silk Road

Wu, Xiyan ; Ning, Chao ; Key, Felix M. ; [et al.]

Public Library of Science (PLoS) ; 2021

In: PLOS Pathogens Vol. 17, No. 9 ( 2021-9-21), p. e1009886-

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In: PLOS Pathogens, Public Library of Science (PLoS), Vol. 17, No. 9 ( 2021-9-21), p. e1009886-

Abstract: Salmonella enterica ( S . enterica ) has infected humans for a long time, but its evolutionary history and geographic spread across Eurasia is still poorly understood. Here, we screened for pathogen DNA in 14 ancient individuals from the Bronze Age Quanergou cemetery (XBQ), Xinjiang, China. In 6 individuals we detected S . enterica . We reconstructed S . enterica genomes from those individuals, which form a previously undetected phylogenetic branch basal to Paratyphi C, Typhisuis and Choleraesuis–the so-called Para C lineage. Based on pseudogene frequency, our analysis suggests that the ancient S . enterica strains were not host adapted. One genome, however, harbors the Salmonella pathogenicity island 7 (SPI-7), which is thought to be involved in (para)typhoid disease in humans. This offers first evidence that SPI-7 was acquired prior to the emergence of human-adapted Paratyphi C around 1,000 years ago. Altogether, our results show that Salmonella enterica infected humans in Eastern Eurasia at least 3,000 years ago, and provide the first ancient DNA evidence for the spread of a pathogen along the Proto-Silk Road.

Type of Medium: Online Resource

ISSN: 1553-7374

URL: Article

DOI: 10.1371/journal.ppat.1009886

DOI: 10.1371/journal.ppat.1009886.g001

DOI: 10.1371/journal.ppat.1009886.g002

DOI: 10.1371/journal.ppat.1009886.g003

DOI: 10.1371/journal.ppat.1009886.g004

DOI: 10.1371/journal.ppat.1009886.g005

DOI: 10.1371/journal.ppat.1009886.t001

DOI: 10.1371/journal.ppat.1009886.s001

DOI: 10.1371/journal.ppat.1009886.s002

DOI: 10.1371/journal.ppat.1009886.s003

DOI: 10.1371/journal.ppat.1009886.s004

DOI: 10.1371/journal.ppat.1009886.s005

DOI: 10.1371/journal.ppat.1009886.s006

DOI: 10.1371/journal.ppat.1009886.s007

DOI: 10.1371/journal.ppat.1009886.s008

DOI: 10.1371/journal.ppat.1009886.s009

DOI: 10.1371/journal.ppat.1009886.s010

DOI: 10.1371/journal.ppat.1009886.s011

DOI: 10.1371/journal.ppat.1009886.s012

DOI: 10.1371/journal.ppat.1009886.s013

DOI: 10.1371/journal.ppat.1009886.s014

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2021

detail.hit.zdb_id: 2205412-1

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Comparative genomic analysis of Helicobacter pylori from Malaysia identifies three distinct lineages suggestive of differential evolution

Kumar, Narender ; Mariappan, Vanitha ; Baddam, Ramani ; [et al.]

Oxford University Press (OUP) ; 2015

In: Nucleic Acids Research Vol. 43, No. 1 ( 2015-01-09), p. 324-335

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In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 43, No. 1 ( 2015-01-09), p. 324-335

Type of Medium: Online Resource

ISSN: 1362-4962 , 0305-1048

URL: Article

DOI: 10.1093/nar/gku1271

RVK:

WA 15000

Language: English

Publisher: Oxford University Press (OUP)

Publication Date: 2015

detail.hit.zdb_id: 1472175-2

SSG: 12

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Historic Treponema pallidum genomes from Colonial Mexico retrieved from archaeological remains

Schuenemann, Verena J. ; Kumar Lankapalli, Aditya ; Barquera, Rodrigo ; [et al.]

Public Library of Science (PLoS) ; 2018

In: PLOS Neglected Tropical Diseases Vol. 12, No. 6 ( 2018-6-21), p. e0006447-

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In: PLOS Neglected Tropical Diseases, Public Library of Science (PLoS), Vol. 12, No. 6 ( 2018-6-21), p. e0006447-

Type of Medium: Online Resource

ISSN: 1935-2735

URL: Article

DOI: 10.1371/journal.pntd.0006447

DOI: 10.1371/journal.pntd.0006447.g001

DOI: 10.1371/journal.pntd.0006447.g002

DOI: 10.1371/journal.pntd.0006447.t001

DOI: 10.1371/journal.pntd.0006447.s001

DOI: 10.1371/journal.pntd.0006447.s002

DOI: 10.1371/journal.pntd.0006447.s003

DOI: 10.1371/journal.pntd.0006447.s004

DOI: 10.1371/journal.pntd.0006447.s005

DOI: 10.1371/journal.pntd.0006447.s006

DOI: 10.1371/journal.pntd.0006447.s007

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2018

detail.hit.zdb_id: 2429704-5

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Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens

Bos, Kirsten I. ; Kühnert, Denise ; Herbig, Alexander ; [et al.]

Annual Reviews ; 2019

In: Annual Review of Microbiology Vol. 73, No. 1 ( 2019-09-08), p. 639-666

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In: Annual Review of Microbiology, Annual Reviews, Vol. 73, No. 1 ( 2019-09-08), p. 639-666

Abstract: The last century has witnessed progress in the study of ancient infectious disease from purely medical descriptions of past ailments to dynamic interpretations of past population health that draw upon multiple perspectives. The recent adoption of high-throughput DNA sequencing has led to an expanded understanding of pathogen presence, evolution, and ecology across the globe. This genomic revolution has led to the identification of disease-causing microbes in both expected and unexpected contexts, while also providing for the genomic characterization of ancient pathogens previously believed to be unattainable by available methods. In this review we explore the development of DNA-based ancient pathogen research, the specialized methods and tools that have emerged to authenticate and explore infectious disease of the past, and the unique challenges that persist in molecular paleopathology. We offer guidelines to mitigate the impact of these challenges, which will allow for more reliable interpretations of data in this rapidly evolving field of investigation.

Type of Medium: Online Resource

ISSN: 0066-4227 , 1545-3251

URL: Issue

URL: Article

DOI: 10.1146/micro.2019.73.issue-1

DOI: 10.1146/annurev-micro-090817-062436

RVK:

WA 15000

Language: English

Publisher: Annual Reviews

Publication Date: 2019

detail.hit.zdb_id: 1470471-7

SSG: 12

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Contig-Layout-Authenticator (CLA): A Combinatorial Approach to Ordering and Scaffolding of Bacterial Contigs for Comparative Genomics and Molecular Epidemiology

Shaik, Sabiha ; Kumar, Narender ; Lankapalli, Aditya K. ; [et al.]

Public Library of Science (PLoS) ; 2016

In: PLOS ONE Vol. 11, No. 6 ( 2016-6-1), p. e0155459-

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In: PLOS ONE, Public Library of Science (PLoS), Vol. 11, No. 6 ( 2016-6-1), p. e0155459-

Type of Medium: Online Resource

ISSN: 1932-6203

URL: Article

DOI: 10.1371/journal.pone.0155459

DOI: 10.1371/journal.pone.0155459.g001

DOI: 10.1371/journal.pone.0155459.g002

DOI: 10.1371/journal.pone.0155459.t001

DOI: 10.1371/journal.pone.0155459.t002

DOI: 10.1371/journal.pone.0155459.t003

DOI: 10.1371/journal.pone.0155459.t004

DOI: 10.1371/journal.pone.0155459.t005

DOI: 10.1371/journal.pone.0155459.s001

DOI: 10.1371/journal.pone.0155459.s002

DOI: 10.1371/journal.pone.0155459.s003

DOI: 10.1371/journal.pone.0155459.s004

DOI: 10.1371/journal.pone.0155459.s005

DOI: 10.1371/journal.pone.0155459.s006

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2016

detail.hit.zdb_id: 2267670-3

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