Comparative Genomic Analysis Reveals Genetic Mechanisms of the Variety of Pathogenicity, Antibiotic Resistance, and Environmental Adaptation of  Providencia  Genus

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

The bacterial genus Providencia is Gram-negative opportunistic pathogens, which have been isolated from a variety of environments and organisms, ranging from humans to animals. Providencia alcalifaciens, Providencia rettgeri, and Providencia stuartii are the most common clinical isolates, however, these three species differ in their pathogenicity, antibiotic resistance and environmental adaptation. Genomes of 91 isolates of the genus Providencia were investigated to clarify their genetic diversity, focusing on virulence factors, antibiotic resistance genes, and environmental adaptation genes. Our study revealed an open pan-genome for the genus Providencia containing 14,720 gene families. Species of the genus Providencia exhibited different functional constraints, with the core genes, accessory genes, and unique genes. A maximum-likelihood phylogeny reconstructed with concatenated single-copy core genes classified all Providencia isolates into 11 distant groups. Comprehensive and systematic comparative genomic analyses revealed that specific distributions of virulence genes, which were highly homologous to virulence genes of the genus Proteus, contributed to diversity in pathogenicity of Providencia alcalifaciens, Providencia rettgeri, and Providencia stuartii. Furthermore, multidrug resistance (MDR) phenotypes of isolates of Providencia rettgeri and Providencia stuartii were predominantly due to resistance genes from class 1 and 2 integrons. In addition, Providencia rettgeri and Providencia stuartii harbored more genes related to material transport and energy metabolism, which conferred a stronger ability to adapt to diverse environments. Overall, our study provided valuable insights into the genetic diversity and functional features of the genus Providencia, and revealed genetic mechanisms underlying diversity in pathogenicity, antibiotic resistance and environmental adaptation of members of this genus.

Related collections

Most cited references 75

Record: found
Abstract: found
Article: found

Is Open Access

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh, Daron Standley (2013)

We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.

0 comments Cited 13026 times – based on 0 reviews      Review now

Record: found
Abstract: found
Article: not found

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

Sudhir Kumar, Glen Stecher, Koichiro Tamura (2016)

We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.

0 comments Cited 8943 times – based on 0 reviews      Review now

Record: found
Abstract: found
Article: found

Is Open Access

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Donovan Parks, Michael Imelfort, Connor Skennerton … (2015)

Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of “marker” genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities.

0 comments Cited 3924 times – based on 0 reviews      Review now

All references

Author and article information

Contributors

Chao Yuan: URI : http://loop.frontiersin.org/people/1098709/overview

Si Zhang: URI : http://loop.frontiersin.org/people/1086641/overview

Yuhui Wang: URI : http://loop.frontiersin.org/people/1064845/overview

Yang Zhang: URI : http://loop.frontiersin.org/people/1087050/overview

Zhiqiu Yin: URI : http://loop.frontiersin.org/people/1006395/overview

Hong Chen: URI : http://loop.frontiersin.org/people/1004844/overview

Journal

Journal ID (nlm-ta): Front Microbiol

Journal ID (iso-abbrev): Front Microbiol

Journal ID (publisher-id): Front. Microbiol.

Title: Frontiers in Microbiology

Publisher: Frontiers Media S.A.

ISSN (Electronic): 1664-302X

Publication date (Electronic): 27 October 2020

Publication date Collection: 2020

Volume: 11

Electronic Location Identifier: 572642

Affiliations

[1] ¹Department of Sanitary Toxicology and Chemistry, School of Public Health, Tianjin Medical University , Tianjin, China

[2] ²Tianjin Key Laboratory of Environment Nutrition and Public Health, Tianjin Medical University , Tianjin, China

[3] ³Center for International Collaborative Research on Environment Nutrition and Public Health, Tianjin Medical University , Tianjin, China

[4] ⁴Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Tianjin Economic-Technological Development Area , Tianjin, China

[5] ⁵Center for Microbial Functional Genomics and Detection Technology, Ministry of Education, Nankai University , Tianjin, China

[6] ⁶Department of Dermatology, Tianjin Union Medical Center , Tianjin, China

[7] ⁷College of Life Science, Nankai University , Tianjin, China

[8] ⁸National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University , Tai’an, China

Author notes

Edited by: Santiago Castillo Ramírez, National Autonomous University of Mexico, Mexico

Reviewed by: Lorenzo Segovia, National Autonomous University of Mexico, Mexico; Timothy Read, Emory University, United States

*Correspondence: Zhiqiu Yin, yzq7873728@ 123456126.com

Hong Chen, baixue20042006@ 123456126.com

^†These authors have contributed equally to this work

This article was submitted to Evolutionary and Genomic Microbiology, a section of the journal Frontiers in Microbiology

Article

DOI: 10.3389/fmicb.2020.572642

PMC ID: 7652902

PubMed ID: 33193173

SO-VID: d46566b9-5f1a-486c-a2d4-7423f0a68b8a

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

History

Date received : 10 July 2020

Date accepted : 17 September 2020

Page count

Figures: 9, Tables: 0, Equations: 0, References: 75, Pages: 15, Words: 0

Funding

Funded by: National Natural Science Foundation of China 10.13039/501100001809

Award ID: 31820103002

Award ID: 31770144

Award ID: 81772148

Award ID: 81871624

Funded by: Natural Science Foundation of Tianjin City 10.13039/501100006606

Comments

Comment on this article

Cited by 17

See all cited by

Most referenced authors 908

See all reference authors

Comparative Genomic Analysis Reveals Genetic Mechanisms of the Variety of Pathogenicity, Antibiotic Resistance, and Environmental Adaptation of Providencia Genus

Read this article at