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Article: Average Nucleotide Identity based

Raghuram, Vishnu / Petit, Robert A / Karol, Zach / Mehta, Rohan / Weissman, Daniel B / Read, Timothy D

bioRxiv : the preprint server for biology

2024

Abstract: Staphylococcus ... ...

Abstract	Staphylococcus aureus
Language	English
Publishing date	2024-01-31
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.01.29.577756
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes.

Mehta, Rohan S / Petit, Robert A / Read, Timothy D / Weissman, Daniel B

BMC bioinformatics

2023 Volume 24, Issue 1, Page(s) 243

Abstract: Bacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecting coevolving genes from large datasets of ... ...

Abstract	Bacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecting coevolving genes from large datasets of bacterial genomes based on pairwise comparisons of closely related individuals, analogous to a pedigree study in eukaryotic populations. We apply our method to pairs of genes from the Staphylococcus aureus accessory genome of over 75,000 annotated gene families using a database of over 40,000 whole genomes. We find many pairs of genes that appear to be gained or lost in a coordinated manner, as well as pairs where the gain of one gene is associated with the loss of the other. These pairs form networks of rapidly coevolving genes, primarily consisting of genes involved in virulence, mechanisms of horizontal gene transfer, and antibiotic resistance, particularly the SCCmec complex. While we focus on gene gain and loss, our method can also detect genes that tend to acquire substitutions in tandem, or genotype-phenotype or phenotype-phenotype coevolution. Finally, we present the R package DeCoTUR that allows for the computation of our method.
MeSH term(s)	Humans ; Staphylococcus aureus/genetics ; Genome, Bacterial ; Virulence/genetics ; Staphylococcal Infections/genetics ; Staphylococcal Infections/microbiology ; Anti-Bacterial Agents
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2023-06-09
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-023-05363-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Development of an Amplicon Nanopore Sequencing Strategy for Detection of Mutations Conferring Intermediate Resistance to Vancomycin in Staphylococcus aureus Strains.

Moller, Abraham G / Petit, Robert A / Davis, Michelle H / Read, Timothy D

Microbiology spectrum

2023 Volume 11, Issue 1, Page(s) e0272822

Abstract: Staphylococcus aureus is a major cause of bacteremia and other hospital-acquired infections. The cell-wall active antibiotic vancomycin is commonly used to treat both methicillin-resistant (MRSA) and sensitive (MSSA) infections. Vancomycin intermediate S. ...

Abstract	Staphylococcus aureus is a major cause of bacteremia and other hospital-acquired infections. The cell-wall active antibiotic vancomycin is commonly used to treat both methicillin-resistant (MRSA) and sensitive (MSSA) infections. Vancomycin intermediate S. aureus (VISA) variants can arise through
MeSH term(s)	Humans ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Bacteremia/drug therapy ; Microbial Sensitivity Tests ; Mutation ; Nanopore Sequencing ; Staphylococcal Infections/drug therapy ; Staphylococcus aureus/genetics ; Vancomycin/pharmacology ; Vancomycin/therapeutic use ; Vancomycin-Resistant Staphylococcus aureus/genetics
Chemical Substances	Anti-Bacterial Agents ; Vancomycin (6Q205EH1VU)
Language	English
Publishing date	2023-01-23
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.02728-22
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Species-Scale Genomic Analysis of Staphylococcus aureus Genes Influencing Phage Host Range and Their Relationships to Virulence and Antibiotic Resistance Genes.

Moller, Abraham G / Petit, Robert A / Read, Timothy D

mSystems

2022 Volume 7, Issue 1, Page(s) e0108321

Abstract: Phage therapy has been proposed as a possible alternative treatment for infections caused by the ubiquitous bacterial pathogen Staphylococcus aureus. However, successful therapy requires understanding the genetic basis of host range-the subset of strains ...

Abstract	Phage therapy has been proposed as a possible alternative treatment for infections caused by the ubiquitous bacterial pathogen Staphylococcus aureus. However, successful therapy requires understanding the genetic basis of host range-the subset of strains in a species that could be killed by a particular phage. We searched diverse sets of S. aureus public genome sequences against a database of genes suggested from prior studies to influence host range to look for patterns of variation across the species. We found that genes encoding biosynthesis of molecules that were targets of S. aureus phage adsorption to the outer surface of the cell were the most conserved in the pangenome. Putative phage resistance genes that were core components of the pangenome genes had similar nucleotide diversity, ratio of nonsynonymous to synonymous substitutions, and functionality (measured by delta-bitscore) to other core genes. However, phage resistance genes that were not part of the core genome were significantly less consistent with the core genome phylogeny than all noncore genes in this set, suggesting more frequent movement between strains by horizontal gene transfer. Only superinfection immunity genes encoded by temperate phages inserted in the genome correlated with experimentally determined temperate phage resistance. Taken together, these results suggested that, while phage adsorption genes are heavily conserved in the S. aureus species, HGT may play a significant role in strain-specific evolution of host range patterns.
Language	English
Publishing date	2022-01-18
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN	2379-5077
DOI	10.1128/msystems.01083-21
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes.

Petit, Robert A / Read, Timothy D

mSystems

2020 Volume 5, Issue 4

Abstract: Sequencing of bacterial genomes using Illumina technology has become such a standard procedure that often data are generated faster than can be conveniently analyzed. We created a new series of pipelines called Bactopia, built using Nextflow workflow ... ...

Abstract	Sequencing of bacterial genomes using Illumina technology has become such a standard procedure that often data are generated faster than can be conveniently analyzed. We created a new series of pipelines called Bactopia, built using Nextflow workflow software, to provide efficient comparative genomic analyses for bacterial species or genera. Bactopia consists of a data set setup step (Bactopia Data Sets [BaDs]), which creates a series of customizable data sets for the species of interest, the Bactopia Analysis Pipeline (BaAP), which performs quality control, genome assembly, and several other functions based on the available data sets and outputs the processed data to a structured directory format, and a series of Bactopia Tools (BaTs) that perform specific postprocessing on some or all of the processed data. BaTs include pan-genome analysis, computing average nucleotide identity between samples, extracting and profiling the 16S genes, and taxonomic classification using highly conserved genes. It is expected that the number of BaTs will increase to fill specific applications in the future. As a demonstration, we performed an analysis of 1,664 public
Language	English
Publishing date	2020-08-04
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN	2379-5077
DOI	10.1128/mSystems.00190-20
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Article ; Online: Extended time-of-flight measurements down to 100 keV at the AMANDE facility with a stilbene scintillator.

Petit, Michael / Di Chicco, Augusto / Sardet, Alix / Babut, Richard / Jacqmin, Robert / Stout, Brian

Radiation protection dosimetry

2023 Volume 199, Issue 15-16, Page(s) 1894–1897

Abstract: The time-of-flight (ToF) method with scintillators is routinely used for determining neutron energy. However, a technical difficulty related to the loss of scintillator efficiency below 1 MeV makes this technique difficult to implement for the energy ... ...

Abstract	The time-of-flight (ToF) method with scintillators is routinely used for determining neutron energy. However, a technical difficulty related to the loss of scintillator efficiency below 1 MeV makes this technique difficult to implement for the energy decade [100 keV-1 MeV]. New crystal production techniques provide stilbene scintillators efficient in this low neutron energy region, making it possible to extend the ToF technique below 1 MeV. In this manner, measurements of secondary reactions (d,n) on carbon or oxygen nuclei in this range become feasible, which should lead to improved reference calibration conditions in neutron fields produced by a deuterium ion beam.
MeSH term(s)	Radiation Dosage ; Equipment Design ; Neutrons ; Calibration
Language	English
Publishing date	2023-10-24
Publishing country	England
Document type	Journal Article
ZDB-ID	225912-6
ISSN	1742-3406 ; 0144-8420
ISSN (online)	1742-3406
ISSN	0144-8420
DOI	10.1093/rpd/ncac256
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Article: Staphylococcus aureus

Petit, Robert A / Read, Timothy D

PeerJ

2018 Volume 6, Page(s) e5261

Abstract: Low-cost Illumina sequencing of clinically-important bacterial pathogens has generated thousands of publicly available genomic datasets. Analyzing these genomes and extracting relevant information for each pathogen and the associated clinical phenotypes ... ...

Abstract	Low-cost Illumina sequencing of clinically-important bacterial pathogens has generated thousands of publicly available genomic datasets. Analyzing these genomes and extracting relevant information for each pathogen and the associated clinical phenotypes requires not only resources and bioinformatic skills but organism-specific knowledge. In light of these issues, we created Staphopia, an analysis pipeline, database and application programming interface, focused on
Language	English
Publishing date	2018-07-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.5261
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Article ; Online: Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes

Rohan S Mehta / Robert A Petit / Timothy D Read / Daniel B Weissman

BMC Bioinformatics, Vol 24, Iss 1, Pp 1-

2023 Volume 16

Abstract: Abstract Bacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecting coevolving genes from large ... ...

Abstract	Abstract Bacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecting coevolving genes from large datasets of bacterial genomes based on pairwise comparisons of closely related individuals, analogous to a pedigree study in eukaryotic populations. We apply our method to pairs of genes from the Staphylococcus aureus accessory genome of over 75,000 annotated gene families using a database of over 40,000 whole genomes. We find many pairs of genes that appear to be gained or lost in a coordinated manner, as well as pairs where the gain of one gene is associated with the loss of the other. These pairs form networks of rapidly coevolving genes, primarily consisting of genes involved in virulence, mechanisms of horizontal gene transfer, and antibiotic resistance, particularly the SCCmec complex. While we focus on gene gain and loss, our method can also detect genes that tend to acquire substitutions in tandem, or genotype-phenotype or phenotype-phenotype coevolution. Finally, we present the R package DeCoTUR that allows for the computation of our method.
Keywords	Genomics ; Genetic interaction ; Horizontal gene transfer ; Staphylococcus aureus ; Software ; Microbial genomics ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Staphylococcus aureus viewed from the perspective of 40,000+ genomes

Robert A. Petit III / Timothy D. Read

PeerJ, Vol 6, p e

2018 Volume 5261

Abstract	Low-cost Illumina sequencing of clinically-important bacterial pathogens has generated thousands of publicly available genomic datasets. Analyzing these genomes and extracting relevant information for each pathogen and the associated clinical phenotypes requires not only resources and bioinformatic skills but organism-specific knowledge. In light of these issues, we created Staphopia, an analysis pipeline, database and application programming interface, focused on Staphylococcus aureus, a common colonizer of humans and a major antibiotic-resistant pathogen responsible for a wide spectrum of hospital and community-associated infections. Written in Python, Staphopia’s analysis pipeline consists of submodules running open-source tools. It accepts raw FASTQ reads as an input, which undergo quality control filtration, error correction and reduction to a maximum of approximately 100× chromosome coverage. This reduction significantly reduces total runtime without detrimentally affecting the results. The pipeline performs de novo assembly-based and mapping-based analysis. Automated gene calling and annotation is performed on the assembled contigs. Read-mapping is used to call variants (single nucleotide polymorphisms and insertion/deletions) against a reference S. aureus chromosome (N315, ST5). We ran the analysis pipeline on more than 43,000 S. aureus shotgun Illumina genome projects in the public European Nucleotide Archive database in November 2017. We found that only a quarter of known multi-locus sequence types (STs) were represented but the top 10 STs made up 70% of all genomes. methicillin-resistant S. aureus (MRSA) were 64% of all genomes. Using the Staphopia database we selected 380 high quality genomes deposited with good metadata, each from a different multi-locus ST, as a non-redundant diversity set for studying S. aureus evolution. In addition to answering basic science questions, Staphopia could serve as a potential platform for rapid clinical diagnostics of S. aureus isolates in the future. The system ...
Keywords	Database ; MSSA ; MRSA ; Antibiotic resistance ; MLST ; S. aureus ; Medicine ; R ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2018-07-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Accelerating bioinformatics implementation in public health.

Libuit, Kevin G / Doughty, Emma L / Otieno, James R / Ambrosio, Frank / Kapsak, Curtis J / Smith, Emily A / Wright, Sage M / Scribner, Michelle R / Petit Iii, Robert A / Mendes, Catarina Inês / Huergo, Marcela / Legacki, Gregory / Loreth, Christine / Park, Daniel J / Sevinsky, Joel R

Microbial genomics

2023 Volume 9, Issue 7

Abstract: We have adopted an open bioinformatics ecosystem to address the challenges of bioinformatics implementation in public health laboratories (PHLs). Bioinformatics implementation for public health requires practitioners to undertake standardized ... ...

Abstract	We have adopted an open bioinformatics ecosystem to address the challenges of bioinformatics implementation in public health laboratories (PHLs). Bioinformatics implementation for public health requires practitioners to undertake standardized bioinformatic analyses and generate reproducible, validated and auditable results. It is essential that data storage and analysis are scalable, portable and secure, and that implementation of bioinformatics fits within the operational constraints of the laboratory. We address these requirements using Terra, a web-based data analysis platform with a graphical user interface connecting users to bioinformatics analyses without the use of code. We have developed bioinformatics workflows for use with Terra that specifically meet the needs of public health practitioners. These Theiagen workflows perform genome assembly, quality control, and characterization, as well as construction of phylogeny for insights into genomic epidemiology. Additonally, these workflows use open-source containerized software and the WDL workflow language to ensure standardization and interoperability with other bioinformatics solutions, whilst being adaptable by the user. They are all open source and publicly available in Dockstore with the version-controlled code available in public GitHub repositories. They have been written to generate outputs in standardized file formats to allow for further downstream analysis and visualization with separate genomic epidemiology software. Testament to this solution meeting the requirements for bioinformatic implementation in public health, Theiagen workflows have collectively been used for over 5 million sample analyses in the last 2 years by over 90 public health laboratories in at least 40 different countries. Continued adoption of technological innovations and development of further workflows will ensure that this ecosystem continues to benefit PHLs.
MeSH term(s)	Public Health ; Ecosystem ; Software ; Computational Biology/methods ; Genomics
Language	English
Publishing date	2023-07-20
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	2835258-0
ISSN	2057-5858 ; 2057-5858
ISSN (online)	2057-5858
ISSN	2057-5858
DOI	10.1099/mgen.0.001051
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