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Artikel ; Online: The Scourge of Antibiotic-resistant Infections in Cystic Fibrosis.

Price, Erin P / Sarovich, Derek S

2019 Band 27, Heft 4, Seite(n) 289–291

Abstract: Bacterial infections are the primary cause of respiratory decline and mortality in cystic fibrosis (CF) patients. In a recent study, Diaz Caballero and colleagues [1] (PLoS Pathog. 2018;14:e1007453) catalogued the molecular adaptation of a decade-long ... ...

Abstract	Bacterial infections are the primary cause of respiratory decline and mortality in cystic fibrosis (CF) patients. In a recent study, Diaz Caballero and colleagues [1] (PLoS Pathog. 2018;14:e1007453) catalogued the molecular adaptation of a decade-long Burkholderia multivorans infection in a Canadian CF patient, which evolved to become resistant towards multiple classes of antibiotics.
Mesh-Begriff(e)	Anti-Bacterial Agents ; Burkholderia ; Burkholderia Infections ; Canada ; Cystic Fibrosis ; Drug Resistance, Bacterial/drug effects ; Genome-Wide Association Study ; Humans ; Recombination, Genetic
Chemische Substanzen	Anti-Bacterial Agents
Sprache	Englisch
Erscheinungsdatum	2019-01-29
Erscheinungsland	England
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	1158963-2
ISSN	1878-4380 ; 0966-842X
ISSN (online)	1878-4380
ISSN	0966-842X
DOI	10.1016/j.tim.2019.01.003
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Comparative genomics confirms a rare melioidosis human-to-human transmission event and reveals incorrect phylogenomic reconstruction due to polyclonality.

Aziz, Ammar / Currie, Bart J / Mayo, Mark / Sarovich, Derek S / Price, Erin P

Microbial genomics

2020 Band 6, Heft 2

Abstract: Human-to-human transmission of the melioidosis bacterium, ...

Abstract	Human-to-human transmission of the melioidosis bacterium,
Mesh-Begriff(e)	Burkholderia pseudomallei/classification ; Burkholderia pseudomallei/genetics ; Burkholderia pseudomallei/isolation & purification ; Genome, Bacterial ; Genomics ; Genotype ; Humans ; Melioidosis/microbiology ; Melioidosis/transmission ; Multilocus Sequence Typing ; Phylogeny
Sprache	Englisch
Erscheinungsdatum	2020-01-17
Erscheinungsland	England
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2835258-0
ISSN	2057-5858 ; 2057-5858
ISSN (online)	2057-5858
ISSN	2057-5858
DOI	10.1099/mgen.0.000326
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: SPANDx: a genomics pipeline for comparative analysis of large haploid whole genome re-sequencing datasets.

Sarovich, Derek S / Price, Erin P

BMC research notes

2014 Band 7, Seite(n) 618

Abstract: Background: Next-generation sequencing (NGS) is now a commonplace tool for molecular characterisation of virtually any species of interest. Despite the ever-increasing use of NGS in laboratories worldwide, analysis of whole genome re-sequencing (WGS) ... ...

Abstract	Background: Next-generation sequencing (NGS) is now a commonplace tool for molecular characterisation of virtually any species of interest. Despite the ever-increasing use of NGS in laboratories worldwide, analysis of whole genome re-sequencing (WGS) datasets from start to finish remains nontrivial due to the fragmented nature of NGS software and the lack of experienced bioinformaticists in many research teams. Findings: We describe SPANDx (Synergised Pipeline for Analysis of NGS Data in Linux), a new tool for high-throughput comparative analysis of haploid WGS datasets comprising one through thousands of genomes. SPANDx consolidates several well-validated, open-source packages into a single tool, mitigating the need to learn and manipulate individual NGS programs. SPANDx incorporates BWA for alignment of raw NGS reads against a reference genome or pan-genome, followed by data filtering, variant calling and annotation using Picard, GATK, SAMtools and SnpEff. BEDTools has also been included for genetic locus presence/absence (P/A) determination to easily visualise the core and accessory genomes. Additional SPANDx features include construction of error-corrected single-nucleotide polymorphism (SNP) and insertion-deletion matrices, and P/A matrices, to enable user-friendly visualisation of genetic variants. The SNP matrices generated using VCFtools and GATK are directly importable into PAUP, PHYLIP or RAxML for downstream phylogenetic analysis. SPANDx has been developed to handle NGS data from Illumina, Ion Personal Genome Machine (PGM) and 454 platforms, and we demonstrate that it has comparable performance across Illumina MiSeq/HiSeq2000 and Ion PGM data. Conclusion:* SPANDx is an all-in-one tool for comprehensive haploid WGS analysis. SPANDx is open source and is freely available at: http://sourceforge.net/projects/spandx/.
Mesh-Begriff(e)	Genome ; Haploidy ; Phylogeny ; Polymorphism, Single Nucleotide
Sprache	Englisch
Erscheinungsdatum	2014-09-08
Erscheinungsland	England
Dokumenttyp	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2413336-X
ISSN	1756-0500 ; 1756-0500
ISSN (online)	1756-0500
ISSN	1756-0500
DOI	10.1186/1756-0500-7-618
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Loss of Methyltransferase Function and Increased Efflux Activity Leads to Doxycycline Resistance in Burkholderia pseudomallei.

Webb, Jessica R / Price, Erin P / Currie, Bart J / Sarovich, Derek S

Antimicrobial agents and chemotherapy

2017 Band 61, Heft 6

Abstract: The soil-dwelling ... ...

Abstract	The soil-dwelling bacterium
Sprache	Englisch
Erscheinungsdatum	2017-06
Erscheinungsland	United States
Dokumenttyp	Journal Article
ZDB-ID	217602-6
ISSN	1098-6596 ; 0066-4804
ISSN (online)	1098-6596
ISSN	0066-4804
DOI	10.1128/AAC.00268-17
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Genomic diversity and antimicrobial resistance of

Webb, Kasey A / Olagoke, Olusola / Baird, Timothy / Neill, Jane / Pham, Amy / Wells, Timothy J / Ramsay, Kay A / Bell, Scott C / Sarovich, Derek S / Price, Erin P

Microbial genomics

2022 Band 8, Heft 2

Abstract: Cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) are characterized by increasingly frequent acute pulmonary exacerbations that reduce life quality and length. Human airways are home to a rich polymicrobial environment, which includes ...

Abstract	Cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) are characterized by increasingly frequent acute pulmonary exacerbations that reduce life quality and length. Human airways are home to a rich polymicrobial environment, which includes members of the obligately anaerobic genus
Mesh-Begriff(e)	Anti-Bacterial Agents/pharmacology ; Cystic Fibrosis/microbiology ; Drug Resistance, Bacterial/genetics ; Genomics ; Humans ; Lung ; Microbial Sensitivity Tests ; Prevotella/drug effects ; Prevotella/genetics ; Prevotella/isolation & purification ; Pulmonary Disease, Chronic Obstructive/microbiology ; Sputum/microbiology
Chemische Substanzen	Anti-Bacterial Agents
Sprache	Englisch
Erscheinungsdatum	2022-03-25
Erscheinungsland	England
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2835258-0
ISSN	2057-5858 ; 2057-5858
ISSN (online)	2057-5858
ISSN	2057-5858
DOI	10.1099/mgen.0.000754
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Comparative genomics of

Le, Cuong T / Price, Erin P / Sarovich, Derek S / Nguyen, Thu T A / Powell, Daniel / Vu-Khac, Hung / Kurtböke, D İpek / Knibb, Wayne / Chen, Shih-Chu / Katouli, Mohammad

Microbial genomics

2022 Band 8, Heft 7

Abstract: Between 2010 and 2015, nocardiosis outbreaks caused ... ...

Abstract	Between 2010 and 2015, nocardiosis outbreaks caused by
Mesh-Begriff(e)	Animals ; Aquaculture ; Fish Diseases/epidemiology ; Fish Diseases/genetics ; Genomics ; Nocardia ; Nocardia Infections/epidemiology ; Nocardia Infections/veterinary ; Vietnam/epidemiology
Sprache	Englisch
Erscheinungsdatum	2022-07-04
Erscheinungsland	England
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2835258-0
ISSN	2057-5858 ; 2057-5858
ISSN (online)	2057-5858
ISSN	2057-5858
DOI	10.1099/mgen.0.000845
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Express Yourself: Quantitative Real-Time PCR Assays for Rapid Chromosomal Antimicrobial Resistance Detection in Pseudomonas aeruginosa.

Madden, Danielle E / Olagoke, Olusola / Baird, Timothy / Neill, Jane / Ramsay, Kay A / Fraser, Tamieka A / Bell, Scott C / Sarovich, Derek S / Price, Erin P

Antimicrobial agents and chemotherapy

2022 Band 66, Heft 5, Seite(n) e0020422

Abstract: The rise of antimicrobial-resistant (AMR) bacteria is a global health emergency. One critical facet of tackling this epidemic is more rapid AMR diagnosis in serious multidrug-resistant pathogens like Pseudomonas aeruginosa. Here, we designed and then ... ...

Abstract	The rise of antimicrobial-resistant (AMR) bacteria is a global health emergency. One critical facet of tackling this epidemic is more rapid AMR diagnosis in serious multidrug-resistant pathogens like Pseudomonas aeruginosa. Here, we designed and then validated two multiplex quantitative real-time PCR (qPCR) assays to simultaneously detect differential expression of the resistance-nodulation-division efflux pumps MexAB-OprM, MexCD-OprJ, MexEF-OprN, and MexXY-OprM, the AmpC β-lactamase, and the porin OprD, which are commonly associated with chromosomally encoded AMR. Next, qPCRs were tested on 15 sputa from 11 participants with P. aeruginosa respiratory infections to determine AMR profiles
Mesh-Begriff(e)	Anti-Bacterial Agents/therapeutic use ; Bacterial Outer Membrane Proteins/genetics ; Bacterial Proteins/metabolism ; Carbapenems/therapeutic use ; Cystic Fibrosis/complications ; Drug Resistance, Bacterial ; Humans ; Membrane Transport Proteins/genetics ; Microbial Sensitivity Tests ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa ; Real-Time Polymerase Chain Reaction
Chemische Substanzen	Anti-Bacterial Agents ; Bacterial Outer Membrane Proteins ; Bacterial Proteins ; Carbapenems ; Membrane Transport Proteins
Sprache	Englisch
Erscheinungsdatum	2022-04-25
Erscheinungsland	United States
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	217602-6
ISSN	1098-6596 ; 0066-4804
ISSN (online)	1098-6596
ISSN	0066-4804
DOI	10.1128/aac.00204-22
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: A Persisting Nontropical Focus of Burkholderia pseudomallei with Limited Genome Evolution over Five Decades.

Webb, Jessica R / Buller, Nicky / Rachlin, Audrey / Golledge, Clayton / Sarovich, Derek S / Price, Erin P / Mayo, Mark / Currie, Bart J

mSystems

2020 Band 5, Heft 6

Abstract: Burkholderia ... ...

Abstract	Burkholderia pseudomallei
Sprache	Englisch
Erscheinungsdatum	2020-11-10
Erscheinungsland	United States
Dokumenttyp	Journal Article
ISSN	2379-5077
ISSN	2379-5077
DOI	10.1128/mSystems.00726-20
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Duplex real-time PCR assay for the simultaneous detection of

Price, Erin P / Soler Arango, Valentina / Kidd, Timothy J / Fraser, Tamieka A / Nguyen, Thuy-Khanh / Bell, Scott C / Sarovich, Derek S

Microbial genomics

2020 Band 6, Heft 7

Abstract: Several members of the Gram-negative environmental bacterial ... ...

Abstract	Several members of the Gram-negative environmental bacterial genus
Mesh-Begriff(e)	Achromobacter/classification ; Achromobacter/genetics ; Achromobacter/isolation & purification ; Achromobacter denitrificans/classification ; Achromobacter denitrificans/genetics ; Achromobacter denitrificans/isolation & purification ; Cystic Fibrosis/microbiology ; Early Diagnosis ; Genomics/methods ; Gram-Negative Bacterial Infections/diagnosis ; Gram-Negative Bacterial Infections/microbiology ; Humans ; Multilocus Sequence Typing ; Phenotype ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sputum
Chemische Substanzen	RNA, Ribosomal, 16S
Sprache	Englisch
Erscheinungsdatum	2020-07-15
Erscheinungsland	England
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2835258-0
ISSN	2057-5858 ; 2057-5858
ISSN (online)	2057-5858
ISSN	2057-5858
DOI	10.1099/mgen.0.000406
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Taking the next-gen step: Comprehensive antimicrobial resistance detection from Burkholderia pseudomallei.

Madden, Danielle E / Webb, Jessica R / Steinig, Eike J / Currie, Bart J / Price, Erin P / Sarovich, Derek S

EBioMedicine

2020 Band 63, Seite(n) 103152

Abstract: Background: Antimicrobial resistance (AMR) poses a major threat to human health. Whole-genome sequencing holds great potential for AMR identification; however, there remain major gaps in accurately and comprehensively detecting AMR across the spectrum ... ...

Abstract	Background: Antimicrobial resistance (AMR) poses a major threat to human health. Whole-genome sequencing holds great potential for AMR identification; however, there remain major gaps in accurately and comprehensively detecting AMR across the spectrum of AMR-conferring determinants and pathogens. Methods: Using 16 wild-type Burkholderia pseudomallei and 25 with acquired AMR, we first assessed the performance of existing AMR software (ARIBA, CARD, ResFinder, and AMRFinderPlus) for detecting clinically relevant AMR in this pathogen. B. pseudomallei was chosen due to limited treatment options, high fatality rate, and AMR caused exclusively by chromosomal mutation (i.e. single-nucleotide polymorphisms [SNPs], insertions-deletions [indels], copy-number variations [CNVs], inversions, and functional gene loss). Due to poor performance with existing tools, we developed ARDaP (Antimicrobial Resistance Detection and Prediction) to identify the spectrum of AMR-conferring determinants in B. pseudomallei. Findings: CARD, ResFinder, and AMRFinderPlus failed to identify any clinically-relevant AMR in B. pseudomallei; ARIBA identified AMR encoded by SNPs and indels that were manually added to its database. However, none of these tools identified CNV, inversion, or gene loss determinants, and ARIBA could not differentiate AMR determinants from natural genetic variation. In contrast, ARDaP accurately detected all SNP, indel, CNV, inversion, and gene loss AMR determinants described in B. pseudomallei (n≈50). Additionally, ARDaP accurately predicted three previously undescribed determinants. In mixed strain data, ARDaP identified AMR to as low as ~5% allelic frequency. Interpretation: Existing AMR software packages are inadequate for chromosomal AMR detection due to an inability to detect resistance conferred by CNVs, inversions, and functional gene loss. ARDaP overcomes these major shortcomings. Further, ARDaP enables AMR prediction from mixed sequence data down to 5% allelic frequency, and can differentiate natural genetic variation from AMR determinants. ARDaP databases can be constructed for any microbial species of interest for comprehensive AMR detection. Funding: National Health and Medical Research Council (BJC, EPP, DSS); Australian Government (DEM, ES); Advance Queensland (EPP, DSS).
Mesh-Begriff(e)	Anti-Bacterial Agents/pharmacology ; Burkholderia pseudomallei/drug effects ; Burkholderia pseudomallei/genetics ; Burkholderia pseudomallei/isolation & purification ; Computational Biology/methods ; Drug Resistance, Bacterial ; Genes, Bacterial ; Genome, Bacterial ; Genomics/methods ; Humans ; Melioidosis/drug therapy ; Melioidosis/microbiology ; Microbial Sensitivity Tests ; Mutation ; Sequence Analysis, DNA ; Whole Genome Sequencing
Chemische Substanzen	Anti-Bacterial Agents
Sprache	Englisch
Erscheinungsdatum	2020-12-04
Erscheinungsland	Netherlands
Dokumenttyp	Journal Article
ZDB-ID	2851331-9
ISSN	2352-3964
ISSN (online)	2352-3964
DOI	10.1016/j.ebiom.2020.103152
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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