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Article ; Online: AusTrakka

Tuyet Hoang / Anders Gonçalves da Silva / Amy V. Jennison / Deborah A. Williamson / Benjamin P. Howden / Torsten Seemann

Nature Communications, Vol 13, Iss 1, Pp 1-

Fast-tracking nationalized genomics surveillance in response to the COVID-19 pandemic

2022 Volume 4

Abstract: The COVID-19 pandemic has accelerated the demand for near real-time analysis and dissemination of pathogen genomic data. In this comment, the authors describe how Australia has developed and rolled out its SARS-CoV-2 genomics platform, AusTrakka, and ... ...

Abstract	The COVID-19 pandemic has accelerated the demand for near real-time analysis and dissemination of pathogen genomic data. In this comment, the authors describe how Australia has developed and rolled out its SARS-CoV-2 genomics platform, AusTrakka, and used it to support public health action.
Keywords	Science ; Q
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Niche-specific genome degradation and convergent evolution shaping Staphylococcus aureus adaptation during severe infections

Stefano G Giulieri / Romain Guérillot / Sebastian Duchene / Abderrahman Hachani / Diane Daniel / Torsten Seemann / Joshua S Davis / Steven YC Tong / Bernadette C Young / Daniel J Wilson / Timothy P Stinear / Benjamin P Howden

eLife, Vol

2022 Volume 11

Abstract: During severe infections, Staphylococcus aureus moves from its colonising sites to blood and tissues and is exposed to new selective pressures, thus, potentially driving adaptive evolution. Previous studies have shown the key role of the agr locus in S. ... ...

Abstract	During severe infections, Staphylococcus aureus moves from its colonising sites to blood and tissues and is exposed to new selective pressures, thus, potentially driving adaptive evolution. Previous studies have shown the key role of the agr locus in S. aureus pathoadaptation; however, a more comprehensive characterisation of genetic signatures of bacterial adaptation may enable prediction of clinical outcomes and reveal new targets for treatment and prevention of these infections. Here, we measured adaptation using within-host evolution analysis of 2590 S. aureus genomes from 396 independent episodes of infection. By capturing a comprehensive repertoire of single nucleotide and structural genome variations, we found evidence of a distinctive evolutionary pattern within the infecting populations compared to colonising bacteria. These invasive strains had up to 20-fold enrichments for genome degradation signatures and displayed significantly convergent mutations in a distinctive set of genes, linked to antibiotic response and pathogenesis. In addition to agr-mediated adaptation, we identified non-canonical, genome-wide significant loci including sucA-sucB and stp1. The prevalence of adaptive changes increased with infection extent, emphasising the clinical significance of these signatures. These findings provide a high-resolution picture of the molecular changes when S. aureus transitions from colonisation to severe infection and may inform correlation of infection outcomes with adaptation signatures.
Keywords	within-host evolution ; adaptation ; Staphylococcus aureus ; genomics ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	572
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Optimising genomic approaches for identifying vancomycin-resistant Enterococcus faecium transmission in healthcare settings

Charlie Higgs / Norelle L. Sherry / Torsten Seemann / Kristy Horan / Hasini Walpola / Paul Kinsella / Katherine Bond / Deborah A. Williamson / Caroline Marshall / Jason C. Kwong / M. Lindsay Grayson / Timothy P. Stinear / Claire L. Gorrie / Benjamin P. Howden

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 11

Abstract: Vancomycin-resistant Enterococcus faecium is an important healthcare-associated pathogen and genomic analyses could inform targeted interventions. Here, the authors optimise an analysis pipeline for identification of putative transmission events using ... ...

Abstract	Vancomycin-resistant Enterococcus faecium is an important healthcare-associated pathogen and genomic analyses could inform targeted interventions. Here, the authors optimise an analysis pipeline for identification of putative transmission events using core genome multilocus sequence type clustering and split kmer analysis.
Keywords	Science ; Q
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Correspondence

Ian R. Monk / Benjamin P. Howden / Torsten Seemann / Timothy P. Stinear

Nature Communications, Vol 8, Iss 1, Pp 1-

Spontaneous secondary mutations confound analysis of the essential two-component system WalKR in Staphylococcus aureus

2017 Volume 4

Keywords	Science ; Q
Language	English
Publishing date	2017-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genomic Evidence of In-Flight SARS-CoV-2 Transmission, India to Australia, April 2021

Emerging Infectious Diseases, Vol 28, Iss 7, Pp 1527-

2022 Volume 1530

Abstract: Epidemiologic and genomic investigation of SARS-CoV-2 infections associated with 2 repatriation flights from India to Australia in April 2021 indicated that 4 passengers transmitted SARS-CoV-2 to >11 other passengers. Results suggest transmission despite ...

Abstract	Epidemiologic and genomic investigation of SARS-CoV-2 infections associated with 2 repatriation flights from India to Australia in April 2021 indicated that 4 passengers transmitted SARS-CoV-2 to >11 other passengers. Results suggest transmission despite mandatory mask use and predeparture testing. For subsequent flights, predeparture quarantine and expanded predeparture testing were implemented.
Keywords	COVID-19 ; 2019 novel coronavirus disease ; coronavirus disease ; severe acute respiratory syndrome coronavirus 2 ; SARS-CoV-2 ; viruses ; Medicine ; R ; Infectious and parasitic diseases ; RC109-216
Language	English
Publishing date	2022-07-01T00:00:00Z
Publisher	Centers for Disease Control and Prevention
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Multi-site implementation of whole genome sequencing for hospital infection control

Norelle L. Sherry / Claire L. Gorrie / Jason C. Kwong / Charlie Higgs / Rhonda L. Stuart / Caroline Marshall / Susan A. Ballard / Michelle Sait / Tony M. Korman / Monica A. Slavin / Robyn S. Lee / Maryza Graham / Marcel Leroi / Leon J. Worth / Hiu Tat Chan / Torsten Seemann / M. Lindsay Grayson / Benjamin P. Howden

The Lancet Regional Health. Western Pacific, Vol 23, Iss , Pp 100446- (2022)

A prospective genomic epidemiological analysis

2022

Abstract: Summary: Background: Current microbiological methods lack the resolution to accurately identify multidrug-resistant organism (MDRO) transmission, however, whole genome sequencing can identify highly-related patient isolates providing opportunities for ... ...

Abstract	Summary: Background: Current microbiological methods lack the resolution to accurately identify multidrug-resistant organism (MDRO) transmission, however, whole genome sequencing can identify highly-related patient isolates providing opportunities for precision infection control interventions. We investigated the feasibility and potential impact of a prospective multi-centre genomics workflow for hospital infection control. Methods: We conducted a prospective genomics implementation study across eight Australian hospitals over 15 months (2017,2018), collecting all clinical and screening isolates from inpatients with vanA VRE, MRSA, ESBL Escherichia coli (ESBL-Ec), or ESBL Klebsiella pneumoniae (ESBL-Kp). Genomic and epidemiologic data were integrated to assess MDRO transmission. Findings: In total, 2275 isolates were included from 1970 patients, predominantly ESBL-Ec (40·8%) followed by MRSA (35·6%), vanA VRE (15·2%), and ESBL-Kp (8·3%).Overall, hospital and genomic epidemiology showed 607 patients (30·8%) acquired their MDRO in hospital, including the majority of vanA VRE (266 patients, 86·4%), with lower proportions of ESBL-Ec (186 patients, 23·0%), ESBL-Kp (42 patients, 26·3%), and MRSA (113 patients, 16·3%). Complex patient movements meant the majority of MDRO transmissions would remain undetected without genomic data.The genomics implementation had major impacts, identifying unexpected MDRO transmissions prompting new infection control interventions, and contributing to vanA VRE becoming a notifiable condition. We identified barriers to implementation and recommend strategies for mitigation. Interpretation: Implementation of a multi-centre genomics-informed infection control workflow is feasible and identifies many unrecognised MDRO transmissions. This provides critical opportunities for interventions to improve patient safety in hospitals. Funding: Melbourne Genomics Health Alliance (supported by State Government of Victoria, Australia), and National Health and Medical Research Council (Australia).
Keywords	Antimicrobial resistance ; Whole genome sequencing ; Infection prevention and control ; Hospital epidemiology ; Public aspects of medicine ; RA1-1270
Subject code	360
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Incursions of Candida auris into Australia, 2018

Courtney R. Lane / Torsten Seemann / Leon J. Worth / Marion Easton / William Pitchers / Jenny Wong / Donna Cameron / Francesca Azzato / Richard Bartolo / Cristina Mateevici / Caroline Marshall / Monica A. Slavin / Benjamin P. Howden / Deborah A. Williamson

Emerging Infectious Diseases, Vol 26, Iss 6, Pp 1326-

2020 Volume 1328

Abstract: Candida auris is an emerging global healthcare-associated pathogen. During July–December 2018, four patients with C. auris were identified in Victoria, Australia, all with previous overseas hospitalization. Phylogenetic analysis revealed putative ... ...

Abstract	Candida auris is an emerging global healthcare-associated pathogen. During July–December 2018, four patients with C. auris were identified in Victoria, Australia, all with previous overseas hospitalization. Phylogenetic analysis revealed putative transmission between 2 patients and suspected overseas acquisition in the others. Vigilant screening of at-risk patients is required.
Keywords	antimicrobial resistance ; public health surveillance ; Candida auris ; infection control ; genomics ; fungi ; Medicine ; R ; Infectious and parasitic diseases ; RC109-216
Language	English
Publishing date	2020-06-01T00:00:00Z
Publisher	Centers for Disease Control and Prevention
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Mitochondrial Genome Sequence of the Scabies Mite Provides Insight into the Genetic Diversity of Individual Scabies Infections.

Ehtesham Mofiz / Torsten Seemann / Melanie Bahlo / Deborah Holt / Bart J Currie / Katja Fischer / Anthony T Papenfuss

PLoS Neglected Tropical Diseases, Vol 10, Iss 2, p e

2016 Volume 0004384

Abstract: The scabies mite, Sarcoptes scabiei, is an obligate parasite of the skin that infects humans and other animal species, causing scabies, a contagious disease characterized by extreme itching. Scabies infections are a major health problem, particularly in ... ...

Abstract	The scabies mite, Sarcoptes scabiei, is an obligate parasite of the skin that infects humans and other animal species, causing scabies, a contagious disease characterized by extreme itching. Scabies infections are a major health problem, particularly in remote Indigenous communities in Australia, where co-infection of epidermal scabies lesions by Group A Streptococci or Staphylococcus aureus is thought to be responsible for the high rate of rheumatic heart disease and chronic kidney disease. We collected and separately sequenced mite DNA from several pools of thousands of whole mites from a porcine model of scabies (S. scabiei var. suis) and two human patients (S. scabiei var. hominis) living in different regions of northern Australia. Our sequencing samples the mite and its metagenome, including the mite gut flora and the wound micro-environment. Here, we describe the mitochondrial genome of the scabies mite. We developed a new de novo assembly pipeline based on a bait-and-reassemble strategy, which produced a 14 kilobase mitochondrial genome sequence assembly. We also annotated 35 genes and have compared these to other Acari mites. We identified single nucleotide polymorphisms (SNPs) and used these to infer the presence of six haplogroups in our samples, Remarkably, these fall into two closely-related clades with one clade including both human and pig varieties. This supports earlier findings that only limited genetic differences may separate some human and animal varieties, and raises the possibility of cross-host infections. Finally, we used these mitochondrial haplotypes to show that the genetic diversity of individual infections is typically small with 1-3 distinct haplotypes per infestation.
Keywords	Arctic medicine. Tropical medicine ; RC955-962 ; Public aspects of medicine ; RA1-1270
Language	English
Publishing date	2016-02-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals

Jean-Baptiste Raina / Dianne Tapiolas / Cherie A. Motti / Sylvain Foret / Torsten Seemann / Jan Tebben / Bette L. Willis / David G. Bourne

PeerJ, Vol 4, p e

2016 Volume 2275

Abstract: Bacterial communities associated with healthy corals produce antimicrobial compounds that inhibit the colonization and growth of invasive microbes and potential pathogens. To date, however, bacteria-derived antimicrobial molecules have not been ... ...

Abstract	Bacterial communities associated with healthy corals produce antimicrobial compounds that inhibit the colonization and growth of invasive microbes and potential pathogens. To date, however, bacteria-derived antimicrobial molecules have not been identified in reef-building corals. Here, we report the isolation of an antimicrobial compound produced by Pseudovibrio sp. P12, a common and abundant coral-associated bacterium. This strain was capable of metabolizing dimethylsulfoniopropionate (DMSP), a sulfur molecule produced in high concentrations by reef-building corals and playing a role in structuring their bacterial communities. Bioassay-guided fractionation coupled with nuclear magnetic resonance (NMR) and mass spectrometry (MS), identified the antimicrobial as tropodithietic acid (TDA), a sulfur-containing compound likely derived from DMSP catabolism. TDA was produced in large quantities by Pseudovibrio sp., and prevented the growth of two previously identified coral pathogens, Vibrio coralliilyticus and V. owensii, at very low concentrations (0.5 μg/mL) in agar diffusion assays. Genome sequencing of Pseudovibrio sp. P12 identified gene homologs likely involved in the metabolism of DMSP and production of TDA. These results provide additional evidence for the integral role of DMSP in structuring coral-associated bacterial communities and underline the potential of these DMSP-metabolizing microbes to contribute to coral disease prevention.
Keywords	Coral-associated bacteria ; Disease ; Alphaproteobacteria ; Antimicrobial compounds ; Medicine ; R ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2016-08-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Key parameters for genomics-based real-time detection and tracking of multidrug-resistant bacteria

Claire L Gorrie, PhD / Anders Gonçalves Da Silva, PhD / Danielle J Ingle, PhD / Charlie Higgs, BSc / Torsten Seemann, PhD / Timothy P Stinear, ProfPhD / Deborah A Williamson, ProfPhD / Jason C Kwong, PhD / M Lindsay Grayson, MD / Norelle L Sherry, MBBS / Benjamin P Howden, ProfPhD

The Lancet Microbe, Vol 2, Iss 11, Pp e575-e

a systematic analysis

2021 Volume 583

Abstract: Summary: Background: Pairwise single nucleotide polymorphisms (SNPs) are a cornerstone of genomic approaches to the inference of transmission of multidrug-resistant (MDR) organisms in hospitals. However, the impact of many key analytical approaches on ... ...

Abstract	Summary: Background: Pairwise single nucleotide polymorphisms (SNPs) are a cornerstone of genomic approaches to the inference of transmission of multidrug-resistant (MDR) organisms in hospitals. However, the impact of many key analytical approaches on these inferences has not yet been systematically assessed. This study aims to make such a systematic assessment. Methods: We conducted a 15-month prospective study (2-month pilot phase, 13-month implementation phase), across four hospital networks including eight hospitals in Melbourne, VIC, Australia. Patient clinical and screening samples containing one or more isolates of meticillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus faecium, and extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae were collected and underwent whole genome sequencing. Using the genome data from the top four most numerous sequence types from each species, 16 in total, we systematically assessed the: (1) impact of sample and reference genome diversity through multiple core genome alignments using different data subsets and reference genomes, (2) effect of masking of prophage and regions of recombination in the core genome alignments by assessing SNP distances before and after masking, (3) differences between a cumulative versus a 3-month sliding-window approach to sample genome inclusion in the dataset over time, and (4) the comparative effects each of these approaches had when applying a previously defined SNP threshold for inferring likely transmission. Findings: 2275 samples were collected (397 during the pilot phase from April 4 to June 18, 2017; 1878 during the implementation phase from Oct 30, 2017, to Nov 30, 2018) from 1870 patients. Of these 2275 samples, 1537 were identified as arising from the four most numerous sequence types from each of the four target species of MDR organisms in this dataset (16 sequence types in total: S aureus ST5, ST22, ST45, and ST93; E faecium ST80, ST203, ST1421, and ST1424; K pneumoniae ST15, ST17, ...
Keywords	Medicine (General) ; R5-920 ; Microbiology ; QR1-502
Subject code	571
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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