Publications by authors named "Kathryn E Holt"

100Publications

Impact of insertion sequences on convergent evolution of Shigella species.

PLoS Genet 2020 07 9;16(7):e1008931. Epub 2020 Jul 9.

Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia.

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http://dx.doi.org/10.1371/journal.pgen.1008931DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7373316PMC
July 2020

Benchmarking of long-read assemblers for prokaryote whole genome sequencing.

F1000Res 2019 23;8:2138. Epub 2019 Dec 23.

Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia.

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http://dx.doi.org/10.12688/f1000research.21782.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6966772.2PMC
June 2020

Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales.

ISME J 2020 Jul 6;14(7):1713-1730. Epub 2020 Apr 6.

Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK.

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http://dx.doi.org/10.1038/s41396-020-0628-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7305143PMC
July 2020

Identification of loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with .

Microb Genom 2020 03;6(3)

Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia.

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http://dx.doi.org/10.1099/mgen.0.000339DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7200062PMC
March 2020

Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016.

PLoS Negl Trop Dis 2020 02 27;14(2):e0008036. Epub 2020 Feb 27.

Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.

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http://dx.doi.org/10.1371/journal.pntd.0008036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7064254PMC
February 2020

Population genomics of Klebsiella pneumoniae.

Nat Rev Microbiol 2020 06 13;18(6):344-359. Epub 2020 Feb 13.

Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia.

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http://dx.doi.org/10.1038/s41579-019-0315-1DOI Listing
June 2020

Persistent circulation of a fluoroquinolone-resistant Salmonella enterica Typhi clone in the Indian subcontinent.

J Antimicrob Chemother 2020 02;75(2):337-341

Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, OX3 7LE, UK.

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http://dx.doi.org/10.1093/jac/dkz435DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223262PMC
February 2020

Systems biology and big data in asthma and allergy: recent discoveries and emerging challenges.

Eur Respir J 2020 01 9;55(1). Epub 2020 Jan 9.

Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia.

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http://dx.doi.org/10.1183/13993003.00844-2019DOI Listing
January 2020

Complete Genome Sequence of A388, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 1 Isolate from Greece.

Microbiol Resour Announc 2019 Oct 10;8(41). Epub 2019 Oct 10.

School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia

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http://dx.doi.org/10.1128/MRA.00971-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6787325PMC
October 2019

Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers.

PLoS Negl Trop Dis 2019 09 12;13(9):e0007620. Epub 2019 Sep 12.

Gastrointestinal Bacteria Reference Unit, Bacteriology Reference Department, National Infection Service, Public Health England, London, United Kingdom.

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http://dx.doi.org/10.1371/journal.pntd.0007620DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6741848PMC
September 2019

Z/I1 Hybrid Virulence Plasmids Carrying Antimicrobial Resistance genes in Typhimurium from Australian Food Animal Production.

Microorganisms 2019 Aug 29;7(9). Epub 2019 Aug 29.

Asia Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3052, Australia.

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http://dx.doi.org/10.3390/microorganisms7090299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6780720PMC
August 2019

Performance of neural network basecalling tools for Oxford Nanopore sequencing.

Genome Biol 2019 06 24;20(1):129. Epub 2019 Jun 24.

Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, 3004, Australia.

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http://dx.doi.org/10.1186/s13059-019-1727-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6591954PMC
June 2019

Empirical ways to identify novel Bedaquiline resistance mutations in AtpE.

PLoS One 2019 29;14(5):e0217169. Epub 2019 May 29.

Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria, Australia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0217169PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6541270PMC
January 2020

Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198.

Microb Genom 2019 07 20;5(7). Epub 2019 May 20.

Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella , World Health Organization Collaborative Centre for the Typing and Antibiotic Resistance of Salmonella , Institut Pasteur, 75015 Paris, France.

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http://dx.doi.org/10.1099/mgen.0.000269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6700661PMC
July 2019

hicap: Serotyping of the Haemophilus influenzae Capsule Locus.

J Clin Microbiol 2019 06 24;57(6). Epub 2019 May 24.

Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia.

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http://dx.doi.org/10.1128/JCM.00190-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6535587PMC
June 2019

Convergence of virulence and MDR in a single plasmid vector in MDR Klebsiella pneumoniae ST15.

J Antimicrob Chemother 2019 05;74(5):1218-1222

Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway.

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http://dx.doi.org/10.1093/jac/dkz028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6477991PMC
May 2019

Co-circulation of Multidrug-resistant Shigella Among Men Who Have Sex With Men in Australia.

Clin Infect Dis 2019 10;69(9):1535-1544

Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne.

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http://dx.doi.org/10.1093/cid/ciz005DOI Listing
October 2019

Small IncQ1 and Col-Like Plasmids Harboring and Non-Tn Elements (NTE-IId) in High-Risk Lineages of CG258.

Antimicrob Agents Chemother 2019 03 26;63(3). Epub 2019 Feb 26.

Department of Clinical Analysis, School of Pharmacy, Universidade de São Paulo, São Paulo, Brazil

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http://dx.doi.org/10.1128/AAC.02140-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6395902PMC
March 2019

Complete Genome Sequence of WM99c, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 2 (GC2) Strain Representing an Australian GC2 Lineage.

Microbiol Resour Announc 2018 Dec 6;7(22). Epub 2018 Dec 6.

School of Life and Environmental Sciences, University of Sydney, Sydney, Australia.

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http://dx.doi.org/10.1128/MRA.01199-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6284088PMC
December 2018

Comment on: CG258 Klebsiella pneumoniae isolates without β-lactam resistance at the onset of the carbapenem-resistant Enterobacteriaceae epidemic in New York City.

J Antimicrob Chemother 2019 03;74(3):831-833

Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia.

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http://dx.doi.org/10.1093/jac/dky472DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6376848PMC
March 2019

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa.

Nat Commun 2018 11 30;9(1):5094. Epub 2018 Nov 30.

The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quant 5, Ho Chi Minh City, Vietnam.

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http://www.nature.com/articles/s41467-018-07370-z
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http://dx.doi.org/10.1038/s41467-018-07370-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6269545PMC
November 2018

Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307.

J Antimicrob Chemother 2019 03;74(3):577-581

Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia.

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http://dx.doi.org/10.1093/jac/dky492DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6376852PMC
March 2019

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks.

PLoS Comput Biol 2018 11 20;14(11):e1006583. Epub 2018 Nov 20.

Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia.

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http://dx.plos.org/10.1371/journal.pcbi.1006583
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http://dx.doi.org/10.1371/journal.pcbi.1006583DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6245502PMC
November 2018

Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae.

Genome Med 2018 10 29;10(1):77. Epub 2018 Oct 29.

Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia.

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https://genomemedicine.biomedcentral.com/articles/10.1186/s1
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http://dx.doi.org/10.1186/s13073-018-0587-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6205773PMC
October 2018

Airway Microbiota Dynamics Uncover a Critical Window for Interplay of Pathogenic Bacteria and Allergy in Childhood Respiratory Disease.

Cell Host Microbe 2018 09;24(3):341-352.e5

Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia; Telethon Kids Institute, The University of Western Australia, West Perth, WA, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia; The Alan Turing Institute, London, UK. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2018.08.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6291254PMC
September 2018

FastSpar: rapid and scalable correlation estimation for compositional data.

Bioinformatics 2019 03;35(6):1064-1066

Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia.

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http://dx.doi.org/10.1093/bioinformatics/bty734DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6419895PMC
March 2019

Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating.

Trends Microbiol 2018 12 20;26(12):1008-1021. Epub 2018 Jul 20.

Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia; The London School of Hygiene and Tropical Medicine, London, United Kingdom.

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http://dx.doi.org/10.1016/j.tim.2018.06.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6249986PMC
December 2018

Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination.

Nat Commun 2018 07 13;9(1):2703. Epub 2018 Jul 13.

Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia.

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http://dx.doi.org/10.1038/s41467-018-05114-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6045662PMC
July 2018

Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods.

BMC Evol Biol 2018 06 19;18(1):95. Epub 2018 Jun 19.

Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3020, Australia.

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http://dx.doi.org/10.1186/s12862-018-1210-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6006949PMC
June 2018

Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria.

Curr Opin Microbiol 2018 10 1;45:131-139. Epub 2018 May 1.

Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3010, Australia.

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http://dx.doi.org/10.1016/j.mib.2018.04.004DOI Listing
October 2018

Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes.

J Clin Microbiol 2018 06 25;56(6). Epub 2018 May 25.

Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria, Australia.

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http://dx.doi.org/10.1128/JCM.00197-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5971559PMC
June 2018

Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection.

Microb Genom 2018 03 16;4(3). Epub 2018 Mar 16.

1​Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.

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http://www.microbiologyresearch.org/content/journal/mgen/10.
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http://dx.doi.org/10.1099/mgen.0.000165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5885017PMC
March 2018

Multidrug-resistant Shigella sonnei carrying the plasmid-mediated mcr-1 gene in China.

Int J Antimicrob Agents 2018 Jul 28;52(1):14-21. Epub 2018 Feb 28.

Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China. Electronic address:

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http://dx.doi.org/10.1016/j.ijantimicag.2018.02.019DOI Listing
July 2018

Completing bacterial genome assemblies with multiplex MinION sequencing.

Microb Genom 2017 10 14;3(10):e000132. Epub 2017 Sep 14.

Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville Victoria 3010, Australia.

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http://dx.doi.org/10.1099/mgen.0.000132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5695209PMC
October 2017

Corrigendum: serotyping of from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages.

Microb Genom 2017 07 1;3(7):e000109. Epub 2017 Aug 1.

3​Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.

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http://dx.doi.org/10.1099/mgen.0.000109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5605953PMC
July 2017

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.

PLoS Comput Biol 2017 Jun 8;13(6):e1005595. Epub 2017 Jun 8.

Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia.

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http://dx.doi.org/10.1371/journal.pcbi.1005595DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5481147PMC
June 2017

The diversity of surface polysaccharides.

Microb Genom 2016 08 25;2(8):e000073. Epub 2016 Aug 25.

2​The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1099/mgen.0.000073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320592PMC
August 2016

Repeated local emergence of carbapenem-resistant in a single hospital ward.

Microb Genom 2016 03 2;2(3):e000050. Epub 2016 Mar 2.

1​Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.

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http://dx.doi.org/10.1099/mgen.0.000050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320574PMC
March 2016

Identification of capsule synthesis loci from whole genome data.

Microb Genom 2016 12 12;2(12):e000102. Epub 2016 Dec 12.

2​Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia.

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http://dx.doi.org/10.1099/mgen.0.000102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5359410PMC
December 2016

Genome-scale rates of evolutionary change in bacteria.

Microb Genom 2016 11 30;2(11):e000094. Epub 2016 Nov 30.

1​Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.

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http://dx.doi.org/10.1099/mgen.0.000094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320706PMC
November 2016

Variants of AbGRI3 carrying the armA gene in extensively antibiotic-resistant Acinetobacter baumannii from Singapore.

J Antimicrob Chemother 2017 04;72(4):1031-1039

School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia.

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http://dx.doi.org/10.1093/jac/dkw542DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5400096PMC
April 2017

Prediction of antibiotic resistance from antibiotic resistance genes detected in antibiotic-resistant commensal Escherichia coli using PCR or WGS.

J Antimicrob Chemother 2017 03;72(3):700-704

School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia.

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http://dx.doi.org/10.1093/jac/dkw511DOI Listing
March 2017

Are Pathotypes Still Relevant in the Era of Whole-Genome Sequencing?

Front Cell Infect Microbiol 2016 18;6:141. Epub 2016 Nov 18.

Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne Parkville, VIC, Australia.

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http://dx.doi.org/10.3389/fcimb.2016.00141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5114240PMC
September 2017

Erratum: Global phylogeography and evolutionary history of Shigella dysenteriae type 1.

Nat Microbiol 2016 10 3;1(11):16209. Epub 2016 Oct 3.

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http://dx.doi.org/10.1038/nmicrobiol.2016.209DOI Listing
October 2016

Klebsiella pneumoniae Population Genomics and Antimicrobial-Resistant Clones.

Trends Microbiol 2016 12 11;24(12):944-956. Epub 2016 Oct 11.

Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.tim.2016.09.007DOI Listing
December 2016

Vitamin D over the first decade and susceptibility to childhood allergy and asthma.

J Allergy Clin Immunol 2017 02 7;139(2):472-481.e9. Epub 2016 Oct 7.

Telethon Kids Institute, University of Western Australia, Perth, Australia; University of Queensland, Brisbane, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.jaci.2016.07.032DOI Listing
February 2017

Microbial mercury methylation in Antarctic sea ice.

Nat Microbiol 2016 08 1;1(10):16127. Epub 2016 Aug 1.

School of Earth Sciences, University of Melbourne, Parkville, Victoria 3010, Australia.

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http://dx.doi.org/10.1038/nmicrobiol.2016.127DOI Listing
August 2016

Global phylogeography and evolutionary history of Shigella dysenteriae type 1.

Nat Microbiol 2016 03 21;1:16027. Epub 2016 Mar 21.

Institut Pasteur, Unité des Bactéries Pathogènes Entériques, 75724 Paris Cedex 15, France.

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http://dx.doi.org/10.1038/nmicrobiol.2016.27DOI Listing
March 2016

A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets.

Cell Syst 2016 07;3(1):71-82

Centre for Systems Genomics, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Pathology, The University of Melbourne, Parkville, VIC 3010, Australia; School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2016.06.012DOI Listing
July 2016

The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia.

PLoS Negl Trop Dis 2016 06 22;10(6):e0004785. Epub 2016 Jun 22.

The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.

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http://dx.doi.org/10.1371/journal.pntd.0004785DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4917249PMC
June 2016

Inducible colistin resistance via a disrupted plasmid-borne mcr-1 gene in a 2008 Vietnamese Shigella sonnei isolate.

J Antimicrob Chemother 2016 08 30;71(8):2314-7. Epub 2016 May 30.

Centre for Systems Genomics, The University of Melbourne, Melbourne, Australia Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Australia.

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http://dx.doi.org/10.1093/jac/dkw173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4954929PMC
August 2016

Cross-validation to select Bayesian hierarchical models in phylogenetics.

BMC Evol Biol 2016 05 26;16(1):115. Epub 2016 May 26.

Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.

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http://dx.doi.org/10.1186/s12862-016-0688-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4880944PMC
May 2016

Comparative genomics of Crohn's disease-associated adherent-invasive .

Gut 2017 08 20;66(8):1382-1389. Epub 2016 Apr 20.

Medical School, Australian National University, Canberra, Australian Capital Territory, Australia.

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http://dx.doi.org/10.1136/gutjnl-2015-311059DOI Listing
August 2017

The genomic signatures of Shigella evolution, adaptation and geographical spread.

Nat Rev Microbiol 2016 Apr 29;14(4):235-50. Epub 2016 Feb 29.

The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam.

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http://dx.doi.org/10.1038/nrmicro.2016.10DOI Listing
April 2016

pCERC3 from a commensal ST95 Escherichia coli: A ColV virulence-multiresistance plasmid carrying a sul3-associated class 1 integron.

Plasmid 2016 Mar-May;84-85:11-9. Epub 2016 Feb 18.

School of Life and Environmental Sciences, The University of Sydney, NSW, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.plasmid.2016.02.002DOI Listing
March 2017

Genome Sequence of Acinetobacter baumannii Strain D36, an Antibiotic-Resistant Isolate from Lineage 2 of Global Clone 1.

Genome Announc 2015 Dec 17;3(6). Epub 2015 Dec 17.

School of Molecular Bioscience, The University of Sydney, Sydney, Australia

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http://dx.doi.org/10.1128/genomeA.01478-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4683233PMC
December 2015

Multiple Genetic Mutations Associated with Polymyxin Resistance in Acinetobacter baumannii.

Antimicrob Agents Chemother 2015 Dec 5;59(12):7899-902. Epub 2015 Oct 5.

Yong Loo Lin School of Medicine, National University Health System, Singapore Saw Swee Hock School of Public Health, National University Health System, Singapore

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http://dx.doi.org/10.1128/AAC.01884-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4649193PMC
December 2015

A small Acinetobacter plasmid carrying the tet39 tetracycline resistance determinant.

J Antimicrob Chemother 2016 Jan 27;71(1):269-71. Epub 2015 Sep 27.

School of Molecular Bioscience, The University of Sydney, NSW 2006, Australia.

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http://dx.doi.org/10.1093/jac/dkv293DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681370PMC
January 2016

Draft Genome Sequence of a Clinical Isolate of Serratia marcescens, Strain AH0650_Sm1.

Genome Announc 2015 Sep 3;3(5). Epub 2015 Sep 3.

Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria, Australia Centre for Systems Genomics, University of Melbourne, Victoria, Australia

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http://genomea.asm.org/content/3/5/e01007-15.full.pdf
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http://genomea.asm.org/lookup/doi/10.1128/genomeA.01007-15
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http://dx.doi.org/10.1128/genomeA.01007-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4559744PMC
September 2015

ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data.

BMC Genomics 2015 Sep 3;16:667. Epub 2015 Sep 3.

Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia.

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http://dx.doi.org/10.1186/s12864-015-1860-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4558774PMC
September 2015

Bandage: interactive visualization of de novo genome assemblies.

Bioinformatics 2015 Oct 22;31(20):3350-2. Epub 2015 Jun 22.

Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne and.

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http://dx.doi.org/10.1093/bioinformatics/btv383DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595904PMC
October 2015

Genomic resistance island AGI1 carrying a complex class 1 integron in a multiply antibiotic-resistant ST25 Acinetobacter baumannii isolate.

J Antimicrob Chemother 2015 Sep 28;70(9):2519-23. Epub 2015 May 28.

School of Molecular Bioscience, The University of Sydney, NSW 2006, Australia

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http://dx.doi.org/10.1093/jac/dkv137DOI Listing
September 2015

Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events.

Nat Genet 2015 Jun 11;47(6):632-9. Epub 2015 May 11.

Wellcome Trust Sanger Institute, Hinxton, UK.

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http://dx.doi.org/10.1038/ng.3281DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4921243PMC
June 2015

A platform for leveraging next generation sequencing for routine microbiology and public health use.

Health Inf Sci Syst 2015 24;3(Suppl 1 HISA Big Data in Biomedicine and Healthcare 2013 Con):S7. Epub 2015 Feb 24.

Department of Biochemistry and Molecular Biology and Bio21 MolecularScience and Biotechnology Institute, The University of Melbourne, Parkville VIC 3010, Victoria, Australia.

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http://dx.doi.org/10.1186/2047-2501-3-S1-S7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383055PMC
April 2015

The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development.

Cell Host Microbe 2015 May 9;17(5):704-15. Epub 2015 Apr 9.

Medical Systems Biology, Department of Pathology and Department of Microbiology & Immunology, The University of Melbourne, Parkville, VIC 3010, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2015.03.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4433433PMC
May 2015