By Dr Michael Payne

Journal articles

Bandaranayake S; Williamson S; Stewart J; Payne M; Kaur S; Pavic A; Lan R, 2025, 'Comparative genomic analysis of Salmonella enterica serovar Typhimurium isolates from the chicken production chain and table egg livestock in New South Wales, Australia', Food Microbiology, 132, http://dx.doi.org/10.1016/j.fm.2025.104855

Luu LDW; Rafique R; Payne M; Octavia S; Robson J; Sintchenko V; Lan R, 2024, 'Deciphering Bordetella pertussis epidemiology through culture-independent multiplex amplicon and metagenomic sequencing', Journal of Clinical Microbiology, 62, http://dx.doi.org/10.1128/jcm.01178-24

Luo Y; Payne M; Kaur S; Octavia S; Lan R, 2024, 'Genomic evidence of two-staged transmission of the early seventh cholera pandemic', Nature Communications, 15, http://dx.doi.org/10.1038/s41467-024-52800-w

Okoh EB; Payne M; Lan R; Riegler M; Chapman TA; Bogema DR, 2024, 'A Multilocus Sequence Typing Scheme for Rapid Identification of Xanthomonas citri Based on Whole-Genome Sequencing Data', Phytopathology, 114, pp. 1480 - 1489, http://dx.doi.org/10.1094/PHYTO-12-23-0490-R

Payne M; Hu D; Wang Q; Sullivan G; Graham RM; Rathnayake IU; Jennison AV; Sintchenko V; Lan R, 2024, 'DODGE: automated point source bacterial outbreak detection using cumulative long term genomic surveillance', Bioinformatics, 40, http://dx.doi.org/10.1093/bioinformatics/btae427

Payne M; Williamson S; Wang Q; Zhang X; Sintchenko V; Pavic A; Lan R, 2024, 'Emergence of Poultry-Associated Human Salmonella enterica Serovar Abortusovis Infections, New South Wales, Australia', Emerging Infectious Diseases, 30, pp. 691 - 700, http://dx.doi.org/10.3201/eid3004.230958

Wu R; Payne M; Zhang L; Lan R, 2024, 'Uncovering the boundaries of Campylobacter species through large-scale phylogenetic and nucleotide identity analyses', Msystems, 9, http://dx.doi.org/10.1128/msystems.01218-23

Bandaranayake S; Williamson S; Stewart J; Payne M; Kaur S; Wang Q; Sintchenko V; Pavic A; Lan R, 2024, 'Genomic diversity of Salmonella enterica serovar Typhimurium isolated from chicken processing facilities in New South Wales, Australia', Frontiers in Microbiology, 15, http://dx.doi.org/10.3389/fmicb.2024.1440777

Cheney L; Payne M; Kaur S; Lan R, 2024, 'SaLTy: a novel Staphylococcus aureus Lineage Typer', Microbial Genomics, 10, http://dx.doi.org/10.1099/mgen.0.001250

Luo Y; Payne M; Kaur S; Octavia S; Jiang J; Lan R, 2023, 'Emergence and genomic insights of non-pandemic O1 Vibrio cholerae in Zhejiang, China', Microbiology Spectrum, 11, http://dx.doi.org/10.1128/spectrum.02615-23

Luo L; Payne M; Wang Q; Kaur S; Rathnayake IU; Graham R; Gall M; Draper J; Martinez E; Octavia S; Tanaka MM; Jennison AV; Sintchenko V; Lan R, 2023, 'Genomic Epidemiology and Multilevel Genome Typing of Australian Salmonella enterica Serovar Enteritidis', Microbiology Spectrum, 11, http://dx.doi.org/10.1128/spectrum.03014-22

Payne M; Xu Z; Hu D; Kaur S; Octavia S; Sintchenko V; Lan R, 2023, 'Genomic epidemiology and multilevel genome typing of Bordetella pertussis', Emerging Microbes and Infections, 12, http://dx.doi.org/10.1080/22221751.2023.2239945

Luo Y; Ye J; Payne M; Hu D; Jiang J; Lan R, 2022, 'Genomic Epidemiology of Vibrio cholerae O139, Zhejiang Province, China, 1994–2018', Emerging Infectious Diseases, 28, pp. 2253 - 2260, http://dx.doi.org/10.3201/eid2811.212066

Zhang X; Payne M; Kaur S; Lan R, 2022, 'Improved Genomic Identification, Clustering, and Serotyping of Shiga Toxin-Producing Escherichia coli Using Cluster/Serotype-Specific Gene Markers', Frontiers in Cellular and Infection Microbiology, 11, pp. 772574, http://dx.doi.org/10.3389/fcimb.2021.772574

Kaur S; Payne M; Luo L; Octavia S; Tanaka MM; Sintchenko V; Lan R, 2022, 'MGTdb: A web service and database for studying the global and local genomic epidemiology of bacterial pathogens', Database, 2022, http://dx.doi.org/10.1093/database/baac094

Zhang X; Payne M; Nguyen T; Kaur S; Lan R, 2021, 'Cluster-specific gene markers enhance Shigella and Enteroinvasive Escherichia coli in silico serotyping', Microbial Genomics, 7, pp. 000704, http://dx.doi.org/10.1099/mgen.0.000704

Luo L; Wang H; Payne M; Liang C; Bai L; Zheng H; Zhang Z; Zhang L; Zhang X; yan G; Zou N; Chen X; Wan Z; Xiong Y; Lan R; Li Q, 2021, 'Comparative genomics of Chinese and international isolates of Escherichia albertii: population structure and evolution of virulence and antimicrobial resistance', Microbial Genomics, 7, pp. 000710, http://dx.doi.org/10.1099/mgen.0.000710

Luu LDW; Payne M; Zhang X; Luo L; Lan R, 2021, 'Development and comparison of novel multiple cross displacement amplification (MCDA) assays with other nucleic acid amplification methods for SARS-CoV-2 detection', Scientific Reports, 11, pp. 1873, http://dx.doi.org/10.1038/s41598-021-81518-8

Luo Y; Wang H; Liang J; Qian H; Ye J; Chen L; Yang X; Chen Z; Wang F; Octavia S; Payne M; Song X; Jiang J; Jin D; Lan R, 2021, 'Population Structure and Multidrug Resistance of Non-O1/Non-O139 Vibrio cholerae in Freshwater Rivers in Zhejiang, China', Microbial Ecology, 82, pp. 319 - 333, http://dx.doi.org/10.1007/s00248-020-01645-z

Cheney L; Payne M; Kaur S; Lan R, 2021, 'Multilevel genome typing describes short- And long-term vibrio cholerae molecular epidemiology', Msystems, 6, pp. 10.1128/msystems.00134 - 10.1128/msystems.00121, http://dx.doi.org/10.1128/mSystems.00134-21

Zhang X; Payne M; Nguyen T; Kaur S; Lan R, 2021, 'Cluster-specific gene markers enhance Shigella and Enteroinvasive Escherichia coli in silico serotyping', , pp. 2021.01.30.428723, http://dx.doi.org/10.1101/2021.01.30.428723

Luo L; Payne M; Kaur S; Hu D; Cheney L; Octavia S; Wang Q; Tanaka MM; Sintchenko V; Lan R, 2021, 'Elucidation of global and national genomic epidemiology of salmonella enterica serovar enteritidis through multilevel genome typing', Microbial Genomics, 7, pp. 000605, http://dx.doi.org/10.1099/MGEN.0.000605

Payne M; Octavia S; Luu LDW; Sotomayor-Castillo C; Wang Q; Tay ACY; Sintchenko V; Tanaka MM; Lan R, 2021, 'Enhancing genomics-based outbreak detection of endemic salmonella enterica serovar typhimurium using dynamic thresholds', Microbial Genomics, 7, pp. 000310, http://dx.doi.org/10.1099/MGEN.0.000310

Payne M; Kaur S; Wang Q; Hennessy D; Luo L; Octavia S; Tanaka MM; Sintchenko V; Lan R, 2020, 'Multilevel genome typing: Genomics-guided scalable resolution typing of microbial pathogens', Eurosurveillance, 25, pp. 1900519, http://dx.doi.org/10.2807/1560-7917.ES.2020.25.20.1900519

Zhang X; Payne M; Wang Q; Sintchenko V; Lan R, 2020, 'Highly Sensitive and Specific Detection and Serotyping of Five Prevalent Salmonella Serovars by Multiple Cross-Displacement Amplification', Journal of Molecular Diagnostics, 22, pp. 708 - 719, http://dx.doi.org/10.1016/j.jmoldx.2020.02.006

Luo L; Chen X; Payne M; Cao X; Wang Y; Zhang J; Deng J; Wang H; Zhang Z; Li Q; Lan R; Ye C, 2019, 'Case report: Whole genome sequencing based investigation of maternal-neonatal listeriosis in Sichuan, China', BMC Infectious Diseases, 19, pp. 893, http://dx.doi.org/10.1186/s12879-019-4551-9

Xu Z; Octavia S; Luu LDW; Payne M; Timms V; Tay CY; Keil AD; Sintchenko V; Guiso N; Lan R, 2019, 'Pertactin-negative and filamentous hemagglutinin-negative Bordetella pertussis, Australia, 2013-2017', Emerging Infectious Diseases, 25, pp. 1196 - 1199, http://dx.doi.org/10.3201/eid2506.180240

Payne M; Weerasinghe H; Tedja I; Andrianopoulos A, 2019, 'A unique aspartyl protease gene expansion in Talaromyces marneffei plays a role in growth inside host phagocytes', Virulence, 10, pp. 277 - 291, http://dx.doi.org/10.1080/21505594.2019.1593776

Xu Z; Wang Z; Luan Y; Li Y; Liu X; Peng X; Octavia S; Payne M; Lan R, 2019, 'Genomic epidemiology of erythromycin-resistant Bordetella pertussis in China', Emerging Microbes and Infections, 8, pp. 461 - 470, http://dx.doi.org/10.1080/22221751.2019.1587315

Zhang X; Payne M; Lan R, 2019, 'In silico identification of serovar-specific genes for salmonella serotyping', Frontiers in Microbiology, 10, pp. 835, http://dx.doi.org/10.3389/fmicb.2019.00835

Weerasinghe H; Payne M; Beard S; Andrianopoulos A, 2016, 'Organism-wide studies into pathogenicity and morphogenesis in Talaromyces marneffei', Future Microbiology, 11, pp. 511 - 526, http://dx.doi.org/10.2217/fmb.16.9

Pasricha S; Payne M; Canovas D; Pase L; Ngaosuwankul N; Beard S; Oshlack A; Smyth GK; Chaiyaroj SC; Boyce KJ; Andrianopoulos A, 2013, 'Cell-type-specific transcriptional profiles of the dimorphic pathogen penicillium marneffei reflect distinct reproductive, morphological, and environmental demands', G3 Genes Genomes Genetics, 3, pp. 1997 - 2014, http://dx.doi.org/10.1534/g3.113.006809

Bugeja HE; Boyce KJ; Weerasinghe H; Beard S; Jeziorowski A; Pasricha S; Payne M; Schreider L; Andrianopoulos A, 2012, 'Tools for high efficiency genetic manipulation of the human pathogen Penicillium marneffei', Fungal Genetics and Biology, 49, pp. 772 - 778, http://dx.doi.org/10.1016/j.fgb.2012.08.003

Boyce KJ; Bugeja HE; Weerasinghe H; Payne MJ; Schreider L, 2012, 'Strategies for the molecular genetic manipulation and visualization of the human fungal pathogen Penicillium marneffei', Fungal Genetics Reports, 59, pp. 1 - 12, http://dx.doi.org/10.4148/1941-4765.1009

Conference Papers

Andrianopoulos A; Weerasinghe H; Payne M, 2018, 'Morphological and metabolic adaptation to environmental conditions by Talaromyces marneffei and its role in the host.', in MEDICAL MYCOLOGY, OXFORD UNIV PRESS, pp. S63 - S63, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000434852700347&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Preprints

Kaur S; Payne M; Partridge S; Sintchenko V; Lan R, 2024, A dissection of the genomic antimicrobial resistance epidemiology ofSalmonellaTyphimurium, http://dx.doi.org/10.1101/2024.05.12.593721

Cheney L; Payne M; Kaur S; McKew G; Lan R, 2024, CharacterisingStaphylococcus aureusgenomic epidemiology with Multilevel Genome Typing, http://dx.doi.org/10.1101/2024.05.09.593273

Payne M; Hu D; Wang Q; Sullivan G; Graham R; Rathnayake I; Jennison A; Sintchenko V; Lan R, 2024, DODGE: Automated point source bacterial outbreak detection using cumulative long term genomic surveillance, http://dx.doi.org/10.1101/2024.01.21.24301506

Payne M; Xu Z; Hu D; Kaur S; Octavia S; Sintchenko V; Lan R, 2023, Genomic epidemiology and multilevel genome typing ofBordetella pertussis, http://dx.doi.org/10.1101/2023.04.26.538362

Cheney L; Payne M; Kaur S; Lan R, 2023, SaLTy: a novelStaphylococcus aureusLineage Typer, http://dx.doi.org/10.1101/2023.02.03.527095

Luo L; Payne M; Wang Q; Kaur S; Rathnayake I; Graham R; Gall M; Draper J; Martinez E; Octavia S; Tanaka M; Jennison A; Sintchenko V; Lan R, 2022, Genomic epidemiology and multilevel genome typing of Australian Salmonella enterica serovar Enteritidis, http://dx.doi.org/10.1101/2022.05.18.492204

Kaur S; Payne M; Luo L; Octavia S; Tanaka M; Sintchenko V; Lan R, 2022, MGTdb: A web service and database for studying the global and local genomic epidemiology of bacterial pathogens, http://dx.doi.org/10.1101/2022.06.14.496187

Zhang X; Payne M; Nguyen T; Kaur S; Lan R, 2021, Cluster-specific gene markers enhance Shigella and Enteroinvasive Escherichia coli in silico serotyping, http://dx.doi.org/10.1101/2021.01.30.428723

Luo L; Wang H; Payne M; Liang C; Bai L; Zheng H; Zhang Z; Zhang L; Zhang X; yan G; Zou N; Chen X; Wan Z; Xiong Y; Lan R; Li Q, 2021, Comparative genomics of Chinese and international isolates of Escherichia albertii: population structure and evolution of virulence and antimicrobial resistance, http://dx.doi.org/10.1101/2021.02.01.429068

Wai Luu LD; Payne M; Zhang X; Luo L; Lan R, 2020, Development and comparison of a novel multiple cross displacement amplification (MCDA) assay with other nucleic acid amplification methods for SARS-CoV-2 detection, http://dx.doi.org/10.1101/2020.10.03.20206193

Luo L; Payne M; Kaur S; Hu D; Cheney L; Octavia S; Wang Q; Tanaka M; Sintchenko V; Lan R, 2020, Elucidation of global and local genomic epidemiology ofSalmonella entericaserovar Enteritidis through multilevel genome typing, http://dx.doi.org/10.1101/2020.06.30.169953

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