Select Publications

Book Chapters

Lan R; Octavia S, 2018, 'Vaccine driven selection and the changing molecular epidemiology of Bordetella pertussis', in Rohani P; Scarpino S (ed.), Pertussis Epidemiology, Immunology, and Evolution, Oxford University Press, USA, pp. 166 - 180

Octavia S; Lan R, 2015, 'Chapter 65 Shigella and Shigellosis Genetics, Epidemiology and Pathogenesis', in Molecular Medical Microbiology, pp. 1147 - 1168,

Octavia S; Lan R, 2014, 'The Family Enterobacteriaceae', in DeLong EF; Lory S; Stackebrandt E; Thompson F (ed.), The Prokaryotes, Springer, pp. 225 - 286,

Octavia S; Lan R, 2014, 'Shigella and Shigellosis: Genetics, Epidemiology and Pathogenesis', in Tang Y-W; Sussman M; Liu D; Poxton I; Schwartzman J (ed.), Molecular Medical Microbiology, Three-Volume Set, Academic Press, pp. 1147 - 1168,

Lan R; Reeves PR, 2007, 'Amplified Fragment Length Polymorphism Analysis of Salmonella enterica', in Schatten H; Eisenstark A (ed.), Methods in Molecular Biology, vol. 394: Salmonella: Methods and Protocols, Humana Press, Totawa, Netherlands, pp. 119 - 132

Lan R; Reeves PR, 2006, 'Evolution of Enteric Pathogens', in Seifert HS; DiRita VJ (ed.), Evolution of Microbial Pathogens, ASM Press, Washington, DC, pp. 273,

Journal articles

Wang Y; Luo L; Ji S; Li Q; Wang H; Zhang Z; Mao P; Sun H; Li L; Wang Y; Xu J; Lan R; Ye C, 2022, 'Dissecting Listeria monocytogenes Persistent Contamination in a Retail Market Using Whole-Genome Sequencing', MICROBIOLOGY SPECTRUM,

Xu Z; Hu D; Wai Luu LD; Octavia S; Keil AD; Sintchenko V; Tanaka MM; Mooi FR; Robson J; Lan R, 2022, 'Genomic dissection of the microevolution of Australian epidemic Bordetella pertussis.', Emerg Microbes Infect, pp. 1 - 122,

Fu S; Wang Q; Wang R; Zhang Y; Lan R; He F; Yang Q, 2022, 'Horizontal transfer of antibiotic resistance genes within the bacterial communities in aquacultural environment', Science of the Total Environment, vol. 820, pp. 153286,

Fu S; Yang Q; Sheng Y; Wang Q; Wu J; Qiu Z; Lan R; Wang Y; Liu Y, 2022, 'Metagenomics combined with comprehensive validation as a public health risk assessment tool for urban and agricultural run-off', Water Research, vol. 209, pp. 117941,

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, vol. 11,

Luu LDW; Lan R, 2022, 'Rapid Surface Shaving for Proteomic Identification of Novel Surface Antigens for Vaccine Development', Methods Mol Biol, vol. 2414, pp. 47 - 62,

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, vol. 11, pp. 1873,

Safarchi A; Saedi S; Octavia S; Sedaghatpour M; Bolourchi N; Tay CY; Lamichhane B; Shahcheraghi F; Lan R, 2021, 'Evolutionary genomics of recent clinical Bordetella pertussis isolates from Iran: wide circulation of multiple ptxP3 lineages and report of the first ptxP3 filamentous hemagglutinin-negative B. pertussis', Infection, Genetics and Evolution, vol. 93, pp. 104970,

Liu L; Zhang L; Zhou H; Yuan M; Hu D; Wang Y; Sun H; Xu J; Lan R, 2021, 'Antimicrobial Resistance and Molecular Characterization of Citrobacter spp. Causing Extraintestinal Infections', Frontiers in Cellular and Infection Microbiology, vol. 11,

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, vol. 82, pp. 319 - 333,

Cheney L; Payne M; Kaur S; Lan R, 2021, 'Multilevel genome typing describes short- And long-term vibrio cholerae molecular epidemiology', mSystems, vol. 6, pp. e0013421,

Liu L; Song L; Deng R; Lan R; Jin W; Tran Van Nhieu G; Cao H; Liu Q; Xiao Y; Li X; Meng G; Ren Z, 2021, 'Citrobacter freundii Activation of NLRP3 Inflammasome via the Type VI Secretion System', Journal of Infectious Diseases, vol. 223, pp. 2174 - 2185,

Zhu W; Yang J; Lu S; Lan R; Jin D; Luo XL; Pu J; Wu S; Xu J, 2021, 'Beta- and Novel Delta-Coronaviruses Are Identified from Wild Animals in the Qinghai-Tibetan Plateau, China', Virologica Sinica, vol. 36, pp. 402 - 411,

Luu LDW; Zhong L; Kaur S; Raftery MJ; Lan R, 2021, 'Comparative Phosphoproteomics of Classical Bordetellae Elucidates the Potential Role of Serine, Threonine and Tyrosine Phosphorylation in Bordetella Biology and Virulence', Frontiers in Cellular and Infection Microbiology, vol. 11, pp. 660280,

Wang X; Zhou H; Du P; Lan R; Chen D; Dong A; Lin X; Qiu X; Xu S; Ji X; Li M; Hou X; Sun L; Li D; Han L; Li Z, 2021, 'Genomic epidemiology of Corynebacterium striatum from three regions of China: an emerging national nosocomial epidemic', Journal of Hospital Infection, vol. 110, pp. 67 - 75,

Yu K; Huang Z; Li Y; Fu Q; Lin L; Wu S; Dai H; Cai H; Xiao Y; Lan R; Wang D, 2021, 'Establishment and Application of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry for Detection of Shewanella Genus', Frontiers in Microbiology, vol. 12, pp. 625821,

Fu S; Yang Q; Wang Q; Pang B; Lan R; Wei D; Qu B; Liu Y, 2021, 'Continuous genomic surveillance monitored the in vivo evolutionary trajectories of vibrio parahaemolyticus and identified a new virulent genotype', mSystems, vol. 6,

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, vol. 7,

Luo L; Wang H; Payne MJ; 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, vol. 7,

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, vol. 7,

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, vol. 7,

Liu F; Chen S; Luu LDW; Lee SA; Tay ACY; Wu R; Riordan SM; Lan R; Liu L; Zhang L, 2020, 'Analysis of complete Campylobacter concisus genomes identifies genomospecies features, secretion systems and novel plasmids and their association with severe ulcerative colitis', Microbial Genomics,

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', ,

Sy BM; Lan R; Tree JJ, 2020, 'Early termination of the Shiga toxin transcript generates a regulatory small RNA', Proceedings of the National Academy of Sciences of the United States of America, vol. 117, pp. 25055 - 25065,

Gong L; Tang N; Chen D; Sun K; Lan R; Zhang W; Zhou H; Yuan M; Chen X; Zhao X; Che J; Bai X; Zhang Y; Xu H; Walsh TR; Lu J; Xu J; Li J; Feng J, 2020, 'A Nosocomial Respiratory Infection Outbreak of Carbapenem-Resistant Escherichia coli ST131 With Multiple Transmissible blaKPC–2 Carrying Plasmids', Frontiers in Microbiology, vol. 11,

Luo Y; Huang C; Ye J; Octavia S; Wang H; Dunbar SA; Jin D; Tang YW; Lan R, 2020, 'Comparison of xMAP Salmonella Serotyping Assay With Traditional Serotyping and Discordance Resolution by Whole Genome Sequencing', Frontiers in Cellular and Infection Microbiology, vol. 10,

Jayasundara D; Lee E; Octavia S; Lan R; Tanaka MM; Wood JG, 2020, 'Emergence of pertactin-deficient pertussis strains in Australia can be explained by models of vaccine escape', Epidemics, vol. 31, pp. 100388,

Fu S; Yang Q; He F; Lan R; Hao J; Ni P; Liu Y; Li R, 2020, 'National safety survey of animal-use commercial probiotics and their spillover effects from farm to humans: An emerging threat to public health', Clinical Infectious Diseases, vol. 70, pp. 2386 - 2395,

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, vol. 25,

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, vol. 22, pp. 708 - 719,

Liu L; Qin L; Hao S; Lan R; Xu B; Guo Y; Jiang R; Sun H; Chen X; Lv X; Xu J; Zhao C, 2020, 'Lineage, antimicrobial resistance and virulence of citrobacter spp', Pathogens, vol. 9,

Luu LDW; Octavia S; Aitken C; Zhong L; Raftery MJ; Sintchenko V; Lan R, 2020, 'Surfaceome analysis of Australian epidemic Bordetella pertussis reveals potential vaccine antigens', Vaccine, vol. 38, pp. 539 - 548,

Fu S; Wei D; Yang Q; Xie G; Pang B; Wang Y; Lan R; Wang Q; Dong X; Zhang X; Huang J; Feng J; Liu Y, 2020, 'Horizontal plasmid transfer promotes the dissemination of Asian acute hepatopancreatic necrosis disease and provides a novel mechanism for genetic exchange and environmental adaptation', mSystems, vol. 5,

Loo SL; Ong A; Kyaw W; Thibaut LM; Lan R; Tanaka MM, 2020, 'Nonsynonymous Polymorphism Counts in Bacterial Genomes: a Comparative Examination', Applied and Environmental Microbiology, vol. 87, pp. 1 - 16,

Wang Y; Luo L; Li Q; Wang H; Wang Y; Sun H; Xu J; Lan R; Ye C, 2019, 'Genomic dissection of the most prevalent Listeria monocytogenes clone, sequence type ST87, in China', BMC Genomics, vol. 20, pp. 1014,

Liu S; Feng J; Pu J; Xu X; Lu S; Yang J; Wang Y; Jin D; Du X; Meng X; Luo X; Sun H; Xiong Y; Ye C; Lan R; Xu J, 2019, 'Genomic and molecular characterisation of Escherichia marmotae from wild rodents in Qinghai-Tibet plateau as a potential pathogen', Scientific Reports, vol. 9, pp. 10619,

Wang M; Du P; Wang J; Lan R; Huang J; Luo M; Jiang Y; Zeng J; Quan Y; Shi Z; Zheng H, 2019, 'Genomic epidemiology of Streptococcus suis sequence type 7 sporadic infections in the Guangxi Zhuang Autonomous Region of China', Pathogens, vol. 8,

Fu S; Hao J; Yang Q; Lan R; Wang Y; Ye S; Liu Y; Li R, 2019, 'Long-distance transmission of pathogenic Vibrio species by migratory waterbirds: a potential threat to the public health', Scientific Reports, vol. 9,

Xu X; Zhang H; Huang Y; Zhang Y; Wu C; Gao P; Teng Z; Luo X; Peng X; Wang X; Wang D; Pu J; Zhao H; Lu X; Lu S; Ye C; Dong Y; Lan R; Xu J, 2019, 'Beyond a Ribosomal RNA Methyltransferase, the Wider Role of MraW in DNA Methylation, Motility and Colonization in Escherichia coli O157:H7', Frontiers in Microbiology, vol. 10,

Kamachi K; Otsuka N; Fumimoto R; Ozawa K; Yao SM; Chiang CS; Luu LDW; Lan R; Shibayama K; Watanabe M, 2019, 'A novel multilocus variable-number tandem repeat analysis for Bordetella parapertussis', Journal of medical microbiology, vol. 68, pp. 1671 - 1676,

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, vol. 19, pp. 893,

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, vol. 25, pp. 1196 - 1199,

Gan L; Cao X; Wang Y; Wang Y; Jiang H; Lan R; Xu J; Ye C, 2019, 'Carriage and potential long distance transmission of Listeria monocytogenes by migratory black-headed gulls in Dianchi Lake, Kunming', Emerging Microbes and Infections, vol. 8, pp. 1195 - 1204,

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, vol. 8, pp. 461 - 470,

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