By Professor Ruiting Lan

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, Elsevier, pp. 1147 - 1168, http://dx.doi.org/10.1016/b978-0-12-397169-2.00065-2

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

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

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.', J Clin Microbiol, pp. e0117824, http://dx.doi.org/10.1128/jcm.01178-24

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

Yang C; Lan R; Zhao L; Pu J; Hu D; Yang J; Zhou H; Han L; Ye L; Jin D; Xu J; Liu L, 2024, 'Prevotella copri alleviates hyperglycemia and regulates gut microbiota and metabolic profiles in mice', mSystems, 9, http://dx.doi.org/10.1128/msystems.00532-24

Fu S; Wang Q; Wang R; Zhang Y; Lan R; He F; Yang Q, 2024, 'Corrigendum to “Horizontal transfer of antibiotic resistance genes within the bacterial communities in aquacultural environment” [Sci. Total Environ. 820 (2022) 153286] (Science of the Total Environment (2022) 820, (S0048969722003771), (10.1016/j.scitotenv.2022.153286))', Science of the Total Environment, 922, http://dx.doi.org/10.1016/j.scitotenv.2024.171434

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

Yu K; Huang Z; Lan R; Morris JG; Xiao Y; Fu S; Gao H; Bai X; Li K; Wang D, 2023, 'Genomic Characteristion of Opportunistic Pathogen Kluyvera Reveals a Novel CTX-M Subgroup', Microorganisms, 11, http://dx.doi.org/10.3390/microorganisms11122836

Lee SA; Liu F; Yuwono C; Phan M; Chong S; Biazik J; Tay ACY; Janitz M; Riordan SM; Lan R; Wehrhahn MC; Zhang L, 2023, 'Emerging Aeromonas enteric infections: their association with inflammatory bowel disease and novel pathogenic mechanisms', Microbiology Spectrum, 11, http://dx.doi.org/10.1128/spectrum.01088-23

Xu M; Lan R; Qiao L; Lin X; Hu D; Zhang S; Yang J; Zhou J; Ren Z; Li X; Liu G; Liu L; Xu J, 2023, 'Bacteroides vulgatus Ameliorates Lipid Metabolic Disorders and Modulates Gut Microbial Composition in Hyperlipidemic Rats', Microbiology Spectrum, 11, http://dx.doi.org/10.1128/spectrum.02517-22

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

Suyama H; Luu LDW; Zhong L; Raftery MJ; Lan R, 2023, 'Integrating proteomic data with metabolic modeling provides insight into key pathways of Bordetella pertussis biofilms', Frontiers in Microbiology, 14, http://dx.doi.org/10.3389/fmicb.2023.1169870

Huang Z; Yu K; Lan R; Glenn Morris J; Xiao Y; Ye J; Zhang L; Luo L; Gao H; Bai X; Wang D, 2023, 'Vibrio metschnikovii as an emergent pathogen: analyses of phylogeny and O-antigen and identification of possible virulence characteristics', Emerging Microbes and Infections, 12, http://dx.doi.org/10.1080/22221751.2023.2252522

Liu L; Xu M; Lan R; Hu D; Li X; Qiao L; Zhang S; Lin X; Yang J; Ren Z; Xu J, 2022, 'Bacteroides vulgatus attenuates experimental mice colitis through modulating gut microbiota and immune responses', Frontiers in Immunology, 13, http://dx.doi.org/10.3389/fimmu.2022.1036196

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

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, 10, http://dx.doi.org/10.1128/spectrum.00185-22

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, 820, http://dx.doi.org/10.1016/j.scitotenv.2022.153286

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, 209, http://dx.doi.org/10.1016/j.watres.2021.117941

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, 11, pp. 772574, http://dx.doi.org/10.3389/fcimb.2021.772574

Liang J; Zhu Z; Lan R; Meng J; Vrancken B; Lu S; Jin D; Yang J; Wang J; Qin T; Pu J; Zhang L; Dong K; Xu M; Tian H; Jiang T; Xu J, 2022, 'Evolutionary and genomic insights into the long-term colonization of Shigella flexneri in animals', Emerging Microbes and Infections, 11, pp. 2069 - 2079, http://dx.doi.org/10.1080/22221751.2022.2109514

Xu Z; Hu D; Luu LDW; 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', Emerging Microbes and Infections, 11, pp. 1460 - 1473, http://dx.doi.org/10.1080/22221751.2022.2077129

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

Luu LDW; Lan R, 2022, 'Rapid Surface Shaving for Proteomic Identification of Novel Surface Antigens for Vaccine Development', , 2414, pp. 47 - 62, http://dx.doi.org/10.1007/978-1-0716-1900-1_4

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. 2021.01.30.428723, 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. 2021.02.01.429068, 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

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, 93, http://dx.doi.org/10.1016/j.meegid.2021.104970

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, 11, http://dx.doi.org/10.3389/fcimb.2021.737636

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

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, 223, pp. 2174 - 2185, http://dx.doi.org/10.1093/infdis/jiaa692

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, 36, pp. 402 - 411, http://dx.doi.org/10.1007/s12250-020-00325-z

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, 11, http://dx.doi.org/10.3389/fcimb.2021.660280

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, 110, pp. 67 - 75, http://dx.doi.org/10.1016/j.jhin.2020.10.005

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, 12, http://dx.doi.org/10.3389/fmicb.2021.625821

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, 6, http://dx.doi.org/10.1128/mSystems.01254-20

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 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, 7, pp. 000710, http://dx.doi.org/10.1099/MGEN.0.000710

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

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