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, http://dx.doi.org/10.1007/978-3-642-38922-1_167

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, http://dx.doi.org/10.1016/B978-0-12-397169-2.00065-2

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, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000278637000016&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a

Journal articles

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, vol. 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, vol. 11, http://dx.doi.org/10.1128/spectrum.03014-22

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, vol. 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, vol. 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, vol. 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, vol. 820, pp. 153286, 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, vol. 209, pp. 117941, 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, vol. 11, 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, vol. 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, vol. 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, vol. 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', Methods Mol Biol, vol. 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, vol. 7, 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, vol. 7, 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, vol. 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, vol. 93, pp. 104970, 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, vol. 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, vol. 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, vol. 6, pp. e0013421, 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, vol. 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, vol. 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, vol. 11, pp. 660280, 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, vol. 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, vol. 12, pp. 625821, 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, vol. 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, vol. 7, 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, vol. 7, 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, vol. 7, 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, vol. 7, http://dx.doi.org/10.1099/MGEN.0.000310

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, http://dx.doi.org/10.1099/mgen.0.000457

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, http://dx.doi.org/10.1073/pnas.2006730117

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, http://dx.doi.org/10.3389/fmicb.2020.02068

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, http://dx.doi.org/10.3389/fcimb.2020.00452

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, http://dx.doi.org/10.1016/j.epidem.2020.100388

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, http://dx.doi.org/10.1093/cid/ciz642

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, 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, vol. 22, pp. 708 - 719, http://dx.doi.org/10.1016/j.jmoldx.2020.02.006

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, http://dx.doi.org/10.3390/pathogens9030195

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, http://dx.doi.org/10.1016/j.vaccine.2019.10.062

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, http://dx.doi.org/10.1128/mSystems.00799-19

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, http://dx.doi.org/10.1128/AEM.02002-20

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

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, http://dx.doi.org/10.1186/s12864-019-6399-1

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, http://dx.doi.org/10.1038/s41598-019-46831-3

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