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

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

Lu Y; Lan R; Fan Q; Tang H; Hu D; Zhang S; Lin X; Wang R; Zhao R; Sun H; Liu L; Xu J, 2025, 'Eubacterium limosum modulates tumor microenvironments and produces antitumor metabolites active against colorectal cancer.', ISME J, http://dx.doi.org/10.1093/ismejo/wraf130

Zhang S; Wang R; Zhao R; Lu Y; Xu M; Lin X; Lan R; Zhang S; Tang H; Fan Q; Yang J; Liu L; Xu J, 2025, 'Alistipes putredinis Ameliorates Metabolic Dysfunction-Associated Steatotic Liver Disease in Rats via Gut Microbiota Remodeling and Inflammatory Suppression', Nutrients, 17, http://dx.doi.org/10.3390/nu17122013

Zhang S; Zhao R; Wang R; Lu Y; Xu M; Lin X; Lan R; Zhang S; Tang H; Fan Q; Yang J; Liu L; Xu J, 2025, 'Weissella viridescens Attenuates Hepatic Injury, Oxidative Stress, and Inflammation in a Rat Model of High-Fat Diet-Induced MASLD', Nutrients, 17, http://dx.doi.org/10.3390/nu17091585

Lin X; Xu M; Lan R; Hu D; Zhang S; Zhang S; Lu Y; Sun H; Yang J; Liu L; Xu J, 2025, 'Gut commensal Alistipes shahii improves experimental colitis in mice with reduced intestinal epithelial damage and cytokine secretion', Msystems, 10, http://dx.doi.org/10.1128/msystems.01607-24

Dewasmika WAPM; Dissanayake DRA; Neelawala NGDAK; Dissanayake BGN; Prasada DVP; Francis VR; Octavia S; Lan R, 2025, 'High Occurrence of ST131 Among Extraintestinal Pathogenic Escherichia coli in Humans and Dogs in Sri Lanka', Zoonoses and Public Health, 72, pp. 200 - 206, http://dx.doi.org/10.1111/zph.13199

Tang H; Fan Q; Lu Y; Lin X; Lan R; Hu D; Zhang S; Wang R; Zhao R; Liu L; Xu J, 2025, 'Weissella confusa alleviates experimental colitis in mice by regulating inflammatory pathways and gut microbiota', Frontiers in Microbiology, 16, http://dx.doi.org/10.3389/fmicb.2025.1574548

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

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. 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

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

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