Ruiting Lan

Professor

Research Contribution

Dr Lan came from a population genetics background and lectured in genetics before doing his PhD in molecular genetics. He combined the two fields in his research on bacterial population structures and evolution of pathogens, making unique contributions to this research field. He has made major advances in the studying of enteric pathogens and evolution of bacterial clones:

Dr Lan initiated the use of genomic subtraction to study genome variation before the genome sequencing era and discovered that horizontal gene transfer is a major factor in bacterial evolution. Although that observation was met with skepticism at the time, the findings have now been confirmed by genome sequence data. Based on that study and genome data he proposed the species genome concept which has been widely cited, and the proposal has been vindicated by microarray studies and rapidly accumulating intraspecies genome data.

His significant work on the origins of Shigella within E. coli resolved the long standing misnomer of Shigella as a separate genus with 4 species. The work was published in the prestigious journal, Proceedings of National Academy of Science, USA, and attracted commentaries in Science and Current Biology. Subsequently he and his colleagues elucidated the relationships of Shigella and enteroinvasive E. coli through a series of studies. His contributions have attracted invitations to write reviews.

Dr Lan work on V. cholerae centered on the origins and evolution of the pandemic clones. He and his colleagues determined the population structure of V. cholerae and recently resolved the relationship of the pandemic clones and their closely related toxigenic isolates. His work on the 7th pandemic clone revealed a temporal pattern of genetic changes during the global spread of the pandemic and showed multiple independent introductions of cholera into Africa during 1970s and 1990s.

Two of his major works on S. enterica were using it as a model organism to study the effect on variation of neighbouring genes by locus under selection pressure for change (the O antigen locus) and to determine the extent of horizontal gene transfer at genome level as discussed above. His studies on serovar Typhimurium, a predominant Salmonella clone, have yielded significant insights into the clone and lay the foundation for the development of a molecular phage typing scheme. His discovery of frequent recombination in subspecies I has a significant impact on our understanding of S. enterica. He also has made contributions in bioinformatics with development of software applications to studying population genetics of bacteria. He maintains two bioinformatics programs MULTICOMP and MLEECOMP, which have been distributed to the research community worldwide.

Professional Experience

  • Postdoc/Research fellow, University of Sydney

Honours & Awards

  • Guest Professor, Chinese Centre for Disease Control and Prevention
  • Division Chair, the Australia Society for Microbiology
  • Fellow of Australian Society for Microbiology
Book Chapters
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Lan R; Octavia S, 2018, 'Vaccine driven selection and the changing molecular epidemiology of Bordetella pertussis', in Rohani P; Scarpino S (ed.), , Oxford University Press, USA, pp. 166 - 180
2018
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
2014
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
2014
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
2007
Lan R; Reeves PR, 2006, 'Evolution of Enteric Pathogens', in Seifert SF; DiRita V (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
2006
Conference Abstracts
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Mahendran V; Lee HY; Tan YS; Riordan SM; Grimm MC; Day AS; Lemberg DA; Octavia S; Lan R; Zhang L, 2013, 'The association between a tight junction toxin gene in Campylobacter concisus and inflammatory bowel disease', in JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, WILEY-BLACKWELL, Vol. 28, pp. 14 - 14, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000324106900026&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
2013
Journal articles
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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
2020
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 : an official publication of the Infectious Diseases Society of America, vol. 70, pp. 2386 - 2395, http://dx.doi.org/10.1093/cid/ciz642
2020
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
2020
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
2020
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
2020
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
2020
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
2020
Payne M; Octavia S; Luu LDW; Sotomayor-Castillo C; Wang Q; Tay ACY; Sintchenko V; Tanaka MM; Lan R, 2019, 'Enhancing genomics-based outbreak detection of endemic Salmonellaenterica serovar Typhimurium using dynamic thresholds.', Microb Genom, http://dx.doi.org/10.1099/mgen.0.000310
2019
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, http://dx.doi.org/10.1186/s12879-019-4551-9
2019
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, http://dx.doi.org/10.1099/jmm.0.001095
2019
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, http://dx.doi.org/10.1038/s41598-019-52791-5
2019
Zhang X; Payne M; Lan R, 2019, 'In silico identification of serovar-specific genes for salmonella serotyping', Frontiers in Microbiology, vol. 10, pp. 835, http://dx.doi.org/10.3389/fmicb.2019.00835
2019
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
2019
Safarchi A; Octavia S; Nikbin VS; Lotfi MN; Zahraei SM; Tay CY; Lamichhane B; Shahcheraghi F; Lan R, 2019, 'Genomic epidemiology of Iranian Bordetella pertussis: 50 years after the implementation of whole cell vaccine', Emerging Microbes and Infections, vol. 8, pp. 1416 - 1427, http://dx.doi.org/10.1080/22221751.2019.1665479
2019
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, http://dx.doi.org/10.3201/eid2506.180240
2019
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, http://dx.doi.org/10.3389/fmicb.2019.02520
2019
Wang X; Zhou H; Chen D; Du P; Lan R; Qiu X; Hou X; Liu Z; Sun L; Xu S; Ji X; Li H; Li D; Zhang J; Zeng H; Li Z, 2019, 'Whole-genome sequencing reveals a prolonged and persistent intrahospital transmission of Corynebacterium striatum, an emerging multidrug-resistant pathogen', Journal of Clinical Microbiology, vol. 57, http://dx.doi.org/10.1128/JCM.00683-19
2019
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
2019
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, http://dx.doi.org/10.3390/pathogens8040187
2019
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, http://dx.doi.org/10.1080/22221751.2019.1647764
2019
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, http://dx.doi.org/10.1080/22221751.2019.1587315
2019
Dhakal R; Wang Q; Lan R; Howard P; Sintchenko V, 2018, 'Novel multiplex PCR assay for identification and subtyping of enteroinvasive escherichia coli and differentiation from shigella based on target genes selected by comparative genomics', Journal of Medical Microbiology, vol. 67, pp. 1257 - 1264, http://dx.doi.org/10.1099/jmm.0.000784
2018
Sotomayor C; Wang Q; Arnott A; Howard P; Hope K; Lan R; Sintchenko V, 2018, 'Novel salmonella enterica serovar typhimurium genotype levels as herald of seasonal salmonellosis epidemics', Emerging Infectious Diseases, vol. 24, pp. 1079 - 1082, http://dx.doi.org/10.3201/eid2406.171096
2018
Luu LDW; Octavia S; Zhong L; Raftery MJ; Sintchenko V; Lan R, 2018, 'Proteomic Adaptation of Australian Epidemic Bordetella pertussis', Proteomics, vol. 18, http://dx.doi.org/10.1002/pmic.201700237
2018
Wai Luu LD; Octavia S; Zhong L; Raftery MJ; Sintchenko V; Lan R, 2018, 'Comparison of the whole cell proteome and secretome of epidemic bordetella pertussis strains from the 2008–2012 Australian epidemic under sulfate-modulating conditions', Frontiers in Microbiology, vol. 9, http://dx.doi.org/10.3389/fmicb.2018.02851
2018
Liu L; Chen D; Liu L; Lan R; Hao S; Jin W; Sun H; Wang Y; Liang Y; Xu J, 2018, 'Genetic diversity, multidrug resistance, and virulence of citrobacter freundii from diarrheal patients and healthy individuals', Frontiers in Cellular and Infection Microbiology, vol. 8, http://dx.doi.org/10.3389/fcimb.2018.00233
2018
Li H; Wang P; Lan R; Luo L; Cao X; Wang Y; Wang Y; Li H; Zhang L; Ji S; Ye C, 2018, 'Risk factors and level of Listeria monocytogenes contamination of raw pork in retail markets in China', Frontiers in Microbiology, vol. 9, http://dx.doi.org/10.3389/fmicb.2018.01090
2018
Liu F; Ma R; Tay CYA; Octavia S; Lan R; Chung HKL; Riordan SM; Grimm MC; Leong RW; Tanaka MM; Connor S; Zhang L, 2018, 'Genomic analysis of oral Campylobacter concisus strains identified a potential bacterial molecular marker associated with active Crohn's disease', Emerging Microbes and Infections, vol. 7, http://dx.doi.org/10.1038/s41426-018-0065-6
2018
Jones M; Octavia S; Lammers G; Heller J; Lan R, 2017, 'Population and evolutionary dynamics of Shiga-toxin producing Escherichia coli O157 in a beef herd: A longitudinal study', Environmental Microbiology, vol. 19, pp. 1836 - 1844, http://dx.doi.org/10.1111/1462-2920.13679
2017
Ahlstrom C; Muellner P; Lammers G; Jones M; Octavia S; Lan R; Heller J, 2017, 'Shiga toxin-producing Escherichia coli O157 shedding dynamics in an Australian beef herd', Frontiers in Veterinary Science, vol. 4, http://dx.doi.org/10.3389/fvets.2017.00200
2017
Chen X; Zhao X; Che J; Xiong Y; Xu Y; Zhang L; Lan R; Xia L; Walsh TR; Xu J; Lu J; Li J, 2017, 'Detection and dissemination of the colistin resistance gene, mcr-1, from isolates and faecal samples in China', Journal of Medical Microbiology, vol. 66, pp. 119 - 125, http://dx.doi.org/10.1099/jmm.0.000425
2017
Luu LDW; Octavia S; Zhong L; Raftery M; Sintchenko V; Lan R, 2017, 'Characterisation of the Bordetella pertussis secretome under different media', Journal of Proteomics, vol. 158, pp. 43 - 51, http://dx.doi.org/10.1016/j.jprot.2017.02.010
2017
Luo L; Zhang Z; Wang H; Wang P; Lan R; Deng J; Miao Y; Wang Y; Wang Y; Xu J; Zhang L; Sun S; Liu X; Zhou Y; Chen X; Li Q; Ye C, 2017, 'A 12-month longitudinal study of Listeria monocytogenes contamination and persistence in pork retail markets in China', Food Control, vol. 76, pp. 66 - 73, http://dx.doi.org/10.1016/j.foodcont.2016.12.037
2017
Fu S; Hiley L; Octavia S; Tanaka MM; Sintchenko V; Lan R, 2017, 'Comparative genomics of Australian and international isolates of Salmonella Typhimurium: Correlation of core genome evolution with CRISPR and prophage profiles', Scientific Reports, vol. 7, http://dx.doi.org/10.1038/s41598-017-06079-1
2017
Du P; Zheng H; Zhou J; Lan R; Ye C; Jing H; Jin D; Cui Z; Bai X; Liang J; Liu J; Xu L; Zhang W; Chen C; Xu J, 2017, 'Detection of multiple parallel transmission outbreak of streptococcus suis human infection by use of genome epidemiology, China, 2005', Emerging Infectious Diseases, vol. 23, pp. 204 - 211, http://dx.doi.org/10.3201/eid2302.160297
2017
Meng X; Lu S; Wang Y; Lai X-H; Wen Y; Jin D; Yang J; Bai X; Zhang G; Pu J; Lan R; Xu J, 2017, 'Corrigendum: Actinomyces vulturis sp. nov., isolated from Gyps himalayensis.', Int J Syst Evol Microbiol, vol. 67, pp. 3134, http://dx.doi.org/10.1099/ijsem.0.002235
2017
Wang Y; Lu L; Lan R; Salazar JK; Liu J; Xu J; Ye C, 2017, 'Isolation and characterization of Listeria species from rodents in natural environments in China', Emerging Microbes and Infections, vol. 6, http://dx.doi.org/10.1038/emi.2017.28
2017
Chung HKL; Tay A; Octavia S; Chen J; Liu F; Ma R; Lan R; Riordan SM; Grimm MC; Zhang L, 2017, 'Erratum: Genome analysis of Campylobacter concisus strains from patients with inflammatory bowel disease and gastroenteritis provides new insights into pathogenicity', Scientific reports, vol. 7, pp. 41113, http://dx.doi.org/10.1038/srep41113
2017
Octavia S; Wang Q; Tanaka MM; Sintchenko V; Lan R, 2017, 'Genomic heterogeneity of Salmonella enterica serovar Typhimurium bacteriuria from chronic infection', Infection, Genetics and Evolution, vol. 51, pp. 17 - 20, http://dx.doi.org/10.1016/j.meegid.2017.03.004
2017
Niu L; Lu S; Lai XH; Hu S; Chen C; Zhang G; Yang J; Jin D; Wang Y; Lan R; Lu G; Xie Y; Ye C; Xu J, 2017, 'Streptococcus himalayensis sp. Nov., isolated from the respiratory tract of marmota himalayana', International Journal of Systematic and Evolutionary Microbiology, vol. 67, pp. 256 - 261, http://dx.doi.org/10.1099/ijsem.0.001609
2017
Bai L; Wang L; Yang X; Wang J; Gan X; Wang W; Xu J; Chen Q; Lan R; Fanning S; Li F, 2017, 'Prevalence and molecular characteristics of extended-spectrum ß-lactamase genes in Escherichia coli isolated from diarrheic patients in China', Frontiers in Microbiology, vol. 8, http://dx.doi.org/10.3389/fmicb.2017.00144
2017
Carbonetti NH; Wirsing von König CH; Lan R; Jacob-Dubuisson F; Cotter PA; Deora R; Merkel TJ; van Els CA; Locht C; Hozbor D; Rodriguez ME, 2017, 'Erratum for Carbonetti et al., "Highlights of the 11th International Bordetella Symposium: from Basic Biology to Vaccine Development".', Clin Vaccine Immunol, vol. 24, http://dx.doi.org/10.1128/CVI.00071-17
2017
Liu L; Lan R; Liu L; Wang Y; Zhang Y; Wang Y; Xu J, 2017, 'Antimicrobial resistance and cytotoxicity of Citrobacter spp. in Maanshan Anhui Province, China', Frontiers in Microbiology, vol. 8, http://dx.doi.org/10.3389/fmicb.2017.01357
2017
Octavia S; Wu SZ; Kaur S; Valinsky L; Marva E; Moran-Gilad J; Lan R, 2017, 'Whole-genome sequencing and comparative genomic analysis of Bordetella pertussis isolates from the 2007–2008 epidemic in Israel', Journal of Infection, vol. 74, pp. 204 - 207, http://dx.doi.org/10.1016/j.jinf.2016.11.012
2017
Meng X; Lu S; Wang Y; Lai XH; Wen Y; Jin D; Yang J; Bai X; Zhang G; Pu J; Lan R; Xu J, 2017, 'Actinomyces vulturis sp. Nov., isolated from gyps himalayensis', International Journal of Systematic and Evolutionary Microbiology, vol. 67, pp. 1720 - 1726, http://dx.doi.org/10.1099/ijsem.0.001851
2017
Qiu X; Bai X; Lan R; Zheng H; Xu J, 2016, 'Novel capsular polysaccharide loci and new diagnostic tools for high-throughput capsular gene typing in Streptococcus suis', Applied and Environmental Microbiology, vol. 82, pp. 7102 - 7112, http://dx.doi.org/10.1128/AEM.02102-16
2016
Carbonetti NH; Von König CHW; Lan R; Jacob-Dubuisson F; Cotter PA; Deora R; Merkel TJ; Van Els CA; Locht C; Hozbor D; Rodriguez ME, 2016, 'Highlights of the 11th international Bordetella symposium: From basic biology to vaccine development', Clinical and Vaccine Immunology, vol. 23, pp. 842 - 850, http://dx.doi.org/10.1128/CVI.00388-16
2016
Safarchi A; Octavia S; Wu SZ; Kaur S; Sintchenko V; Gilbert GL; Wood N; McIntyre P; Marshall H; Keil AD; Lan R, 2016, 'Genomic dissection of Australian Bordetella pertussis isolates from the 2008-2012 epidemic', Journal of Infection, vol. 72, pp. 468 - 477, http://dx.doi.org/10.1016/j.jinf.2016.01.005
2016
Safarchi A; Octavia S; Luu LDW; Tay CY; Sintchenko V; Wood N; Marshall H; McIntyre P; Lan R, 2016, 'Better colonisation of newly emerged Bordetella pertussis in the co-infection mouse model study', Vaccine, vol. 34, pp. 3967 - 3971, http://dx.doi.org/10.1016/j.vaccine.2016.06.052
2016
Clarke M; McIntyre PB; Blyth CC; Wood N; Octavia S; Sintchenko V; Giles L; Quinn H; Hill V; Hanly G; Lan R; Marshall HS, 2016, 'The relationship between Bordetella pertussis genotype and clinical severity in Australian children with pertussis', Journal of Infection, vol. 72, pp. 171 - 178, http://dx.doi.org/10.1016/j.jinf.2015.11.004
2016
Chan CHS; Octavia S; Sintchenko V; Lan R, 2016, 'SnpFilt: A pipeline for reference-free assembly-based identification of SNPs in bacterial genomes', Computational Biology and Chemistry, vol. 65, pp. 178 - 184, http://dx.doi.org/10.1016/j.compbiolchem.2016.09.004
2016
Qin T; Zhang W; Liu W; Zhou H; Ren H; Shao Z; Lan R; Xu J, 2016, 'Population structure and minimum core genome typing of Legionella pneumophila', Scientific Reports, vol. 6, http://dx.doi.org/10.1038/srep21356
2016
Niu L; Lu S; Hu S; Jin D; Lai X; Yang J; Chen C; Wang Y; Bai X; Lan R; Lv G; Xie Y; Ye C; Xu J, 2016, 'Streptococcus halotolerans sp. nov. isolated from the respiratory tract of Marmota himalayana in Qinghai-Tibet plateau of China', International Journal of Systematic and Evolutionary Microbiology, vol. 66, pp. 4211 - 4217, http://dx.doi.org/10.1099/ijsem.0.001337
2016
Chen D; Gong L; Walsh TR; Lan R; Wang T; Zhang J; Mai W; Ni N; Lu J; Xu J; Li J, 2016, 'Infection by and dissemination of NDM-5-producing Escherichia coli in China', Journal of Antimicrobial Chemotherapy, vol. 71, pp. 563 - 565, http://dx.doi.org/10.1093/jac/dkv352
2016
Fu S; Octavia S; Wang Q; Tanaka MM; Tay CY; Sintchenko V; Lan R, 2016, 'Evolution of variable number tandem repeats and its relationship with genomic diversity in Salmonella typhimurium', Frontiers in Microbiology, vol. 7, http://dx.doi.org/10.3389/fmicb.2016.02002
2016
Luo Y; Octavia S; Jin D; Ye J; Miao Z; Jiang T; Xia S; Lan R, 2016, 'US Gulf-like toxigenic O1 Vibrio cholerae causing sporadic cholera outbreaks in China', Journal of Infection, vol. 72, pp. 564 - 572, http://dx.doi.org/10.1016/j.jinf.2016.02.005
2016
Li H; Lan R; Peng N; Sun J; Zhu Y, 2016, 'High resolution melting curve analysis with MATLAB-based program', Measurement: Journal of the International Measurement Confederation, vol. 90, pp. 178 - 186, http://dx.doi.org/10.1016/j.measurement.2016.04.057
2016
Lu S; Jin D; Wu S; Yang J; Lan R; Bai X; Liu S; Meng Q; Yuan X; Zhou J; Pu J; Chen Q; Dai H; Hu Y; Xiong Y; Ye C; Xu J, 2016, 'Insights into the evolution of pathogenicity of Escherichia coli from genomic analysis of intestinal E. coli of Marmota himalayana in Qinghai-Tibet plateau of China', Emerging Microbes and Infections, vol. 5, http://dx.doi.org/10.1038/emi.2016.122
2016
Phillips A; Sotomayor C; Wang Q; Holmes N; Furlong C; Ward K; Howard P; Octavia S; Lan R; Sintchenko V, 2016, 'Whole genome sequencing of Salmonella Typhimurium illuminates distinct outbreaks caused by an endemic multi-locus variable number tandem repeat analysis type in Australia, 2014', BMC Microbiology, vol. 16, http://dx.doi.org/10.1186/s12866-016-0831-3
2016
Chung HKL; Tay A; Octavia S; Chen J; Liu F; Ma R; Lan R; Riordan SM; Grimm MC; Zhang L, 2016, 'Genome analysis of Campylobacter concisus strains from patients with inflammatory bowel disease and gastroenteritis provides new insights into pathogenicity', Scientific Reports, vol. 6, http://dx.doi.org/10.1038/srep38442
2016
Niu L; Lu S; Hu S; Jin D; Lai X; Yangn J; Chen C; Wang Y; Wang Y; Bai X; Lan R; Lv G; Xie Y; Ye C; Xu J, 2016, 'Streptococcus marmotae sp. Nov., isolated from the respiratory tract of marmota himalayana', International Journal of Systematic and Evolutionary Microbiology, vol. 66, pp. 4315 - 4322, http://dx.doi.org/10.1099/ijsem.0.001350
2016
Liu F; Lee H; Lan R; Zhang L, 2016, 'Zonula occludens toxins and their prophages in Campylobacter species', Gut Pathogens, vol. 8, http://dx.doi.org/10.1186/s13099-016-0125-1
2016
Octavia S; Wang Q; Tanaka MM; Sintchenko V; Lan R, 2015, 'Genomic variability of serial human isolates of salmonella enterica serovar typhimurium associated with prolonged carriage', Journal of Clinical Microbiology, vol. 53, pp. 3507 - 3514, http://dx.doi.org/10.1128/JCM.01733-15
2015
Wang Y; Jiao Y; Lan R; Xu X; Liu G; Wang X; Zhang L; Pang H; Jin D; Dai H; Yuan X; Zhang W; Xu J; Ye C, 2015, 'Characterization of Listeria monocytogenes isolated from human Listeriosis cases in China', Emerging Microbes and Infections, vol. 4, pp. 1 - 3, http://dx.doi.org/10.1038/emi.2015.50
2015
Liu S; Jin D; Lan R; Wang Y; Meng Q; Dai H; Lu S; Hu S; Xu J, 2015, 'Escherichia marmotae sp. nov., isolated from faeces of Marmota himalayana', International Journal of Systematic and Evolutionary Microbiology, vol. 65, pp. 2130 - 2134, http://dx.doi.org/10.1099/ijs.0.000228
2015
Safarchi A; Octavia S; Luu LDW; Tay CY; Sintchenko V; Wood N; Marshall H; McIntyre P; Lan R, 2015, 'Pertactin negative Bordetella pertussis demonstrates higher fitness under vaccine selection pressure in a mixed infection model', Vaccine, vol. 33, pp. 6277 - 6281, http://dx.doi.org/10.1016/j.vaccine.2015.09.064
2015
Octavia S; Sara J; Lan R, 2015, 'Characterization of a large novel phage-like plasmid in Salmonella enterica serovar Typhimurium', FEMS Microbiology Letters, vol. 362, http://dx.doi.org/10.1093/femsle/fnv044
2015
Fung CC; Octavia S; Mooney AM; Lan R, 2015, 'Virulence variations in Shigella and enteroinvasive Escherichia coli using the Caenorhabditis elegans model', FEMS Microbiology Letters, vol. 362, http://dx.doi.org/10.1093/femsle/fnu045
2015
Liu L; Hao S; Lan R; Wang G; Xiao D; Sun H; Xu J, 2015, 'The type VI secretion system modulates flagellar gene expression and secretion in Citrobacter freundii and contributes to adhesion and cytotoxicity to host cells', Infection and Immunity, vol. 83, pp. 2596 - 2604, http://dx.doi.org/10.1128/IAI.03071-14
2015
Bai L; Lan R; Zhang X; Cui S; Xu J; Guo Y; Li F; Zhang D, 2015, 'Prevalence of salmonella isolates from chicken and pig slaughterhouses and emergence of ciprofloxacin and cefotaxime co-resistant S. enterica serovar Indiana in Henan, China', PLoS ONE, vol. 10, http://dx.doi.org/10.1371/journal.pone.0144532
2015
Octavia S; Wang Q; Tanaka MM; Kaur S; Sintchenko V; Lan R, 2015, 'Delineating community outbreaks of Salmonella enterica serovar typhimurium by use of whole-genome sequencing: Insights into genomic variability within an outbreak', Journal of Clinical Microbiology, vol. 53, pp. 1063 - 1071, http://dx.doi.org/10.1128/JCM.03235-14
2015
Wang Y; Wang Y; Lan R; Xu H; Ma A; Li D; Dai H; Yuan X; Xu J; Ye C, 2015, 'Multiple endonuclease restriction real-time loop-mediated isothermal amplification: A novel analytically rapid, sensitive, multiplex loop-mediated isothermal amplification detection technique', Journal of Molecular Diagnostics, vol. 17, pp. 392 - 401, http://dx.doi.org/10.1016/j.jmoldx.2015.03.002
2015
Zheng H; Ji S; Liu Z; Lan R; Huang Y; Bai X; Gottschalk M; Xu J, 2015, 'Eight novel capsular polysaccharide synthesis gene loci identified in nontypeable Streptococcus suis isolates', Applied and Environmental Microbiology, vol. 81, pp. 4111 - 4119, http://dx.doi.org/10.1128/AEM.00315-15
2015
Fu S; Liu Y; Li X; Tu J; Lan R; Tian H, 2015, 'A preliminary stochastic model for managing microorganisms in a recirculating aquaculture system', Annals of Microbiology, vol. 65, pp. 1119 - 1129, http://dx.doi.org/10.1007/s13213-014-0958-0
2015
Bai L; Guo Y; Lan R; Dong Y; Wang W; Hu Y; Gan X; Yan S; Fu P; Pei X; Xu J; Liu X; Li F, 2015, 'Genotypic characterization of Shiga toxin-producing Escherichia coli O157:H7 isolates in food products from china between 2005 and 2010', Food Control, vol. 50, pp. 209 - 214, http://dx.doi.org/10.1016/j.foodcont.2014.08.045
2015
Mahendran V; Octavia S; Demirbas OF; Sabrina S; Ma R; Lan R; Riordan SM; Grimm MC; Zhang L, 2015, 'Delineation of genetic relatedness and population structure of oral and enteric Campylobacter concisus strains by analysis of housekeeping genes', Microbiology (United Kingdom), vol. 161, pp. 1600 - 1612, http://dx.doi.org/10.1099/mic.0.000112
2015
Fu S; Octavia S; Tanaka MM; Sintchenko V; Lan R, 2015, 'Defining the core genome of salmonella enterica serovar typhimurium for genomic surveillance and epidemiological typing', Journal of Clinical Microbiology, vol. 53, pp. 2530 - 2538, http://dx.doi.org/10.1128/JCM.03407-14
2015
Zhang N; Lan R; Sun Q; Wang J; Wang Y; Zhang J; Yu D; Hu W; Hu S; Dai H; Du P; Wang H; Xu J, 2014, 'Genomic portrait of the evolution and epidemic spread of a recently emerged multidrug-resistant shigella flexneri clone in China', Journal of Clinical Microbiology, vol. 52, pp. 1119 - 1126, http://dx.doi.org/10.1128/JCM.02669-13
2014
Chen C; Zhang W; Zheng H; Lan R; Wang H; Du P; Bai X; Ji S; Meng Q; Jin D; Liu K; Jing H; Ye C; Gao GF; Wang L; Gottschalk EM; Xu J, 2014, 'Erratum: Correction for Chen et al., minimum core genome sequence typing of bacterial pathogens: A unified approach for clinical and public health microbiology (J. Clin. Microbiol. (2014) 52:11 (4120) 10.1128/JCM.02282-14)', Journal of Clinical Microbiology, vol. 52, pp. 4120, http://dx.doi.org/10.1128/JCM.02282-14
2014
Wang J; Knirel YA; Lan R; Senchenkova SN; Luo X; Perepelov AV; Wang Y; Shashkov AS; Xu J; Sun Q, 2014, 'Identification of an O-acyltransferase gene (oacB) that mediates 3-and 4-O-acetylation of Rhamnose III in Shigella flexneri O antigens', Journal of Bacteriology, vol. 196, pp. 1525 - 1531, http://dx.doi.org/10.1128/JB.01393-13
2014
Dadigamuwage A, 2014, 'Population structure and virulence content of avian pathogenic Escherichia coli isolated from outbreaks in Sri Lanka', Veterinary Microbiology, vol. 168, pp. 403 - 412, http://dx.doi.org/10.1016/j.vetmic.2013.11.028
2014
Sun Q; Knirel YA; Wang J; Luo X; Senchenkova SN; Lan R; Shashkov AS; Xu J, 2014, 'Serotype-converting bacteriophage SfII encodes an acyltransferase protein that mediates 6-O-acetylation of GlcNAc in Shigella flexneri O-antigens, conferring on the host a novel O-antigen epitope', Journal of Bacteriology, vol. 196, pp. 3656 - 3666, http://dx.doi.org/10.1128/JB.02009-14
2014
Lee H; Ma R; Grimm MC; Riordan SM; Lan R; Zhong L; Raftery M; Zhang L, 2014, 'Examination of the anaerobic growth of Campylobacter concisus strains', International Journal of Microbiology, vol. 2014, http://dx.doi.org/10.1155/2014/476047
2014
Wang J; Lan R; Knirel YA; Luo X; Senchenkova SN; Shashkov AS; Xu J; Sun Q, 2014, 'Serological identification and prevalence of a novel o-antigen epitope linked to 3-and 4-o-acetylated rhamnose III of lipopolysaccharide in shigella flexneri', Journal of Clinical Microbiology, vol. 52, pp. 2033 - 2038, http://dx.doi.org/10.1128/JCM.00197-14
2014
Lam C; Octavia S; Ricafort L; Sintchenko V; Gilbert GL; Wood N; McIntyre P; Marshall H; Guiso N; Keil AD; Lawrence A; Robson J; Hogg G; Lan R, 2014, 'Rapid increase in pertactin-deficient Bordetella pertussis isolates, Australia', Emerging Infectious Diseases, vol. 20, pp. 626 - 633, http://dx.doi.org/10.3201/eid2004.131478
2014
Li J; Lan R; Xiong Y; Ye C; Yuan M; Liu X; Chen X; Yu D; Liu B; Lin W; Bai X; Wang Y; Sun Q; Wang Y; Zhao H; Meng Q; Chen Q; Zhao A; Xu J, 2014, 'Sequential isolation in a patient of Raoultella planticola and Escherichia coli bearing a novel IS CR1 element carrying blaNDM-1', PLoS ONE, vol. 9, http://dx.doi.org/10.1371/journal.pone.0089893
2014
Bart MJ; Harris SR; Advani A; Arakawa Y; Bottero D; Bouchez V; Cassiday PK; Chiang CS; Dalby T; Fry NK; Gaillard ME; van Gent M; Guiso N; Hallander HO; Harvill ET; He Q; van der Heide HGJ; Heuvelman K; Hozbor DF; Kamachi K; Karataev GI; Lan R; Lutyńska A; Maharjan RP; Mertsola J; Miyamura T; Octavia S; Preston A; Quail MA; Sintchenko V; Stefanelli P; Tondella ML; Tsang RSW; Xu Y; Yao SM; Zhang S; Parkhill J; Mooi FR, 2014, 'Global population structure and evolution of Bordetella pertussis and their relationship with vaccination', mBio, vol. 5, http://dx.doi.org/10.1128/mBio.01074-14
2014
Sun Q; Knirel YA; Lan R; Wang J; Senchenkova SN; Shashkov AS; Wang Y; Wang Y; Luo X; Xu J, 2014, 'Dissemination and serotype modification potential of pSFxv-2, an O-antigen PEtN modification plasmid in Shigella flexneri', Glycobiology, vol. 24, pp. 305 - 313, http://dx.doi.org/10.1093/glycob/cwt115
2014
Zheng H; Ji S; Lan R; Liu Z; Bai X; Zhang W; Gottschalk M; Xu J, 2014, 'Population analysis of Streptococcus suis Isolates from slaughtered swine by use of minimum core genome sequence typing', Journal of Clinical Microbiology, vol. 52, pp. 3568 - 3572, http://dx.doi.org/10.1128/JCM.00536-14
2014
Lam C; Octavia S; Sintchenko V; Gilbert GL; Lan R, 2014, 'Investigating genome reduction of Bordetella pertussis using a multiplex PCR-based reverse line blot assay (mPCR/RLB)', BMC Research Notes, vol. 7, http://dx.doi.org/10.1186/1756-0500-7-727
2014
Meng Q; Bai X; Zhao A; Lan R; Du H; Wang T; Shi C; Yuan X; Bai X; Ji S; Jin D; Yu B; Wang Y; Sun H; Liu K; Xu J; Xiong Y, 2014, 'Characterization of Shiga toxin-producing Escherichia coli isolated from healthy pigs in China', BMC Microbiology, vol. 14, http://dx.doi.org/10.1186/1471-2180-14-5
2014
Zheng H; Lan R; Zheng X; Cui Z; Liu Z; Bai X; Ji S; Gottschalk M; Xu J, 2014, 'Comparative genomic hybridization identifies virulence differences in Streptococcus suis', PLoS ONE, vol. 9, http://dx.doi.org/10.1371/journal.pone.0087866
2014
Knirel YA; Wang J; Luo X; Senchenkova SN; Lan R; Shpirt AM; Du P; Shashkov AS; Zhang N; Xu J; Sun Q, 2014, 'Genetic and structural identification of an O-acyltransferase gene (oacC) responsible for the 3/4-O-acetylation on rhamnose III in Shigella flexneri serotype 6', BMC Microbiology, vol. 14, http://dx.doi.org/10.1186/s12866-014-0266-7
2014
Shashkov AS; Senchenkova SN; Sun QZ; Lan R; Wang J; Perepelov AV; Knirel YA; Xu J, 2013, 'Structure of the O-antigen of a novel Shigella flexneri serotype, 1d (I: 7,8)', Carbohydrate Research, vol. 373, pp. 93 - 96, http://dx.doi.org/10.1016/j.carres.2013.03.015
2013
Bai X; Zhao A; Lan R; Xin Y; Xie H; Meng Q; Jin D; Yu B; Sun H; Lu S; Xu J; Xiong Y, 2013, 'Shiga Toxin-Producing Escherichia coli in Yaks (Bos grunniens) from the Qinghai-Tibetan Plateau, China', PLoS ONE, vol. 8, http://dx.doi.org/10.1371/journal.pone.0065537
2013
Liu Z; Zheng H; Gottschalk M; Bai X; Lan R; Ji S; Liu H; Xu J, 2013, 'Development of Multiplex PCR Assays for the Identification of the 33 Serotypes of Streptococcus suis', PLoS ONE, vol. 8, pp. e72070 - e72070, http://dx.doi.org/10.1371/journal.pone.0072070
2013
Xu YM; Xu XF; Lan R; Xiong Y; Ye C; Ren ZH; Liu L; Zhao A; Wu LF; Xu J, 2013, 'An O Island 172 Encoded RNA Helicase Regulates the Motility of Escherichia coli O157:H7', PLoS ONE, vol. 8, pp. Article number e64211, http://dx.doi.org/10.1371/journal.pone.0064211
2013
Chen C; Zhang W; Zheng H; Lan R; Wang H; Du P; Bai X; Ji S; Meng Q; Jin D; Liu K; Jing H; Ye C; Gao GF; Wang L; Gottschalk M; Xu J, 2013, 'Minimum core genome sequence typing of bacterial pathogens: A unified approach for clinical and public health microbiology', Journal of Clinical Microbiology, vol. 51, pp. 2582 - 2591, http://dx.doi.org/10.1128/JCM.00535-13
2013
Knirel YA; Lan R; Senchenkova SN; Wang J; Shashkov AS; Wang YM; Perepelov AV; Xiong Y; Xu J; Sun QZ, 2013, 'O-antigen structure of Shigella flexneri serotype Yv and effect of the lpt-O gene variation on phosphoethanolamine modification of S. flexneri O-antigens', Glycobiology, vol. 23, pp. 475 - 485, http://dx.doi.org/10.1093/glycob/cws222
2013
Octavia S; Salim A; Kurniawan J; Lam C; Leung Q; Ahsan S; Reeves PR; Nair GB; Lan R, 2013, 'Population Structure and Evolution of Non-O1/Non-O139 Vibrio cholerae by Multilocus Sequence Typing', PLoS ONE, vol. 8, http://dx.doi.org/10.1371/journal.pone.0065342
2013
Pang S; Octavia S; Feng L; Liu B; Reeves PR; Lan R; Wang L, 2013, 'Genomic diversity and adaptation of Salmonella enterica serovar Typhimurium from analysis of six genomes of different phage types', BMC Genomics, vol. 14, http://dx.doi.org/10.1186/1471-2164-14-718
2013
Meng Q; Xiong Y; Lan R; Ye C; Wang T; Qi T; Wang Y; Wang H; Bai X; Bai X; Ji S; Jin D; Yuan X; Zhao A; Sun H; Jing H; Xu J, 2013, 'SNP genotyping of enterohemorrhagic Escherichia coli O157: H7 isolates from China and genomic identity of the 1999 Xuzhou outbreak', Infection, Genetics and Evolution, vol. 16, pp. 275 - 281, http://dx.doi.org/10.1016/j.meegid.2013.02.018
2013
Sun Q; Lan R; Wang Y; Wang J; Wang Y; Li P; Du P; Xu J, 2013, 'Isolation and genomic characterization of SfI, a serotype-converting bacteriophage of Shigella flexneri', BMC Microbiology, vol. 13, http://dx.doi.org/10.1186/1471-2180-13-39
2013
Sun Q; Lan R; Wang J; Xia S; Wang Y; Wang Y; Jin D; Yu B; Knirel YA; Xu J, 2013, 'Identification and Characterization of a Novel Shigella flexneri Serotype Yv in China', PLoS ONE, vol. 8, http://dx.doi.org/10.1371/journal.pone.0070238
2013
Sun Q; Lan R; Wang Y; Wang J; Xia S; Wang Y; Zhang J; Yu D; Li Z; Jing H; Xu J, 2013, 'Identification of a divergent O-acetyltransferase gene oac1b from Shigella flexneri serotype 1b strains.', Emerging Microbes & Infections, vol. 1, pp. 1 - 7, http://dx.doi.org/10.1038/emi.2012.22
2013
Luo Y; Ye J; Jin D; Ding G; Zhang Z; Mei L; Octavia S; Lan R, 2013, 'Molecular analysis of non-O1/non-O139 Vibrio cholerae isolated from hospitalised patients in China', BMC Microbiology, vol. 13, http://dx.doi.org/10.1186/1471-2180-13-52
2013
Zhao H; Chen C; Xiong Y; Lan R; Wang H; Yao X; Zhang X; Sun H; Zhao A; Bai X; Cheng Q; Ye C; Xu J, 2013, 'Global Transcriptional and Phenotypic Analyses of Escherichia coli O157:H7 Strain Xuzhou21 and Its pO157_Sal Cured Mutant', PLoS ONE, vol. 8, pp. Article numbere65466, http://dx.doi.org/10.1371/journal.pone.0065466
2013
Mahendran V; Tan YS; Riordan SM; Grimm MC; Day AS; Lemberg DA; Octavia S; Lan R; Zhang L, 2013, 'The Prevalence and Polymorphisms of Zonula Occluden Toxin Gene in Multiple Campylobacter concisus Strains Isolated from Saliva of Patients with Inflammatory Bowel Disease and Controls', PLoS ONE, vol. 8, http://dx.doi.org/10.1371/journal.pone.0075525
2013
Octavia S; Sintchenko V; Gilbert GL; Lawrence AL; Keil AD; Hogg G; Lan R, 2012, 'Newly emerging clones of bordetella pertussis carrying prn2 and ptxP3 alleles implicated in Australian pertussis epidemic in 2008-2010', Journal of Infectious Diseases, vol. 205, pp. 1220 - 1224, http://dx.doi.org/10.1093/infdis/jis178
2012
Lam C; Octavia S; Reeves PR; Lan R, 2012, 'Multi-locus variable number tandem repeat analysis of 7th pandemic vibrio cholerae.', BMC Microbiology, vol. 12, pp. 1 - 11, http://dx.doi.org/10.1186/1471-2180-12-82
2012
Bai L; Xia S; Lan R; Liu L; Ye C; Wang Y; Jin D; Cui Z; Jing H; Xiong Y; Bai X; Sun H; Zhang J; Wang L; Xu J, 2012, 'Isolation and characterization of cytotoxic,aggregative Citrobacter freundii.', PLoS One, vol. 7, pp. e33054, http://dx.doi.org/10.1371/journal.pone.0033054
2012
Lam C; Octavia S; Bahrame Z; Sintchenko V; Gilbert GL; Lan R, 2012, 'Selection and emergence of pertussis toxin promoter ptxP3 allele in the evolution of Bordetella pertussis', Infection Genetics and Evolution, vol. 12, pp. 492 - 495, http://dx.doi.org/10.1016/j.meegid.2012.01.001
2012
Xiong Y; Wang P; Lan R; Ye C; Wang H; Ren J; Jing H; Wang Y; Zhou Z; Bai X; Cui Z; Luo X; Zhao A; Wang Y; Zhang S; Sun H; Wang L; Xu J, 2012, 'A novel escherichia coli O157:H7 clone causing a major hemolytic uremic syndrome outbreak in China', PLoS ONE, vol. 7, pp. e36144, http://dx.doi.org/10.1371/journal.pone.0036144
2012
Pang S; Octavia S; Reeves PR; Wang Q; Gilbert GL; Sintchenko V; Lan R, 2012, 'Genetic relationships of phage types and single nucleotide polymorphism typing of Salmonella enterica serovar Typhimurium', Journal of Clinical Microbiology, vol. 50, pp. 727 - 734, http://dx.doi.org/10.1128/JCM.01284-11
2012
Ismail Y; Mahendran V; Octavia S; Day AS; Riordan S; Grimm M; Lan R; Lemberg DA; Tran TAT; Zhang L, 2012, 'Investigation of the enteric pathogenic potential of oral campylobacter concisus strains isolated from patients with inflammatory bowel disease', PLoS One, vol. 7(5), pp. 1 - 11, http://dx.doi.org/10.1371/journal.pone.0038217
2012
Luo X; Sun Q; Lan R; Wang J; Li Z; Xia S; Zhang J; Wang Y; Jin D; Wang Y; Wang Y; Yu B; Cui Z; Xu J, 2012, 'Emergence of a novel Shigella flexneri serotype 1d in China.', Diagnostic Microbiology and Infectious Disease, vol. 74, pp. 316 - 319, http://dx.doi.org/10.1016/j.diagmicrobio.2012.06.022
2012
Sun Q; Knirel YA; Lan R; Wang J; Senchenkova SN; Jin D; Shashkov AS; Xia S; Perepelov AV; Chen Q; Wang Y; Wang H; Xu J, 2012, 'A novel plasmid-encoded serotype conversion mechanism through addition of phosphoethanolamine to the O-antigen of shigella flexneri.', PLoS ONE, vol. 7, pp. e46095, http://dx.doi.org/10.1371/journal.pone.0046095
2012
Wang Y; Zhao A; Zhu R; Lan R; Jin D; Cui Z; Wang Y; Li Z; Wang Y; Xu J; Ye C, 2012, 'Genetic diversity and molecular typing of Listeria monocytogenes in China.', BMC Microbiology, vol. 12, pp. 1 - 9, http://dx.doi.org/10.1186/1471-2180-12-119
2012
Octavia S; Maharjan RP; Sintchenko V; Stevenson GM; Reeves PR; Gilbert GL; Lan R, 2011, 'Insight into evolution of Bordetella pertussis from comparative genomic analysis: Evidence of vaccine-driven selection', Molecular Biology and Evolution, vol. 28, pp. 707 - 715, http://dx.doi.org/10.1093/molbev/msq245
2011
Wang P; Xiong Y; Lan R; Ye C; Wang H; Ren J; Jing H; Wang Y; Zhou Z; Cui Z; Zhao H; Chen Y; Jin D; Bai X; Zhao A; Wang Y; Zhang S; Sun H; Li J; Wang T; Wang L; Xu J, 2011, 'PO157-Sal, a novel conjugative plasmid detected in outbreak isolates of Escherichia coli O157:H7', Journal of Clinical Microbiology, vol. 49, pp. 1594 - 1597, http://dx.doi.org/10.1128/JCM.02530-10
2011
Lin FP; Lan R; Sintchenko V; Kong F; Gilbert GL; Coiera E, 2011, 'Computational genome-wide analysis of phylogenetic profiles reveal potential virulence genes of Streptococcus agalactiae', PLoS One, vol. 6, pp. e17964, http://dx.doi.org/10.1371/journal.pone.0017964
2011
Sun Q; Lan R; Wang Y; Zhao A; Zhang S; Wang J; Wang Y; Xia S; Jin D; Cui Z; Zhao H; Li Z; Ye C; Zhang S; Jing H; Xu J, 2011, 'Development of a multiplex PCR assay targeting O-antigen modification genes for molecular serotyping of Shigella flexneri', Journal of Clinical Microbiology, vol. 49, pp. 3766 - 3770, http://dx.doi.org/10.1128/JCM.01259-11
2011
Sun Q; Lan R; Wang Y; Wang J; Luo X; Zhang S; Li P; Wang Y; Ye C; Jing H; Xu J, 2011, 'Genesis of a novel Shigella flexneri serotype by sequential infection of serotype-converting bacteriophages SfX and SfI', BMC Microbiology, vol. 11, pp. 269, http://dx.doi.org/10.1186/1471-2180-11-269
2011
Octavia S; Ch''ng SL; Xia Q; Duong A; Tanaka M; Fukushima H; Lan R, 2011, 'Population structure and evolution of pathogenicity of Yersinia pseudotuberculosis', Applied and Environmental Microbiology, vol. 77, pp. 768 - 775, http://dx.doi.org/10.1128/AEM.01993-10
2011
Zheng X; Zheng H; Lan R; Ye C; Wang Y; Zhang J; Jing H; Chen C; Segura M; Gottschalk M; Xu J, 2011, 'Identification of genes and genomic islands correlated with high pathogenicity in Streptococcus suis using whole genome tiling microarrays', PLoS One, vol. 6, pp. e17987, http://dx.doi.org/10.1371/journal.pone.0017987
2011
Reeves PR; Liu B; Zhou Z; Li D; Guo D; Ren Y; Clabots C; Lan R; Johnson J; Wang L, 2011, 'Rates of mutation and host transmission for an escherichia coli clone over 3 years', PLoS One, vol. 6, pp. Article number e26907, http://dx.doi.org/10.1371/journal.pone.0026907
2011
Cashmore AW; Lan R; Macartney K, 2011, 'Bug breakfast in the Bulletin. Pertussis in NSW and its prevention in infants and children.', NSW Public Health Bulletin, vol. 22, pp. 236 - 236
2011
Cashmore AW; Lan R; Macartney KK, 2011, 'Bug breakfast in the Bulletin. Pertussis in NSW and its prevention in infants and children.', New South Wales public health bulletin, vol. 22, pp. 236, http://dx.doi.org/10.1071/nb11032
2011
Ballouz S; Lan R; Francis AR; Tanaka M, 2010, 'Conditions for the evolution of gene clusters in bacterial genomes.', PLoS Computational Biology, vol. 6, pp. e1000672 - e1000672, http://dx.doi.org/10.1371/journal.pcbi.1000672
2010
Lam C; Octavia S; Reeves PR; Wang L; Lan R, 2010, 'Evolution of seventh cholera pandemic and origin of 1991 epidemic, Latin America', Emerging Infectious Diseases, vol. 16, pp. 1130 - 1132, http://dx.doi.org/10.3201/eid1607.100131
2010
Zhou Z; Li X; Liu B; Beutin L; Xu J; Ren Y; Feng L; Lan R; Reeves PR; Wang L, 2010, 'Derivation of Escherichia coli O157:H7 from its O55:H7 precursor', PLoS One, vol. 5, pp. e8700, http://dx.doi.org/10.1371/journal.pone.0008700
2010
Octavia S; Lan R, 2010, 'Single nucleotide polymorphism typing of global Salmonella enterica serovar Typhi isolates by use of a hairpin primer real-time PCR assay', Journal of Clinical Microbiology, vol. 48, pp. 3504 - 3509, http://dx.doi.org/10.1128/JCM.00709-10
2010
Lan R, 2010, 'Bordetella pertussis clones identified by multilocus variable-number tandem-repeat analysis', Emerging Infectious Diseases, vol. 16, pp. 297 - 300, http://dx.doi.org/10.3201/eid1602.081707
2010
Ye C; Lan R; Xia S; Zhang J; Sun Q; Zhang S; Jing H; Jing H; Wang L; Li Z; Zhou Z; Zhao A; Cui Z; Cui J; Jin D; Huang L; Wang Y; Luo X; Bai X; Wang Y; Wang P; Xu Q; Xu J, 2010, 'Emergence of a new multidrug-resistant serotype X variant in an epidemic clone of Shigella flexneri', Journal of Clinical Microbiology, vol. 48, pp. 419 - 426, http://dx.doi.org/10.1128/JCM.00614-09
2010
Lin FP; Coiera E; Lan R; Sintchenko V, 2009, 'In silico prioritisation of candidate genes for prokaryotic gene function discovery: an application of phylogenetic profiles.', BMC bioinformatics, vol. 10, pp. 86 - 86, http://dx.doi.org/10.1186/1471-2105-10-86
2009
Chan W; Maharjan RP; Reeves PR; Sintchenko V; Gilbert GL; Lan R, 2009, 'Rapid and accurate typing of Bordetella pertussis targeting genes encoding acellular vaccine antigens using real time PCR and High Resolution Melt analysis', Journal of Microbiological Methods, vol. 77, pp. 326 - 329, http://dx.doi.org/10.1016/j.mimet.2009.03.007
2009
Lan R; Reeves PR; Octavia S, 2009, 'Population structure, origins and evolution of major Salmonella enterica clones', Infection Genetics and Evolution, vol. 9, pp. 996 - 1005, http://dx.doi.org/10.1016/j.meegid.2009.04.011
2009
Tay CY; Mitchell HM; Dong Q; Goh K; Dawes IW; Lan R, 2009, 'Population structure of Helicobacter pylori among ethnic groups in Malaysia: Recent acquisition of the bacterium by the Malay population', BMC Microbiology, vol. 9, pp. 126, http://dx.doi.org/10.1186/1471-2180-9-126
2009
Octavia S; Lan R, 2009, 'Multiple-locus variable-number tandem-repeat analysis of Salmonella enterica serovar Typhi', Journal of Clinical Microbiology, vol. 47, pp. 2369 - 2376, http://dx.doi.org/10.1128/JCM.00223-09
2009
Feng L; Reeves PR; Lan R; Ren Y; Gao C; Zhou Z; Ren Y; Cheng J; Weng W; Wang J; Qian WL; Li D; Wang L, 2008, 'A recalibrated molecular clock and independent origins for the cholera pandemic clones', PLoS One, vol. 3, pp. 4053 - 4063, http://dx.doi.org/10.1371/journal.pone.0004053
2008
Tay CY; Reeves PR; Lan R, 2008, 'Importation of the major pilin TcpA gene and frequent recombination drive the divergence of the Vibrio pathogenicity island in Vibrio cholerae', FEMS Microbiology Letters, vol. 289, pp. 210 - 218, http://dx.doi.org/10.1111/j.1574-6968.2008.01385.x
2008
Maharjan RP; Gu C; Reeves PR; Sintchenko V; Gilbert GL; Lan R, 2008, 'Genome-wide analysis of single nucleotide polymorphisms in Bordetella pertussis using comparative genomic sequencing', Research in Microbiology, vol. 159, pp. 602 - 608, http://dx.doi.org/10.1016/j.resmic.2008.08.004
2008
Lan R; Stevenson G; Donohoe K; Ward LA; Reeves PR, 2007, 'Molecular markers with potential to replace phage typing for Salmonella enterica serovar typhimurium', Journal of Microbiological Methods, vol. 68, pp. 145 - 156, http://dx.doi.org/10.1016/j.mimet.2006.07.004
2007
Zaghloul L; Tang C; Chin H; Bek EJ; Lan R; Tanaka M, 2007, 'The distribution of insertion sequences in the genome of Shigella flexneri strain 2457T', FEMS Microbiology Letters, vol. 277, pp. 197 - 204, http://dx.doi.org/10.1111/j.1574-6968.2007.00957.x
2007
Octavia S; Lan R, 2007, 'Single-Nucleotide-Polymorphism Typing and Genetic Relationships of Salmonella enterica Serovar Typhi Isolates', Journal of Clinical Microbiology, vol. 45, pp. 3795 - 3801, http://dx.doi.org/10.1128/JCM.00720-07
2007
Wirth T; Falush D; Lan R; Colles F; Mensa P; Wieler L; Karch H; Reeves PR; Maiden M; Ochman H; Achtman M, 2006, 'Sex and virulence in Escherichia coli: an evolutionary perspective', Molecular Microbiology, vol. 60, pp. 1136 - 1151, http://dx.doi.org/10.1111/j.1365-2958.2006.05172.x
2006
Hu H; Lan R; Reeves PR, 2006, 'Adaptation of multilocus sequencing for studying variation within a major clone: Evolutionary relationships of Salmonella enterica serovar typhimurium', Genetics, vol. 172, pp. 743 - 750, http://dx.doi.org/10.1534/genetics.105.046466
2006
Octavia S; Lan R, 2006, 'Frequent recombination and low level of clonality within Salmonella enterica subspecies I', Microbiology, vol. 152, pp. 1099 - 1108, http://dx.doi.org/10.1099/mic.0.28486-0
2006
Tominaga A; Lan R; Reeves PR, 2005, 'Evolutionary changes of the flhDC flagellar master operon in Shigella strains', Journal of Bacteriology, vol. 187, pp. 4295 - 4302, http://dx.doi.org/10.1128/JB.187.12.4295-4302.2005
2005
Salim A; Lan R; Reeves PR, 2005, 'Vibrio cholerae pathogenic clones', Emerging Infectious Diseases, vol. 11, pp. 1758 - 1760, http://dx.doi.org/10.3201/eid1111.041170
2005
Lan R; Alles MC; Donohoe K; Martinez M; Reeves PR, 2004, 'Molecular evolutionary relationships of enteroinvasive Escherichia coli and Shigella spp', Infection and Immunity, vol. 72, pp. 5080 - 5088, http://dx.doi.org/10.1128/IAI.72.9.5080-5088.2004
2004
Rezwan F; Lan R; Reeves PR, 2004, 'Molecular basis of the indole-negative reaction in Shigella strains:extensive damages to the tna operon by insertion sequences', Journal of Bacteriology, vol. 186, pp. 7460 - 7465, http://dx.doi.org/10.1128/JB.186.21.7460-7465.2004
2004
Lan R; Davison AM; Reeves PR; Ward LR, 2003, 'AFLP analysis of Salmonella enterica serovar Typhimurium isolates of phage types DT 9 and DT 135: Diversity within phage types and its epidemiological significance', Microbes and Infection, vol. 5, pp. 841 - 850, http://dx.doi.org/10.1016/S1286-4579(03)00174-6
2003
Lan R; Stevenson G; Reeves PR, 2003, 'Comparison of two major forms of the Shigella virulence plasmid pINV: positive selection is a major force driving the divergence', Infection and Immunity, vol. 71, pp. 6298 - 6306, http://dx.doi.org/10.1128/IAI.71.11.6298-6306.2003
2003
Hu H; Lan R; Reeves PR, 2002, 'Fluorescent amplified fragment length polymorphism analysis of Salmonella enterica serovar Typhimurium reveals phage-type-specific markers and potential for microarray typing', Journal of Clinical Microbiology, vol. 40, pp. 3406 - 3415, http://dx.doi.org/10.1128/JCM.40.9.3406-3415.2002
2002
Lan R; Reeves PR, 2002, 'Pandemic spread of cholera: Genetic diversity and relationships within the seventh pandemic clone of Vibrio cholerae determined by amplified fragment length polymorphism', Journal of Clinical Microbiology, vol. 40, pp. 172 - 181, http://dx.doi.org/10.1128/JCM.40.1.172-181.2002
2002
Lan R; Reeves PR, 2002, 'Escherichia coli in disguise: Molecular origins of Shigella', Microbes and Infection, vol. 4, pp. 1125 - 1132, http://dx.doi.org/10.1016/S1286-4579(02)01637-4
2002
Lan R; Lumb B; Ryan D; Reeves PR, 2001, 'Molecular evolution of large virulence plasmid in Shigella clones and enteroinvasive Escherichia coli', Infection and Immunity, vol. 69, pp. 6303 - 6309, http://dx.doi.org/10.1128/IAI.69.10.6303-6309.2001
2001
Lan R; Reeves PR, 2001, 'When does a clone deserve a name? A perspective on bacterial species based on population genetics', Trends in Microbiology, vol. 9, pp. 419 - 424, http://dx.doi.org/10.1016/S0966-842X(01)02133-3
2001
Karaolis DKR; Lan R; Kaper JB; Reeves PR, 2001, 'Comparison of Vibrio cholerae pathogenicity islands in sixth and seventh pandemic strains', Infection and Immunity, vol. 69, pp. 1947 - 1952, http://dx.doi.org/10.1128/IAI.69.3.1947-1952.2001
2001
Pupo GM; Lan R; Reeves PR; Baverstock PR, 2000, 'Population genetics of Escherichia coli in a natural population of native Australian rats', Environmental Microbiology, vol. 2, pp. 594 - 610, http://dx.doi.org/10.1046/j.1462-2920.2000.00142.x
2000
Stevenson G; Lan R; Reeves PR, 2000, 'The colanic acid gene cluster of Salmonella enterica has a complex history', FEMS Microbiology Letters, vol. 191, pp. 11 - 16, http://dx.doi.org/10.1016/S0378-1097(00)00361-X
2000
Lan R; Reeves PR, 2000, 'Intraspecies variation in bacterial genomes: The need for a species genome concept', Trends in Microbiology, vol. 8, pp. 396 - 401, http://dx.doi.org/10.1016/S0966-842X(00)01791-1
2000
Pupo GM; Lan R; Reeves PR, 2000, 'Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics', Proceedings of the National Academy of Sciences of the United States of America, vol. 97, pp. 10567 - 10572, http://dx.doi.org/10.1073/pnas.180094797
2000
Lan R; Reeves PR, 2000, 'Unique adaptor design for AFLP fingerprinting', BioTechniques, vol. 29, pp. 745 - 750, http://dx.doi.org/10.2144/00294bm14
2000
Byun R; Elbourne LDH; Lan R; Reeves PR, 1999, 'Evolutionary relationships of pathogenic clones of VIbrio cholerae by sequence analysis of four housekeeping genes', Infection and Immunity, vol. 67, pp. 1116 - 1124, http://dx.doi.org/10.1128/iai.67.3.1116-1124.1999
1999
Lan R; Reeves PR, 1998, 'Molecular Basis of Ribotype Variation in the Seventh Pandemic Clone and its O139 Variant of Vibrio cholerae', Memorias do Instituto Oswaldo Cruz, vol. 93, pp. 595 - 599, http://dx.doi.org/10.1590/s0074-02761998000500007
1998
Reeves PR; Lan R, 1998, 'Cholera in the 1990s', British Medical Bulletin, vol. 54, pp. 611 - 623, http://dx.doi.org/10.1093/oxfordjournals.bmb.a011714
1998
Lan R; Reeves PR, 1998, 'Recombination between rRNA operons created most of the ribotype variation observed in the seventh pandemic clone of Vibrio cholerae', Microbiology, vol. 144, pp. 1213 - 1221, http://dx.doi.org/10.1099/00221287-144-5-1213
1998
Pérez Luz S; Rodríguez-Valera F; Lan R; Reeves PR, 1998, 'Variation of the ribosomal operon 16S-23S gene spacer region in representatives of Salmonella enterica subspecies', Journal of Bacteriology, vol. 180, pp. 2144 - 2151, http://dx.doi.org/10.1128/jb.180.8.2144-2151.1998
1998
Pupo GM; Karaolis DKR; Lan R; Reeves PR, 1997, 'Evolutionary relationships among pathogenic and nonpathogenic Escherichia coli strains inferred from multilocus enzyme electrophoresis and mdh sequence studies', Infection and Immunity, vol. 65, pp. 2685 - 2692, http://dx.doi.org/10.1128/iai.65.7.2685-2692.1997
1997
Lan R; Reeves PR, 1996, 'Gene transfer is a major factor in bacterial evolution', Molecular Biology and Evolution, vol. 13, pp. 47 - 55, http://dx.doi.org/10.1093/oxfordjournals.molbev.a025569
1996
Karaolis DKR; Lan R; Reeves PR, 1995, 'The sixth and seventh cholera pandemics are due to independent clones separately derived from environmental, nontoxigenic, non-O1 Vibrio cholerae', Journal of Bacteriology, vol. 177, pp. 3191 - 3198, http://dx.doi.org/10.1128/jb.177.11.3191-3198.1995
1995
Karaolis DKR; Lan R; Reeves PR, 1994, 'Molecular evolution of the seventh-pandemic clone of Vibrio cholerae and its relationship to other pandemic and epidemic V. cholerae isolates', Journal of Bacteriology, vol. 176, pp. 6199 - 6206, http://dx.doi.org/10.1128/jb.176.20.6199-6206.1994
1994
Lan R; Greenoak GE; Moran C, 1994, 'PYRIMIDINE DIMER INDUCTION AND REMOVAL IN THE EPIDERMIS OF HAIRLESS MICE: INEFFICIENT REPAIR IN THE GENOME OVERALL AND RAPID REPAIR IN THE H‐ras SEQUENCE', Photochemistry and Photobiology, vol. 59, pp. 356 - 361, http://dx.doi.org/10.1111/j.1751-1097.1994.tb05047.x
1994
Karaolis DKR; Lan R; Reeves PR, 1994, 'Sequence variation in Shigella sonnei (Sonnei), a pathogenic clone of Escherichia coli, over four continents and 41 years', Journal of Clinical Microbiology, vol. 32, pp. 796 - 802, http://dx.doi.org/10.1128/jcm.32.3.796-802.1994
1994
Reeves PR; Farnell L; Lan R, 1994, 'Multicomp: A program for preparing sequence data for phylogenetic analysis', Bioinformatics, vol. 10, pp. 281 - 284, http://dx.doi.org/10.1093/bioinformatics/10.3.281
1994
Thampapillai G; Lan R; Reeves PR, 1994, 'Molecular evolution in the gnd locus of Salmonella enterica', Molecular Biology and Evolution, vol. 11, pp. 813 - 828
1994

Bacterial population structures and evolution of pathogens.