Select Publications
Book Chapters
Lan R; Octavia S, 2018, 'Vaccine driven selection and the changing molecular epidemiology of Bordetella pertussis', in Rohani P; Scarpino S (ed.), , Oxford University Press, USA, pp. 166 - 180
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 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
Journal articles
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 : an official publication of the Infectious Diseases Society of America, 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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