Select Publications

Journal articles

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, 2020, 'Genomic epidemiology of Corynebacterium striatum from three regions of China: an emerging national nosocomial epidemic.', J Hosp Infect,

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, 2020, 'Citrobacter freundii activates the NLRP3 inflammasome via T6SS.', J Infect Dis,

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,

Loo SL; Ong A; Kyaw W; Thibaut LM; Lan R; Tanaka MM, 2020, 'A comparative examination of non-synonymous polymorphism counts in bacterial genomes.', Appl Environ Microbiol,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

Zhang X; Payne M; Lan R, 2019, 'In silico identification of serovar-specific genes for salmonella serotyping', Frontiers in Microbiology, vol. 10, pp. 835,

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,

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,

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,

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,

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,

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,

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,

Luu LDW; Octavia S; Zhong L; Raftery MJ; Sintchenko V; Lan R, 2018, 'Proteomic Adaptation of Australian Epidemic Bordetella pertussis', Proteomics, vol. 18,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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,

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