Ruiting Lan

Summary

Affiliation: University of New South Wales
Country: Australia

Publications

  1. ncbi request reprint AFLP analysis of Salmonella enterica serovar Typhimurium isolates of phage types DT 9 and DT 135: diversity within phage types and its epidemiological significance
    Ruiting Lan
    School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia
    Microbes Infect 5:841-50. 2003
  2. pmc Genetic relationships of phage types and single nucleotide polymorphism typing of Salmonella enterica Serovar Typhimurium
    Stanley Pang
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
    J Clin Microbiol 50:727-34. 2012
  3. pmc Population structure and evolution of non-O1/non-O139 Vibrio cholerae by multilocus sequence typing
    Sophie Octavia
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
    PLoS ONE 8:e65342. 2013
  4. pmc Bordetella pertussis clones identified by multilocus variable-number tandem-repeat analysis
    Jacob Kurniawan
    University of New South Wales, Sydney, New South Wales, Australia
    Emerg Infect Dis 16:297-300. 2010
  5. pmc Evolution of seventh cholera pandemic and origin of 1991 epidemic, Latin America
    Connie Lam
    University of New South Wales, Sydney, New South Wales 2052, Australia
    Emerg Infect Dis 16:1130-2. 2010
  6. pmc Genomic diversity and adaptation of Salmonella enterica serovar Typhimurium from analysis of six genomes of different phage types
    Stanley Pang
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
    BMC Genomics 14:718. 2013
  7. pmc Molecular analysis of non-O1/non-O139 Vibrio cholerae isolated from hospitalised patients in China
    Yun Luo
    Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
    BMC Microbiol 13:52. 2013
  8. pmc Genetic diversity and molecular typing of Listeria monocytogenes in China
    Yan Wang
    State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, China CDC, Changbai Road 155, Changping, Beijing, China
    BMC Microbiol 12:119. 2012
  9. pmc Genesis of a novel Shigella flexneri serotype by sequential infection of serotype-converting bacteriophages SfX and SfI
    Qiangzheng Sun
    State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, China CDC, P, O, Box 5, Changping, Beijing, China
    BMC Microbiol 11:269. 2011
  10. ncbi request reprint Molecular markers with potential to replace phage typing for Salmonella enterica serovar typhimurium
    Ruiting Lan
    School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
    J Microbiol Methods 68:145-56. 2007

Collaborators

Detail Information

Publications44

  1. ncbi request reprint AFLP analysis of Salmonella enterica serovar Typhimurium isolates of phage types DT 9 and DT 135: diversity within phage types and its epidemiological significance
    Ruiting Lan
    School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW 2006, Australia
    Microbes Infect 5:841-50. 2003
    ..The value of AFLP is in locating DNA fragments useful for typing, but implementation of a replacement typing scheme would probably involve multiplex PCR or microarray technologies...
  2. pmc Genetic relationships of phage types and single nucleotide polymorphism typing of Salmonella enterica Serovar Typhimurium
    Stanley Pang
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
    J Clin Microbiol 50:727-34. 2012
    ..However, 12 SNP profiles contained more than one phage type, and more SNPs would be needed for further differentiation. SNP typing should be considered as a replacement for phage typing for the identification of S. Typhimurium strains...
  3. pmc Population structure and evolution of non-O1/non-O139 Vibrio cholerae by multilocus sequence typing
    Sophie Octavia
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
    PLoS ONE 8:e65342. 2013
    ..cholerae serogroups O114 to O117 were also analysed and formed a separate population with V. mimicus. The MLST scheme developed in this study provides a framework to identify sporadic cholera isolates by genetic identity...
  4. pmc Bordetella pertussis clones identified by multilocus variable-number tandem-repeat analysis
    Jacob Kurniawan
    University of New South Wales, Sydney, New South Wales, Australia
    Emerg Infect Dis 16:297-300. 2010
    ..Typing of genes encoding acellular vaccine antigens showed changes that may be vaccine driven in 2 MTs prevalent in Australia...
  5. pmc Evolution of seventh cholera pandemic and origin of 1991 epidemic, Latin America
    Connie Lam
    University of New South Wales, Sydney, New South Wales 2052, Australia
    Emerg Infect Dis 16:1130-2. 2010
    ..Isolates from the 1991 epidemic in Latin America shared a profile with 1970s isolates from Africa, suggesting a possible origin in Africa. Data also showed that the observed genotypes spread easily and widely...
  6. pmc Genomic diversity and adaptation of Salmonella enterica serovar Typhimurium from analysis of six genomes of different phage types
    Stanley Pang
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
    BMC Genomics 14:718. 2013
    ..Six Typhimurium strains of different phage types (defined by patterns of susceptibility to lysis by a set of bacteriophages) were analysed using Illumina high-throughput genome sequencing...
  7. pmc Molecular analysis of non-O1/non-O139 Vibrio cholerae isolated from hospitalised patients in China
    Yun Luo
    Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, China
    BMC Microbiol 13:52. 2013
    ..The aim of this study was to determine the genetic diversity of non-O1/non-O139 V. cholerae isolates from hospitalised diarrhoeal patients in Zhejiang Province, China...
  8. pmc Genetic diversity and molecular typing of Listeria monocytogenes in China
    Yan Wang
    State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, China CDC, Changbai Road 155, Changping, Beijing, China
    BMC Microbiol 12:119. 2012
    ..monocytogenes has been isolated from foods and food processing environments in China. However little is known of genetic diversity of Chinese L. monocytogenes isolates and their relationships with global isolates...
  9. pmc Genesis of a novel Shigella flexneri serotype by sequential infection of serotype-converting bacteriophages SfX and SfI
    Qiangzheng Sun
    State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, China CDC, P, O, Box 5, Changping, Beijing, China
    BMC Microbiol 11:269. 2011
    ..The genesis of new S. flexneri serotypes is commonly mediated by serotype-converting bacteriophages. Untypeable or novel serotypes from natural infections had been reported worldwide but have not been generated in laboratory...
  10. ncbi request reprint Molecular markers with potential to replace phage typing for Salmonella enterica serovar typhimurium
    Ruiting Lan
    School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
    J Microbiol Methods 68:145-56. 2007
    ..Eight patterns can unambiguously identify 8 phage types and a further 12 correlated with phage type distribution, showing the usefulness of these markers for molecular phage typing...
  11. ncbi request reprint Population structure, origins and evolution of major Salmonella enterica clones
    Ruiting Lan
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
    Infect Genet Evol 9:996-1005. 2009
    ..The fully resolved phylogenetic tree allows one to trace the mutational changes occurred during clonal diversification. Genome wide SNPs have greatly enhanced our understanding of the evolution of Salmonella clones...
  12. pmc Molecular evolutionary relationships of enteroinvasive Escherichia coli and Shigella spp
    Ruiting Lan
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Australia
    Infect Immun 72:5080-8. 2004
    ..Two strains were found in the pINV B form by using the ipgD sequence, with one strain having an mxiA sequence similar to the divergent sequence of D1. Clearly, EIEC and Shigella spp. form a pathovar of E. coli...
  13. ncbi request reprint Escherichia coli in disguise: molecular origins of Shigella
    Ruiting Lan
    School of Molecular and Microbial Biosciences, The University of Sydney, NSW 2006, Australia
    Microbes Infect 4:1125-32. 2002
    ..The chromosomally determined phenotypic properties of Shigella result from convergent evolution during niche adaptation, most due to loss of function, some from negative selection pressure...
  14. ncbi request reprint Genome-wide analysis of single nucleotide polymorphisms in Bordetella pertussis using comparative genomic sequencing
    Ram P Maharjan
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
    Res Microbiol 159:602-8. 2008
    ..The data also allowed us to compare genomic diversity with other "clonal" human pathogens such as Mycobacterium tuberculosis and Yersinia pestis, showing that B. pertussis may be one of the least variable pathogenic bacterial species...
  15. doi request reprint Insight into evolution of Bordetella pertussis from comparative genomic analysis: evidence of vaccine-driven selection
    Sophie Octavia
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
    Mol Biol Evol 28:707-15. 2011
    ..Our findings suggest that B. pertussis, despite its high population homogeneity, is evolving in response to vaccination pressure with recent expansion of clones carrying variants of genes encoding ACV antigens...
  16. ncbi request reprint Population structure and virulence content of avian pathogenic Escherichia coli isolated from outbreaks in Sri Lanka
    D R A Dissanayake
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
    Vet Microbiol 168:403-12. 2014
    ..Our results enhanced the understanding of APEC population structure and virulence association...
  17. pmc Multiple-locus variable-number tandem-repeat analysis of Salmonella enterica serovar Typhi
    Sophie Octavia
    University of New South Wales, Sydney, NSW, Australia
    J Clin Microbiol 47:2369-76. 2009
    ..We suggest that seven of the nine most polymorphic VNTRs be used as a standardized typing scheme for epidemiological typing...
  18. doi request reprint Rapid and accurate typing of Bordetella pertussis targeting genes encoding acellular vaccine antigens using real time PCR and High Resolution Melt analysis
    Wai Fong Chan
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
    J Microbiol Methods 77:326-9. 2009
    ..These rapid methods are suitable for large-scale studies of vaccine-driven evolution of Bordetella pertussis...
  19. pmc Vibrio cholerae pathogenic clones
    Anna Salim
    School of Molecular and Microbial Biosciences, University of Sydney, Sydney, New South Wales 2006, Australia
    Emerg Infect Dis 11:1758-60. 2005
    ..The sixth pandemic clone was well separated from them...
  20. ncbi request reprint Frequent recombination and low level of clonality within Salmonella enterica subspecies I
    Sophie Octavia
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
    Microbiology 152:1099-108. 2006
    ..enterica. These results showed that the genes studied have undergone frequent recombination, suggesting a low level of clonality within subspecies I of S. enterica...
  21. pmc Fluorescent amplified fragment length polymorphism analysis of Salmonella enterica serovar typhimurium reveals phage-type- specific markers and potential for microarray typing
    Honghua Hu
    School of Molecular and Microbial Biosciences, The University of Sydney, Sydney, New South Wales 2006, Australia
    J Clin Microbiol 40:3406-15. 2002
    ....
  22. pmc Adaptation of multilocus sequencing for studying variation within a major clone: evolutionary relationships of Salmonella enterica serovar Typhimurium
    Honghua Hu
    School of Molecular and Microbial Biosciences, The University of Sydney, New South Wales, Australia
    Genetics 172:743-50. 2006
    ..We found that sequencing intergenic regions provides a good strategy for detection of mutational polymorphisms and study of phylogenetic relationships of closely related isolates and would be applicable to many other species...
  23. ncbi request reprint Importation of the major pilin TcpA gene and frequent recombination drive the divergence of the Vibrio pathogenicity island in Vibrio cholerae
    Chin Yen Tay
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
    FEMS Microbiol Lett 289:210-8. 2008
    ..These findings enhance our understanding of variation in the VPI, and of the pathogenic potential of VPI-positive environmental isolates...
  24. pmc Multi-locus variable number tandem repeat analysis of 7th pandemic Vibrio cholerae
    Connie Lam
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, Australia
    BMC Microbiol 12:82. 2012
    ..In this study we use multilocus variable number of tandem repeats (VNTRs) analysis (MLVA) to discriminate between isolates of the 7th pandemic clone of Vibrio cholerae...
  25. pmc Computational bacterial genome-wide analysis of phylogenetic profiles reveals potential virulence genes of Streptococcus agalactiae
    Frank Po Yen Lin
    Centre for Health Informatics, University of New South Wales, Sydney, Australia
    PLoS ONE 6:e17964. 2011
    ..This computational pipeline can also be extended to in silico analysis of virulence determinants of other bacterial pathogens...
  26. pmc Population structure and evolution of pathogenicity of Yersinia pseudotuberculosis
    Shear Lane Ch'ng
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
    Appl Environ Microbiol 77:768-75. 2011
    ..The differences in pathogenicity among Y. pseudotuberculosis strains are likely due to the variable presence and instability of the virulence factors...
  27. doi request reprint Newly emerging clones of Bordetella pertussis carrying prn2 and ptxP3 alleles implicated in Australian pertussis epidemic in 2008-2010
    Sophie Octavia
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Australia
    J Infect Dis 205:1220-4. 2012
    ..The data suggest increasing selection among the B. pertussis population in Australia in favor of strains carrying prn2 and ptxP3 under the pressure of acellular vaccine-induced immunity...
  28. pmc Evolutionary changes of the flhDC flagellar master operon in Shigella strains
    Akira Tominaga
    School of Molecular and Microbial Biosciences GO8, The University of Sydney, Sydney, NSW 2006, Australia
    J Bacteriol 187:4295-302. 2005
    ..Two cluster 2 strains were found to have unique flhDC sequences, which are most probably due to recombination during the exchange of the adjacent O-antigen gene clusters...
  29. pmc Single nucleotide polymorphism typing of global Salmonella enterica serovar Typhi isolates by use of a hairpin primer real-time PCR assay
    Sophie Octavia
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
    J Clin Microbiol 48:3504-9. 2010
    ..These clusters can be identified by using five SNPs, while the full differentiation of the 25 SNP profiles requires a minimum of 24 SNPs. This real-time PCR-based SNP typing method will be useful for global epidemiological analysis...
  30. pmc 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
    Vikneswari Mahendran
    The School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
    PLoS ONE 8:e75525. 2013
    ..concisus strains and the polymorphisms of C. concisus zot gene. The data suggest that the possible role of C. concisus strains containing specific polymorphic forms of zot gene in human IBD should be investigated. ..
  31. doi request reprint Selection and emergence of pertussis toxin promoter ptxP3 allele in the evolution of Bordetella pertussis
    Connie Lam
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
    Infect Genet Evol 12:492-5. 2012
    ..pertussis and its emergence is concurrent with the change to the non-vaccine prn2 allele. Our results suggest that the globally distributed cluster I of B. pertussis has the ability to evade vaccine induced selection pressure...
  32. pmc Population structure of Helicobacter pylori among ethnic groups in Malaysia: recent acquisition of the bacterium by the Malay population
    Chin Yen Tay
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
    BMC Microbiol 9:126. 2009
    ..Malaysia is made up of three major ethnic populations, Malay, Chinese and Indian, providing a good population for studying recent H. pylori migration and admixture...
  33. pmc Conditions for the evolution of gene clusters in bacterial genomes
    Sara Ballouz
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales, Australia
    PLoS Comput Biol 6:e1000672. 2010
    ..Under these conditions the selfish operon model is still viable as an explanation for the evolution of gene clusters...
  34. pmc Single-nucleotide-polymorphism typing and genetic relationships of Salmonella enterica serovar Typhi isolates
    Sophie Octavia
    School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
    J Clin Microbiol 45:3795-801. 2007
    ..87, and a minimum of 16 SNPs may be used to achieve the same level of differentiation. The SNP typing method we developed will be a valuable tool for global epidemiology studies of serovar Typhi...
  35. pmc Rates of mutation and host transmission for an Escherichia coli clone over 3 years
    Peter R Reeves
    School of Molecular and Microbial Biosciences, University of Sydney, Sydney, Australia
    PLoS ONE 6:e26907. 2011
    ..The ability of a UTI strain to persist for 2 years and also to transfer readily within a household has implications for epidemiology, diagnosis, and clinical intervention...
  36. ncbi request reprint Amplified fragment length polymorphism analysis of Salmonella enterica
    Ruiting Lan
    Microbiology and Immunology, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
    Methods Mol Biol 394:119-32. 2007
    ..We present here protocols for both radioactively labeled and fluorescent dye-labeled AFLP analyses that are also applicable to other bacterial species. Fluorescent AFLP has proved to be reproducible and capable of standardization...
  37. pmc Molecular basis of the indole-negative reaction in Shigella strains: extensive damages to the tna operon by insertion sequences
    Ferdousi Rezwan
    School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia
    J Bacteriol 186:7460-5. 2004
    ..coli. Parallel loss of the trait and prevalence of indole-negative strains suggest that the trait is deleterious in Shigella strains and advantages those without it...
  38. pmc Comparison of two major forms of the Shigella virulence plasmid pINV: positive selection is a major force driving the divergence
    Ruiting Lan
    School of Molecular and Microbial Biosciences, University of Sydney, Sydney, Australia
    Infect Immun 71:6298-306. 2003
    ..flexneri serotype 5. The incompatibility of the two pINV forms appears to be due to either small differences in the mvpAT postsegregational killing system or the presence of an unknown system in pINVA...
  39. pmc Pandemic spread of cholera: genetic diversity and relationships within the seventh pandemic clone of Vibrio cholerae determined by amplified fragment length polymorphism
    Ruiting Lan
    Department of Microbiology, University of Sydney, NSW 2006, Australia
    J Clin Microbiol 40:172-81. 2002
    ..These observations have major implications for our understanding of cholera epidemiology...
  40. pmc In silico prioritisation of candidate genes for prokaryotic gene function discovery: an application of phylogenetic profiles
    Frank P Y Lin
    Centre for Health Informatics, University of New South Wales, Sydney, Australia
    BMC Bioinformatics 10:86. 2009
    ..Here we present two prokaryotic CGP methods, based on phylogenetic profiles, to assist with this task...
  41. pmc Investigation of the enteric pathogenic potential of oral Campylobacter concisus strains isolated from patients with inflammatory bowel disease
    Yazan Ismail
    The School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
    PLoS ONE 7:e38217. 2012
    ..This study investigated if patients with IBD are colonized with specific oral C. concisus strains that have potential to cause enteric diseases...
  42. ncbi request reprint The distribution of insertion sequences in the genome of Shigella flexneri strain 2457T
    Lamia Zaghloul
    FEMS Microbiol Lett 277:197-204. 2007
    ..Of the genes disrupted by ISs, those involved in signal transduction, intracellular trafficking, and cell motility are most commonly targeted, suggesting selection against genes in these categories...
  43. pmc Sex and virulence in Escherichia coli: an evolutionary perspective
    Thierry Wirth
    Department of Molecular Biology, Schumannstrasse 21 22, Max Planck Institut für Infektionsbiologie, 10117 Berlin, Germany
    Mol Microbiol 60:1136-51. 2006
    ..This long-term pattern of evolution was observed in genes distributed throughout the genome, and thereby is the likely result of episodic selection for strains that can escape the host immune response...