Select Publications
Book Chapters
2018, 'Vaccine driven selection and the changing molecular epidemiology of Bordetella pertussis', in Rohani P; Scarpino S (ed.), Pertussis Epidemiology, Immunology, and Evolution, Oxford University Press, USA, pp. 166 - 180
,2015, 'Chapter 65 Shigella and Shigellosis Genetics, Epidemiology and Pathogenesis', in Molecular Medical Microbiology, Elsevier, pp. 1147 - 1168, http://dx.doi.org/10.1016/b978-0-12-397169-2.00065-2
,2014, 'The Family Enterobacteriaceae', in DeLong EF; Lory S; Stackebrandt E; Thompson F (ed.), The Prokaryotes, Springer, pp. 225 - 286
,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
,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
,2006, 'Evolution of Enteric Pathogens', in Seifert HS; DiRita VJ (ed.), Evolution of Microbial Pathogens, ASM Press, Washington, DC, pp. 273
,Journal articles
2024, 'Genomic evidence of two-staged transmission of the early seventh cholera pandemic.', Nat Commun, 15, pp. 8504, http://dx.doi.org/10.1038/s41467-024-52800-w
,2024, 'A Multilocus Sequence Typing Scheme for Rapid Identification of Xanthomonas citri Based on Whole-Genome Sequencing Data', Phytopathology, 114, pp. 1480 - 1489, http://dx.doi.org/10.1094/PHYTO-12-23-0490-R
,2024, 'DODGE: automated point source bacterial outbreak detection using cumulative long term genomic surveillance', Bioinformatics, 40, http://dx.doi.org/10.1093/bioinformatics/btae427
,2024, 'Prevotella copri alleviates hyperglycemia and regulates gut microbiota and metabolic profiles in mice', mSystems, 9, http://dx.doi.org/10.1128/msystems.00532-24
,2024, 'Corrigendum to “Horizontal transfer of antibiotic resistance genes within the bacterial communities in aquacultural environment” [Sci. Total Environ. 820 (2022) 153286] (Science of the Total Environment (2022) 820, (S0048969722003771), (10.1016/j.scitotenv.2022.153286))', Science of the Total Environment, 922, http://dx.doi.org/10.1016/j.scitotenv.2024.171434
,2024, 'Emergence of Poultry-Associated Human Salmonella enterica Serovar Abortusovis Infections, New South Wales, Australia', Emerging Infectious Diseases, 30, pp. 691 - 700, http://dx.doi.org/10.3201/eid3004.230958
,2024, 'Uncovering the boundaries of Campylobacter species through large-scale phylogenetic and nucleotide identity analyses', mSystems, 9, http://dx.doi.org/10.1128/msystems.01218-23
,2024, 'Genomic diversity of Salmonella enterica serovar Typhimurium isolated from chicken processing facilities in New South Wales, Australia', Frontiers in Microbiology, 15, http://dx.doi.org/10.3389/fmicb.2024.1440777
,2024, 'SaLTy: a novel Staphylococcus aureus Lineage Typer', Microbial Genomics, 10, http://dx.doi.org/10.1099/mgen.0.001250
,2023, 'Emergence and genomic insights of non-pandemic O1 Vibrio cholerae in Zhejiang, China', Microbiology Spectrum, 11, http://dx.doi.org/10.1128/spectrum.02615-23
,2023, 'Genomic Characteristion of Opportunistic Pathogen Kluyvera Reveals a Novel CTX-M Subgroup', Microorganisms, 11, http://dx.doi.org/10.3390/microorganisms11122836
,2023, 'Emerging Aeromonas enteric infections: their association with inflammatory bowel disease and novel pathogenic mechanisms', Microbiology Spectrum, 11, http://dx.doi.org/10.1128/spectrum.01088-23
,2023, 'Bacteroides vulgatus Ameliorates Lipid Metabolic Disorders and Modulates Gut Microbial Composition in Hyperlipidemic Rats', Microbiology Spectrum, 11, http://dx.doi.org/10.1128/spectrum.02517-22
,2023, 'Genomic Epidemiology and Multilevel Genome Typing of Australian Salmonella enterica Serovar Enteritidis', Microbiology Spectrum, 11, http://dx.doi.org/10.1128/spectrum.03014-22
,2023, 'Genomic epidemiology and multilevel genome typing of Bordetella pertussis', Emerging Microbes and Infections, 12, http://dx.doi.org/10.1080/22221751.2023.2239945
,2023, 'Integrating proteomic data with metabolic modeling provides insight into key pathways of Bordetella pertussis biofilms', Frontiers in Microbiology, 14, http://dx.doi.org/10.3389/fmicb.2023.1169870
,2023, 'Vibrio metschnikovii as an emergent pathogen: analyses of phylogeny and O-antigen and identification of possible virulence characteristics', Emerging Microbes and Infections, 12, http://dx.doi.org/10.1080/22221751.2023.2252522
,2022, 'Bacteroides vulgatus attenuates experimental mice colitis through modulating gut microbiota and immune responses', Frontiers in Immunology, 13, http://dx.doi.org/10.3389/fimmu.2022.1036196
,2022, 'Genomic Epidemiology of Vibrio cholerae O139, Zhejiang Province, China, 1994–2018', Emerging Infectious Diseases, 28, pp. 2253 - 2260, http://dx.doi.org/10.3201/eid2811.212066
,2022, 'Dissecting Listeria monocytogenes Persistent Contamination in a Retail Market Using Whole-Genome Sequencing', Microbiology Spectrum, 10, http://dx.doi.org/10.1128/spectrum.00185-22
,2022, 'Horizontal transfer of antibiotic resistance genes within the bacterial communities in aquacultural environment', Science of the Total Environment, 820, http://dx.doi.org/10.1016/j.scitotenv.2022.153286
,2022, 'Metagenomics combined with comprehensive validation as a public health risk assessment tool for urban and agricultural run-off', Water Research, 209, http://dx.doi.org/10.1016/j.watres.2021.117941
,2022, 'Improved Genomic Identification, Clustering, and Serotyping of Shiga Toxin-Producing Escherichia coli Using Cluster/Serotype-Specific Gene Markers', Frontiers in Cellular and Infection Microbiology, 11, pp. 772574, http://dx.doi.org/10.3389/fcimb.2021.772574
,2022, 'Evolutionary and genomic insights into the long-term colonization of Shigella flexneri in animals', Emerging Microbes and Infections, 11, pp. 2069 - 2079, http://dx.doi.org/10.1080/22221751.2022.2109514
,2022, 'Genomic dissection of the microevolution of Australian epidemic Bordetella pertussis', Emerging Microbes and Infections, 11, pp. 1460 - 1473, http://dx.doi.org/10.1080/22221751.2022.2077129
,2022, 'MGTdb: A web service and database for studying the global and local genomic epidemiology of bacterial pathogens', Database, 2022, http://dx.doi.org/10.1093/database/baac094
,2022, 'Rapid Surface Shaving for Proteomic Identification of Novel Surface Antigens for Vaccine Development', , 2414, pp. 47 - 62, http://dx.doi.org/10.1007/978-1-0716-1900-1_4
,2021, 'Cluster-specific gene markers enhance Shigella and Enteroinvasive Escherichia coli in silico serotyping', Microbial Genomics, 7, pp. 2021.01.30.428723, http://dx.doi.org/10.1099/mgen.0.000704
,2021, 'Comparative genomics of Chinese and international isolates of Escherichia albertii: population structure and evolution of virulence and antimicrobial resistance', Microbial Genomics, 7, pp. 2021.02.01.429068, http://dx.doi.org/10.1099/mgen.0.000710
,2021, 'Development and comparison of novel multiple cross displacement amplification (MCDA) assays with other nucleic acid amplification methods for SARS-CoV-2 detection', Scientific Reports, 11, pp. 1873, http://dx.doi.org/10.1038/s41598-021-81518-8
,2021, 'Evolutionary genomics of recent clinical Bordetella pertussis isolates from Iran: wide circulation of multiple ptxP3 lineages and report of the first ptxP3 filamentous hemagglutinin-negative B. pertussis', Infection, Genetics and Evolution, 93, http://dx.doi.org/10.1016/j.meegid.2021.104970
,2021, 'Antimicrobial Resistance and Molecular Characterization of Citrobacter spp. Causing Extraintestinal Infections', Frontiers in Cellular and Infection Microbiology, 11, http://dx.doi.org/10.3389/fcimb.2021.737636
,2021, 'Population Structure and Multidrug Resistance of Non-O1/Non-O139 Vibrio cholerae in Freshwater Rivers in Zhejiang, China', Microbial Ecology, 82, pp. 319 - 333, http://dx.doi.org/10.1007/s00248-020-01645-z
,2021, 'Multilevel genome typing describes short- And long-term vibrio cholerae molecular epidemiology', mSystems, 6, pp. 10.1128/msystems.00134 - 10.1128/msystems.00121, http://dx.doi.org/10.1128/mSystems.00134-21
,2021, 'Citrobacter freundii Activation of NLRP3 Inflammasome via the Type VI Secretion System', Journal of Infectious Diseases, 223, pp. 2174 - 2185, http://dx.doi.org/10.1093/infdis/jiaa692
,2021, 'Beta- and Novel Delta-Coronaviruses Are Identified from Wild Animals in the Qinghai-Tibetan Plateau, China', Virologica Sinica, 36, pp. 402 - 411, http://dx.doi.org/10.1007/s12250-020-00325-z
,2021, 'Comparative Phosphoproteomics of Classical Bordetellae Elucidates the Potential Role of Serine, Threonine and Tyrosine Phosphorylation in Bordetella Biology and Virulence', Frontiers in Cellular and Infection Microbiology, 11, http://dx.doi.org/10.3389/fcimb.2021.660280
,2021, 'Genomic epidemiology of Corynebacterium striatum from three regions of China: an emerging national nosocomial epidemic', Journal of Hospital Infection, 110, pp. 67 - 75, http://dx.doi.org/10.1016/j.jhin.2020.10.005
,2021, 'Establishment and Application of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry for Detection of Shewanella Genus', Frontiers in Microbiology, 12, http://dx.doi.org/10.3389/fmicb.2021.625821
,2021, 'Continuous genomic surveillance monitored the in vivo evolutionary trajectories of vibrio parahaemolyticus and identified a new virulent genotype', mSystems, 6, http://dx.doi.org/10.1128/mSystems.01254-20
,2021, 'Cluster-specific gene markers enhance Shigella and enteroinvasive Escherichia coli in silico serotyping', Microbial Genomics, 7, pp. 000704, http://dx.doi.org/10.1099/MGEN.0.000704
,2021, 'Comparative genomics of Chinese and international isolates of Escherichia albertii: population structure and evolution of virulence and antimicrobial resistance', Microbial Genomics, 7, pp. 000710, http://dx.doi.org/10.1099/MGEN.0.000710
,2021, 'Elucidation of global and national genomic epidemiology of salmonella enterica serovar enteritidis through multilevel genome typing', Microbial Genomics, 7, pp. 000605, http://dx.doi.org/10.1099/MGEN.0.000605
,2021, 'Enhancing genomics-based outbreak detection of endemic salmonella enterica serovar typhimurium using dynamic thresholds', Microbial Genomics, 7, pp. 000310, http://dx.doi.org/10.1099/MGEN.0.000310
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