标题/作者	年份
Open-access bacterial population genomics: BIGSdb software, the PubMLST. org website and their applications KA Jolley, JE Bray, MCJ Maiden Wellcome open research 3	2018
GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens Z Zhou, NF Alikhan, MJ Sergeant, N Luhmann, C Vaz, AP Francisco, ... Genome research 28 (9), 1395-1404	2018
The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity Z Zhou, NF Alikhan, K Mohamed, Y Fan, M Achtman, D Brown, ... Genome research 30 (1), 138-152	2020
MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies J Robertson, JHE Nash Microbial genomics 4 (8)	2018
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0 F Asnicar, AM Thomas, F Beghini, C Mengoni, S Manara, P Manghi, ... Nature communications 11 (1), 2500	2020
Fast and flexible bacterial genomic epidemiology with PopPUNK JA Lees, SR Harris, G Tonkin-Hill, RA Gladstone, SW Lo, JN Weiser, ... Genome research 29 (2), 304-316	2019
Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder MHK Johansson, V Bortolaia, S Tansirichaiya, FM Aarestrup, AP Roberts, ... Journal of Antimicrobial Chemotherapy 76 (1), 101-109	2021
Ancient pathogen genomics as an emerging tool for infectious disease research MA Spyrou, KI Bos, A Herbig, J Krause Nature Reviews Genetics 20 (6), 323-340	2019
Persistent infection and long-term carriage of typhoidal and nontyphoidal salmonellae O Gal-Mor Clinical microbiology reviews 32 (1), 10.1128/cmr. 00088-18	2018
Molecular mechanism of azithromycin resistance among typhoidal Salmonella strains in Bangladesh identified through passive pediatric surveillance Y Hooda, MSI Sajib, H Rahman, SP Luby, J Bondy-Denomy, ... PLoS neglected tropical diseases 13 (11), e0007868	2019
Embracing diversity: differences in virulence mechanisms, disease severity, and host adaptations contribute to the success of nontyphoidal Salmonella as a foodborne pathogen RA Cheng, CR Eade, M Wiedmann Frontiers in microbiology 10, 1368	2019
Metabolism the difficile way: the key to the success of the pathogen Clostridioides difficile M Neumann-Schaal, D Jahn, K Schmidt-Hohagen Frontiers in microbiology 10, 219	2019
Integrating whole-genome sequencing data into quantitative risk assessment of foodborne antimicrobial resistance: a review of opportunities and challenges L Collineau, P Boerlin, CA Carson, B Chapman, A Fazil, B Hetman, ... Frontiers in Microbiology 10, 1107	2019
Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms EFSA Panel on Biological Hazards (EFSA BIOHAZ Panel), ... EFSA Journal 17 (12), e05898	2019
Molecular epidemiology of Salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid P Alba, P Leekitcharoenphon, V Carfora, R Amoruso, G Cordaro, ... Microbial genomics 6 (5)	2020
Pan-genome analysis of ancient and modern Salmonella enterica demonstrates genomic stability of the invasive para C lineage for millennia Z Zhou, I Lundstrøm, A Tran-Dien, S Duchêne, NF Alikhan, MJ Sergeant, ... Current Biology 28 (15), 2420-2428. e10	2018
Emergence of human-adapted Salmonella enterica is linked to the Neolithization process FM Key, C Posth, LR Esquivel-Gomez, R Hübler, MA Spyrou, ... Nature ecology & evolution 4 (3), 324-333	2020
Whole genome sequencing: bridging one-health surveillance of foodborne diseases P Gerner-Smidt, J Besser, J Concepción-Acevedo, JP Folster, J Huffman, ... Frontiers in Public Health 7, 172	2019
Assessment and comparison of molecular subtyping and characterization methods for Salmonella S Tang, RH Orsi, H Luo, C Ge, G Zhang, RC Baker, A Stevenson, ... Frontiers in microbiology 10, 1591	2019
INNUENDO: a cross‐sectoral platform for the integration of genomics in the surveillance of food‐borne pathogens AK Llarena, BF Ribeiro‐Gonçalves, D Nuno Silva, J Halkilahti, ... EFSA Supporting Publications 15 (11), 1498E	2018

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