VFDB 2022: a general classification scheme for bacterial virulence factors

Liu, Bo; Zheng, Dan; Zhou, Siyu; Chen, Lihong; Yang, Jian

doi:10.1093/nar/gkab1107

Cited by 757 publications

(424 citation statements)

References 31 publications

Supporting

Mentioning

424

Contrasting

Order By: Relevance

“…The site allows construction of sophisticated search strategies and options for analysing host-pathogen interactions are a future priority. The third, the popular VFDB ( 66 ), returns with a novel hierarchical classification of its bacterial virulence factors (VFs) into 14 categories and >100 subcategories. Chromosome maps and genomic loci can be visualised with VFs colour-coded according to their categorisation.…”

Section: New and Updated Databasesmentioning

confidence: 99%

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

Rigden

Fernández

2021

Nucleic Acids Research

View full text Add to dashboard Cite

The 2022 Nucleic Acids Research Database Issue contains 185 papers, including 87 papers reporting on new databases and 85 updates from resources previously published in the Issue. Thirteen additional manuscripts provide updates on databases most recently published elsewhere. Seven new databases focus specifically on COVID-19 and SARS-CoV-2, including SCoV2-MD, the first of the Issue's Breakthrough Articles. Major nucleic acid databases reporting updates include MODOMICS, JASPAR and miRTarBase. The AlphaFold Protein Structure Database, described in the second Breakthrough Article, is the stand-out in the protein section, where the Human Proteoform Atlas and GproteinDb are other notable new arrivals. Updates from DisProt, FuzDB and ELM comprehensively cover disordered proteins. Under the metabolism and signalling section Reactome, ConsensusPathDB, HMDB and CAZy are major returning resources. In microbial and viral genomes taxonomy and systematics are well covered by LPSN, TYGS and GTDB. Genomics resources include Ensembl, Ensembl Genomes and UCSC Genome Browser. Major returning pharmacology resource names include the IUPHAR/BPS guide and the Therapeutic Target Database. New plant databases include PlantGSAD for gene lists and qPTMplants for post-translational modifications. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). Our latest update to the NAR online Molecular Biology Database Collection brings the total number of entries to 1645. Following last year's major cleanup, we have updated 317 entries, listing 89 new resources and trimming 80 discontinued URLs. The current release is available at http://www.oxfordjournals.org/nar/database/c/.

show abstract

Section: New and Updated Databasesmentioning

confidence: 99%

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

Rigden

Fernández

2021

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…In this study, we assembled a set of STEC O145:H28 environmental and clinical strains, all with high quality complete genome sequences, and used E. coli K-12 substrain MG-1655, the O157:H7 strain EDL933, and two O145:H25 strains as references. We first examined the conservation of 333 E. coli virulence genes deposited in the Virulence Factor DataBase [ 32 , 33 ], followed by comparative genomic analyses of ten PAIs/GIs known to contribute to pathogenicity and fitness traits in STEC to assess the pathogenicity potential in STEC environmental isolates.…”

Section: Introductionmentioning

confidence: 99%

Comparative Genomics Applied to Systematically Assess Pathogenicity Potential in Shiga Toxin-Producing Escherichia coli O145:H28

Carter

Laniohan

et al. 2022

Microorganisms

View full text Add to dashboard Cite

Shiga toxin-producing Escherichia coli (STEC) O145:H28 can cause severe disease in humans and is a predominant serotype in STEC O145 environmental isolates. Here, comparative genomics was applied to a set of clinical and environmental strains to systematically evaluate the pathogenicity potential in environmental strains. While the core genes-based tree separated all O145:H28 strains from the non O145:H28 reference strains, it failed to segregate environmental strains from the clinical. In contrast, the accessory genes-based tree placed all clinical strains in the same clade regardless of their genotypes or serotypes, apart from the environmental strains. Loss-of-function mutations were common in the virulence genes examined, with a high frequency in genes related to adherence, autotransporters, and the type three secretion system. Distinct differences in pathogenicity islands LEE, OI-122, and OI-57, the acid fitness island, and the tellurite resistance island were detected between the O145:H28 and reference strains. A great amount of genetic variation was detected in O145:H28, which was mainly attributed to deletions, insertions, and gene acquisition at several chromosomal “hot spots”. Our study demonstrated a distinct virulence gene repertoire among the STEC O145:H28 strains originating from the same geographical region and revealed unforeseen contributions of loss-of-function mutations to virulence evolution and genetic diversification in STEC.

show abstract

“…The resistance and virulence genes were detected using ABRicate (https://github.com/tseemann/abricate) employing ResFinder 4.1 (Bortolaia et al, 2020), VFDB 2022 (Liu et al, 2022) and MEGARes 2.0 (Doster et al, 2020) databases, respectively with 90% threshold for both gene identity and coverage. The typing of capsule-encoding loci (KL) and lipooligosaccharide outer core (OCL) were determined using Kaptive (Wick et al, 2018; Wyres et al, 2020) after manual curation of the corresponding loci by mapping the short reads on anticipated reference sequence of the KL using Geneious R9 (Biomatters, NZ).…”

Section: Methodsmentioning

confidence: 99%

What are the reference strains of Acinetobacter baumannii referring to?

Philippe

Valček

Whiteway

et al. 2022

Preprint

View full text Add to dashboard Cite

We assembled the whole genome sequence (WGS) of a collection of 43 non-redundant modern clinical isolates and four broadly used reference strains of Acinetobacter baumannii. Comparison of these isolates and their WGS confirmed the high heterogeneity in capsule loci, sequence types, the presence of virulence and antibiotic resistance genes. However, a significant portion of clinical isolates strongly differ when compared to several reference strains in the light of colony morphology, cellular density, capsule production, natural transformability and in vivo virulence. These genetic and phenotypic differences between current circulating strains of A. baumannii and established reference strains could hamper the study of A. baumannii as an entity. The broadly used reference strains led to the current state of the art of the A. baumannii field, however, we propose that established reference strains in the A. baumannii field should be carefully used, because of the high genetic and phenotypic heterogeneities. In this study, we generated a collection of high-quality nucleotide sequences of 43 modern and non-redundant clinical isolates with the corresponding multi-level phenotypic characterizations. Beside the contribution of novel fundamental observations generated in this study, the phenotypic and genetic data, along with the bacterial strains themselves, will be further accessible using the first open access online platform called Acinetobase. Therefore, a rational choice of modern strains will be possible to select the ones that suit the needs of specific biological questions.

show abstract

VFDB 2022: a general classification scheme for bacterial virulence factors

Cited by 757 publications

References 31 publications

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

Comparative Genomics Applied to Systematically Assess Pathogenicity Potential in Shiga Toxin-Producing Escherichia coli O145:H28

What are the reference strains of Acinetobacter baumannii referring to?

Contact Info

Product

Resources

About