Prophage Hunter: an integrative hunting tool for active prophages

Song, Wenchen; Sun, Hai Xi; Zhang, Carolyn; Cheng, Li; Peng, Ye; Deng, Ziqing; Wang, Dan; Wang, Yun; Hu, Ming; Liu, Wenen; Yang, Huanming; Shen, Yue; Li, Junhua; Li, You; Xiao, Mei

doi:10.1093/nar/gkz380

Cited by 190 publications

(168 citation statements)

References 34 publications

Supporting

Mentioning

162

Contrasting

Order By: Relevance

“…Plasmids were detected using PlasmidFinder 2.0 [16] and by BLAST searches against a local version of the Enterobacteriaceae plasmid database [47]. Prophages were annotated using the recent tool Prophage Hunter [48], which is also able to differentiate active from inactive prophages. Only active prophages were selected into the final annotation.…”

Section: Genome Sequencing and Annotationmentioning

confidence: 99%

Sequencing of five poultry strains elucidates phylogenetic relationships and divergence in virulence genes in Morganella morganii

Palmieri

Heß

et al. 2020

BMC Genomics

View full text Add to dashboard Cite

Background: M. morganii is a bacterium frequently associated with urinary infections in humans. While many human strains are sequenced, only the genomes of few poultry strains are available. Here, we performed a detailed characterization of five highly resistant Morganella morganii strains isolated in association with Escherichia coli from diseased domestic Austrian poultry flocks, namely geese, turkeys and chicken layers. Additionally, we sequenced the genomes of these strains by NGS and analyzed phylogenetic clustering, resistance and virulence genes in the context of host-specificity. Results: Two strains were identified to be Extended Spectrum Beta Lactamase (ESBL) and one as AmpC betalactamases (AMP-C) phenotype, while two were ESBL negative. By integrating the genome sequences of these five poultry strains with all the available M. morganii genomes, we constructed a phylogenetic tree that clearly separates the Morganella genus into two clusters (M1 and M2), which approximately reflect the proposed subspecies classification (morganii and sibonii). Additionally, we found no association between phylogenetic structure and host, suggesting interspecies transmission. All five poultry strains contained genes for resistance to aminocoumarins, betalactams, colistin, elfamycins, fluoroquinolones, phenicol, rifampin and tetracycline. A comparative genomics analysis of virulence genes showed acquisition of novel virulence genes involved in secretion system and adherence in cluster M2. We showed that some of these genes were acquired by horizontal gene transfer from closely related Morganellaceae species and propose that novel virulence genes could be responsible for expansion of tissue tropism in M. morganii. Finally, we detected variability in copy number and high sequence divergence in toxin genes and provided evidence for positive selection in insecticidal toxins genes, likely reflecting host-related adaptations. Conclusions: In summary, this study describes i) the first isolation and characterization of M. morganii from goose and turkey, ii) a large-scale genetic analysis of M. morganii and an attempt to generate a global picture of the M. morganii intraspecific phylogenetic structure.

show abstract

Section: Genome Sequencing and Annotationmentioning

confidence: 99%

Sequencing of five poultry strains elucidates phylogenetic relationships and divergence in virulence genes in Morganella morganii

Palmieri

Heß

et al. 2020

BMC Genomics

View full text Add to dashboard Cite

show abstract

“…286Assessment of prevalence of the RcGTA-like clusters among putative prophages 287Putative prophages in the 1,423 alphaproteobacterial genomes were predicted using the 288 PHASTER web server(Arndt et al [2016]; accessed in January, 2019). The PHASTER program was 289 chosen due to its solid performance in benchmarking studies(Sousa et al 2018) and its useful scoring 290 system that ranks predictions based on a prophage region completeness(Song et al 2019). To restrict our 291 evaluation to likely functional prophages, only predicted prophages with the PHASTER score >90 (i.e., 292 classified as "intact" prophages) were retained for further analyses.…”

mentioning

confidence: 99%

Machine-learning classification suggests that many alphaproteobacterial prophages may instead be gene transfer agents

Kogay

Neely

Burnbaum

et al. 2019

Preprint

View full text Add to dashboard Cite

21Many of the sequenced bacterial and archaeal genomes encode regions of viral provenance. Yet, not all of 22 these regions encode bona fide viruses. Gene transfer agents (GTAs) are thought to be former viruses that 23 are now maintained in genomes of some bacteria and archaea and are hypothesized to enable exchange of 24 DNA within bacterial populations. In Alphaproteobacteria, genes homologous to the 'head-tail' gene 25 cluster that encodes structural components of the Rhodobacter capsulatus GTA (RcGTA) are found in 26 many taxa, even if they are only distantly related to Rhodobacter capsulatus. Yet, in most genomes 27 available in GenBank RcGTA-like genes have annotations of typical viral proteins, and therefore are not 28 easily distinguished from their viral homologs without additional analyses. Here, we report a 'support 29 vector machine' classifier that quickly and accurately distinguishes RcGTA-like genes from their viral 30 homologs by capturing the differences in the amino acid composition of the encoded proteins. Our open-31 source classifier is implemented in Python and can be used to scan homologs of the RcGTA genes in 32 newly sequenced genomes. The classifier can also be trained to identify other types of GTAs, or even to 33 detect other elements of viral ancestry. Using the classifier trained on a manually curated set of 34 homologous viruses and GTAs, we detected RcGTA-like 'head-tail' gene clusters in 57.5% of the 1,423 35 examined alphaproteobacterial genomes. We also demonstrated that more than half of the in silico 36prophage predictions are instead likely to be GTAs, suggesting that in many alphaproteobacterial 37 genomes the RcGTA-like elements remain unrecognized. 38 39 Keywords 40 Virus exaptation, GTA, Rhodobacter capsulatus, support vector machine, binary classification, carbon 41 depletion 42 43 7 value < 0.001; query and subject overlap by at least 60% of their length) and PSI-BLASTP searches (E-132 value < 0.001; query and subject overlap by at least 40% of their length; maximum of six iterations) of 133 the viral RefSeq database release 90 (last accessed in November 2018; accession numbers of the viral 134 entries are provided in Supplementary Table S2). BLASTP and PSI-BLAST executables were from the 135 BLAST v. 2.6.0+ package (Altschul et al. 1997) . The obtained homologs are listed in Supplementary 136

show abstract

“…The tool used to identify prophages in A. baumannii genomes was Prophage Hunter (Song et al 2019; available at https://pro-hunter.bgi.com/). Here, we obtained data on the start, end, length, score, category, and the name of the closest phage.…”

Section: Methodsmentioning

confidence: 99%

A Biological Inventory of Prophages inA. baumanniiGenomes Reveal Distinct Distributions in Classes, Length and Genomic Positions

Loh

Chen

Manohar

et al. 2020

Preprint

View full text Add to dashboard Cite

Acinetobacter baumannii is of major clinical importance as the bacterial pathogen often causes hospital acquired infections, further complicated by the high prevalence of antibiotic resistant strains. Aside from natural tolerance to certain antibiotic classes, resistance is often acquired by the exchange of genetic information via conjugation but also by the high natural competence exhibited by A. baumannii. In addition, bacteriophages are able to introduce resistance genes but also toxins and virulence factors via phage mediated transduction. In this work, we analysed the complete genomes of 177 A. baumannii strains for the occurrence of prophages, and analysed their taxonomy, size and positions of insertion. Among all the prophages that were detected, Siphoviridae and Myoviridae were the two most commonly found families, while the average genome size was determined as 3.98 Mbp. Our data shows the wide variation in the number of prophages in A. baumannii genomes and the prevalence of certain prophages within strains that are most successful or potentially beneficial to the host. Our study also revealed that only two specific sites of insertion within the genome of the host bacterium are being used, with few exceptions only. Lastly, we analysed the existence of genes that are encoded in the prophages, which confer antimicrobial resistance (AMR). Several phages carry AMR genes, including OXA-23 and NDM-1, illustrating the importance of lysogenic phages in the acquisition of resistance genes.

show abstract

Prophage Hunter: an integrative hunting tool for active prophages

Cited by 190 publications

References 34 publications

Sequencing of five poultry strains elucidates phylogenetic relationships and divergence in virulence genes in Morganella morganii

Sequencing of five poultry strains elucidates phylogenetic relationships and divergence in virulence genes in Morganella morganii

Machine-learning classification suggests that many alphaproteobacterial prophages may instead be gene transfer agents

A Biological Inventory of Prophages inA. baumanniiGenomes Reveal Distinct Distributions in Classes, Length and Genomic Positions

Contact Info

Product

Resources

About