-
MBio Mar 2021is an emerging pathogen that is often refractory to antibiotic control. Treatment is further complicated by considerable variation among clinical isolates in both their...
is an emerging pathogen that is often refractory to antibiotic control. Treatment is further complicated by considerable variation among clinical isolates in both their genetic constitution and their clinical manifestations. Here, we show that the prophage and plasmid mobilome is a likely contributor to this variation. Prophages and plasmids are common, abundant, and highly diverse, and code for large repertoires of genes influencing virulence, antibiotic susceptibility, and defense against viral infection. At least 85% of the strains we describe carry one or more prophages, representing at least 17 distinct and diverse sequence "clusters," integrated at 18 different locations. The prophages code for 19 distinct configurations of polymorphic toxin and toxin-immunity systems, each with WXG-100 motifs for export through type VII secretion systems. These are located adjacent to attachment junctions, are lysogenically expressed, and are implicated in promoting growth in infected host cells. Although the plethora of prophages and plasmids confounds the understanding of pathogenicity, they also provide an abundance of tools for engineering. is an important emerging pathogen that is challenging to treat with current antibiotic regimens. There is substantial genomic variation in clinical isolates, but little is known about how this influences pathogenicity and growth. Much of the genomic variation is likely due to the large and varied mobilome, especially a large and diverse array of prophages and plasmids. The prophages are unrelated to previously characterized phages of mycobacteria and code for a diverse array of genes implicated in both viral defense and growth. Prophage-encoded polymorphic toxin proteins secreted via the type VII secretion system are common and highly varied and likely contribute to strain-specific pathogenesis.
Topics: Bacterial Proteins; Bacterial Toxins; Bacteriophages; Genetic Variation; Humans; Mycobacterium Infections, Nontuberculous; Mycobacterium abscessus; Phylogeny; Plasmids; Prophages; Type VII Secretion Systems
PubMed: 33785627
DOI: 10.1128/mBio.03441-20 -
Nucleic Acids Research Jul 2022Advances in genome sequencing have produced hundreds of thousands of bacterial genome sequences, many of which have integrated prophages derived from temperate...
Advances in genome sequencing have produced hundreds of thousands of bacterial genome sequences, many of which have integrated prophages derived from temperate bacteriophages. These prophages play key roles by influencing bacterial metabolism, pathogenicity, antibiotic resistance, and defense against viral attack. However, they vary considerably even among related bacterial strains, and they are challenging to identify computationally and to extract precisely for comparative genomic analyses. Here, we describe DEPhT, a multimodal tool for prophage discovery and extraction. It has three run modes that facilitate rapid screening of large numbers of bacterial genomes, precise extraction of prophage sequences, and prophage annotation. DEPhT uses genomic architectural features that discriminate between phage and bacterial sequences for efficient prophage discovery, and targeted homology searches for precise prophage extraction. DEPhT is designed for prophage discovery in Mycobacterium genomes but can be adapted broadly to other bacteria. We deploy DEPhT to demonstrate that prophages are prevalent in Mycobacterium strains but are absent not only from the few well-characterized Mycobacterium tuberculosis strains, but also are absent from all ∼30 000 sequenced M. tuberculosis strains.
Topics: Bacteriophages; Genomics; Mycobacteriophages; Mycobacterium; Prophages
PubMed: 35451479
DOI: 10.1093/nar/gkac273 -
PLoS Pathogens Jul 2019Temperate phages are bacterial viruses that as part of their life cycle reside in the bacterial genome as prophages. They are found in many species including most...
Temperate phages are bacterial viruses that as part of their life cycle reside in the bacterial genome as prophages. They are found in many species including most clinical strains of the human pathogens, Staphylococcus aureus and Salmonella enterica serovar Typhimurium. Previously, temperate phages were considered as only bacterial predators, but mounting evidence point to both antagonistic and mutualistic interactions with for example some temperate phages contributing to virulence by encoding virulence factors. Here we show that generalized transduction, one type of bacterial DNA transfer by phages, can create conditions where not only the recipient host but also the transducing phage benefit. With antibiotic resistance as a model trait we used individual-based models and experimental approaches to show that antibiotic susceptible cells become resistant to both antibiotics and phage by i) integrating the generalized transducing temperate phages and ii) acquiring transducing phage particles carrying antibiotic resistance genes obtained from resistant cells in the environment. This is not observed for non-generalized transducing temperate phages, which are unable to package bacterial DNA, nor for generalized transducing virulent phages that do not form lysogens. Once established, the lysogenic host and the prophage benefit from the existence of transducing particles that can shuffle bacterial genes between lysogens and for example disseminate resistance to antibiotics, a trait not encoded by the phage. This facilitates bacterial survival and leads to phage population growth. We propose that generalized transduction can function as a mutualistic trait where temperate phages cooperate with their hosts to survive in rapidly-changing environments. This implies that generalized transduction is not just an error in DNA packaging but is selected for by phages to ensure their survival.
Topics: Bacteriophages; Computer Simulation; DNA Packaging; Drug Resistance, Bacterial; Evolution, Molecular; Humans; Lysogeny; Models, Biological; Prophages; Salmonella typhimurium; Staphylococcus aureus; Transduction, Genetic; Virulence
PubMed: 31276485
DOI: 10.1371/journal.ppat.1007888 -
Genes & Genomics Nov 2021The Gram-negative intracellular bacterium Mycoplasma anatis is a pathogen of respiratory infectious diseases in ducks and has caused significant economic losses in the...
BACKGROUND
The Gram-negative intracellular bacterium Mycoplasma anatis is a pathogen of respiratory infectious diseases in ducks and has caused significant economic losses in the poultry industry.
OBJECTIVE
This study, as the first report of the structure and function of the pan-genome of Mycoplasma anatis, may provide a valuable genetic basis for many aspects of future research on the pathogens of waterfowl.
METHODS
We sequenced the whole genomes of 15 Mycoplasma anatis isolated from ducks in China. Draft genome sequencing was carried out and whole-genome sequencing was performed by the sequencers of the PacBio Sequel and an IonTorrent Personal Genome Machine (PGM). Then the common genic elements of protein-coding genes, tRNAs, and rRNAs of Mycoplasma anatis genomes were predicted by using the pipeline Prokka v1.13.7. To investigate homologous protein clusters across Mycoplasma anatis genomes, we adopted Roary v3.13.0 to cluster orthologous genes (OGs) based on the following criteria.
RESULTS
We obtained one complete genome and 14 genome sketches. Microbial mobile genetic element analysis revealed the distribution of insertion sequences (IS30, IS3, and IS1634), prophage regions, and CRISPR arrays in the genome of Mycoplasma anatis. Comparative genomic analysis decoded the genetic components and functional classification of the pan-genome of Mycoplasma anatis that comprised 646 core genes, 231 dispensable genes and among them 110 was strain-specific. Virulence-related gene profiles of Mycoplasma anatis were systematically identified, and the products of these genes included bacterial ABC transporter systems, iron transport proteins, toxins, and secretion systems.
CONCLUSION
A complete virulence-related gene profile of Mycoplasma anatis has been identified, most of the genes are highly conserved in all strains. Sequencing results are relevant to the molecular mechanisms of drug resistance, adaptive evolution of pathogens, population structure, and vaccine development.
Topics: Base Sequence; China; Comparative Genomic Hybridization; Genome, Bacterial; Molecular Sequence Annotation; Mycoplasma; Phylogeny; Prophages; Sequence Analysis, DNA; Vaccine Development; Virulence; Virulence Factors; Whole Genome Sequencing
PubMed: 34181213
DOI: 10.1007/s13258-021-01129-5 -
Infection, Genetics and Evolution :... Aug 2021Mycoplasma anserisalpingitidis is a bacterial waterfowl pathogen. In these days of growing antibiotic resistance, it is necessary to search for alternative methods of...
Mycoplasma anserisalpingitidis is a bacterial waterfowl pathogen. In these days of growing antibiotic resistance, it is necessary to search for alternative methods of defense against Mycoplasma impacts in flocks. In order to identify prophage-like sequences, three established bioinformatics tools (PHASTER, PhiSpy, Prophage Hunter) were used in this study for the in silico screening of 82 M. anserisalpingitidis whole genomes. The VIBRANT software was used as a novel approach to further investigate the possibility of prophages in the sequences. The commonly used softwares found prophage-like sequences in the strains, but the results were inconclusive. The VIBRANT search resulted in multiple hits, and many of them were over 10,000 base pairs (bp). These putative prophages are comparable in size to the few described mycoplasma phages. The translated coding DNA sequences of the putative prophages were checked with protein BLAST. The functions of the proteins found by the BLASTP search are common among bacteriophages. The BLASTN search of the sequences found that many of these were more similar to the M. anatis NCTC 10156 strain, rather than the available M. anserisalpingitidis strains. The initial screening pointed at the presence of novel bacteriophages in the M. anserisalpingitidis and M. anatis strains. The VIBRANT search results were very similar to each other and none of these sequences were part of the core genome of M. anserisalpingitidis, with a few exceptions. The VIBRANT analysis explored presumably intact, novel prophages.
Topics: Mycoplasma; Prophages
PubMed: 33932611
DOI: 10.1016/j.meegid.2021.104886 -
NPJ Biofilms and Microbiomes Oct 2023Elimination of specific enteropathogenic microorganisms is critical to gut health. However, the complexity of the gut community makes it challenging to target specific...
Elimination of specific enteropathogenic microorganisms is critical to gut health. However, the complexity of the gut community makes it challenging to target specific bacterial organisms. Accumulating evidence suggests that various foods can change the abundance of intestinal bacteria by modulating prophage induction. By using pathogenic Escherichia coli (E. coli) ATCC 25922 as a model in this research, we explored the potential of dietary modulation of prophage induction and subsequent bacterial survival. Among a panel of sugars tested in vitro, D-xylose was shown to efficiently induce prophages in E. coli ATCC 25922, which depends, in part, upon the production of D-lactic acid. In an enteric mouse model, prophage induction was found to be further enhanced in response to propionic acid. Dietary D-xylose increased the proportion of Clostridia which converted D-lactic acid to propionic acid. Intestinal propionic acid levels were diminished, following either oral gavage with the dehydrogenase gene (ldhA)-deficient E. coli ATCC 25922 or depletion of intestinal Clostridia by administration of streptomycin. D-Xylose metabolism and exposure to propionic acid triggered E. coli ATCC 25922 SOS response that promoted prophage induction. E. coli ATCC 25922 mutant of RecA, a key component of SOS system, exhibited decreased phage production. These findings suggest the potential of using dietary components that can induce prophages as antimicrobial alternatives for disease control and prevention by targeted elimination of harmful gut bacteria.
Topics: Mice; Animals; Bacteriophages; Escherichia coli; Xylose; Prophages; Lactic Acid
PubMed: 37821428
DOI: 10.1038/s41522-023-00445-w -
Frontiers in Microbiology 2022Prophages have long been regarded as an important contributor to the evolution of and Verotoxin-producing (VTEC), members of the that cause millions of cases of...
Prophages have long been regarded as an important contributor to the evolution of and Verotoxin-producing (VTEC), members of the that cause millions of cases of foodborne illness in North America. In . Typhimurium, prophages provide many of the genes required for invasion; similarly, in VTEC, the Verotoxin-encoding genes are located in cryptic prophages. The ability of prophages to quickly acquire and lose genes have driven their rapid evolution, leading to highly diversified populations of phages that can infect distantly-related bacterial hosts. To defend against foreign genetic materials (i.e., phages), bacteria have evolved Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) immunity, consisting of variable spacer regions that match short nucleic acid sequences of invaders previously encountered. The number of spacer regions varies widely amongst , and there is currently no clear consensus if the accumulation of spacers is linked to genomic prophage abundance. Given the immense prophage diversity and contribution to bacterial host phenotypes, we analyzed the prophage sequences within 118 strains of and VTEC, 117 of which are of agricultural origin. Overall, 130 unique prophage sequences were identified and they were found to be remarkably diverse with <50% nucleotide similarity, particularly with the Gifsy-1 group which was identified in several serovars and interestingly, a strain of VTEC. Additionally, we identified a novel plasmid-like phage that carried antibiotic resistance and bacteriocin resistance genes. The strains analyzed carried at least six distinct spacers which did not possess homology to prophages identified in the same genome. In fact, only a fraction of all identified spacers (14%) possessed significant homology to known prophages. Regression models did not discern a correlation between spacer and prophage abundance in our strains, although the relatively high number of spacers in our strains (an average of 27 in and 19 in VTEC) suggest that high rates of infection may occur in agricultural niches and be a contributing driver in bacterial evolution. Cumulatively, these results shed insight into prophage diversity of and VTEC, which will have further implications when informing development of phage therapies against these foodborne pathogens.
PubMed: 35935192
DOI: 10.3389/fmicb.2022.853703 -
Microbiology (Reading, England) Mar 2022subspecies serovar Typhimurium (. Typhimurium) definitive phage type 104 (DT104), . Worthington, and produce ArtAB toxin, which catalyses ADP-ribosylation of...
subspecies serovar Typhimurium (. Typhimurium) definitive phage type 104 (DT104), . Worthington, and produce ArtAB toxin, which catalyses ADP-ribosylation of pertussis toxin-sensitive G protein. ArtAB gene () is encoded on a prophage in , and prophage induction by SOS-inducing agents is associated with increases in ArtAB production . However, little is known about the expression of . Here, we showed a significant increase in transcription of DT104 within macrophage-like RAW264.7 cells. Intracellular expression of ArtAB was also observed by immunofluorescence staining. The induced expression of in DT104 and was enhanced by treatment of RAW264.7 cells with phorbol 12-myristate 13-acetate (PMA), which stimulates the production of reactive oxygen species (ROS); however, such induction was not observed in . Worthington. Upregulation of , a major regulator of oxidative stress, and a repressor of prophage induction, was observed in . Worthington within RAW264.7 cells treated with PMA but not in the DT104 strain. Although the expression of was increased, was upregulated in which lacks the gene in the incomplete -encoded prophage. Taken together, oxidative stress plays a role in the production of toxins in macrophages, and high expression levels of and are responsible for the low expression of . Therefore, strain variation in the level of expression within macrophages could be explained by differences in the oxidative stress response of bacteria and might be reflected in its virulence.
Topics: Macrophages; Prophages; Salmonella typhimurium; Virulence
PubMed: 35333707
DOI: 10.1099/mic.0.001152 -
MBio Feb 2024Many temperate phages encode prophage-expressed functions that interfere with superinfection of the host bacterium by external phages. phage P22 has four such systems...
Many temperate phages encode prophage-expressed functions that interfere with superinfection of the host bacterium by external phages. phage P22 has four such systems that are expressed from the prophage in a lysogen that are encoded by the (repressor), , , and genes. Here we report that the P22-encoded SieA protein is necessary and sufficient for exclusion by the SieA system and that it is an inner membrane protein that blocks DNA injection by P22 and its relatives, but has no effect on infection by other tailed phage types. The P22 virion injects its DNA through the host cell membranes and periplasm via a conduit assembled from three "ejection proteins" after their release from the virion. Phage P22 mutants that overcome the SieA block were isolated, and they have amino acid changes in the C-terminal regions of the gene and encoded ejection proteins. Three different single-amino acid changes in these proteins are required to obtain nearly full resistance to SieA. Hybrid P22 phages that have phage HK620 ejection protein genes are also partially resistant to SieA. There are three sequence types of extant phage-encoded SieA proteins that are less than 30% identical to one another, yet comparison of two of these types found no differences in phage target specificity. Our data strongly suggest a model in which the inner membrane protein SieA interferes with the assembly or function of the periplasmic gp20 and membrane-bound gp16 DNA delivery conduit.IMPORTANCEThe ongoing evolutionary battle between bacteria and the viruses that infect them is a critical feature of bacterial ecology on Earth. Viruses can kill bacteria by infecting them. However, when their chromosomes are integrated into a bacterial genome as a prophage, viruses can also protect the host bacterium by expressing genes whose products defend against infection by other viruses. This defense property is called "superinfection exclusion." A significant fraction of bacteria harbor prophages that encode such protective systems, and there are many different molecular strategies by which superinfection exclusion is mediated. This report is the first to describe the mechanism by which bacteriophage P22 SieA superinfection exclusion protein protects its host bacterium from infection by other P22-like phages. The P22 prophage-encoded inner membrane SieA protein prevents infection by blocking transport of superinfecting phage DNA across the inner membrane during injection.
Topics: Humans; Bacteriophage P22; Superinfection; Bacteriophages; Prophages; Membrane Proteins; DNA; Amino Acids
PubMed: 38236051
DOI: 10.1128/mbio.02169-23 -
Virus Research Apr 2023Bacteriophages are viruses that exclusively infect bacteria which require local degradation of cell barriers. This degradation is accomplished by various lysins located...
Bacteriophages are viruses that exclusively infect bacteria which require local degradation of cell barriers. This degradation is accomplished by various lysins located mainly within the phage tail structure. In this paper we surveyed and analysed the genomes of 506 isolated bacteriophage and prophage infecting or harboured within the genomes of the medically important Enterococcus faecalis and faecium. We highlight and characterise the major features of the genomes of phage in the morphological groups podovirus, siphovirus and myovirus, and explore their categorisation according to the new ICTV classifications, with a focus on putative extracellular lysins chiefly within tail modules. Our analysis reveals a range of potential cell-wall targeting enzyme domains that are part of tail, tape measure or other predicted base structures of these phages or prophages. These largely fall into protein domains targeting pentapeptide or glycosidic linkages within peptidoglycan but also potentially the enterococcal polysaccharide antigen (EPA) and wall teichoic acids of these species (i.e., Pectinesterases and Phosphodiesterases). Notably, there is a great variety of domain architectures that reveal the diversity of evolutionary solutions to attack the Enterococcus cell wall. Despite this variety, most phage and prophage possess a putative endopeptidase (70%), reflecting the ubiquity of this cell surface barrier. We also identified a predicted lytic transglycosylase domain belonging to the glycosyl hydrolase (GH) family 23 and present exclusively within tape measure proteins. Our data also reveal distinct features of the genomes of podo-, sipho- and myo-type viruses that most likely relate to their size and complexity. Overall, we lay a foundation for expression of recombinant TAL proteins and engineering of enterococcal and other phage that will be invaluable for researchers in this field.
Topics: Bacteriophages; Prophages; Biological Evolution; Bacteria; Enterococcus
PubMed: 36787848
DOI: 10.1016/j.virusres.2023.199073