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Viruses Nov 2020(group B Streptococcus, GBS) represents a leading cause of invasive bacterial infections in newborns and is also responsible for diseases in older and immunocompromised...
(group B Streptococcus, GBS) represents a leading cause of invasive bacterial infections in newborns and is also responsible for diseases in older and immunocompromised adults. Prophages represent an important factor contributing to the genome plasticity and evolution of new strains. In the present study, prophage content was analyzed in human GBS isolates. Thirty-seven prophages were identified in genomes of 20 representative sequenced strains. On the basis of the sequence comparison, we divided the prophages into eight groups named A-H. This division also corresponded to the clustering of phage integrase, even though several different integration sites were observed in some relative prophages. Next, PCR method was used for detection of the prophages in 123 GBS strains from adult hospitalized patients and from pregnancy screening. At least one prophage was present in 105 isolates (85%). The highest prevalence was observed for prophage group A (71%) and satellite prophage group B (62%). Other groups were detected infrequently (1-6%). Prophage distribution did not differ between clinical and screening strains, but it was unevenly distributed in MLST (multi locus sequence typing) sequence types. High content of full-length and satellite prophages detected in present study implies that prophages could be beneficial for the host bacterium and could contribute to evolution of more adapted strains.
Topics: Adaptation, Physiological; Adolescent; Adult; Aged; Aged, 80 and over; Bacterial Typing Techniques; Carrier State; Female; Genetic Variation; Genome, Bacterial; Humans; Middle Aged; Multilocus Sequence Typing; Phylogeny; Pregnancy; Prophages; Streptococcal Infections; Streptococcus agalactiae; Virus Integration; Whole Genome Sequencing; Young Adult
PubMed: 33217933
DOI: 10.3390/v12111323 -
The ISME Journal Dec 2023Environmental bacteria host an enormous number of prophages, but their diversity and natural functions remain largely elusive. Here, we investigate prophage activity and...
Environmental bacteria host an enormous number of prophages, but their diversity and natural functions remain largely elusive. Here, we investigate prophage activity and diversity in 63 Erwinia and Pseudomonas strains isolated from flag leaves of wheat grown in a single field. Introducing and validating Virion Induction Profiling Sequencing (VIP-Seq), we identify and quantify the activity of 120 spontaneously induced prophages, discovering that some phyllosphere bacteria produce more than 10 virions/mL in overnight cultures, with significant induction also observed in planta. Sequence analyses and plaque assays reveal E. aphidicola prophages contribute a majority of intraspecies genetic diversity and divide their bacterial hosts into antagonistic factions engaged in widespread microbial warfare, revealing the importance of prophage-mediated microdiversity. When comparing spontaneously active prophages with predicted prophages we also find insertion sequences are strongly correlated with non-active prophages. In conclusion, we discover widespread and largely unknown prophage diversity and function in phyllosphere bacteria.
Topics: Prophages; Triticum; Bacteria
PubMed: 37919394
DOI: 10.1038/s41396-023-01547-1 -
PloS One 2023Due to its frequent association with urinary tract infections (UTIs), Escherichia coli is the best characterized constituent of the urinary microbiota (urobiome)....
Due to its frequent association with urinary tract infections (UTIs), Escherichia coli is the best characterized constituent of the urinary microbiota (urobiome). However, uropathogenic E. coli is just one member of the urobiome. In addition to bacterial constituents, the urobiome of both healthy and symptomatic individuals is home to a diverse population of bacterial viruses (bacteriophages). A prior investigation found that most bacterial species in the urobiome are lysogens, harboring one or more phages integrated into their genome (prophages). Many of these prophages are temperate phages, capable of entering the lytic cycle and thus lysing their bacterial host. This transition from the lysogenic to lytic life cycle can impact the bacterial diversity of the urobiome. While many phages that infect E. coli (coliphages) have been studied for decades in the laboratory setting, the coliphages within the urobiome have yet to be cataloged. Here, we investigated the diversity of urinary coliphages by first identifying prophages in all publicly available urinary E. coli genomes. We detected 3,038 intact prophage sequences, representative of 1,542 unique phages. These phages include both novel species as well as species also found within the gut microbiota. Ten temperate phages were isolated from urinary E. coli strains included in our analysis, and we assessed their ability to infect and lyse urinary E. coli strains. We also included in these host range assays other urinary coliphages and laboratory coliphages. The temperate phages and other urinary coliphages were successful in lysing urinary E. coli strains. We also observed that coliphages from non-urinary sources were most efficient in killing urinary E. coli strains. The two phages, T2 and N4, were capable of lysing 83.5% (n = 86) of strains isolated from females with UTI symptoms. In conclusion, our study finds a diverse community of coliphages in the urobiome, many of which are predicted to be temperate phages, ten of which were confirmed here. Their ability to infect and lyse urinary E. coli strains suggests that urinary coliphages may play a role in modulating the E. coli strain diversity of the urobiome.
Topics: Female; Humans; Escherichia coli; Coliphages; Bacteriophages; Lysogeny; Prophages; Microbiota; Bacteria
PubMed: 37053131
DOI: 10.1371/journal.pone.0283930 -
Avicenna Journal of Medical... 2022Bacteriophages are bacterial parasites. Unlike lytic bacteriophages, lysogenic bacteriophages do not multiply immediately after entering the host cells and may integrate...
BACKGROUND
Bacteriophages are bacterial parasites. Unlike lytic bacteriophages, lysogenic bacteriophages do not multiply immediately after entering the host cells and may integrate their genomes into the bacterial genomes as prophages. Prophages can include various phenotypic and genotypic effects on the host bacteria. spp. are Gram-positive bacteria that cause infections in humans and animals. In recent decades, these bacteria have become resistant to various antimicrobials, including vancomycin. The aim of this study was to analyze genome of an enterococcal prophage.
METHODS
In this study, EntfacYE was isolated from biological samples and its genome was analyzed using next-generation sequencing method.
RESULTS
Overall, 254 prophage genes were identified in the bacterial genome. The prophage included 39 housekeeping, 41 replication and regulation, 80 structural and packaging, and 48 lysis genes. Moreover, 46 genes with unknown functions were identified. All genes were annotated in DNA Data Bank of Japan.
CONCLUSION
In general, most prophage genes were linked to packaging and structure (31.5%) gene group. However, genes with unknown functions included a high proportion (18.11%), which indicated necessity of further analyses. Genomic analysis of the prophages can be effective in better understanding of their roles in development of bacterial resistance to antibiotics. Moreover, identification and study of prophages can help researchers develop genetic engineering tools and novel infection therapies.
PubMed: 36061127
DOI: 10.18502/ajmb.v14i3.9826 -
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 -
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 -
Food Microbiology Apr 2022Prophage distribution and phage characteristics based on the genome of Lactobacillus plantarum derived from kimchi were investigated. Prophage genomes retrieved from a...
Prophage distribution and phage characteristics based on the genome of Lactobacillus plantarum derived from kimchi were investigated. Prophage genomes retrieved from a database were analyzed in silico with prophage inducibility. Twenty-one kimchi-derived L. plantarum had at least one intact prophage, including a putative cryptic state on the chromosome. They were all confirmed to belong to the Siphoviridae family. Intact prophages can be classified into three different groups: PM411-like, Sha1-like, and unclassified phage groups. Some prophage regions were encoded with superinfection exclusion proteins and orphan methylases, suggesting that the phages co-evolved with their hosts. Interestingly, prophage inducibility showed that only DNA damage could induce prophages and that pH stresses by organic acids could not. Therefore, the prophage of L. plantarum did not affect the host unless DNA was damaged, and it would hardly affect the viability of the host through phage induction during kimchi fermentation. Our results might provide insights into the distribution and non-inducibility of prophages, existence of phage-immunity genes, and role of plant-derived L. plantarum prophages in host survival during late acidic kimchi fermentation.
Topics: Brassica; Fermented Foods; Genome, Viral; Lactobacillus plantarum; Prophages
PubMed: 34809939
DOI: 10.1016/j.fm.2021.103913 -
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 -
Genome Jul 2021is a zoonotic pathogen whose genetic heterogeneity is well known. Five serogroups (A, B, D, E, and F) and 16 serotypes of have been recognized thus far based on...
is a zoonotic pathogen whose genetic heterogeneity is well known. Five serogroups (A, B, D, E, and F) and 16 serotypes of have been recognized thus far based on capsular polysaccharide typing and lipopolysaccharide typing, respectively. Progressive atrophic rhinitis in domestic pigs is caused by strains containing , which encodes a 146 kDa heat-labile toxin. Among the five serogroups, only some strains of serogroups A and D are toxigenic. In this study, by comparative analyses of the genomes of many strains, it has been shown that is sparsely distributed in . Furthermore, full-length homologs of were found only in two other bacterial species. It has also been shown that is usually associated with a prophage, and that some strains contain an orthologous prophage but not . Among the -containing prophages that were compared, an operon putatively encoding a type II restriction-modification system was present only in strains LFB3, HN01, and HN06. These results indicate that the selection and maintenance of the heat-labile toxin and the type II restriction-modification system are evolutionarily less favorable among strains. Phylogenetic analysis using the alignment- and parameter-free method CVTree3 showed that deduced proteome sequences can be used as effectively as whole/core genome single nucleotide polymorphisms to group strains in relation to their serotypes and (or) genotypes. It remains to be determined if the -containing prophages in strains HN01 and HN06 are inducible, and if they can be used for lysogenic transfer of to other bacteria.
Topics: Bacterial Proteins; Bacterial Toxins; Comparative Genomic Hybridization; DNA Restriction-Modification Enzymes; DNA, Bacterial; Genomics; Pasteurella multocida; Phylogeny; Prophages
PubMed: 33471631
DOI: 10.1139/gen-2020-0176