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Microbial Genomics Jan 2022has emerged as an important opportunistic pathogen worldwide, being responsible for large outbreaks for nosocomial infections, primarily in intensive care units. ATCC... (Comparative Study)
Comparative Study
has emerged as an important opportunistic pathogen worldwide, being responsible for large outbreaks for nosocomial infections, primarily in intensive care units. ATCC 19606 is the species type strain, and a reference organism in many laboratories due to its low virulence, amenability to genetic manipulation and extensive antibiotic susceptibility. We wondered if frequent propagation of ATCC 19606 in different laboratories may have driven micro- and macro-evolutionary events that could determine inter-laboratory differences of genome-based data. By combining Illumina MiSeq, MinION and Sanger technologies, we generated a high-quality whole-genome sequence of ATCC 19606, then performed a comparative genome analysis between ATCC 19606 strains from several research laboratories and a reference collection. Differences between publicly available ATCC 19606 genome sequences were observed, including SNPs, macro- and micro-deletions, and the uneven presence of a 52 kb prophage belonging to genus . Two plasmids, pMAC and p1ATCC19606, were invariably detected in all tested strains. The presence of a putative replicase, a replication origin containing four 22-mer direct repeats, and a toxin-antitoxin system implicated in plasmid stability were predicted by analysis of p1ATCC19606, and experimentally confirmed. This work refines the sequence, structure and functional annotation of the ATCC 19606 genome, and highlights some remarkable differences between domesticated strains, likely resulting from genetic drift.
Topics: Acinetobacter baumannii; Cross Infection; Evolution, Molecular; Genetic Variation; Genome, Bacterial; High-Throughput Nucleotide Sequencing; Humans; Intensive Care Units; Plasmids; Polymorphism, Single Nucleotide; Prophages; Sequence Deletion; Whole Genome Sequencing
PubMed: 35084299
DOI: 10.1099/mgen.0.000749 -
Journal of Bacteriology Feb 2015Bacteriophages and genetic elements, such as prophage-like elements, pathogenicity islands, and phage morons, make up a considerable amount of bacterial genomes. Their... (Review)
Review
Bacteriophages and genetic elements, such as prophage-like elements, pathogenicity islands, and phage morons, make up a considerable amount of bacterial genomes. Their transfer and subsequent activity within the host's genetic circuitry have had a significant impact on bacterial evolution. In this review, we consider what underlying mechanisms might cause the spontaneous activity of lysogenic phages in single bacterial cells and how the spontaneous induction of prophages can lead to competitive advantages for and influence the lifestyle of bacterial populations or the virulence of pathogenic strains.
Topics: Adaptation, Biological; Bacteria; Host-Pathogen Interactions; Prophages; Virus Activation
PubMed: 25404701
DOI: 10.1128/JB.02230-14 -
MSystems Aug 2022Phages and prophages are one of the principal modulators of microbial populations. However, much of their diversity is still poorly understood. Here, we extracted 33,624...
Phages and prophages are one of the principal modulators of microbial populations. However, much of their diversity is still poorly understood. Here, we extracted 33,624 prophages from 13,713 complete prokaryotic genomes to explore the prophage diversity and their relationships with their host. Our results reveal that prophages were present in 75% of the genomes studied. In addition, Enterobacterales were significantly enriched in prophages. We also found that pathogens are a significant reservoir of prophages. Finally, we determined that the prophage relatedness and the range of genomic hosts were delimited by the evolutionary relationships of their hosts. On a broader level, we got insights into the prophage population, identified in thousands of publicly available prokaryotic genomes, by comparing the prophage distribution and relatedness between them and their hosts. Phages and prophages play an essential role in controlling their host populations either by modulating the host abundance or providing them with genes that benefit the host. The constant growth in next-generation sequencing technology has caused the development of powerful computational tools to identify phages and prophages with high precision. Making it possible to explore the prophage populations integrated into host genomes on a large scale. However, it is still a new and under-explored area, and efforts are still required to identify prophage populations to understand their dynamics with their hosts.
Topics: Prophages; Host Specificity; Bacteriophages; Genomics; Genome, Viral
PubMed: 35880895
DOI: 10.1128/msystems.00326-22 -
Theoretical Population Biology Jun 2020Genome sequencing has revealed that prophages, viral sequences integrated in a bacterial chromosome, are abundant, accounting for as much as 20% of the bacterial genome....
Genome sequencing has revealed that prophages, viral sequences integrated in a bacterial chromosome, are abundant, accounting for as much as 20% of the bacterial genome. These sequences can confer fitness benefits to the bacterial host, but may also instigate cell death through induction. Several recent investigations have revealed that the distribution of prophage lengths is bimodal, with a clear distinction between small and large prophages. Here we develop a mathematical model of the evolutionary forces affecting the prophage size distribution, and fit this model to three recent data sets. This approach offers quantitative estimates for the relative rates of lysogeny, induction, mutational degradation and selection acting on a wide class of prophage sequences. The model predicts that large prophages are predominantly maintained by the introduction of new prophage sequences through lysogeny, whereas shorter prophages can be enriched when they no longer encode the genes necessary for induction, but still offer selective benefits to their hosts.
Topics: Base Sequence; Biological Evolution; Genome, Bacterial; Lysogeny; Prophages
PubMed: 31758948
DOI: 10.1016/j.tpb.2019.11.003 -
International Journal of Molecular... Apr 2022In this study, several different depolymerases encoded in the prophage regions of genomes have been bioinformatically predicted and recombinantly produced. The...
In this study, several different depolymerases encoded in the prophage regions of genomes have been bioinformatically predicted and recombinantly produced. The identified depolymerases possessed multi-domain structures and were identical or closely homologous to various proteins encoded in other genomes. This means that prophage-derived depolymerases are widespread, and different bacterial genomes can be the source of proteins with polysaccharide-degrading activities. For two depolymerases, the specificity to capsular polysaccharides (CPSs) of belonging to K1 and K92 capsular types (K types) was determined. The data obtained showed that the prophage-derived depolymerases were glycosidases that cleaved the CPSs by the hydrolytic mechanism to yield monomers and oligomers of the K units. The recombinant proteins with established enzymatic activity significantly reduced the mortality of larvae infected with of K1 and K92 capsular types. Therefore, these enzymes can be considered as suitable candidates for the development of new antibacterials against corresponding K types.
Topics: Acinetobacter baumannii; Bacterial Capsules; Bacteriophages; Glycoside Hydrolases; Polysaccharides; Polysaccharides, Bacterial; Prophages
PubMed: 35563361
DOI: 10.3390/ijms23094971 -
Archives of Virology Oct 2022Little is known about the prophages in Hafniaceae bacteria. A novel Hafnia phage, yong2, was induced from Hafnia paralvei by treatment with mitomycin C. The phage has an...
Little is known about the prophages in Hafniaceae bacteria. A novel Hafnia phage, yong2, was induced from Hafnia paralvei by treatment with mitomycin C. The phage has an elliptical head with dimensions of approximately 45 × 38 nm and a long noncontractile tail of approximately 157 × 4 nm. The complete genome of Hafnia phage yong2 is a 39,546-bp double-stranded DNA with a G+C content of 49.9%, containing 59 open reading frames (ORFs) and having at least one fixed terminus (GGGGCAGCGACA). In phylogenetic analysis, Hafnia phage yong2 clustered with four predicted Hafnia prophages and one predicted Enterobacteriaceae prophage. These prophages and members of the family Drexlerviridae together formed two distinct subclades nested within a clade, suggesting the existence of a novel class of prophages with conserved sequences and a unique evolutionary status not yet studied before in Hafniaceae and Enterobacteriaceae bacteria.
Topics: Bacteriophages; Genome, Viral; Genomics; Hafnia; Open Reading Frames; Phylogeny; Prophages
PubMed: 35752683
DOI: 10.1007/s00705-022-05498-4 -
BMC Microbiology Sep 2023Over the past two decades, Corynebacterium striatum has been increasingly isolated from clinical cultures with most isolates showing increased antimicrobial resistance...
BACKGROUND
Over the past two decades, Corynebacterium striatum has been increasingly isolated from clinical cultures with most isolates showing increased antimicrobial resistance (AMR) to last resort agents. Advances in the field of pan genomics would facilitate the understanding of the clinical significance of such bacterial species previously thought to be among commensals paving the way for identifying new drug targets and control strategies.
METHODS
We constructed a pan-genome using 310 genome sequences of C. striatum. Pan-genome analysis was performed using three tools including Roary, PIRATE, and PEPPAN. AMR genes and virulence factors have been studied in relation to core genome phylogeny. Genomic Islands (GIs), Integrons, and Prophage regions have been explored in detail.
RESULTS
The pan-genome ranges between a total of 5253-5857 genes with 2070 - 1899 core gene clusters. Some antimicrobial resistance genes have been identified in the core genome portion, but most of them were located in the dispensable genome. In addition, some well-known virulence factors described in pathogenic Corynebacterium species were located in the dispensable genome. A total of 115 phage species have been identified with only 44 intact prophage regions.
CONCLUSION
This study presents a detailed comparative pangenome report of C. striatum. The species show a very slowly growing pangenome with relatively high number of genes in the core genome contributing to lower genomic variation. Prophage elements carrying AMR and virulence elements appear to be infrequent in the species. GIs appear to offer a prominent role in mobilizing antibiotic resistance genes in the species and integrons occur at a frequency of 50% in the species. Control strategies should be directed against virulence and resistance determinants carried on the core genome and those frequently occurring in the accessory genome.
Topics: Corynebacterium; Genomics; Multigene Family; Anti-Bacterial Agents; Prophages
PubMed: 37684624
DOI: 10.1186/s12866-023-02996-6 -
Cell Host & Microbe Nov 2021Temperate phages are pervasive in bacterial genomes, existing as vertically inherited islands termed prophages. Prophages are vulnerable to predation of their host...
Temperate phages are pervasive in bacterial genomes, existing as vertically inherited islands termed prophages. Prophages are vulnerable to predation of their host bacterium by exogenous phages. Here, we identify BstA, a family of prophage-encoded phage-defense proteins in diverse Gram-negative bacteria. BstA localizes to sites of exogenous phage DNA replication and mediates abortive infection, suppressing the competing phage epidemic. During lytic replication, the BstA-encoding prophage is not itself inhibited by BstA due to self-immunity conferred by the anti-BstA (aba) element, a short stretch of DNA within the bstA locus. Inhibition of phage replication by distinct BstA proteins from Salmonella, Klebsiella, and Escherichia prophages is generally interchangeable, but each possesses a cognate aba element. The specificity of the aba element ensures that immunity is exclusive to the replicating prophage, preventing exploitation by variant BstA-encoding phages. The BstA protein allows prophages to defend host cells against exogenous phage attack without sacrificing the ability to replicate lytically.
Topics: Bacteriophages; Genome, Bacterial; Prophages; Salmonella
PubMed: 34597593
DOI: 10.1016/j.chom.2021.09.002 -
Advances in Virus Research 2019The viruses that infect bacteria, known as phages, are the most abundant biological entity on earth. They play critical roles in controlling bacterial populations... (Review)
Review
The viruses that infect bacteria, known as phages, are the most abundant biological entity on earth. They play critical roles in controlling bacterial populations through phage-mediated killing, as well as through formation of bacterial lysogens. In this form, the survival of the phage depends on the survival of the bacterial host in which it resides. Thus, it is advantageous for phages to encode genes that contribute to bacterial fitness and expand the environmental niche. In many cases, these fitness factors also make the bacteria better able to survive in human infections and are thereby considered pathogenesis or virulence factors. The genes that encode these fitness factors, known as "morons," have been shown to increase bacterial fitness through a wide range of mechanisms and play important roles in bacterial diseases. This review outlines the benefits provided by phage morons in various aspects of bacterial life, including phage and antibiotic resistance, motility, adhesion and quorum sensing.
Topics: Bacteria; Bacterial Adhesion; Bacterial Physiological Phenomena; Bacterial Toxins; Bacteriophages; CRISPR-Cas Systems; Drug Resistance, Bacterial; Host-Pathogen Interactions; Humans; Lysogeny; Phage Therapy; Prophages; Quorum Sensing; Virulence
PubMed: 30635074
DOI: 10.1016/bs.aivir.2018.08.001 -
Microbial Biotechnology Apr 2022Gram-positive bacterial extracellular membrane vesicles (EVs) have been drawing more attention in recent years. However, mechanistic insights are still lacking on how...
Gram-positive bacterial extracellular membrane vesicles (EVs) have been drawing more attention in recent years. However, mechanistic insights are still lacking on how EVs are released through the cell walls in Gram-positive bacteria. In this study, we characterized underlying mechanisms of EV production and provide evidence for a role of prophage activation in EV release using the Gram-positive bacterium Lactococcus lactis as a model. By applying a standard EV isolation procedure, we observed the presence of EVs in the culture supernatant of a lysogenic L. lactis strain FM-YL11, for which the prophage-inducing condition led to an over 10-fold increase in EV production in comparison with the non-inducing condition. In contrast, the prophage-encoded holin-lysin knockout mutant YL11ΔHLH and the prophage-cured mutant FM-YL12 produced constantly low levels of EVs. Under the prophage-inducing condition, FM-YL11 did not show massive cell lysis. Defective phage particles were found to be released in and associated with holin-lysin-induced EVs from FM-YL11, as demonstrated by transmission electron microscopic images, flow cytometry and proteomics analysis. Findings from this study further generalized the EV-producing phenotype to Gram-positive L. lactis, and provide additional insights into the EV production mechanism involving prophage-encoded holin-lysin system. The knowledge on bacterial EV production can be applied to all Gram-positive bacteria and other lactic acid bacteria with important roles in fermentations and probiotic formulations, to enable desired release and delivery of cellular components with nutritional values or probiotic effects.
Topics: Bacteriophages; Extracellular Vesicles; Lactococcus lactis; Lysogeny; Prophages
PubMed: 35229476
DOI: 10.1111/1751-7915.13972