-
BMC Research Notes Oct 2019Staphylococcus aureus is considered an important pathogen with a variety of virulence factors in communities and hospitals all around the world. Prophage typing is a...
OBJECTIVE
Staphylococcus aureus is considered an important pathogen with a variety of virulence factors in communities and hospitals all around the world. Prophage typing is a practical technique for categorizing this bacterium. In this study, we focused on the detection of prophage patterns in methicillin-resistant S. aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) strains based on their virulence factors, antimicrobial resistance patterns, and molecular typing by rep-PCR.
RESULTS
Out of 126 S. aureus isolates, 45 (35.7%) were identified as MRSA. In total, 17 different prophage types were detected and 112 strains out of 126 strains contained at least one prophage. There was a statistically significant relationship between hld, hlg, eta and SGA, SGA, and SGFb, respectively. The results of the rep-PCR analysis revealed 14 different patterns among the MRSA and MSSA isolates. In conclusion, the presence of different prophage-encoded virulence factors and antibiotic-resistant genes among MRSA strains enables them to produce a broad range of diseases. Thus, diverse MRSA strains which have these prophages can be considered as a potential threat to the patient's health in either the hospital or the community.
Topics: Anti-Bacterial Agents; Community-Acquired Infections; Drug Resistance, Bacterial; Gene Expression; Genes, Bacterial; Humans; Iran; Methicillin-Resistant Staphylococcus aureus; Microbial Sensitivity Tests; Polymerase Chain Reaction; Prophages; Staphylococcal Infections; Staphylococcus aureus; Virulence Factors
PubMed: 31639052
DOI: 10.1186/s13104-019-4711-4 -
Scientific Reports Mar 2023Actinobacteria represent one of the largest bacterial phyla harboring many species of high medical, biotechnological and ecological relevance. Prophage elements are...
Actinobacteria represent one of the largest bacterial phyla harboring many species of high medical, biotechnological and ecological relevance. Prophage elements are major contributors to bacterial genome diversity and were shown to significantly shape bacterial fitness and host-microbe interactions. In this study, we performed a systematic analysis of prophage elements in 2406 complete actinobacterial genomes. Overall, 2106 prophage elements were predicted to be present in about 50% (1172/2406) of the analyzed datasets. Interestingly, these identified sequences compose a high prevalence of cryptic prophage elements, indicating genetic decay and domestication. Analysis of the sequence relationship of predicted prophages with known actinobacteriophage genomes revealed an exceptional high phylogenetic diversity of prophage elements. As a trend, we observed a higher prevalence of prophage elements in vicinity to the terminus. Analysis of the prophage-encoded gene functions revealed that prophage sequences significantly contribute to the bacterial antiviral immune system, but no biosynthetic gene clusters involved in the synthesis of known antiphage molecules were identified in prophage genomes. Overall, the current study highlights the remarkable diversity of prophages in actinobacterial genomes, with highly divergent prophages in actinobacterial genomes and thus provides an important basis for further investigation of phage-host interactions in this important bacterial phylum.
Topics: Prophages; Phylogeny; Bacteriophages; Genome, Bacterial
PubMed: 36932119
DOI: 10.1038/s41598-023-30829-z -
Viruses Nov 2021Prophage 919TP is widely distributed among and is induced to produce free φ919TP phage particles. However, the interactions between prophage φ919TP, the induced phage...
Prophage 919TP is widely distributed among and is induced to produce free φ919TP phage particles. However, the interactions between prophage φ919TP, the induced phage particle, and its host remain unknown. In particular, phage resistance mechanisms and potential fitness trade-offs, resulting from phage resistance, are unresolved. In this study, we examined a prophage 919TP-deleted variant of and its interaction with a modified lytic variant of the induced prophage (φ919TP ). Specifically, the phage-resistant mutant was isolated by challenging a prophage-deleted variant with lytic phage φ919TP . Further, the comparative genomic analysis of wild-type and φ919TP -resistant mutant predicted that phage φ919TP selects for phage-resistant mutants harboring a mutation in key steps of lipopolysaccharide (LPS) O-antigen biosynthesis, causing a single-base-pair deletion in gene . Our study showed that the -mediated O-antigen defect can cause pleiotropic phenotypes, e.g., cell autoaggregation and reduced swarming motility, emphasizing the role of phage-driven diversification in . The developed approach assists in the identification of genetic determinants of host specificity and is used to explore the molecular mechanism underlying phage-host interactions. Our findings contribute to the understanding of prophage-facilitated horizontal gene transfer and emphasize the potential for developing new strategies to optimize the use of phages in bacterial pathogen control.
Topics: Bacterial Proteins; Cholera; Host Microbial Interactions; Host Specificity; Lysogeny; O Antigens; Prophages; Vibrio cholerae O1; Virus Activation
PubMed: 34960610
DOI: 10.3390/v13122342 -
Nature Communications Nov 2019Bacterial pathogens often carry multiple prophages and other phage-derived elements within their genome, some of which can produce viral particles in response to stress....
Bacterial pathogens often carry multiple prophages and other phage-derived elements within their genome, some of which can produce viral particles in response to stress. Listeria monocytogenes 10403S harbors two phage elements in its chromosome, both of which can trigger bacterial lysis under stress: an active prophage (ϕ10403S) that promotes the virulence of its host and can produce infective virions, and a locus encoding phage tail-like bacteriocins. Here, we show that the two phage elements are co-regulated, with the bacteriocin locus controlling the induction of the prophage and thus its activity as a virulence-associated molecular switch. More specifically, a metalloprotease encoded in the bacteriocin locus is upregulated in response to stress and acts as an anti-repressor for CI-like repressors encoded in each phage element. Our results provide molecular insight into the phenomenon of polylysogeny and its intricate adaptation to complex environments.
Topics: Amino Acid Sequence; Bacteriocins; Bacteriolysis; Bacteriophages; Chromosomes, Bacterial; Genome, Bacterial; Genome, Viral; Host-Pathogen Interactions; Listeria monocytogenes; Lysogeny; Metalloproteases; Prophages; Sequence Homology, Amino Acid; Virus Activation
PubMed: 31754112
DOI: 10.1038/s41467-019-13296-x -
Archives of Razi Institute 2021is a well-known commensal and pathogen agent of many wild and domestic animals. A wide variety of infections can be caused by , from suppurative skin infections to...
is a well-known commensal and pathogen agent of many wild and domestic animals. A wide variety of infections can be caused by , from suppurative skin infections to life-threatening septicemia. This study was conducted to determine the prophage typing and the pattern of antibiotic resistance of isolated from broiler poultry before they have been slaughtered. In this study, 200 nasal and cloacal swab samples from 20 different flocks were collected for bacterial isolation. Staphylococci were identified using biochemical and molecular methods before being examined for gene detections in all samples resistant to oxacillin and cefotaxime. The highest value of antibiotic resistance was observed against ciprofloxacin (94%), and the maximum value of susceptibility was to gentamicin (85%). Twenty-eight (27%) samples were resistant to oxacillin. In methicillin-resistance (MRSA) isolates, 5 prophage types were observed, where the prophage with a frequency of 75% was identified as a dominant prophage; in isolates of susceptible to methicillin, 8 prophage types were observed, where prophage with a frequency about 82% was the dominant prophage. The high prevalence of MRSA isolates can indicate the risk of transmission of these bacteria to the food cycle. Furthermore, existence of various prophages in these isolates can be considered a threat to public health in producing pathogenicity factors in this bacterium while also empowering other bacterial pathogenicity, even other bacterial genera.
Topics: Animals; Chickens; Microbial Sensitivity Tests; Poultry; Prophages; Staphylococcus aureus
PubMed: 34824743
DOI: 10.22092/ari.2020.343199.1498 -
Microbial Physiology 2021As an opportunistic pathogen of humans and animals, Staphylococcus aureus asymptomatically colonizes the nasal cavity but is also a leading cause of life-threatening... (Review)
Review
As an opportunistic pathogen of humans and animals, Staphylococcus aureus asymptomatically colonizes the nasal cavity but is also a leading cause of life-threatening acute and chronic infections. The evolution of S. aureus resulting from short- and long-term adaptation to diverse hosts is tightly associated with mobile genetic elements. S. aureus strains can carry up to four temperate phages, many of which possess accessory genes encoding staphylococcal virulence factors. More than 90% of human nasal isolates of S. aureus have been shown to carry Sa3int phages, whereas invasive S. aureus isolates tend to lose these phages. Sa3int phages integrate as prophages into the bacterial hlb gene, disrupting the expression of the sphingomyelinase Hlb, an important virulence factor under specific infection conditions. Virulence factors encoded by genes carried by Sa3int phages include staphylokinase, enterotoxins, chemotaxis-inhibitory protein, and staphylococcal complement inhibitor, all of which are highly human specific and probably essential for bacterial survival in the human host. The transmission of S. aureus from humans to animals is strongly correlated with the loss of Sa3int phages, whereas phages are regained once a strain is transmitted from animals to humans. Thus, both the insertion and excision of prophages may confer a fitness advantage to this bacterium. There is also growing evidence that Sa3int phages may perform "active lysogeny," a process during which prophages are temporally excised from the chromosome without forming intact phage particles. The molecular mechanisms controlling the peculiar life cycle of Sa3int phages remain largely unclear. Nevertheless, their regulation is likely fine-tuned to ensure bacterial survival within different hosts.
Topics: Animals; Bacteriophages; Humans; Lysogeny; Prophages; Staphylococcal Infections; Staphylococcus aureus
PubMed: 34126612
DOI: 10.1159/000516645 -
Microorganisms Dec 2020The role of prophages in the evolution, diversification, or virulence of the fish pathogen has not been studied thus far. Here, we describe a functional spontaneously...
The role of prophages in the evolution, diversification, or virulence of the fish pathogen has not been studied thus far. Here, we describe a functional spontaneously inducing prophage fF4 from the type strain ATCC 23463, which is not detectable with commonly used prophage search methods. We show that this prophage type has a global distribution and is present in strains isolated from Finland, Thailand, Japan, and North America. The virions of fF4 are myoviruses with contractile tails and infect only bacterial strains originating from Northern Finland. The fF4 resembles transposable phages by similar genome organization and several gene orthologs. Additional bioinformatic analyses reveal several species in the phylum Bacteroidetes that host a similar type of putative prophage, including bacteria that are important animal and human pathogens. Furthermore, a survey of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) spacers indicate a shared evolutionary history between strains and the fF4 phage, and another putative prophage in the strain ATCC 49512, named p49512. First, CRISPR spacer content from the two CRISPR loci (types II-C and VI-B) of the fF4 lysogen ATCC 23463 revealed a phage terminase protein-matching spacer in the VI-B locus. This spacer is also present in two Chinese strains. Second, CRISPR analysis revealed four strains that contain unique spacers targeting different regions of the putative prophage p49512 in the strain ATCC 49512, despite the geographical distance or genomovar of the different strains. This suggests a common ancestry for the prophages and different host strains.
PubMed: 33276599
DOI: 10.3390/microorganisms8121919 -
Microbial Genomics Jan 2020Phages and plasmids play important roles in bacterial evolution and diversification. Although many draft genomes have been generated, phage and plasmid genomes are...
Phages and plasmids play important roles in bacterial evolution and diversification. Although many draft genomes have been generated, phage and plasmid genomes are usually fragmented, limiting our understanding of their dynamics. Here, we performed a systematic analysis of 239 draft genomes and 7 complete genomes of Shiga toxin (Stx)-producing O145:H28, the major virulence factors of which are encoded by prophages (PPs) or plasmids. The results indicated that PPs are more stably maintained than plasmids. A set of ancestrally acquired PPs was well conserved, while various PPs, including Stx phages, were acquired by multiple sublineages. In contrast, gains and losses of a wide range of plasmids have frequently occurred across the O145:H28 lineage, and only the virulence plasmid was well conserved. The different dynamics of PPs and plasmids have differentially impacted the pangenome of O145:H28, with high proportions of PP- and plasmid-associated genes in the variably present and rare gene fractions, respectively. The dynamics of PPs and plasmids have also strongly impacted virulence gene repertoires, such as the highly variable distribution of genes and the high conservation of a set of type III secretion effectors, which probably represents the core effectors of O145:H28 and the genes on the virulence plasmid in the entire O145:H28 population. These results provide detailed insights into the dynamics of PPs and plasmids, and show the application of genomic analyses using a large set of draft genomes and appropriately selected complete genomes.
Topics: Genome, Bacterial; Phylogeny; Plasmids; Polymorphism, Single Nucleotide; Prophages; Shiga-Toxigenic Escherichia coli; Siphoviridae; Virulence Factors
PubMed: 31935184
DOI: 10.1099/mgen.0.000323 -
Viruses Nov 2021The interaction between gut bacterial and viral microbiota is thought to be important in human health. While fluctuations in female genital tract (FGT) bacterial...
The interaction between gut bacterial and viral microbiota is thought to be important in human health. While fluctuations in female genital tract (FGT) bacterial microbiota similarly determine sexual health, little is known about the presence, persistence, and function of vaginal bacteriophages. We conducted shotgun metagenome sequencing of cervicovaginal samples from South African adolescents collected longitudinally, who received no antibiotics. We annotated viral reads and circular bacteriophages, identified CRISPR loci and putative prophages, and assessed their diversity, persistence, and associations with bacterial microbiota composition. was the most prevalent bacteriophage family, followed by , , , and . Full-length siphoviruses targeting bacterial vaginosis (BV)-associated bacteria were identified, suggesting their presence in vivo. CRISPR loci and prophage-like elements were common, and genomic analysis suggested higher diversity among than prophages. We found that some prophages were highly persistent within participants, and identical prophages were present in cervicovaginal secretions of multiple participants, suggesting that prophages, and thus bacterial strains, are shared between adolescents. The number of CRISPR loci and prophages were associated with vaginal microbiota stability and absence of BV. Our analysis suggests that (pro)phages are common in the FGT and vaginal bacteria and (pro)phages may interact.
Topics: Adolescent; Bacteriophages; Cohort Studies; Female; Humans; Metagenome; Microbiota; South Africa; Vagina
PubMed: 34960611
DOI: 10.3390/v13122341 -
MSystems Jun 2022The genus includes two pathogenic species, N. gonorrhoeae and N. meningitidis, and numerous commensal species. species frequently exchange DNA with one another,...
The genus includes two pathogenic species, N. gonorrhoeae and N. meningitidis, and numerous commensal species. species frequently exchange DNA with one another, primarily via transformation and homologous recombination and via multiple types of mobile genetic elements (MGEs). Few bacteriophages (phages) have been identified, and their impact on bacterial physiology is poorly understood. Furthermore, little is known about the range of species that phages can infect. In this study, we used three virus prediction tools to scan 248 genomes of 21 different species and identified 1,302 unique predicted prophages. Using comparative genomics, we found that many predictions are dissimilar from prophages and other MGEs previously described to infect species. We also identified similar predicted prophages in genomes of different species. Additionally, we examined CRISPR-Cas targeting of each genome and predicted prophage. While CRISPR targeting of chromosomal DNA appears to be common among several species, we found that 20% of the prophages we predicted are targeted significantly more than the rest of the bacterial genome in which they were identified (i.e., backbone). Furthermore, many predicted prophages are targeted by CRISPR spacers encoded by other species. We then used these results to infer additional host species of known prophages and predictions that are highly targeted relative to the backbone. Together, our results suggest that we have identified novel prophages, several of which may infect multiple species. These findings have important implications for understanding horizontal gene transfer between members of this genus. Drug-resistant Neisseria gonorrhoeae is a major threat to human health. Commensal species are thought to serve as reservoirs of antibiotic resistance and virulence genes for the pathogenic species N. gonorrhoeae and N. meningitidis. Therefore, it is important to understand both the diversity of mobile genetic elements (MGEs) that can mediate horizontal gene transfer within this genus and the breadth of species these MGEs can infect. In particular, few bacteriophages (phages) are known to infect species. In this study, we identified a large number of candidate phages integrated in the genomes of commensal and pathogenic species, many of which appear to be novel phages. Importantly, we discovered extensive interspecies targeting of predicted phages by CRISPR-Cas systems, which may reflect their movement between different species. Uncovering the diversity and host range of phages is essential for understanding how they influence the evolution of their microbial hosts.
Topics: Humans; Prophages; Neisseria; Host Specificity; Bacteriophages; Genomics; Neisseria gonorrhoeae; Neisseria meningitidis
PubMed: 35418239
DOI: 10.1128/msystems.00083-22