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Comparative map of J2315_chr1_1 phage region: (a) general location of the phage on the host chromosome; (b) genes characterization based on PHASTER annotation; (c) genes characterization based on manual annotation.
Source publication
Burkholderia cenocepacia, is a Gram-negative opportunistic pathogen that belongs to Burkholderia cepacia complex (BCC) group. BCC representatives carry various pathogenicity factors and can infect humans and plants. Phages as bacterial viruses play a significant role in biodiversity and ecological balance in the environment. Specifically, horizonta...
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Citations
... One alternative source of Burkholderia-targeting phages are prophages found within the genomes of Burkholderia spp. isolates [24]. This is because prophages that have integrated into bacterial genomes are the result of successful prior phage infection and therefore could be useful for phage therapy [25,26]. ...
... Polylysogeny in Burkholderia appears to be common [24], and prophages present in Burkholderia genomes likely represent a rich hunting ground for clinically useful bacteriophages [42]. Triggering the bacterial DNA damage response using a mutagen like mitomycin C is a simple way to activate the lysogenic-lytic switch for some prophages [43], and the prophages we induced with this method showed lytic activity against both conspecific and heterospecific bacterial isolates. ...
Burkholderia spp. are often resistant to antibiotics, and infections with these organisms are difficult to treat. A potential alternative treatment for Burkholderia spp. infections is bacteriophage (phage) therapy; however, it can be difficult to locate phages that target these bacteria. Prophages incorporated into the bacterial genome have been identified within Burkholderia spp. and may represent a source of useful phages for therapy. Here, we investigate whether prophages within Burkholderia spp. clinical isolates can kill conspecific and heterospecific isolates. Thirty-two Burkholderia spp. isolates were induced for prophage release, and harvested phages were tested for lytic activity against the same 32 isolates. Temperate phages were passaged and their host ranges were determined, resulting in four unique phages of prophage origin that showed different ranges of lytic activity. We also analyzed the prophage content of 35 Burkholderia spp. clinical isolate genomes and identified several prophages present in the genomes of multiple isolates of the same species. Finally, we observed that Burkholdera cenocepacia isolates were more phage-susceptible than Burkholderia multivorans isolates. Overall, our findings suggest that prophages present within Burkholderia spp. genomes are a potentially useful starting point for the isolation and development of novel phages for use in phage therapy.
... Therefore, understanding the biology of the phages has several implementations in selecting phages as antibacterial agents, the evolution of bacterial strains, and typing for epidemiological studies [10]. Previously, characterization and comparative analysis of prophages present in several pathogenic strains of Burkholderia cenocepacia [11], Helicobacter pylori [12], Streptococcus mutans [13], Acinetobacter baumannii [14,15], Acinetobacter pittii [16], Klebsiella pneumoniae [17,18], Desulfovibrio [19], Staphylococcus aureus [20] have been performed to understand the roles of prophages in the evolution, fitness, and pathogenicity of the host bacteria. ...
Citrobacter freundii is a Gram-negative opportunistic bacterium that can cause infections, sepsis, and meningitis, predominantly in infants and immunocompromised adults. This study is aimed at investigating the distribution of prophages in C. freundii strains and their potential effects on the host strains using genomic characterization. In-silico analysis of 144 complete chromosomal sequences of C. freundii strains was performed, and 574 intact prophages were identified from 1178 prophages in the host. The genome sizes of the intact prophages were 6.74-115.15 kb; on average, the host chromosomes were predicted to have around 3.98% of intact prophage genomes. At least three intact prophages were most frequently predicted, while only three host chromosomes were found to have the highest number of nine intact prophages. The GC content of prophages is 50.75%, slightly lower than the average GC content (51.85%) of C. freundii. Most of the prophages in C. freundii strains were classified into four families, Myoviridae (48.16%), Siphoviridae (42%), Podoviridae (4.67%), Inoviridae (0.17%), and 5% of the intact prophages could not be assigned into any family. Phylogenomic analysis of intact prophages divided the genomes into three distinct clades. Virulence gene analysis revealed the variable distribution of 7 virulence genes (hcp, higB, hipA, msgA, rtx, yeeV, and ykfI) among the intact prophages. Overall, this study provides insights into the diversity and characteristics of prophages associated with C. freundii strains, which will help in understanding the genetic evolution and pathogenesis of the bacteria.
... The coordinates and annotation of phages in the CC31 isolates were fetched using the PHASTER server (Arndt et al., 2016). The GenBank files of 39 phages previously reported in the Burkholderia genus (Roszniowski et al., 2018) were extracted and compared to phages in CC31 isolates using clinker v0.0.23 with default settings (Gilchrist and Chooi, 2021). It performs protein sequence alignment and generates results based on sequence similarity of default 30% identity. ...
... Phages carry toxin genes and enzymes, enabling their host to infect other organisms by overcoming their defense system and eventually contribute to host pathogenicity. We compared Bcc phages in the NCBI database in the CC31 lineage (Roszniowski et al., 2018). Out of 39 phages, 13 phages were present in the CC31 lineage. ...
... Phage phiE202 belongs to the Myoviridae family and is a phage of B. thaliandensis, whereas phages BcepMu and KS10 are phages of B. cenocepacia, and KL3 is phage of B. amfibaria. KS9 belongs to Siphoviridae and is a phage of B. pyrrocinia (Roszniowski et al., 2018). Apart from basic phage machinery, phages carry additional genes conferring special advantages to their host. ...
Introduction
Burkholderia cepacia complex (Bcc) clonal complex (CC) 31, the predominant lineage causing devastating outbreaks globally, has been a growing concern of infections in non-cystic fibrosis (NCF) patients in India. B. cenocepacia is very challenging to treat owing to its virulence determinants and antibiotic resistance. Improving the management of these infections requires a better knowledge of their resistance patterns and mechanisms.
Methods
Whole-genome sequences of 35 CC31 isolates obtained from patient samples, were analyzed against available 210 CC31 genomes in the NCBI database to glean details of resistance, virulence, mobile elements, and phylogenetic markers to study genomic diversity and evolution of CC31 lineage in India.
Results
Genomic analysis revealed that 35 isolates belonging to CC31 were categorized into 11 sequence types (ST), of which five STs were reported exclusively from India. Phylogenetic analysis classified 245 CC31 isolates into eight distinct clades (I-VIII) and unveiled that NCF isolates are evolving independently from the global cystic fibrosis (CF) isolates forming a distinct clade. The detection rate of seven classes of antibiotic-related genes in 35 isolates was 35 (100%) for tetracyclines, aminoglycosides, and fluoroquinolones; 26 (74.2%) for sulphonamides and phenicols; 7 (20%) for beta-lactamases; and 1 (2.8%) for trimethoprim resistance genes. Additionally, 3 (8.5%) NCF isolates were resistant to disinfecting agents and antiseptics. Antimicrobial susceptibility testing revealed that majority of NCF isolates were resistant to chloramphenicol (77%) and levofloxacin (34%). NCF isolates have a comparable number of virulence genes to CF isolates. A well-studied pathogenicity island of B. cenocepacia, GI11 is present in ST628 and ST709 isolates from the Indian Bcc population. In contrast, genomic island GI15 (highly similar to the island found in B. pseudomallei strain EY1) is exclusively reported in ST839 and ST824 isolates from two different locations in India. Horizontal acquisition of lytic phage ST79 of pathogenic B. pseudomallei is demonstrated in ST628 isolates Bcc1463, Bcc29163, and BccR4654 amongst CC31 lineage.
Discussion
The study reveals a high diversity of CC31 lineages among B. cenocepacia isolates from India. The extensive information from this study will facilitate the development of rapid diagnostic and novel therapeutic approaches to manage B. cenocepacia infections.
... Therefore, understanding the biology of the phages has several implementations in selecting phages as antibacterial agents, the evolution of bacterial strains, and typing for epidemiological studies [10]. Previously, characterization and comparative analysis of prophages present in several pathogenic strains of Burkholderia cenocepacia [11], Helicobacter pylori [12], Streptococcus mutans [13], Acinetobacter baumannii [14,15], Acinetobacter pittii [16], Klebsiella pneumoniae [17,18], Desulfovibrio [19], Staphylococcus aureus [20] have been performed to understand the roles of prophages in the evolution, fitness, and pathogenicity of the host bacteria. ...
Citrobacter freundii is a Gram-negative opportunistic bacterium that can cause infections, sepsis, and meningitis, predominantly in infants and immunocompromised adults. This study is aimed at investigating the distribution of prophages in C. freundii strains and their potential effects on the host strains using genomic characterization. In-silico analysis of 144 complete chromosomal sequences of C. freundii strains was performed, and 574 intact prophages were identified from 1178 prophages in the host. The genome sizes of the intact prophages were 6.74-115.15 kb; on average, the host chromosomes were predicted to have around 3.98% of intact prophage genomes. At least three intact prophages were most frequently predicted, while only three host chromosomes were found to have the highest number of nine intact prophages. The GC content of prophages is 50.75%, slightly lower than the average GC content (51.85%) of C. freundii. Most of the prophages in C. freundii strains were classified into four families, Myoviridae (48.16%), Siphoviridae (42%), Podoviridae (4.67%), Inoviridae (0.17%), and 5% of the intact prophages could not be assigned into any family. Phylogenomic analysis of intact prophages divided the genomes into three distinct clades. Virulence gene analysis revealed the variable distribution of 7 virulence genes (hcp, higB, hipA, msgA, rtx, yeeV, and ykfI) among the intact prophages. Overall, this study provides insights into the diversity and characteristics of prophages associated with C. freundii strains, which will help in understanding the genetic evolution and pathogenesis of the bacteria.
... To test this hypothesis, experiments will need to be conducted, especially for these genera. A literature search for reports of HGT in Burkholderia and Paraburkholderia showed that HGT has been either demonstrated or suggested for several species in these two genera and it is said that it may confer advantages for the acquisition of MGE that might benefit them in their ecological environments (Wang et al., 2007(Wang et al., , 2021Roszniowski et al. 2018;Pratama and Van Elsas, 2019). Of note, the strains studied in these reports do not contain complete CRISPR-Cas systems (Burkholderia cenocepacia, Burkholderia seminalis, Paraburkholderia caribensis, Paraburkholderia terrae and Paraburkholderia phymatum). ...
CRISPR-Cas systems are composed of repeated sequences separated by non-repeated sequences that are near genes coding for Cas proteins, which are involved in the function of these systems. Their function has been mostly related to “genetic immunity” against foreign genetic material, among other roles. Interest in them increased after their use in genetic manipulation was uncovered and surveys to find and classify them have been done in several bacterial groups. To determine the presence of these genetic elements in the Burkholderiaceae family members, a bioinformatic approach was followed. Attention in this family comes as it is formed by a great diversity of microorganisms that include opportunistic and true pathogens, and symbiotic and saprophytic organisms, among others. Results show that, in contrast to other bacterial groups, only 8.4% of family members harbor complete CRISPR-Cas systems and the rest either do not have one or have remains or sections of one. Analyses of the spacer sequences indicated that most of them have identity to sections of the same genomes they were found, while a few had identities with either plasmids or phages. The genus with the higher proportion of self-directed spacers is Ralstonia, and their possible roles are discussed. Most of the systems (60%) belong to the class I subtype I-E and a few to subtypes I-C (13.3%), I-F (18.3%), II-C (5%), IV-A (1.7%) and V-C (1.7%). To the best of our knowledge, this is the first study to uncover the CRISPR-Cas system for the whole Burkholderiaceae family.
... For example, prophages of some of the most destructive plant pathogens including Pseudomonas [23], Xylella [24], and Xanthomonas [25] spp., have been associated with auxiliary genes that encode plant immune response inhibitors [26,27], secretion system proteins, degradative enzymes, and toxin exporters [28,29,30]. Plant pathogen competitiveness can also be mediated by prophages that encode competitor-repressing bacteriocins [31], provide resistance to environmental stresses such as toxic metal ions [32] and antimicrobials [33], or encourage survival during nutrient scarcity by increasing metabolic potential [34]. However, the distribution, diversity, and functional potential of prophages are still relatively understudied at the pangenome-level with plant pathogenic bacteria. ...
... While prophages are known to affect plant pathogen fitness by mediating host growth, competitiveness, and virulence [26,27,28,29,30,31,32,33,34,37,84], only very little is known about their diversity and distribution at the pangenome-level. In this study, we analysed the prophage content of the plant pathogenic RSSC bacterium using a representative, global collection of new 192 draft genome assemblies. ...
Background
Ralstonia solanacearum species complex (RSSC) strains are destructive plant pathogenic bacteria and the causative agents of bacterial wilt disease, infecting over 200 plant species worldwide. In addition to chromosomal genes, their virulence is mediated by mobile genetic elements including integrated DNA of bacteriophages, i.e. , prophages, which may carry fitness-associated auxiliary genes or modulate host gene expression. Although experimental studies have characterised several prophages that shape RSSC virulence, the global diversity, distribution, and wider functional gene content of RSSC prophages are unknown. In this study, prophages were identified in a diverse collection of 192 RSSC draft genome assemblies originating from six continents.
Results
Prophages were identified bioinformatically and their diversity investigated using genetic distance measures, gene content, GC, and total length. Prophage distributions were characterised using metadata on RSSC strain geographic origin and lineage classification (phylotypes), and their functional gene content was assessed by identifying putative prophage-encoded auxiliary genes. In total, 313 intact prophages were identified, forming ten genetically distinct clusters. These included six prophage clusters with similarity to the Inoviridae , Myoviridae , and Siphoviridae phage families, and four uncharacterised clusters, possibly representing novel, previously undescribed phages. The prophages had broad geographical distributions, being present across multiple continents. However, they were generally host phylogenetic lineage-specific, and overall, prophage diversity was proportional to the genetic diversity of their hosts. The prophages contained many auxiliary genes involved in metabolism and virulence of both phage and bacteria.
Conclusions
Our results show that while RSSC prophages are highly diverse globally, they make lineage-specific contributions to the RSSC accessory genome, which could have resulted from shared coevolutionary history.
... Something similar happens with bacteriophages. The finding of putative ARGs in prophages inserted in the chromosomes of different B. cenocepacia strains suggest that these genetic elements might be involved in the spread of resistance among Bcc [290]. However, detailed studies about the contribution of these elements in Bcc AR remain to be established. ...
The use and misuse of antibiotics have made antibiotic-resistant bacteria widespread nowadays, constituting one of the most relevant challenges for human health at present. Among these bacteria, opportunistic pathogens with an environmental, non-clinical, primary habitat stand as an increasing matter of concern at hospitals. These organisms usually present low susceptibility to antibiotics currently used for therapy. They are also proficient in acquiring increased resistance levels, a situation that limits the therapeutic options for treating the infections they cause. In this article, we analyse the most predominant opportunistic pathogens with an environmental origin, focusing on the mechanisms of antibiotic resistance they present. Further, we discuss the functions, beyond antibiotic resistance, that these determinants may have in the natural ecosystems that these bacteria usually colonize. Given the capacity of these organisms for colonizing different habitats, from clinical settings to natural environments, and for infecting different hosts, from plants to humans, deciphering their population structure, their mechanisms of resistance and the role that these mechanisms may play in natural ecosystems is of relevance for understanding the dissemination of antibiotic resistance under a One-Health point of view.
... Crucially, the capability of many of these phages to form lysogens has done little to inhibit their antibacterial effects, with lysogeny-capable phages, such as KS14 and KS4-M, demonstrating remarkable effectiveness in both in vitro and in vivo settings [166,170,244,256,259]. Interestingly, several Bcc phages have been isolated from the Bcc strains that they lysogenize, but these strains nevertheless remain susceptible to several other Bcc phages-suggesting that although prophages may provide superinfection immunity against phages of the same type, they do not provide protection against all Bcc phages [175,252,[259][260][261][262]. In spite of over two decades of research, very little is known about the receptors that Bcc phages use to enter their target cells, with only the primary receptors known for a small number of phages. ...
The increasing prevalence and worldwide distribution of multidrug-resistant bacterial pathogens is an imminent danger to public health and threatens virtually all aspects of modern medicine. Particularly concerning, yet insufficiently addressed, are the members of the Burkholderia cepacia complex (Bcc), a group of at least twenty opportunistic, hospital-transmitted, and notoriously drug-resistant species, which infect and cause morbidity in patients who are immunocompromised and those afflicted with chronic illnesses, including cystic fibrosis (CF) and chronic granulomatous disease (CGD). One potential solution to the antimicrobial resistance crisis is phage therapy—the use of phages for the treatment of bacterial infections. Although phage therapy has a long and somewhat checkered history, an impressive volume of modern research has been amassed in the past decades to show that when applied through specific, scientifically supported treatment strategies, phage therapy is highly efficacious and is a promising avenue against drug-resistant and difficult-to-treat pathogens, such as the Bcc. In this review, we discuss the clinical significance of the Bcc, the advantages of phage therapy, and the theoretical and clinical advancements made in phage therapy in general over the past decades, and apply these concepts specifically to the nascent, but growing and rapidly developing, field of Bcc phage therapy.
... However, host lifestyle cannot be the sole predictor for pBGC abundance, since some recurrent facultative pathogens, such as Acinetobacter, Burkholderia, Pseudomonas, or Staphylococcus, for which there is a high abundance of genomes in NCBI, contained no, or very few pBGCs, despite the presence of prophages. [46][47][48] The fact that pBGCs were overrepresented in bacterial genera with lower numbers of gBGCs, especially Escherichia, could suggest that the presence of gBGCs reduces the likelihood of phage infections. This matches previous data on the role of gBGCs in anti-phage defense. ...
Bacteria produce diverse specialized metabolites that mediate ecological interactions and serve as a rich source of industrially relevant natural products. Biosynthetic pathways for these metabolites are encoded by organized groups of genes called biosynthetic gene clusters (BGCs). Understanding the natural function and distribution of BGCs provides insight into the mechanisms through which microorganisms interact and compete. Further, understanding BGCs is extremely important for biocontrol and the mining of new bioactivities. Here, we investigated phage-encoded BGCs (pBGCs), challenging the relationship between phage origin and BGC structure and function. The results demonstrated that pBGCs are rare, and they predominantly reside within temperate phages infecting commensal or pathogenic bacterial hosts. Further, the vast majority of pBGCs were found to encode for bacteriocins. Using the soil- and gut-associated bacterium Bacillus subtilis, we experimentally demonstrated how a temperate phage equips a bacterium with a fully functional BGC, providing a clear competitive fitness advantage over the ancestor. Moreover, we demonstrated a similar transfer of the same phage in prophage form. Finally, using genetic and genomic comparisons, a strong association between pBGC type and phage host range was revealed. These findings suggest that bacteriocins are encoded in temperate phages of a few commensal bacterial genera. In these cases, lysogenic conversion provides an evolutionary benefit to the infected host and, hence, to the phage itself. This study is an important step toward understanding the natural role of bacterial compounds encoded by BGCs, the mechanisms driving their horizontal transfer, and the sometimes mutualistic relationship between bacteria and temperate phages.
... The presence of lysogenic phage may also provide a selective advantage to the host bacterium against secondary phage attack [10]. Several recent studies have been focused on the characterization and comparative analysis of the prophage within pathogen genomes, such as Acinetobacter baumannii [11]; Burkholderia cenocepacia [12]; Helicobacter pylori [13]; Mycobacterium [14]; Streptococcus pneumoniae [7] and Streptococcus mutans [15]. ...
Klebsiella pneumoniae, an opportunistic pathogen found in the environment and human mucosal surfaces, is a leading cause of nosocomial infections. K. pneumoniae is now considered a global threat owing to the emergence of multidrug-resistant strains making its infections untreatable. In this study, 254 strains of K. pneumoniae were screened for the presence of prophages using the PHASTER tool. Very few strains lacked prophages (3.1%), while the remaining harboured both intact (811) and defective prophages (709). A subset of 42 unique strains of K. pneumoniae was chosen for further analysis. Our analysis revealed the presence of 110 complete prophages which were further classified as belonging to Myoviridae (67.3%), Siphoviridae (28.2%) and Podoviridae family (4.5%). An alignment of the 110 complete, prophage genome sequences clustered the prophages into 16 groups and 3 singletons. While none of the prophages encoded for virulence factors, 2 (1.8%) prophages were seen to encode for the antibiotic resistance-related genes. The CRISPR-Cas system was prevalent in 10 (23.8%) out of the 42 strains. Further analysis of the CRISPR spacers revealed 11.42% of the total spacers integrated in K. pneumoniae chromosome to match prophage protein sequences.
