Streptococcus pyogenes Φ1207.3 Is a Temperate Bacteriophage Carrying the Macrolide Resistance Gene Pair
            <i>mef</i>
            (A)-
            <i>msr</i>
            (D) and Capable of Lysogenizing Different Streptococci

Santoro, Francesco; Pastore, Gabiria; Fox, Valeria; Petit, Marie‐Agnès; Iannelli, Francesco; Pozzi, Gianni

doi:10.1128/spectrum.04211-22

Cited by 6 publications

(4 citation statements)

References 41 publications

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“…While carriage of antibiotic resistance genes (ARGs) is not common in prophages [44], there have been reports of ARGs carriage in conjugative elements within prophages of streptococcal species [45,46]. The fact that these elements were found in only a single GBS prophage analysed in this study, highlights the overall low prevalence of ARGs in GBS prophages.…”

Section: Discussionmentioning

confidence: 74%

Revisiting typing systems for group BStreptococcus(GBS) prophages: an application in prophage detection and classification in GBS isolates from Argentina

Kovacec,

Di Gregorio,

Pajón

et al. 2024

Preprint

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Group B Streptococcus (GBS) causes severe infections in neonates and adults with comorbidities. Prophages have been reported to contribute to GBS evolution and pathogenicity. However, no studies are available to date on the presence and diversity of prophages in GBS isolates from humans in South America. This study provides insights into the prophage content of 365 GBS isolates collected from clinical samples in the context of an Argentinean multicentric study. Using whole genome sequence data, we implemented two previously proposed methods for prophage typing: a PCR approach (carried out in silico) coupled with a blastx-based method to classify prophages based on their prophage group and integrase type, respectively. We manually searched the genomes and identified 325 prophages. However, only 80% of prophages could be accurately categorised with the previous approaches. Integration of phylogenetic analysis, prophage group and integrase type allowed for all to be classified into 19 prophage types, which correlated with GBS clonal complex grouping. The revised prophage typing approach was additionally improved by using a blastn search after enriching the database with 10 new genes for prophage group classification combined with the existing integrase typing method. This modified and integrated typing system was applied to the analysis of 615 GBS genomes (365 GBS from Argentina and 250 from public databases), which revealed 29 prophage types, including 2 novel integrase subtypes. Their characterization and comparative analysis revealed major differences in the lysogeny and replication modules. Genes related to bacterial fitness, virulence or adaptation to stressful environments were detected in all prophage types. Considering prophage prevalence, distribution and their association with bacterial virulence, it is important to study their role in GBS epidemiology. In this context, we propose the use of an improved and integrated prophage typing system suitable for rapid phage detection and classification with little computational processing.

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Section: Discussionmentioning

confidence: 74%

Revisiting typing systems for group BStreptococcus(GBS) prophages: an application in prophage detection and classification in GBS isolates from Argentina

Kovacec,

Di Gregorio,

Pajón

et al. 2024

Preprint

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“…Nevertheless, BM6001 could not be transformed in any of our experimental conditions. As observed for ΦBM6001.3, mitomycin C treatment induces the excision of the lysogenic phage Φ1207.3 [ 63 , 64 , 65 , 66 ], which inserts within the pneumococcal comEC / celB competence gene impairing genetic transformation and increases the free locus restoration frequency. Differently from ΦBM6001.3, this restores a low level of competence for genetic transformation (9.96 × 10 −4 transformants/total CFU).…”

Section: Discussionmentioning

confidence: 99%

The Mobilome-Enriched Genome of the Competence-Deficient Streptococcus pneumoniae BM6001, the Original Host of Integrative Conjugative Element Tn5253, Is Phylogenetically Distinct from Historical Pneumococcal Genomes

Colombini,

Cuppone,

Tirziu

et al. 2023

Microorganisms

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Streptococcus pneumoniae is an important human pathogen causing both mild and severe diseases. In this work, we determined the complete genome sequence of the S. pneumoniae clinical isolate BM6001, which is the original host of the ICE Tn5253. The BM6001 genome is organized in one circular chromosome of 2,293,748 base pairs (bp) in length, with an average GC content of 39.54%; the genome harbors a type 19F capsule locus, two tandem copies of pspC, the comC1-comD1 alleles and the type I restriction modification system SpnIII. The BM6001 mobilome accounts for 15.54% (356,521 bp) of the whole genome and includes (i) the ICE Tn5253 composite; (ii) the novel IME Tn7089; (iii) the novel transposon Tn7090; (iv) 3 prophages and 2 satellite prophages; (v) 5 genomic islands (GIs); (vi) 72 insertion sequences (ISs); (vii) 69 RUPs; (viii) 153 BOX elements; and (ix) 31 SPRITEs. All MGEs, except for the GIs, produce excised circular forms and attB site restoration. Tn7089 is 9089 bp long and contains 11 ORFs, of which 6 were annotated and code for three functions: integration/excision, mobilization and adaptation. Tn7090 is 9053 bp in size, flanked by two copies of ISSpn7, and contains seven ORFs organized as a single transcriptional unit, with genes encoding for proteins likely involved in the uptake and binding of Mg2+ cations in the adhesion to host cells and intracellular survival. BM6001 GIs, except for GI-BM6001.4, are variants of the pneumococcal TIGR4 RD5 region of diversity, pathogenicity island PPI1, R6 Cluster 4 and PTS island. Overall, prophages and satellite prophages contain genes predicted to encode proteins involved in DNA replication and lysogeny, in addition to genes encoding phage structural proteins and lytic enzymes carried only by prophages. ΦBM6001.3 has a mosaic structure that shares sequences with prophages IPP69 and MM1 and disrupts the competent comGC/cglC gene after chromosomal integration. Treatment with mitomycin C results in a 10-fold increase in the frequency of ΦBM6001.3 excised forms and comGC/cglC coding sequence restoration but does not restore competence for genetic transformation. In addition, phylogenetic analysis showed that BM6001 clusters in a small lineage with five other historical strains, but it is distantly related to the lineage due to its unique mobilome, suggesting that BM6001 has progressively accumulated many MGEs while losing competence for genetic transformation.

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“…Mitomycin C induction and phage preparation were obtained essentially as previously reported [ 31 ]. Briefly, bacterial cells were grown in 600 ml of MRS broth until early exponential phase, and the culture was then split into three aliquots of which two were treated with 200 and 400 ng ml −1 of mitomycin C. After 21 h of incubation at 37 °C, EDTA was added at a final concentration of 10 mM and the samples were centrifuged twice at 5 000 g for 40 min at 4 °C in 50 ml tubes to eliminate bacterial cells and cellular debris.…”

Section: Methodsmentioning

confidence: 99%

The mobilome of Lactobacillus crispatus M247 includes two novel genetic elements: Tn7088 coding for a putative bacteriocin and the siphovirus prophage ΦM247

Colombini,

Santoro,

Tirziu

et al. 2023

Microbial Genomics

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Lactobacillus crispatus is a member of the vaginal and gastrointestinal human microbiota. Here we determined the complete genome sequence of the probiotic strain M247 combining Nanopore and Illumina technologies. The M247 genome is organized in one circular chromosome of 2 336 109 bp, with a GC content of 37.04 % and 2303 ORFs, of which 1962 could be annotated. Analysis of the M247 mobilome, which accounts for 14 % of the whole genome, revealed the presence of: (i) Tn7088, a novel 14 105 bp long integrative and mobilizable element (IME) containing 16 ORFs; (ii) ΦM247, a novel 42 510 bp long siphovirus prophage containing 52 ORFs; (iii) three clustered regularly interspaced short palindromic repeats (CRISPRs); and (iv) 226 insertion sequences (ISs) belonging to 14 different families. Tn7088 has a modular organization including a mobilization module encoding FtsK homologous proteins and a relaxase, an integration/excision module coding for an integrase and an excisionase, and an adaptation module coding for a class I bacteriocin and homologous to the listeriolysin S (lls) locus of Listeria monocytogenes . Genome-wide homology search analysis showed the presence of Tn7088-like elements in 12 out of 23 L . crispatus complete public genomes. Mobilization and integration/excision modules are essentially conserved, while the adaptation module is variable since it is the target site for the integration of different ISs. Prophage ΦM247 contains genes for phage structural proteins, DNA replication and packaging, lysogenic and lytic cycles. ΦM247-like prophages are present in seven L . crispatus complete genomes, with sequence variability mainly due to the integration of ISs. PCR and sequencing showed that the Tn7088 IME excises from the M247 chromosome producing a circular form at a concentration of 4.32×10−5 copies per chromosome, and reconstitution of the Tn7088 chromosomal target site occurred at 6.65×10−4 copies per chromosome. The ΦM247 prophage produces an excised form and a reconstituted target site at a level of 3.90×10−5 and 2.48×10−5 copies per chromosome, respectively. This study identified two novel genetic elements in L. crispatus . Tn7088 represents the first example of an IME carrying a biosynthetic gene cluster for a class I bacteriocin in L. crispatus .

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Streptococcus pyogenes Φ1207.3 Is a Temperate Bacteriophage Carrying the Macrolide Resistance Gene Pair mef (A)- msr (D) and Capable of Lysogenizing Different Streptococci

Abstract: Bacteriophages play an important role in bacterial physiology and genome evolution. The widespread use of genome sequencing revealed that bacterial genomes can contain several different integrated temperate bacteriophages, which can constitute up to 20% of the genome.

Cited by 6 publications

References 41 publications

Revisiting typing systems for group BStreptococcus(GBS) prophages: an application in prophage detection and classification in GBS isolates from Argentina

Revisiting typing systems for group BStreptococcus(GBS) prophages: an application in prophage detection and classification in GBS isolates from Argentina

The Mobilome-Enriched Genome of the Competence-Deficient Streptococcus pneumoniae BM6001, the Original Host of Integrative Conjugative Element Tn5253, Is Phylogenetically Distinct from Historical Pneumococcal Genomes

The mobilome of Lactobacillus crispatus M247 includes two novel genetic elements: Tn7088 coding for a putative bacteriocin and the siphovirus prophage ΦM247

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