Analysis of intact prophages in genomes of Paenibacillus larvae: An important pathogen for bees

Abstract

Paenibacillus larvae is the etiological agent of American Foulbrood (AFB), a highly contagious and worldwide spread bacterial disease that affects honeybee brood. In this study, all complete P. larvae genomes available on the NCBI database were analyzed in order to detect presence of prophages using the PHASTER software. A total of 55 intact prophages were identified in 11 P. larvae genomes (5.0 ± 2.3 per genome) and were further investigated for the presence of genes encoding relevant traits related to P. larvae. A closer look at the prophage genomes revealed the presence of several putative genes such as metabolic and antimicrobial resistance genes, toxins or bacteriocins, potentially influencing host performance. Some of the coding DNA sequences (CDS) were present in all ERIC-genotypes, while others were only found in a specific genotype. While CDS encoding toxins and antitoxins such as HicB and MazE were found in prophages of all bacterial genotypes, others, from the same category, were provided by prophages particularly to ERIC I (enhancin-like toxin), ERIC II (antitoxin SocA) and ERIC V strains (subunit of Panton-Valentine leukocidin system (PVL) LukF-PV). This is the first in-depth analysis of P. larvae prophages. It provides better knowledge on their impact in the evolution of virulence and fitness of P. larvae, by discovering new features assigned by the viruses.

Diverse Prophage Elements of Salmonella enterica Serovars Show Potential Roles in Bacterial Pathogenicity

“…Besides the diversity of prophage numbers encoded in the genomes of the strains representing the serovars, we also observed clear differences in the genome completeness of the prophages detected in the Salmonella strains ( Figure 1 , Table 1 and Table S1 ) [ 23 , 44 ]. Generally, the numbers of complete (195) and incomplete (332) prophage regions detected across the dataset outweighed the number of questionable (88) prophage elements identified in the genomes examined [ 44 ].…”

“…Besides the diversity of prophage numbers encoded in the genomes of the strains representing the serovars, we also observed clear differences in the genome completeness of the prophages detected in the Salmonella strains ( Figure 1 , Table 1 and Table S1 ) [ 23 , 44 ]. Generally, the numbers of complete (195) and incomplete (332) prophage regions detected across the dataset outweighed the number of questionable (88) prophage elements identified in the genomes examined [ 44 ]. Specifically, the S. Inverness strains showed the greatest number of intact (25) and incomplete (33) prophages, and S. Agona encodes the least intact prophages in their genomes (5 prophages in total, with a single intact prophage in each strain), while S. Javiana encodes the lowest number of questionable prophages (but only one prophage was each identified in 3 (Accession numbers SAMN02335409, SAMN02345148, SAMN02646184) of the 5 examined representative strains) ( Table S1 ).…”

“…We observed a higher number of defective prophages (incomplete and questionable prophages) than intact prophage elements in the genomes studied here, and this concurs with general previous observations in Salmonella strains irrespective of serovar [ 19 , 23 , 42 ]. This is also a common occurrence in many other bacterial pathogens such as Paenibacillus larvae , C. difficile , and Bacillus thuringiensis [ 44 , 59 , 80 ]. The majority of the strains we examined encoded ‘low’ to ‘moderate’ number of prophages, and this is comparable to several other reports on Salmonella strains which reported an average of 5.29 prophages in the pathogen [ 19 ].…”

Characterization of prophages in bacterial genomes from the honey bee (Apis mellifera) gut microbiome

“…However, the high abundance and diversity of putative prophage regions in nearly all P. larvae isolates may imply that there are more prophage-encoded virulence factors to be discovered. For example, the presence of P. larvae prophage regions containing possible antimicrobial resistance genes, as well as carbohydrate, iron and sulfur metabolism genes, may indicate additional ways phage provide fitness to the pathogen (discussed in Ribeiro et al, 2022 ). The presence of three separate carbohydrate-associated genes in a single M. plutonius prophage indicates that prophage-encoded auxiliary metabolic pathways provide additional benefit to M. plutonius , as well.…”