scholarly journals Genomic Analysis of 48 Paenibacillus larvae Bacteriophages

Viruses ◽  
2018 ◽  
Vol 10 (7) ◽  
pp. 377 ◽  
Author(s):  
Casey Stamereilers ◽  
Christopher Fajardo ◽  
Jamison Walker ◽  
Katterinne Mendez ◽  
Eduardo Castro-Nallar ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Dna Packaging ◽  
Paenibacillus Larvae ◽  
Bacterial Disease ◽  
Replication Proteins ◽  
Antibiotic Resistant ◽  
Distinct Cluster ◽  
Antibiotic Resistant Bacterium ◽  
Packaging Strategy ◽  
Assembly Proteins

The antibiotic-resistant bacterium Paenibacillus larvae is the causative agent of American foulbrood (AFB), currently the most destructive bacterial disease in honeybees. Phages that infect P. larvae were isolated as early as the 1950s, but it is only in recent years that P. larvae phage genomes have been sequenced and annotated. In this study we analyze the genomes of all 48 currently sequenced P. larvae phage genomes and classify them into four clusters and a singleton. The majority of P. larvae phage genomes are in the 38–45 kbp range and use the cohesive ends (cos) DNA-packaging strategy, while a minority have genomes in the 50–55 kbp range that use the direct terminal repeat (DTR) DNA-packaging strategy. The DTR phages form a distinct cluster, while the cos phages form three clusters and a singleton. Putative functions were identified for about half of all phage proteins. Structural and assembly proteins are located at the front of the genome and tend to be conserved within clusters, whereas regulatory and replication proteins are located in the middle and rear of the genome and are not conserved, even within clusters. All P. larvae phage genomes contain a conserved N-acetylmuramoyl-l-alanine amidase that serves as an endolysin.

scholarly journals Characterization of CRISPR Spacer and Protospacer Sequences in Paenibacillus larvae and Its Bacteriophages

Viruses ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 459
Author(s):  
Casey Stamereilers ◽  
Simon Wong ◽  
Philippos K. Tsourkas
Keyword(s):  
Comparative Studies ◽  
Point Mutations ◽  
Paenibacillus Larvae ◽  
Bacterial Disease ◽  
American Foulbrood ◽  
Antibiotic Resistant ◽  
Future Studies ◽  
Complete Genomes ◽  
Point Of Reference

The bacterium Paenibacillus larvae is the causative agent of American foulbrood, the most devastating bacterial disease of honeybees. Because P. larvae is antibiotic resistant, phages that infect it are currently used as alternative treatments. However, the acquisition by P. larvae of CRISPR spacer sequences from the phages could be an obstacle to treatment efforts. We searched nine complete genomes of P. larvae strains and identified 714 CRISPR spacer sequences, of which 384 are unique. Of the four epidemiologically important P. larvae strains, three of these have fewer than 20 spacers, while one strain has over 150 spacers. Of the 384 unique spacers, 18 are found as protospacers in the genomes of 49 currently sequenced P. larvae phages. One P. larvae strain does not have any protospacers found in phages, while another has eight. Protospacer distribution in the phages is uneven, with two phages having up to four protospacers, while a third of phages have none. Some phages lack protospacers found in closely related phages due to point mutations, indicating a possible escape mechanism. This study serve a point of reference for future studies on the CRISPR-Cas system in P. larvae as well as for comparative studies of other phage–host systems.

scholarly journals Phylogenetic evidence of headful packaging strategy in gene transfer agents

2020 ◽  
Author(s):  
Emma Esterman ◽  
Yuri I. Wolf ◽  
Roman Kogay ◽  
Eugene V. Koonin ◽  
Olga Zhaxybayeva
Keyword(s):  
Gene Transfer ◽  
Rhodobacter Capsulatus ◽  
Large Subunit ◽  
Dna Packaging ◽  
Host Genome ◽  
Bacterial And Archaeal Communities ◽  
History Of ◽  
Viral Dna Packaging ◽  
Packaging Strategy ◽  
Transfer Agents

AbstractGene transfer agents (GTAs) are virus-like particles encoded and produced by many bacteria and archaea. Unlike viruses, GTAs package fragments of the host genome instead of the genes that encode the components of the GTA itself. As a result of this non-specific DNA packaging, GTAs can transfer genes within bacterial and archaeal communities. GTAs clearly evolved from viruses and are thought to have been maintained in prokaryotic genomes due to the advantages associated with their DNA transfer capacity. The most-studied GTA is produced by the alphaproteobacterium Rhodobacter capsulatus (RcGTA), which packages random portions of the host genome at a lower DNA density than usually observed in tailed bacterial viruses. How the DNA packaging properties of RcGTA evolved from those of the ancestral virus remains unknown. To address this question, we reconstructed the evolutionary history of the large subunit of the terminase (TerL), a highly conserved enzyme used by viruses and GTAs to package DNA. We found that RcGTA-like TerLs grouped within viruses that employ the headful packaging strategy. Because distinct mechanisms of viral DNA packaging correspond to differences in the TerL amino acid sequence, our finding suggests that RcGTA evolved from a headful packaging virus. Headful packaging is the least sequence-specific mode of DNA packaging, which would facilitate the switch from packaging of the viral genome to packaging random pieces of the host genome during GTA evolution.

scholarly journals Antimicrobial Activity against Paenibacillus larvae and Functional Properties of Lactiplantibacillus plantarum Strains: Potential Benefits for Honeybee Health

Antibiotics ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 442 ◽  
Author(s):  
Massimo Iorizzo ◽  
Bruno Testa ◽  
Silvia Jane Lombardi ◽  
Sonia Ganassi ◽  
Mario Ianiro ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Biochemical Properties ◽  
Antagonistic Activity ◽  
Paenibacillus Larvae ◽  
Bacterial Disease ◽  
Osmotic Tolerance ◽  
Potential Benefits ◽  
Honeybee Health ◽  
Exopolysaccharides Production

Paenibacillus larvae is the causative agent of American foulbrood (AFB), a severe bacterial disease that affects larvae of honeybees. The present study evaluated, in vitro, antimicrobial activity of sixty-one Lactiplantibacillus plantarum strains, against P. larvae ATCC 9545. Five strains (P8, P25, P86, P95 and P100) that showed the greatest antagonism against P. larvae ATCC 9545 were selected for further physiological and biochemical characterizations. In particular, the hydrophobicity, auto-aggregation, exopolysaccharides production, osmotic tolerance, enzymatic activity and carbohydrate assimilation patterns were evaluated. The five L. plantarum selected strains showed suitable physical and biochemical properties for their use as probiotics in the honeybee diet. The selection and availability of new selected bacteria with good functional characteristics and with antagonistic activity against P. larvae opens up interesting perspectives for new biocontrol strategies of diseases such as AFB.

The effects of ultraviolet disinfection on vancomycin-resistant Enterococcus faecalis

2020 ◽  
Vol 22 (2) ◽  
pp. 418-429 ◽  
Author(s):  
Jingyu Wang ◽  
Minghao Sui ◽  
Hongwei Li ◽  
Bojie Yuan
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Gene ◽  
Enterococcus Faecalis ◽  
Removal Efficiency ◽  
Antibiotic Resistance Gene ◽  
Vancomycin Resistant Enterococcus ◽  
Ultraviolet Disinfection ◽  
Antibiotic Resistant ◽  
Antibiotic Resistant Bacterium ◽  
Vancomycin Resistant

Ultraviolet disinfection could effectively inactivate the antibiotic resistant bacterium vancomycin resistant Enterococcus faecalis, but had a limited removal efficiency for the antibiotic resistance gene–vanB gene.

scholarly journals Caffeic Acid Esters Are Effective Bactericidal Compounds Against Paenibacillus larvae by Altering Intracellular Oxidant and Antioxidant Levels

Biomolecules ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 312 ◽  
Author(s):  
William Collins ◽  
Noah Lowen ◽  
David J. Blake
Keyword(s):  
Caffeic Acid ◽  
Bacterial Growth ◽  
Bactericidal Effect ◽  
Caffeic Acid Phenethyl Ester ◽  
Benzyl Ester ◽  
Paenibacillus Larvae ◽  
Bacterial Disease ◽  
Bee Foraging ◽  
Caffeic Acid Esters ◽  
Acid Esters

American Foulbrood (AFB) is a deadly bacterial disease affecting pupal and larval honey bees. AFB is caused by the endospore-forming bacterium Paenibacillus larvae (PL). Propolis, which contains a variety of organic compounds, is a product of bee foraging and is a resinous substance derived from botanical substances found primarily in trees. Several compounds from the class of caffeic acid esters, which are commonly found in propolis, have been shown to have antibacterial activity against PL. In this study, six different caffeic acid esters were synthesized, purified, spectroscopically analyzed, and tested for their activity against PL to determine the minimum inhibitory concentrations (MICs) and minimum bactericidal concentrations (MBCs). Caffeic acid isopropenyl ester (CAIE), caffeic acid benzyl ester (CABE), and caffeic acid phenethyl ester (CAPE) were the most effective in inhibiting PL growth and killing PL cell with MICs and MBCs of 125 µg/mL when used individually, and a MIC and MBC of 31.25 µg/mL for each compound alone when CAIE, CABE, and CAPE are used in combination against PL. These compounds inhibited bacterial growth through a bactericidal effect, which revealed cell killing but no lysis of PL cells after 18 h. Incubation with CAIE, CABE, and CAPE at their MICs significantly increased reactive oxygen species levels and significantly changed glutathione levels within PL cells. Caffeic acid esters are potent bactericidal compounds against PL and eliminate bacterial growth through an oxidative stress mechanism.

scholarly journals Application of Combined Genomic and Transfer Analyses to Identify Factors Mediating Regional Spread of Antibiotic-resistant Bacterial Lineages

2020 ◽  
Vol 71 (10) ◽  
pp. e642-e649
Author(s):  
Joyce Wang ◽  
Betsy Foxman ◽  
Ali Pirani ◽  
Zena Lapp ◽  
Lona Mody ◽  
...  
Keyword(s):  
Methicillin Resistant Staphylococcus Aureus ◽  
Genomic Analysis ◽  
Patient Characteristics ◽  
Fourth Generation ◽  
Nursing Facilities ◽  
Antibiotic Resistant ◽  
Patient Level ◽  
Vancomycin Resistant ◽  
Healthcare Associated ◽  
Genomic Similarity

Abstract Background Patients entering nursing facilities (NFs) are frequently colonized with antibiotic-resistant organisms (AROs). To understand the determinants of ARO colonization on NF admission, we applied whole-genome sequencing to track the spread of 4 ARO species across regional NFs and evaluated patient-level characteristics and transfer acute care hospitals (ACHs) as risk factors for colonization. Methods Patients from 6 NFs (n = 584) were surveyed for methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecalis/faecium (VREfc/VREfm), and ciprofloxacin-resistant Escherichia coli (CipREc) colonization. Genomic analysis was performed to quantify ARO spread between NFs and compared to patient-transfer networks. The association between admission colonization and patient-level variables and recent ACH exposures was examined. Results The majority of ARO isolates belonged to major healthcare-associated lineages: MRSA (sequence type [ST] 5); VREfc (ST6); CipREc (ST131), and VREfm (clade A). While the genomic similarity of strains between NF pairs was positively associated with overlap in their feeder ACHs (P < .05 for MRSA, VREfc, and CipREc), limited phylogenetic clustering by either ACH or NF supported regional endemicity. Significant predictors for ARO colonization on NF admission included lower functional status and recent exposure to glycopeptides (adjusted odds ratio [aOR], > 2 for MRSA and VREfc/VREfm) or third-/fourth-generation cephalosporins (aOR, > 2 for MRSA and VREfm). Transfer from specific ACHs was an independent risk factor for only 1 ARO/ACH pair (VREfm/ACH19: aOR, 2.48). Conclusions In this region, healthcare-associated ARO lineages are endemic among connected NFs and ACHs, making patient characteristics more informative of NF admission colonization risk than exposure to specific ACHs.

scholarly journals The Generalized Transducing Salmonella Bacteriophage ES18: Complete Genome Sequence and DNA Packaging Strategy

2005 ◽  
Vol 187 (3) ◽  
pp. 1091-1104 ◽  
Author(s):  
Sherwood R. Casjens ◽  
Eddie B. Gilcrease ◽  
Danella A. Winn-Stapley ◽  
Petra Schicklmaier ◽  
Horst Schmieger ◽  
...  
Keyword(s):  
Shigella Flexneri ◽  
Bioinformatic Analysis ◽  
Dna Packaging ◽  
Phage Group ◽  
Double Stranded Dna ◽  
Functional Classes ◽  
Phage P22 ◽  
Genome Nucleotide Sequence ◽  
Group Members ◽  
Packaging Strategy

ABSTRACT The generalized transducing double-stranded DNA bacteriophage ES18 has an icosahedral head and a long noncontractile tail, and it infects both rough and smooth Salmonella enterica strains. We report here the complete 46,900-bp genome nucleotide sequence and provide an analysis of the sequence. Its 79 genes and their organization clearly show that ES18 is a member of the lambda-like (lambdoid) phage group; however, it contains a novel set of genes that program assembly of the virion head. Most of its integration-excision, immunity, Nin region, and lysis genes are nearly identical to those of the short-tailed Salmonella phage P22, while other early genes are nearly identical to Escherichia coli phages λ and HK97, S. enterica phage ST64T, or a Shigella flexneri prophage. Some of the ES18 late genes are novel, while others are most closely related to phages HK97, lambda, or N15. Thus, the ES18 genome is mosaically related to other lambdoid phages, as is typical for all group members. Analysis of virion DNA showed that it is circularly permuted and about 10% terminally redundant and that initiation of DNA packaging series occurs across an approximately 1-kbp region rather than at a precise location on the genome. This supports a model in which ES18 terminase can move substantial distances along the DNA between recognition and cleavage of DNA destined to be packaged. Bioinformatic analysis of large terminase subunits shows that the different functional classes of phage-encoded terminases can usually be predicted from their amino acid sequence.

Biochemical characterization of different genotypes of Paenibacillus larvae subsp. larvae, a honey bee bacterial pathogen

Microbiology ◽  
2004 ◽  
Vol 150 (7) ◽  
pp. 2381-2390 ◽  
Author(s):  
Sandra Neuendorf ◽  
Kati Hedtke ◽  
Gerhard Tangen ◽  
Elke Genersch
Keyword(s):  
Honey Bee ◽  
Reference Strain ◽  
Biochemical Characterization ◽  
Bacterial Pathogen ◽  
Paenibacillus Larvae ◽  
Bacterial Disease ◽  
System A ◽  
Biolog System ◽  
Far Future

Paenibacillus larvae subsp. larvae (P. l. larvae) is the aetiological agent of American foulbrood (AFB), the most virulent bacterial disease of honey bee brood worldwide. In many countries AFB is a notifiable disease since it is highly contagious, in most cases incurable and able to kill affected colonies. Genotyping of field isolates of P. l. larvae revealed at least four genotypes (AB, Ab, ab and α B) present in Germany which are genotypically different from the reference strain DSM 7030. Therefore, based on these data, five different genotypes of P. l. larvae are now identified with genotype AB standing out with a characteristic brown-orange and circled two-coloured colony morphology. Analysing the metabolic profiles of three German genotypes (AB, Ab and ab) as well as of the reference strain using the Biolog system, a characteristic biochemical fingerprint could be obtained for each strain. Cluster analysis showed that while genotypes Ab, ab and the reference strain DSM 7030 are rather similar, genotype AB is clearly different from the others. Analysis of all isolates for plasmid DNA revealed two different plasmids present only in isolates belonging to genotype AB. Therefore, genotype AB is remarkable in all aspects analysed so far. Future analysis will show whether or not these differences will expand to differences in virulence.

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