Multiple Locus Variable number of tandem repeat Analysis: A molecular genotyping tool for Paenibacillus larvae

Hexanic extract of Achyrocline satureioides: antimicrobial activity and in vitro inhibitory effect on mechanisms related to the pathogenicity of Paenibacillus larvae

INTRODUCTION

Paenibacillus larvae is a spore-forming bacillus, the most important bacterial pathogen of honeybee larvae and the causative agent of American foulbrood (AFB). Control measures are limited and represent a challenge for both beekeepers and researchers. For this reason, many studies focus on the search for alternative treatments based on natural products.

AIM

The objective of this study was to determine the antimicrobial activity of the hexanic extract (HE) of Achyrocline satureioides on P. larvae and the inhibitory activity on some mechanisms related to pathogenicity.

MATERIAL AND METHODS

The Minimum Inhibitory Concentration (MIC) of the HE was determined by the broth microdilution technique and the Minimum Bactericidal Concentration (MBC) by the microdrop technique. Swimming and swarming motility was evaluated in plates with 0.3 and 0.5% agar, respectively. Biofilm formation was evaluated and quantified by the Congo red and crystal violet method. The protease activity was evaluated by the qualitative technique on skim milk agar plates.

RESULTS

It was determined that the MIC of the HE on four strains of P. larvae ranged between 0.3 and 9.37 µg/ml and the MBC between 1.17 and 150 µg/ml. On the other hand, sub-inhibitory concentrations of the HE were able to decrease swimming motility, biofilm formation and the proteases production of P. larvae.

Genomic analysis of Paenibacillus larvae isolates from the Czech Republic and the neighbouring regions of Slovakia

Paenibacillus larvae is the causative agent of American foulbrood (AFB), a devastating disease of honeybee larvae. In the Czech Republic, two large infested regions were recognised. This study aimed to analyse P. larvae strains occurring in the Czech Republic in the years 2016-2017 and to characterise the genetic structure of their population with the use of Enterobacterial Repetitive Intergenic Consensus genotyping (ERIC), multilocus sequence typing (MLST) and whole genome sequence (WGS) analysis. The results were complemented by the analysis of isolates collected in the year 2018 in areas of Slovakia located near the Czechia-Slovakia border. ERIC genotyping revealed that 78.9% of tested isolates belonged to the ERIC II genotype and 21.1% to ERIC I genotype. MLST showed six sequence types with ST10 and ST11 being the most frequent among isolates. Within six isolates we found discrepancies in correlations between MLST and ERIC genotypes. The use of MLST and WGS analysis of isolates revealed that each of the large infested geographic regions had its own dominating P. larvae strains. We assume that these strains represented primary sources of infection in the affected areas. In addition, the sporadic presence of strains identified by core genome analysis as genetically related was unveiled in geographically distant regions suggesting possible human-mediated transmission of AFB.

Molecular diversity of Paenibacillus larvae strains isolated from Lithuanian apiaries

Paenibacillus larvae bacterium is known to be the causative agent of American foulbrood (AFB), a widespread, highly contagious and fatal disease in honey bees (Apis mellifera). There are four genotypes of Paenibacillus larvae that are named after their enterobacterial repetitive consensus (ERIC), and a fifth ERIC genotype has recently been found. In this study, a total of 108 independent P. larvae isolates from different geographical regions in Lithuania collected between 2011 and 2021 were investigated by molecular methods. The aims of this study were to detect which enterobacterial repetitive intergenic consensus (ERIC) genotype is the most common in Lithuania apiaries, identify and differentiate subtypes of the defined genotype by using multiple-locus variable number of tandem-repeat analysis (MLVA), and review how bacterial molecular diversity has changed over time in different parts of Lithuania. The obtained molecular analysis results showed that 100% of P. larvae bacterial isolates from Lithuania belong to the ERIC I genotype and can be differentiated to nine different subtypes by using the MLVA and capillary electrophoresis methods.

Molecular Detection and Differentiation of Arthropod, Fungal, Protozoan, Bacterial and Viral Pathogens of Honeybees

The honeybee Apis mellifera is highly appreciated worldwide because of its products, but also as it is a pollinator of crops and wild plants. The beehive is vulnerable to infections due to arthropods, fungi, protozoa, bacteria and/or viruses that manage to by-pass the individual and social immune mechanisms of bees. Due to the close proximity of bees in the beehive and their foraging habits, infections easily spread within and between beehives. Moreover, international trade of bees has caused the global spread of infections, several of which result in significant losses for apiculture. Only in a few cases can infections be diagnosed with the naked eye, by direct observation of the pathogen in the case of some arthropods, or by pathogen-associated distinctive traits. Development of molecular methods based on the amplification and analysis of one or more genes or genomic segments has brought significant progress to the study of bee pathogens, allowing for: (i) the precise and sensitive identification of the infectious agent; (ii) the analysis of co-infections; (iii) the description of novel species; (iv) associations between geno- and pheno-types and (v) population structure studies. Sequencing of bee pathogen genomes has allowed for the identification of new molecular targets and the development of specific genotypification strategies.

ERIC and WGS Typing of Paenibacillus larvae in Slovenia: Investigation of ERIC I Outbreaks

Simple Summary

American foulbrood is a serious disease of honeybees caused by Paenibacillus larvae. ERIC-PCR is a widely used method for typing of P. larvae that currently divides it into five ERIC types (ERIC I–V); these differ in certain phenotypic characteristics—most importantly, virulence. In the first part of the study, we assessed the distribution of ERIC types in Slovenia in the period 2017–2019 on a set of 506 P. larvae isolates. We identified ERIC II as the predominant type (70.2%), followed by ERIC I (29.8%). In the second part of the study, we typed 59 outbreak-related ERIC I isolates using whole-genome sequencing, which revealed seven ERIC I-ST2 outbreak clusters (≤35 allele differences). The transmission of the outbreak clone within a 3-km radius was observed in all seven clusters and could be explained by the activity of honeybees. The transmission of the outbreak clone between geographically distant apiaries was observed in three clusters and could be explained by migratory beekeeping and trading of bee colonies. The present findings highlight the importance of beekeeping activities in the transmission of P. larvae over large geographic distances.

Abstract

Paenibacillus larvae is the causative agent of American foulbrood (AFB), a fatal disease of honeybee brood. Here, we obtained 506 P. larvae isolates originating from honey or brood samples and from different geographic regions of Slovenia in the period 2017–2019. In the first part of the study, we conducted ERIC-PCR typing to assess the frequency of ERIC types in Slovenia. Capillary electrophoresis was used for the analysis of ERIC patterns, revealing good separation efficiency and enabling easy lane-to-lane comparisons. ERIC II was the predominant type (70.2%), followed by ERIC I (29.8%); two slightly altered ERIC I banding patterns were observed but were not considered relevant for the discrimination of ERIC types. No evident spatiotemporal clustering of ERIC types was observed. To assess the clonality of the outbreak-related P. larvae ERIC I isolates, 59 isolates of this type underwent whole-genome sequencing (WGS). Whole-genome multilocus sequence typing (wgMLST) revealed seven ERIC I-ST2 outbreak clusters (≤35 allele differences) with the median intra-outbreak diversity ranging from 7 to 27 allele differences. In all seven clusters, the transmission of P. larvae outbreak clone within a 3-km radius (AFB zone) was observed, which could be explained by the activity of honeybees. In three clusters, the transmission of the outbreak clone between geographically distant apiaries was revealed, which could be explained by the activities of beekeepers such as migratory beekeeping and trading of bee colonies. The present findings reinforce the importance of beekeeping activities in the transmission of P. larvae. WGS should be used as a reference typing method for the detection of P. larvae transmission clusters.

Development and evaluation of a core genome multilocus sequence typing scheme for Paenibacillus larvae, the deadly American foulbrood pathogen of honeybees

Paenibacillus larvae is the causative agent of the fatal American foulbrood disease in honeybees (Apis mellifera). Strain identification is vital for preventing the spread of the disease. To date, the most accessible and robust scheme to identify strains is the multilocus sequence typing (MLST) method. However, this approach has limited resolution, especially for epidemiological studies. As the cost of whole-genome sequencing has decreased and as it becomes increasingly available to most laboratories, an extended MLST based on the core genome (cgMLST) presents a valuable tool for high-resolution investigations. In this study, we present a standardized, robust cgMLST scheme for P. larvae typing using whole-genome sequencing. A total of 333 genomes were used to identify, validate and evaluate 2419 core genes. The cgMLST allowed fine-scale differentiation between samples that had the same profile using traditional MLST and allowed for the characterization of strains impossible by MLST. The scheme was successfully used to trace a localized Swedish outbreak, where a cluster of 38 isolates was linked to a country-wide beekeeping operation. cgMLST greatly enhances the power of a traditional typing scheme, while preserving the same stability and standardization for sharing results and methods across different laboratories.

Rapid identification and genotyping of the honeybee pathogen Paenibacillus larvae by combining culturing and multiplex quantitative PCR

Background:

American Foulbrood (AFB) is a devastating disease of honey bee (Apis mellifera) larvae caused by the spore-forming, Gram-positive bacterium Paenibacillus larvae. In most countries, the law requires mandatory reporting of AFB to the veterinary authority.

Aim and Methods:

To speed up detection and genotyping of P. larvae spores, we compared different culturing protocols on Columbia sheep blood agar and developed a new multiplex quantitative polymerase chain reaction to distinguish between the two relevant P. larvae genotypes enterobacterial repetitive intergenic consensus (ERIC) I and ERIC II.

Results and Conclusion:

As confirmed by P. larvae reference strains and field isolates, the new identification and genotyping protocol halves the time of current workflows, lessens labor-intension, allows a higher throughput of samples for monitoring, and permits a faster intervention to prevent the spread of AFB.

Discovery of Paenibacillus larvae ERIC V: Phenotypic and genomic comparison to genotypes ERIC I-IV reveal different inventories of virulence factors which correlate with epidemiological prevalences of American Foulbrood

Paenibacillus larvae is the etiological agent of American Foulbrood (AFB), a highly contagious brood disease of honey bees (Apis mellifera). AFB requires mandatory reporting to the veterinary authority in many countries and until now four genotypes, P. larvae ERIC I-IV, have been identified. We isolated a new genotype, ERIC V, from a Spanish honey sample. After a detailed phenotypic comparison with the reference strains of the ERIC I-IV genotypes, including spore morphology, non-ribosomal peptide (NRP) profiling, and in vivo infections of A. mellifera larvae, we established a genomic DNA Macrorestriction Fragment Pattern Analysis (MRFPA) scheme for future epidemiologic discrimination. Whole genome comparison of the reference strains and the new ERIC V genotype (DSM 106052) revealed that the respective virulence gene inventories of the five genotypes corresponded with the time needed to kill 100 % of the infected bee larvae (LT₁₀₀) in in vivo infection assays. The rarely isolated P. larvae genotypes ERIC II I-V with a fast-killing phenotype (LT₁₀₀ 3 days) harbor genes with high homology to virulence factors of other insect pathogens. These virulence genes are absent in the epidemiologically prevalent genotypes ERIC I (LT₁₀₀ 12 days) and ERIC II (LT₁₀₀ 7 days), which exhibit slower killing phenotypes. Since killing-retardation is known to reduce the success of hygienic cleaning by nurse bees, the identified absence of virulence factors might explain the epidemiological prevalences of ERIC genotypes. The discovery of the P. larvae ERIC V isolate suggests that more unknown ERIC genotypes exist in bee colonies. Since inactivation or loss of a few genes can transform a fast-killing phenotype into a more dangerous slow-killing phenotype, these rarely isolated genotypes may represent a hidden reservoir for future AFB outbreaks.

Comprehensive proteomic analysis of exoproteins expressed by ERIC I, II, III and IV Paenibacillus larvae genotypes reveals a wide range of virulence factors

American foulbrood is a quarantine disease of the honeybee Apis mellifera L. in many countries and contributes greatly to colony losses. We performed a label-free proteomics study of exoprotein fractions produced in vitro by Paenibacillus larvae reference strains of the ERIC I-IV genotypes. A quantitative comparison was performed of previous studied protein-based virulence factors and many newly identified putative virulence factors. Among the multiple proteases identified, key virulence factors included the microbial collagenase ColA and immune inhibitor A (InhA, an analog of the Bacillus thuringiensis protein InhA). Both of these virulence factors were detected in ERICs II-IV but were absent from ERIC I. Furthermore, the different S-layer proteins and polysaccharide deacetylases prevailed in ERICs II-IV. Thus, the expression patterns of these virulence factors corresponded with the different speeds at which honeybee larvae are known to be killed by ERICs II-IV compared to ERIC I. In addition, putative novel toxin-like proteins were identified, including vegetative insecticidal protein Vip1, a mosquitocidal toxin, and epsilon-toxin type B, which exhibit similarity to homologs present in Bacillus thuringiensis or Lysinibacillus sphaericus. Furthermore, a putative bacteriocin similar to Lactococcin 972 was identified in all assayed genotypes. It appears that P. larvae shares virulence factors similar to those of the Bacillus cereus group. Overall, the results provide novel information regarding P. larvae virulence potential, and a comprehensive exoprotein comparison of all four ERICs was performed for the first time. The identification of novel virulence factors can explain differences in the virulence of isolates.

Swarming motility and biofilm formation of Paenibacillus larvae, the etiological agent of American Foulbrood of honey bees (Apis mellifera)

American Foulbrood is a worldwide distributed, fatal disease of the brood of the Western honey bee (Apis mellifera). The causative agent of this fatal brood disease is the Gram-positive, spore-forming bacterium Paenibacillus larvae, which can be classified into four different genotypes (ERIC I-IV), with ERIC I and II being the ones isolated from contemporary AFB outbreaks. P. larvae is a peritrichously flagellated bacterium and, hence, we hypothesized that P. larvae is capable of coordinated and cooperative multicellular behaviors like swarming motility and biofilm formation. In order to analyze these behaviors of P. larvae, we firstly established appropriate functional assays. Using these assays we demonstrated that P. larvae ERIC II, but not P. larvae ERIC I, was capable of swarming. Swarming motility was hampered in a P. larvae ERIC II-mutant lacking production of paenilarvin, an iturin-like lipopeptide exclusively expressed by this genotype. Both genotypes were able to form free floating biofilm aggregates loosely attached to the walls of the culture wells. Visualizing the biofilms by Congo red and thioflavin S staining suggested structural differences between the biofilms formed. Biofilm formation was shown to be independent from paenilarvin production because the paenilarvin deficient mutant was comparably able to form a biofilm.

Bacterial pathogens of bees

Pollination is an indispensable ecosystem service provided by many insects, especially by wild and managed bee species. Hence, reports on large scale honey bee colony losses and on population declines of many wild bees were alarming and resulted in increased awareness of the importance of bee health and increased interest in bee pathogens. To serve this interest, this review will give a comprehensive overview on bacterial bee pathogens by covering not only the famous pathogens (Paenibacillus larvae, Melissococcus plutonius), but also the orphan pathogens which have largely been neglected by the scientific community so far (spiroplasmas) and the pathogens which were only recently discovered as being pathogenic to bees (Serratia marcescens, Lysinibacillus sphaericus).

Functionality of Tn916 in Paenibacillus larvae

The conjugative transposon Tn916 was determined to be functional in Paenibacillus larvae in regard to expression of tetracycline resistance and conjugative transfer. Expression of erythromycin resistance, using Tn916ΔE, was also observed. Conjugative transfer experiments employing Paenibacillus popilliae strains Tc1001 and Em1001 as transposon donors and experiments using different P. larvae subspecies or different transposon-containing strains demonstrated interspecies and intraspecies transfer occurred for Tn916 and Tn916ΔE. Southern hybridization analysis of several Tn916-containing P. larvae isolates showed that the transposon randomly inserted into the bacterial chromosome with an indication that hot spot insertion had occurred. Hybridization analysis indicated single-copy insertion of Tn916 into the genome predominated. However, selection of multiple-resistant isolates (i.e., isolates containing Tn916 and Tn916ΔE) demonstrated that multiple copies of the transposon could coexist in the bacterial genome. Growth of transposon-containing isolates in broth medium in the absence of selective antibiotic pressure showed that Tn916 and Tn916ΔE were stably maintained in the bacterium.

Multiple Locus Variable number of tandem repeat Analysis: A molecular genotyping tool for Paenibacillus larvae

American Foulbrood, caused by Paenibacillus larvae, is the most severe bacterial disease of honey bees (Apis mellifera). To perform genotyping of P. larvae in an epidemiological context, there is a need of a fast and cheap method with a high resolution. Here, we propose Multiple Locus Variable number of tandem repeat Analysis (MLVA). MLVA has been used for typing a collection of 209 P. larvae strains from which 23 different MLVA types could be identified. Moreover, the developed methodology not only permits the identification of the four Enterobacterial Repetitive Intergenic Consensus (ERIC) genotypes, but allows also a discriminatory subdivision of the most dominant ERIC type I and ERIC type II genotypes. A biogeographical study has been conducted showing a significant correlation between MLVA genotype and the geographical region where it was isolated.