Host Matters: Medicinal Leech Digestive-Tract Symbionts and Their Pathogenic Potential

Draft Genome Sequence of Plesiomonas shigelloides MD22D9, Isolated from the Digestive Tract of Macrobdella decora

Here, we present a draft genome sequence of Plesiomonas shigelloides MD22D9, isolated from the digestive tract of the North American medicinal leech Macrobdella decora. The gut microbiome of the medicinal leech is hypothesized to be critical for maintaining host fitness. This genome can provide insights into this uncharacterized microbe-host relationship.

Lethal Aeromonas veronii Sepsis in the Course of Medicinal Leech Therapy

A patient with oral squamous cell carcinoma (OSCC) underwent complex surgical tumor therapy, including the reconstruction of soft tissues using a radial forearm flap. Due to venous congestion that could only partly be resolved by revision surgery, leech therapy was started on the second postoperative day. The patient developed pneumonia and sepsis and died as a result of septic shock, despite having received targeted broad-spectrum antibiotic therapy since day 5. Aeromonas spp. were cultured from both the patient’s specimens and unused leeches. Biochemical identification and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) yielded inconsistent identification results. Finally, microbiological identification of Aeromonas spp. was performed via 16S rDNA sequencing and use of the basic local alignment search tool (BLAST), and strains from both the patient and the leeches were identified as Aeromonas veronii. Aeromonas spp. strains derived from the patient and leeches and independent laboratory strains were submitted to randomly amplified polymorphic DNA (RAPD) subtyping. RAPD of A. veronii strains from both sources revealed an identical pattern, strongly suggesting the transmission of A. veronii from the leeches to the patient. Physicians should be aware of the potential for severe lethal infections as a fatal side-effect of leech therapy in critically ill patients, which should be addressed using antibiotic prophylaxis.

Isolation of Hermetia illucens larvae core gut microbiota by two different cultivation strategies

Hermetia illucens larvae (black soldier fly larvae, BSFL) convert efficiently organic waste to high quality biomass. To gain knowledge on the specific functions of gut microbes in this process it is a prerequisite to culture members of the core gut microbiota. Two different cultivation strategies were applied here for this purpose, a dilution-to-extinction cultivation and direct plating using six different media to culture aerobic heterotrophic bacteria. A total of 341 isolates were obtained by the dilution-to-extinction cultivation and 138 isolates by direct plating from guts of BSFL reared on chicken feed. Bacterial isolates were phylogenetically identified at the genus level by 16S rRNA gene sequencing (phylotyping) and differentiated at the strain level by genomic fingerprinting (genotyping). The main proportion of isolates was assigned to Proteobacteria, Firmicutes (Bacilli), and Actinobacteria. Predominant genera discussed in literature as member of a potential BSFL core gut microbiota, Providencia, Proteus, Morganella, Enterococcus, Bacillus, and members of the family Enterobacteriaceae, were isolated. A high intra-phylotype diversity was obtained by genomic fingerprinting which was especially enhanced by the dilution-to-extinction cultivation. This study showed that the application of different cultivation strategies including a dilution-to-extinction cultivation helps to culture a higher diversity of the BSFL gut microbiota and that genomic fingerprinting gives a better picture on the genetic diversity of cultured bacteria which cannot be covered by a 16S rRNA gene sequence based identification alone.

Systematic Detection of Large-Scale Multigene Horizontal Transfer in Prokaryotes

Horizontal gene transfer (HGT) is central to prokaryotic evolution. However, little is known about the “scale” of individual HGT events. In this work, we introduce the first computational framework to help answer the following fundamental question: How often does more than one gene get horizontally transferred in a single HGT event? Our method, called HoMer, uses phylogenetic reconciliation to infer single-gene HGT events across a given set of species/strains, employs several techniques to account for inference error and uncertainty, combines that information with gene order information from extant genomes, and uses statistical analysis to identify candidate horizontal multigene transfers (HMGTs) in both extant and ancestral species/strains. HoMer is highly scalable and can be easily used to infer HMGTs across hundreds of genomes. We apply HoMer to a genome-scale data set of over 22,000 gene families from 103 Aeromonas genomes and identify a large number of plausible HMGTs of various scales at both small and large phylogenetic distances. Analysis of these HMGTs reveals interesting relationships between gene function, phylogenetic distance, and frequency of multigene transfer. Among other insights, we find that 1) the observed relative frequency of HMGT increases as divergence between genomes increases, 2) HMGTs often have conserved gene functions, and 3) rare genes are frequently acquired through HMGT. We also analyze in detail HMGTs involving the zonula occludens toxin and type III secretion systems. By enabling the systematic inference of HMGTs on a large scale, HoMer will facilitate a more accurate and more complete understanding of HGT and microbial evolution.

Activation of the type VI secretion system in the squid symbiont Vibrio fischeri requires the transcriptional regulator TasR and the structural proteins TssM and TssA

Bacteria have evolved diverse strategies to compete for a niche, including the type VI secretion system (T6SS), a contact-dependent killing mechanism. T6SSs are common in bacterial pathogens, commensals, and beneficial symbionts, where they affect the diversity and spatial structure of host-associated microbial communities. Although T6SS gene clusters are often located on genomic islands (GIs), which may be transferred as a unit, the regulatory strategies that promote gene expression once the T6SS genes are transferred into a new cell are not known. We used the squid symbiont, Vibrio fischeri, to identify essential regulatory factors that control expression of a strain-specific T6SS encoded on a GI. We found that a transcriptional reporter for this T6SS is active only in strains that contain the T6SS-encoding GI, suggesting the GI encodes at least one essential regulator. A transposon screen identified seven mutants that could not activate the reporter. These mutations mapped exclusively to three genes on the T6SS-containing GI that encode two essential structural proteins (a TssA-like protein and TssM) and a transcriptional regulator (TasR). Using T6SS reporters, RT-PCR, competition assays, and differential proteomics, we found that all three genes are required for expression of many T6SS components, except for the TssA-like protein and TssM, which are constitutively expressed. Based on these findings, we propose a model whereby T6SS expression requires conserved structural proteins, in addition to the essential regulator TasR, and this ability to self-regulate may be a strategy to activate T6SS expression upon transfer of T6SS-encoding elements into a new bacterial host. Importance Interbacterial weapons like the T6SS are often located on mobile genetic elements and their expression is highly regulated. We found that two conserved structural proteins are required for T6SS expression in Vibrio fischeri. These structural proteins also contain predicted GTPase and GTP binding domains, suggesting their role in promoting T6SS expression may involve sensing the energetic state of the cell. Such a mechanism would provide a direct link between T6SS activation and cellular energy levels, providing a "checkpoint" to ensure the cell has sufficient energy to build such a costly weapon. Because these regulatory factors are encoded within the T6SS gene cluster, they are predicted to move with the genetic element to activate T6SS expression in a new host cell.

Macrobdella decora: Old World Leech Gut Microbial Community Structure Conserved in a New World Leech

Leeches are found in terrestrial, aquatic, and marine habitats on all continents. Sanguivorous leeches have been used in medicine for millennia. Modern scientific uses include studies of neurons, anticoagulants, and gut microbial symbioses. Hirudo verbana, the European medicinal leech, maintains a gut community dominated by two bacterial symbionts, Aeromonas veronii and Mucinivorans hirudinis, which sometimes account for as much as 97% of the total crop microbiota. The highly simplified gut anatomy and microbiome of H. verbana make it an excellent model organism for studying gut microbial dynamics. The North American medicinal leech, Macrobdella decora, is a hirudinid leech native to Canada and the northern United States. In this study, we show that M. decora symbiont communities are very similar to those in H. verbana. We performed an extensive study using field-caught M. decora and purchased H. verbana from two suppliers. Deep sequencing of the V4 region of the 16S rRNA gene allowed us to determine that the core microbiome of M. decora consists of Bacteroides, Aeromonas, Proteocatella, and Butyricicoccus. The analysis revealed that the compositions of the gut microbiomes of the two leech species were significantly different at all taxonomic levels. The R ² value was highest at the genus and amplicon sequence variant (ASV) levels and much lower at the phylum, class, and order levels. The gut and bladder microbial communities were distinct. We propose that M. decora is an alternative to H. verbana for studies of wild-caught animals and provide evidence for the conservation of digestive-tract and bladder symbionts in annelid models.IMPORTANCE Building evidence implicates the gut microbiome in critical animal functions such as regulating digestion, nutrition, immune regulation, and development. Simplified, phylogenetically diverse models for hypothesis testing are necessary because of the difficulty of assigning causative relationships in complex gut microbiomes. Previous research used Hirudo verbana as a tractable animal model of digestive-tract symbioses. Our data show that Macrobdella decora may work just as well without the drawback of being an endangered organism and with the added advantage of easy access to field-caught specimens. The similarity of the microbial community structures of species from two different continents reveals the highly conserved nature of the microbial symbionts in sanguivorous leeches.

Interactions of host-associated multispecies bacterial communities

The oral microbiome comprises microbial communities colonizing biotic (epithelia, mucosa) and abiotic (enamel) surfaces. Different communities are associated with health (eg, immune development, pathogen resistance) and disease (eg, tooth loss and periodontal disease). Like any other host-associated microbiome, colonization and persistence of both beneficial and dysbiotic oral microbiomes are dictated by successful utilization of available nutrients and defense against host and competitor assaults. This chapter will explore these general features of microbe-host interactions through the lens of symbiotic (mutualistic and antagonistic/pathogenic) associations with nonmammalian animals. Investigations in such systems across a broad taxonomic range have revealed conserved mechanisms and processes that underlie the complex associations among microbes and between microbes and hosts.

Closed Genome Sequence of Aeromonas veronii Strain Hm21, an Isolate from the Medicinal Leech Hirudo verbana

Aeromonas veronii strain Hm21 was isolated from the medicinal leech and is used for genetic studies. We present here the 4.71-Mbp genome with a 56-kb plasmid and identify the mutations present in strains commonly used for genetic engineering.

Aeromonas veronii strain Hm21 was isolated from the medicinal leech Hirudo verbana and is used for genetic studies. We present here the 4.71-Mbp genome with a 56-kb plasmid and identify the mutations present in strains commonly used for genetic engineering.

The Hirudo Medicinalis Microbiome Is a Source of New Antimicrobial Peptides

Antimicrobial peptides (AMPs) are considered a promising new class of anti-infectious agents. This study reports new antimicrobial peptides derived from the Hirudo medicinalis microbiome identified by a computational analysis method applied to the H. medicinalis metagenome. The identified AMPs possess a strong antimicrobial activity against Gram-positive and Gram-negative bacteria (MIC range: 5.3 to 22.4 μM), including Staphylococcus haemolyticus, an opportunistic coagulase-negative pathogen. The secondary structure analysis of peptides via CD spectroscopy showed that all the AMPs except pept_352 have mostly disordered structures that do not change under different conditions. For peptide pept_352, the α-helical content increases in the membrane environment. The examination of the mechanism of action of peptides suggests that peptide pept_352 exhibits a direct membranolytic activity. Furthermore, the cytotoxicity assay demonstrated that the nontoxic peptide pept_1545 is a promising candidate for drug development. Overall, the analysis method implemented in the study may serve as an effective tool for the identification of new AMPs.

Complications of leech therapy

OBJECTIVE

The principle of the use of leeches is associated with traditional medicine of many countries and its application has different philosophies for use in different areas of the body. Leeches, with all the benefits, can have dangers.

MATERIALS AND METHODS

A review of complications of leech therapy was done based on English articles indexed in the databases up to July 1, 2018. A strategic search has done independently by members of the research team and then all of the articles were +categorized by subject.

RESULTS

Related articles were mostly case-reports. Complications were divided into five categories including infection, allergy, prolonged bleeding, migration, and others. Infection is the most-reported complication related to leech therapy and Aeromonas spp. has the most participation in infections.

CONCLUSION

Leech therapy can be a therapeutic complementary method if the possible complications are managed properly.

Comparative Study on A Novel Pathogen of European Seabass. Diversity of Aeromonas veronii in the Aegean Sea

Aeromonas veronii is an emerging pathogen causing severe pathology and mortalities in European seabass aquaculture in the Aegean Sea, Mediterranean. More than 50 strains of the pathogen were characterized biochemically and genetically in order to study the epidemiology of the disease, as well as the phylogeny and virulence of the bacterium. Based on the phenotypic characteristics, the isolates form three groups consisting of: (a) the West Aegean Sea, non-motile, non-pigment-producing strains, (b) the West Aegean Sea, motile, and pigment-producing strains and (c) the East Aegean Sea motile strains that produce minute amounts of pigment. All strains were highly similar at the genomic level; however, the pattern of West/East geographic origin was reflected in biochemical properties, in general genomic level comparison and in the putative virulent factors studied. Type VI secretion system was not detected in the western strains. The outer membrane protein (OMP) profile which contains proteins that are putative antigenic factors, was very similar between strains from the different areas. Although most of the OMPs were detected in all strains with great sequence similarity, diversification according to geographic origin was evident in known antigenic factors such as the maltoporin LamB. A systematic comparative analysis of the strains is presented and discussed in view of the emergence of A. veronii as a significant pathogen for the Mediterranean aquaculture.

Model systems for the study of how symbiotic associations between animals and extracellular bacterial partners are established and maintained

This contribution describes the current state of experimental model development and use as a strategy for gaining insight into the form and function of certain types of host-microbe associations. Development of quality models for the study of symbiotic systems will be critical not only to facilitate an understanding of mechanisms underlying symbiosis, but also for providing insights into how drug development can promote healthy animal-microbe interactions as well as the treatment of pathogenic infections. Because of the growing awareness over the last decade of the importance of symbiosis in biology, a number of model systems has emerged to examine how these partnerships are maintained within and across generations of the host. The focus here will be upon host-bacterial symbiotic systems that, as in humans, (i) are acquired from the environment each generation, or horizontally transmitted, and (ii) are defined by interactions at the interface of their cellular boundaries, i.e., extracellular symbiotic associations. As with the use of models in other fields of biology where complexity is daunting (e.g., developmental biology or brain circuitry), each model has its strengths and weaknesses, i.e., no one model system will provide easy access to all the questions defining what is conserved in cell-cell interactions in symbiosis and what creates diversity within such partnerships. Rather, as discussed here, the more models explored, the richer our understanding of these associations is likely to be.

Identification and characterization of putative Aeromonas spp. T3SS effectors

The genetic determinants of bacterial pathogenicity are highly variable between species and strains. However, a factor that is commonly associated with virulent Gram-negative bacteria, including many Aeromonas spp., is the type 3 secretion system (T3SS), which is used to inject effector proteins into target eukaryotic cells. In this study, we developed a bioinformatics pipeline to identify T3SS effector proteins, applied this approach to the genomes of 105 Aeromonas strains isolated from environmental, mutualistic, or pathogenic contexts and evaluated the cytotoxicity of the identified effectors through their heterologous expression in yeast. The developed pipeline uses a two-step approach, where candidate Aeromonas gene families are initially selected using Hidden Markov Model (HMM) profile searches against the Virulence Factors DataBase (VFDB), followed by strict comparisons against positive and negative control datasets, greatly reducing the number of false positives. This approach identified 21 Aeromonas T3SS likely effector families, of which 8 represent known or characterized effectors, while the remaining 13 have not previously been described in Aeromonas. We experimentally validated our in silico findings by assessing the cytotoxicity of representative effectors in Saccharomyces cerevisiae BY4741, with 15 out of 21 assayed proteins eliciting a cytotoxic effect in yeast. The results of this study demonstrate the utility of our approach, combining a novel in silico search method with in vivo experimental validation, and will be useful in future research aimed at identifying and authenticating bacterial effector proteins from other genera.

Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing

Background

Short-read sequencing technologies have made microbial genome sequencing cheap and accessible. However, closing genomes is often costly and assembling short reads from genomes that are repetitive and/or have extreme %GC content remains challenging. Long-read, single-molecule sequencing technologies such as the Oxford Nanopore MinION have the potential to overcome these difficulties, although the best approach for harnessing their potential remains poorly evaluated.

Results

We sequenced nine bacterial genomes spanning a wide range of GC contents using Illumina MiSeq and Oxford Nanopore MinION sequencing technologies to determine the advantages of each approach, both individually and combined. Assemblies using only MiSeq reads were highly accurate but lacked contiguity, a deficiency that was partially overcome by adding MinION reads to these assemblies. Even more contiguous genome assemblies were generated by using MinION reads for initial assembly, but these assemblies were more error-prone and required further polishing. This was especially pronounced when Illumina libraries were biased, as was the case for our strains with both high and low GC content. Increased genome contiguity dramatically improved the annotation of insertion sequences and secondary metabolite biosynthetic gene clusters, likely because long-reads can disambiguate these highly repetitive but biologically important genomic regions.

Conclusions

Genome assembly using short-reads is challenged by repetitive sequences and extreme GC contents. Our results indicate that these difficulties can be largely overcome by using single-molecule, long-read sequencing technologies such as the Oxford Nanopore MinION. Using MinION reads for assembly followed by polishing with Illumina reads generated the most contiguous genomes with sufficient accuracy to enable the accurate annotation of important but difficult to sequence genomic features such as insertion sequences and secondary metabolite biosynthetic gene clusters. The combination of Oxford Nanopore and Illumina sequencing can therefore cost-effectively advance studies of microbial evolution and genome-driven drug discovery.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5381-7) contains supplementary material, which is available to authorized users.

Low-Level Antimicrobials in the Medicinal Leech Select for Resistant Pathogens That Spread to Patients

Fluoroquinolones (FQs) and ciprofloxacin (Cp) are important antimicrobials that pollute the environment in trace amounts. Although Cp has been recommended as prophylaxis for patients undergoing leech therapy to prevent infections by the leech gut symbiont Aeromonas, a puzzling rise in Cp-resistant (Cpr) Aeromonas infections has been reported. We report on the effects of subtherapeutic FQ concentrations on bacteria in an environmental reservoir, the medicinal leech, and describe the presence of multiple antibiotic resistance mutations and a gain-of-function resistance gene. We link the rise of CprAeromonas isolates to exposure of the leech microbiota to very low levels of Cp (0.01 to 0.04 µg/ml), <1/100 of the clinical resistance breakpoint for Aeromonas Using competition experiments and comparative genomics of 37 strains, we determined the mechanisms of resistance in clinical and leech-derived Aeromonas isolates, traced their origin, and determined that the presence of merely 0.01 µg/ml Cp provides a strong competitive advantage for Cpr strains. Deep-sequencing the Cpr-conferring region of gyrA enabled tracing of the mutation-harboring Aeromonas population in archived gut samples, and an increase in the frequency of the Cpr-conferring mutation in 2011 coincides with the initial reports of CprAeromonas infections in patients receiving leech therapy.IMPORTANCE The role of subtherapeutic antimicrobial contamination in selecting for resistant strains has received increasing attention and is an important clinical matter. This study describes the relationship of resistant bacteria from the medicinal leech, Hirudo verbana, with patient infections following leech therapy. While our results highlight the need for alternative antibiotic therapies, the rise of Cpr bacteria demonstrates the importance of restricting the exposure of animals to antibiotics approved for veterinary use. The shift to a more resistant community and the dispersion of Cpr-conferring mechanisms via mobile elements occurred in a natural setting due to the presence of very low levels of fluoroquinolones, revealing the challenges of controlling the spread of antibiotic-resistant bacteria and highlighting the importance of a holistic approach in the management of antibiotic use.

Leech management before application on patient: a nationwide survey of practices in French university hospitals

Background

Leech therapy in plastic/reconstructive microsurgery significantly improves a successful outcome of flap salvage but the drawback is a risk of severe infection that results in a drop of the salvage rates from 70-80% to below 30%. We report the results of a national survey conducted in all the French university hospitals to assess the current extent of use of leech for medical practices in the hospital and to investigate maintenance, delivery practices and prevention of the risk of infection.

Methods

Data concerning conditions of storage, leech external decontamination, microbiological controls, mode of delivery and antibiotic prophylaxis were collected from all the French university hospitals in practicing leech therapy, on the basis of a standardized questionnaire.

Results

Twenty-eight of the 32 centers contacted filled the questionnaire, among which 23 practiced leech therapy, mostly with a centralized storage in the pharmacy; 39.1% of the centers declared to perform leech external decontamination and only 2 centers recurrent microbiological controls of the water storage. Leech delivery was mostly nominally performed (56.5%), but traceability of the leech batch number was achieved in only 39.1% of the cases. Only 5 centers declared that a protocol of antibiotic prophylaxis was systematically administered during leech therapy: either quinolone (2), sulfamethoxazole/trimethoprim (2) or amoxicillin/clavulanic acid (1).

Conclusions

Measures to prevent infectious complications before application to patient have to be better applied and guidelines of good practices are necessary.