Sequencing the Obligate Intracellular Rhabdochlamydia helvetica within Its Tick Host Ixodes ricinus to Investigate Their Symbiotic Relationship

Endosymbiont diversity across native and invasive brown widow spider populations

The invasive brown widow spider, Latrodectus geometricus (Araneae: Theridiidae), has spread in multiple locations around the world and, along with it, brought associated organisms such as endosymbionts. We investigated endosymbiont diversity and prevalence across putative native and invasive populations of this spider, predicting lower endosymbiont diversity across the invasive range compared to the native range. First, we characterized the microbial community in the putative native (South Africa) and invasive (Israel and the United States) ranges via high throughput 16S sequencing of 103 adult females. All specimens were dominated by reads from only 1-3 amplicon sequence variants (ASV), and most individuals were infected with an apparently uniform strain of Rhabdochlamydia. We also found Rhabdochlamydia in spider eggs, indicating that it is a maternally-inherited endosymbiont. Relatively few other ASV were detected, but included two variant Rhabdochlamydia strains and several Wolbachia, Spiroplasma and Enterobacteriaceae strains. We then diagnostically screened 118 adult female spiders from native and invasive populations specifically for Rhabdochlamydia and Wolbachia. We found Rhabdochlamydia in 86% of individuals and represented in all populations, which suggests that it is a consistent and potentially important associate of L. geometricus. Wolbachia was found at lower overall prevalence (14%) and was represented in all countries, but not all populations. In addition, we found evidence for geographic variation in endosymbiont prevalence: spiders from Israel were more likely to carry Rhabdochlamydia than those from the US and South Africa, and Wolbachia was geographically clustered in both Israel and South Africa. Characterizing endosymbiont prevalence and diversity is a first step in understanding their function inside the host and may shed light on the process of spread and population variability in cosmopolitan invasive species.

Spontaneous Aberrant Bodies Formation in Human Pneumocytes Infected with Estrella lausannensis

Estrella lausannensis, a Chlamydia-related bacterium isolated from a Spanish river, is considered as a possible emerging human pathogen. Indeed, it was recently demonstrated to multiply in human macrophages, resisting oxidative burst and causing a strong cytopathic effect. In addition, a preliminary study highlighted a correlation between antibody response to E. lausannensis and pneumonia in children. To clarify the pathogenic potential of these bacteria, we infected a human pneumocyte cell line with E. lausannensis and assessed its replication and cytopathic effect using quantitative real-time PCR and immunofluorescence, as well as confocal and electron microscopy. Our results demonstrated that E. lausannensis enters and replicates rapidly in human pneumocytes, and that it causes a prompt lysis of the host cells. Furthermore, we reported the spontaneous formation of aberrant bodies, a form associated with persistence in Chlamydiae, suggesting that E. lausannensis infection could cause chronic disorders in humans.

Use of gene sequences as type for naming prokaryotes: Recommendations of the international committee on the taxonomy of chlamydiae

The International Committee on Systematics of Prokaryotes (ICSP) discussed and rejected in 2020 a proposal to modify the International Code of Nomenclature of Prokaryotes to allow the use of gene sequences as type for naming prokaryotes. An alternative nomenclatural code, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), which considers genome sequences as type material for naming species, was published in 2022. Members of the ICSP subcommittee for the taxonomy of the phylum Chlamydiae (Chlamydiota) consider that the use of gene sequences as type would benefit the taxonomy of microorganisms that are difficult to culture such as the chlamydiae and other strictly intracellular bacteria. We recommend the registration of new names of uncultured prokaryotes in the SeqCode registry.

Temperature Affects the Host Range of Rhabdochlamydia porcellionis

The Rhabdochlamydiaceae family is a recent addition to the Chlamydiae phylum. Its members were discovered in cockroaches and woodlice, but recent metagenomics surveys demonstrated the widespread distribution of this family in the environment. It was, moreover, estimated to be the largest family of the Chlamydiae phylum based on the diversity of its 16S rRNA encoding gene. Unlike most Chlamydia-like organisms, no Rhabdochlamydiaceae member could be cultivated in amoebae, and its host range remains unknown. We tested the permissivity of various mammalian and arthropod cell lines to determine the host range of Rhabdochlamydia porcellionis, the only cultured representative of this family. While growth could initially be obtained only in the Sf9 cell line, lowering the incubation temperature of the mammalian cells from 37°C to 28°C allowed the growth of R. porcellionis. Furthermore, a 6-h exposure to 37°C was sufficient to irreversibly block the replication of R. porcellionis, suggesting that this bacterium either lost or never acquired the ability to grow at 37°C. We next sought to determine if temperature would also affect the infectivity of elementary bodies. Although we could not purify enough bacteria to reach a conclusive result for R. porcellionis, our experiment showed that the elementary bodies of Chlamydia trachomatis and Waddlia chondrophila lose their infectivity faster at 37°C than at room temperature. Our results demonstrate that members of the Chlamydiae phylum adapt to the temperature of their host organism and that this adaptation can in turn restrict their host range. IMPORTANCE The Rhabdochlamydiaceae family is part of the Chlamydiae, a phylum of bacteria that includes obligate intracellular bacteria sharing the same biphasic developmental cycle. This family has been shown to be highly prevalent in the environment, particularly in freshwater and soil, and despite being estimated to be the largest family in the Chlamydiae phylum is only poorly studied. Members of the Rhabdochlamydiaceae have been detected in various arthropods like ticks, spiders, cockroaches, and woodlice, but the full host range of this family is currently unknown. In this study, we showed that R. porcellionis, the only cultured representative of the Rhabdochlamydiaceae family, cannot grow at 37°C and is quickly inactivated at this temperature. A similar temperature sensitivity was also observed for elementary bodies of chlamydial species adapted to mammals. Our work demonstrates that chlamydiae adapt to the temperature of their reservoir, making a jump between species with different body temperatures unlikely.

The dynamics of the microbiome in Ixodidae are shaped by tick ontogeny and pathogens in Sarawak, Malaysian Borneo

Tick-borne diseases have recently been considered a potential emerging public health threat in Malaysia; however, fundamental studies into tick-borne pathogens and microbiome appear limited. In this study, six tick species (Ixodes granulatus, Haemaphysalis hystricis, Haemaphysalis shimoga, Dermacentor compactus, Dermacentor steini and Dermacentor atrosignatus) collected from two primary forests and an oil palm plantation in Sarawak, Malaysian Borneo, were used for microbiome analysis targeting bacterial 16S rDNA using next-generation sequencing (NGS). In addition, bacterial species were further characterized in conventional PCRs to identify potential pathogens. Sequences generated from NGS were first filtered with the Decontam package in R before subsequent microbial diversity analyses. Alpha and beta analyses revealed that the genus Dermacentor had the highest microbial diversity, and H. shimoga significantly differed in microbial composition from other tick species. Alpha and beta diversities were also significantly different between developmental stages of H. shimoga. Furthermore, we observed that some bacterial groups were significantly more abundant in certain tick species and developmental stages of H. shimoga. We tested the relative abundances using pairwise linear discriminant analysis effect size (LEfSe), which also revealed significant microbial composition differences between Borrelia-positive and Borrelia-negative I. granulatus ticks. Finally, pathogenic and potentially pathogenic bacteria circulating in different tick species, such as Rickettsia heilongjiangensis, Ehrlichia sp., Anaplasma sp. and Bartonella spp. were characterized by PCR and sequencing. Moreover, Coxiella and Francisella-like potential symbionts were identified from H. shimoga and D. steini, respectively. More studies are required to unravel the factors associated with the variations observed in this study.

One to host them all: genomics of the diverse bacterial endosymbionts of the spider Oedothorax gibbosus

Bacterial endosymbionts of the groups Wolbachia, Cardinium and Rickettsiaceae are well known for their diverse effects on their arthropod hosts, ranging from mutualistic relationships to reproductive phenotypes. Here, we analysed a unique system in which the dwarf spider Oedothorax gibbosus is co-infected with up to five different endosymbionts affiliated with Wolbachia, 'Candidatus Tisiphia' (formerly Torix group Rickettsia), Cardinium and Rhabdochlamydia. Using short-read genome sequencing data, we show that the endosymbionts are heterogeneously distributed among O. gibbosus populations and are frequently found co-infecting spider individuals. To study this intricate host-endosymbiont system on a genome-resolved level, we used long-read sequencing to reconstruct closed genomes of the Wolbachia, 'Ca. Tisiphia' and Cardinium endosymbionts. We provide insights into the ecology and evolution of the endosymbionts and shed light on the interactions with their spider host. We detected high quantities of transposable elements in all endosymbiont genomes and provide evidence that ancestors of the Cardinium, 'Ca. Tisiphia' and Wolbachia endosymbionts have co-infected the same hosts in the past. Our findings contribute to broadening our knowledge about endosymbionts infecting one of the largest animal phyla on Earth and show the usefulness of transposable elements as an evolutionary 'contact-tracing' tool.

What do we know about the microbiome of I. ricinus?

I. ricinus is an obligate hematophagous parasitic arthropod that is responsible for the transmission of a wide range of zoonotic pathogens including spirochetes of the genus Borrelia, Rickettsia spp., C. burnetii, Anaplasma phagocytophilum and Francisella tularensis, which are part the tick´s microbiome. Most of the studies focus on "pathogens" and only very few elucidate the role of "non-pathogenic" symbiotic microorganisms in I. ricinus. While most of the members of the microbiome are leading an intracellular lifestyle, they are able to complement tick´s nutrition and stress response having a great impact on tick´s survival and transmission of pathogens. The composition of the tick´s microbiome is not consistent and can be tied to the environment, tick species, developmental stage, or specific organ or tissue. Ovarian tissue harbors a stable microbiome consisting mainly but not exclusively of endosymbiotic bacteria, while the microbiome of the digestive system is rather unstable, and together with salivary glands, is mostly comprised of pathogens. The most prevalent endosymbionts found in ticks are Rickettsia spp., Ricketsiella spp., Coxiella-like and Francisella-like endosymbionts, Spiroplasma spp. and Candidatus Midichloria spp. Since microorganisms can modify ticks' behavior, such as mobility, feeding or saliva production, which results in increased survival rates, we aimed to elucidate the potential, tight relationship, and interaction between bacteria of the I. ricinus microbiome. Here we show that endosymbionts including Coxiella-like spp., can provide I. ricinus with different types of vitamin B (B2, B6, B7, B9) essential for eukaryotic organisms. Furthermore, we hypothesize that survival of Wolbachia spp., or the bacterial pathogen A. phagocytophilum can be supported by the tick itself since coinfection with symbiotic Spiroplasma ixodetis provides I. ricinus with complete metabolic pathway of folate biosynthesis necessary for DNA synthesis and cell division. Manipulation of tick´s endosymbiotic microbiome could present a perspective way of I. ricinus control and regulation of spread of emerging bacterial pathogens.

Ecology and evolution of chlamydial symbionts of arthropods

The phylum Chlamydiae consists of obligate intracellular bacteria including major human pathogens and diverse environmental representatives. Here we investigated the Rhabdochlamydiaceae, which is predicted to be the largest and most diverse chlamydial family, with the few described members known to infect arthropod hosts. Using published 16 S rRNA gene sequence data we identified at least 388 genus-level lineages containing about 14 051 putative species within this family. We show that rhabdochlamydiae are mainly found in freshwater and soil environments, suggesting the existence of diverse, yet unknown hosts. Next, we used a comprehensive genome dataset including metagenome assembled genomes classified as members of the family Rhabdochlamydiaceae, and we added novel complete genome sequences of Rhabdochlamydia porcellionis infecting the woodlouse Porcellio scaber, and of 'Candidatus R. oedothoracis' associated with the linyphiid dwarf spider Oedothorax gibbosus. Comparative analysis of basic genome features and gene content with reference genomes of well-studied chlamydial families with known host ranges, namely Parachlamydiaceae (protist hosts) and Chlamydiaceae (human and other vertebrate hosts) suggested distinct niches for members of the Rhabdochlamydiaceae. We propose that members of the family represent intermediate stages of adaptation of chlamydiae from protists to vertebrate hosts. Within the genus Rhabdochlamydia, pronounced genome size reduction could be observed (1.49-1.93 Mb). The abundance and genomic distribution of transposases suggests transposable element expansion and subsequent gene inactivation as a mechanism of genome streamlining during adaptation to new hosts. This type of genome reduction has never been described before for any member of the phylum Chlamydiae. This study provides new insights into the molecular ecology, genomic diversity, and evolution of representatives of one of the most divergent chlamydial families.

The evolution and role of eukaryotic-like domains in environmental intracellular bacteria: the battle with a eukaryotic cell

Intracellular pathogens that are able to thrive in different environments, such as Legionella spp. which preferentially live in protozoa in aquatic environments or environmental Chlamydiae which replicate either within protozoa or a range of animals, possess a plethora of cellular biology tools to influence their eukaryotic host. The host manipulation tools that evolved in the interaction with protozoa, confer these bacteria the capacity to also infect phylogenetically distinct eukaryotic cells, such as macrophages and thus they can also be human pathogens. To manipulate the host cell, bacteria use protein secretion systems and molecular effectors. Although these molecular effectors are encoded in bacteria, they are expressed and function in a eukaryotic context often mimicking or inhibiting eukaryotic proteins. Indeed, many of these effectors have eukaryotic-like domains. In this review we propose that the main pathways environmental intracellular bacteria need to subvert in order to establish the host eukaryotic cell as a replication niche are chromatin remodelling, ubiquitination signalling, and modulation of protein-protein interactions via tandem repeat domains. We then provide mechanistic insight into how these proteins might have evolved as molecular weapons. Finally, we highlight that in environmental intracellular bacteria the number of eukaryotic-like domains and proteins is considerably higher than in intracellular bacteria specialised to an isolated niche, such as obligate intracellular human pathogens. As mimics of eukaryotic proteins are critical components of host pathogen interactions, this distribution of eukaryotic-like domains suggests that the environment has selected them.

Prevalence and molecular characterization of C. pecorum detected in Swiss fattening pigs

Chlamydia (C.) pecorum, an obligate intracellular bacterial species commonly found in ruminants, can also occur in pigs. However, its significance as a potential porcine pathogen, or commensal, is still unclear. In a previous study (Hoffmann et al. 2015), mixed infections of C. suis and C. pecorum were detected in 14 Swiss fattening pig farms. Using these samples, we aimed to investigate the infection dynamics of C. suis and C. pecorum mixed infections in these farms. In addition, we analyzed the genetic diversity of Swiss porcine C. pecorum strains in relation to globally circulating strains. In total, 1284 conjunctival and rectal swabs from 391 pigs, collected at the beginning and end of the fattening period, were tested during the course of this study. We determined the bacterial loads of C. suis and C. pecorum using species-specific real-time PCR (qPCR) and compared these results to already existing DNA-microarray and Chlamydiaceae qPCR data. Overall, C. suis and Chlamydiaceae copy numbers decreased in the course of the fattening period, whereas C. pecorum copy numbers increased. No association was found between clinical signs (conjunctivitis, lameness and diarrhea) and the bacterial loads. Preventive antibiotic treatment at the beginning of the fattening period significantly lowered the chlamydial load and outdoor access was associated with higher loads. Proximity to the nearest ruminants correlated with increased C. pecorum loads, indicating that C. pecorum could be transmitted from ruminants to pigs. Multi-locus sequence typing (MLST) and major outer membrane protein (ompA) genotyping revealed two novel sequence types (STs) (301, 302) and seven unique ompA genotypes (1-7) that appear to form a specific clade separate from other European C. pecorum strains.

Nested Species Distribution Models of Chlamydiales in Ixodes ricinus (Tick) Hosts in Switzerland

The tick Ixodes ricinus is the vector of various pathogens, including Chlamydiales bacteria, which potentially cause respiratory infections. In this study, we modeled the spatial distribution of I. ricinus and associated Chlamydiales over Switzerland from 2009 to 2019. We used a total of 2,293 ticks and 186 Chlamydiales occurrences provided by a Swiss Army field campaign, a collaborative smartphone application, and a prospective campaign. For each tick location, we retrieved from Swiss federal data sets the environmental factors reflecting the topography, climate, and land cover. We then used the Maxent modeling technique to estimate the suitability of particular areas for I. ricinus and to subsequently build the nested niche of Chlamydiales bacteria. Results indicate that I. ricinus habitat suitability is determined by higher temperature and normalized difference vegetation index (NDVI) values, lower temperature during the driest months, and a higher percentage of artificial and forest areas. The performance of the model was improved when extracting the environmental variables for a 100-m radius buffer around the sampling points and when considering the climatic conditions of the 2 years previous to the sampling date. Chlamydiales bacteria were favored by a lower percentage of artificial surfaces, drier conditions, high precipitation during the coldest months, and short distances to wetlands. From 2009 to 2018, we observed an extension of areas suitable to ticks and Chlamydiales, associated with a shift toward higher altitude. The importance of considering spatiotemporal variations in the environmental conditions for obtaining better prediction was also demonstrated.IMPORTANCEIxodes ricinus is the vector of pathogens including the agent of Lyme disease, the tick-borne encephalitis virus, and the less well-known Chlamydiales bacteria, which are responsible for certain respiratory infections. In this study, we identified the environmental factors influencing the presence of I. ricinus and Chlamydiales in Switzerland and generated maps of their distribution from 2009 to 2018. We found an important expansion of suitable areas for both the tick and the bacteria during the last decade. Results also provided the environmental factors that determine the presence of Chlamydiales within ticks. Distribution maps as generated here are expected to bring valuable information for decision makers in controlling tick-borne diseases in Switzerland and establishing prevention campaigns. The methodological framework presented could be used to predict the distribution and spread of other host-pathogen pairs to identify environmental factors driving their distribution and to develop control or prevention strategies accordingly.

Chlamydiae in the Environment

Chlamydiae have been known for more than a century as major pathogens of humans. Yet they are also found ubiquitously in the environment where they thrive within protists and in an unmatched wide range of animals. This review summarizes recent advances in understanding chlamydial diversity and distribution in nature. Studying these environmental chlamydiae provides a novel perspective on basic chlamydial biology and evolution. A picture is beginning to emerge with chlamydiae representing one of the evolutionarily most ancient and successful groups of obligate intracellular bacteria.

Marine Sediments Illuminate Chlamydiae Diversity and Evolution

The bacterial phylum Chlamydiae is so far composed of obligate symbionts of eukaryotic hosts. Well known for Chlamydiaceae, pathogens of humans and other animals, Chlamydiae also include so-called environmental lineages that primarily infect microbial eukaryotes. Environmental surveys indicate that Chlamydiae are found in a wider range of environments than anticipated previously. However, the vast majority of this chlamydial diversity has been underexplored, biasing our current understanding of their biology, ecological importance, and evolution. Here, we report that previously undetected and active chlamydial lineages dominate microbial communities in deep anoxic marine sediments taken from the Arctic Mid-Ocean Ridge. Reaching relative abundances of up to 43% of the bacterial community, and a maximum diversity of 163 different species-level taxonomic units, these Chlamydiae represent important community members. Using genome-resolved metagenomics, we reconstructed 24 draft chlamydial genomes, expanding by over a third the known genomic diversity in this phylum. Phylogenomic analyses revealed several novel clades across the phylum, including a previously unknown sister lineage of the Chlamydiaceae, providing new insights into the origin of pathogenicity in this family. We were unable to identify putative eukaryotic hosts for these marine sediment chlamydiae, despite identifying genomic features that may be indicative of host-association. The high abundance and genomic diversity of Chlamydiae in these anoxic marine sediments indicate that some members could play an important, and thus far overlooked, ecological role in such environments and may indicate alternate lifestyle strategies.

A predation assay using amoebae to screen for virulence factors unearthed the first W. chondrophila inclusion membrane protein

Waddlia chondrophila is an intracellular bacterium phylogenetically related to the well-studied human and animal pathogens of the Chlamydiaceae family. In the last decade, W. chondrophila was convincingly demonstrated to be associated with adverse pregnancy outcomes in humans and abortions in animals. All members of the phylum Chlamydiae possess a Type Three Secretion System that they use for delivering virulence proteins into the host cell cytosol to modulate their environment and create optimal conditions to complete their life cycle. To identify W. chondrophila virulence proteins, we used an original screening approach that combines a cosmid library with an assay monitoring resistance to predation by phagocytic amoebae. This technique combined with bioinformatic data allowed the identification of 28 candidate virulence proteins, including Wimp1, the first identified inclusion membrane protein of W. chondrophila.