Diversity of the Parachlamydiae in the Environment

Development of a duplex q-PCR for the simultaneous detection of Parachlamydia acanthamoebae and Simkania negevensis in environmental and clinical samples

Parachlamydia acanthamoebae and Simkania negevensis, two Chlamydia-like bacteria, have been recently recognized as emerging human respiratory pathogens. The prevalence and frequency of these bacteria in the environment and among atypical pneumonia patients are still underestimated by classical cultures, immunohistochemistry and serology which are non-specific, long and tedious methods. This study aims to develop a new duplex probe-based q-PCR assay for the simultaneous detection and quantification of P. acanthamoebae and S. negevensis. The selected hydrolysis probes displayed no cross-reaction with the closely related Chlamydia or the other tested waterborne pathogens. The assay achieved a large dynamic range for quantification (from 5 × 10⁶ to 5 DNA copies/reaction). Efficiencies of FAM and JOE label probes weren't affected when they were combined. They were close to 100%, indicating the linear amplification. The application of this diagnostic tool resulted in 9/47 (19%) and 4/47 (8.5%) positive water samples for P. acanthamoebae and S. negevensis, respectively. P. acanthamoebae was also covered from 2/78 (2.5%) respiratory specimens and only one case (1/200 = 0.5%) of P. acanthamoebae and SARS-CoV-2 co-infection was noticed. While S. negevensis wasn't detected in clinical samples, the developed duplex q-PCR was shown to be an accurate, highly sensitive, and robust diagnostic tool for the detection and quantification of P. acanthamoebae and S. negevensis.

A new TaqMan real-time PCR assay to detect Parachlamydia acanthamoebae and to monitor its co-existence with SARS-COV-2 among COVID-19 patients

Human respiratory infections caused by a large variety of microbial pathogens are the most common diseases responsible for hospitalization, morbidity and mortality. Parachlamydia acanthamoebae, a Chlamydia-related bacterium, has been found to be potentially associated with these diseases. An early and accurate diagnosis of this pathogen could be useful to avoid the potential respiratory complications linked especially to COVID-19 patients and to set suitable outbreak control measures. A TaqMan-PCR assay was developed to detect and quantify Parachlamydia acanthamoebae in environmental and clinical samples from patients of all ages with COVID-19. The selected hydrolysis probe displayed no cross-reaction with the closely related Chlamydia or the other tested pathogens. This q-PCR achieved good reproducibility and repeatability with a detection limit of about 5 DNA copies per reaction. Using this q-PCR assay, Parachlamydia acanthamoebae was detected in 2/78 respiratory specimens and 9/47 water samples. Only one case (1.3%) of Parachlamydia acanthamoebae and SARS-COV-2 co-infection was noticed. To our knowledge, the combination of these two respiratory pathogens has not been described yet. This new TaqMan-PCR assay represents an efficient diagnostic tool to survey Parachlamydia acanthamoebae on a large-scale screening programs and also during outbreaks.

Novel Chlamydiae and Amoebophilus endosymbionts are prevalent in wild isolates of the model social amoeba Dictyostelium discoideum

Amoebae interact with bacteria in multifaceted ways. Amoeba predation can serve as a selective pressure for the development of bacterial virulence traits. Bacteria may also adapt to life inside amoebae, resulting in symbiotic relationships. Indeed, particular lineages of obligate bacterial endosymbionts have been found in different amoebae. Here, we screened an extensive collection of Dictyostelium discoideum wild isolates for the presence of these bacterial symbionts using endosymbiont specific PCR primers. We find that these symbionts are surprisingly common, identified in 42% of screened isolates (N = 730). Members of the Chlamydiae phylum are particularly prevalent, occurring in 27% of the amoeba isolated. They are novel and phylogenetically distinct from other Chlamydiae. We also found Amoebophilus symbionts in 8% of screened isolates (N = 730). Antibiotic-cured amoebae behave similarly to their Chlamydiae or Amoebophilus-infected counterparts, suggesting that these endosymbionts do not significantly impact host fitness, at least in the laboratory. We found several natural isolates were co-infected with multiple endosymbionts, with no obvious fitness effect of co-infection under laboratory conditions. The high prevalence and novelty of amoeba endosymbiont clades in the model organism D. discoideum opens the door to future research on the significance and mechanisms of amoeba-symbiont interactions.

Parachlamydia acanthamoebae Detected during a Pneumonia Outbreak in Southeastern Finland, in 2017⁻2018

Community-acquired pneumonia (CAP) is a common disease responsible for significant morbidity and mortality. However, the definite etiology of CAP often remains unresolved, suggesting that unknown agents of pneumonia remain to be identified. The recently discovered members of the order Chlamydiales, Chlamydia-related bacteria (CRB), are considered as possible emerging agents of CAP. Parachlamydia acanthamoebae is the most studied candidate. It survives and replicates inside free-living amoeba, which it might potentially use as a vehicle to infect animals and humans. A Mycoplasma pneumoniae outbreak was observed in Kymenlaakso region in Southeastern Finland during August 2017-January 2018. We determined the occurrence of Chlamydiales bacteria and their natural host, free-living amoeba in respiratory specimens collected during this outbreak with molecular methods. Altogether, 22/278 (7.9%) of the samples contained Chlamydiales DNA. By sequence analysis, majority of the CRBs detected were members of the Parachlamydiaceae family. Amoebal DNA was not detected within the sample material. Our study further proposes that Parachlamydiaceae could be a potential agent causing atypical CAP in children and adolescents.

Detection of novel Chlamydiae and Legionellales from human nasal samples of healthy volunteers

Chlamydiae are intracellular bacterial parasites of eukaryotes, ranging from amoebae to humans. They comprise many novel members and are investigated as emerging pathogens. Environmental studies highlighted similarities between the ecologies of chlamydiae and legionellae, both groups being important agents of respiratory infections. Herein, we analyzed nasal samples from healthy persons, searching for the presence of amoebae, chlamydiae and legionellae. From a total of 25 samples, we recovered by PCR eight samples positive to chlamydiae and six samples positive to legionellae. Among these samples, four were positive to both organisms. The sequencing of 16S rDNAs allowed to identify (i) among Chlamydiae: Parachlamydia acanthamoebae, Chlamydophila psittaci, Chlamydophila felis, and members of Rhabdochlamydiaceae, Simkaniaceae and E6 lineage and (ii) among Legionellaceae: Legionella longbeachae, Legionella bozemanii and Legionella impletisoli. Unexpectedly, we also recovered Diplorickettsia sp. Amoebae collected from nasal mucosae, Acanthamoeba and Vermamoeba, were endosymbiont-free, and chlamydiae revealed refractory to amoeba coculture. This study shows common exposure to chlamydiae and legionellae and suggests open air activities like gardening as a probable additional source of infection.

Developmental cycle and host interaction of Rhabdochlamydia porcellionis, an intracellular parasite of terrestrial isopods

Environmental chlamydiae are a diverse group of obligate intracellular bacteria related to well-known pathogens of humans. To date, only very little is known about chlamydial species infecting arthropods. In this study, we used cocultivation with insect cells for recovery and maintenance of Rhabdochlamydia porcellionis, a parasite of the crustacean host Porcellio scaber. In vitro, the infection cycle of R. porcellionis was completed within 7 days, resulting in the release of infectious particles by host cell lysis. Lack of apoptosis induction during the entire course of infection, combined with a reduced sensitivity of infected cultures to experimentally induced programmed cell death, indicates that R. porcellionis like its human pathogenic relatives counteracts this host defence mechanism. Interestingly, the rod-shaped variant of R. porcellionis, proposed to represent their mature infective stage, was not detected in cell culture, suggesting that its development may require prolonged maturation or may be triggered by specific conditions encountered only in the animal host. This first cell culture-based system for the cultivation and investigation of an arthropod-associated chlamydial species will help to better understand the biology of a so far neglected group of chlamydiae and its recently suggested potential to cause disease in humans.

Metabolic features of Protochlamydia amoebophila elementary bodies--a link between activity and infectivity in Chlamydiae

The Chlamydiae are a highly successful group of obligate intracellular bacteria, whose members are remarkably diverse, ranging from major pathogens of humans and animals to symbionts of ubiquitous protozoa. While their infective developmental stage, the elementary body (EB), has long been accepted to be completely metabolically inert, it has recently been shown to sustain some activities, including uptake of amino acids and protein biosynthesis. In the current study, we performed an in-depth characterization of the metabolic capabilities of EBs of the amoeba symbiont Protochlamydia amoebophila. A combined metabolomics approach, including fluorescence microscopy-based assays, isotope-ratio mass spectrometry (IRMS), ion cyclotron resonance Fourier transform mass spectrometry (ICR/FT-MS), and ultra-performance liquid chromatography mass spectrometry (UPLC-MS) was conducted, with a particular focus on the central carbon metabolism. In addition, the effect of nutrient deprivation on chlamydial infectivity was analyzed. Our investigations revealed that host-free P. amoebophila EBs maintain respiratory activity and metabolize D-glucose, including substrate uptake as well as host-free synthesis of labeled metabolites and release of labeled CO₂ from ¹³C-labeled D-glucose. The pentose phosphate pathway was identified as major route of D-glucose catabolism and host-independent activity of the tricarboxylic acid (TCA) cycle was observed. Our data strongly suggest anabolic reactions in P. amoebophila EBs and demonstrate that under the applied conditions D-glucose availability is essential to sustain metabolic activity. Replacement of this substrate by L-glucose, a non-metabolizable sugar, led to a rapid decline in the number of infectious particles. Likewise, infectivity of Chlamydia trachomatis, a major human pathogen, also declined more rapidly in the absence of nutrients. Collectively, these findings demonstrate that D-glucose is utilized by P. amoebophila EBs and provide evidence that metabolic activity in the extracellular stage of chlamydiae is of major biological relevance as it is a critical factor affecting maintenance of infectivity.

The Chlamydiae are a group of bacteria that strictly rely on eukaryotic host cells as a niche for intracellular growth. This group includes major pathogens of humans and animals as well as symbionts of protists. Unlike most other bacteria, chlamydiae alternate between two distinct developmental stages. Here we provide novel insights into the infective stage, the elementary body (EB), which has been described almost a century ago and is commonly referred to as an inert spore-like particle. Our analyses of EBs of the amoeba symbiont Protochlamydia amoebophila provide a detailed overview of their metabolism outside of, and independent from, their natural host cells. We demonstrated that these EBs are capable of respiration and are active in the major routes of central carbon metabolism, including glucose import, biosynthetic reactions, and catabolism for energy generation. Glucose starvation resulted in a rapid decline of metabolic activity in P. amoebophila EBs and a concomitant decrease in their potential to infect new host cells. The human pathogen Chlamydia trachomatis was also dependent on nutrient availability for extracellular survival. The extent of metabolic activity in chlamydial EBs and its consequences for infectivity challenge long-standing textbook knowledge and demonstrate that the infective stage is far more dependent on its environment than previously recognized.

"Candidatus Mesochlamydia elodeae" (Chlamydiae: Parachlamydiaceae), a novel chlamydia parasite of free-living amoebae

Vannella sp. isolated from waterweed Elodea sp. was found infected by a chlamydia-like organism. This organism behaves like a parasite, causing the death through burst of its host. Once the vannellae degenerated, the parasite was successfully kept in laboratory within a Saccamoeba sp. isolated from the same waterweed sample, which revealed in fine through electron microscopy to harbor two bacterial endosymbionts: the chlamydial parasite we introduce and another endosymbiont initially and naturally present in the host. Herein, we provide molecular-based identification of both the amoeba host and its two endosymbionts, with special focus on the chlamydia parasite. High sequence similarity values of the 18S rDNA permitted to assign the amoeba to the species Saccamoeba lacustris (Amoebozoa, Tubulinea). The bacterial endosymbiont naturally harbored by the host belonged to Sphingomonas koreensis (Alpha-Proteobacteria). The chlamydial parasite showed a strict specificity for Saccamoeba spp., being unable to infect a variety of other amoebae, including Acanthamoeba, and it was itself infected by a bacteriophage. Sequence similarity values of the 16S rDNA and phylogenetic analysis indicated that this strain is a new member of the family Parachlamydiaceae, for which we propose the name "Candidatus Mesochlamydia elodeae."

Environmental chlamydiae alter the growth speed and motility of host acanthamoebae

Symbiosis between living beings is an important driver of evolutionary novelty and ecological diversity; however, understanding the mechanisms underlying obligate mutualism remains a significant challenge. Regarding this, we have previously isolated two different Acanthamoeba strains harboring endosymbiotic bacteria, Protochlamydia (R18 symbiotic amoebae: R18WT) or Neochlamydia (S13 symbiotic amoebae; S13WT). In this study, we treated the symbiotic amoebae R18WT and S13WT with doxycycline (DOX) and rifampicin (RFP), respectively, to establish the aposymbiotic amoebae R18DOX and S13RFP, respectively. Subsequently, we compared the growth speed, motility, phagocytosis, pinocytosis, and morphology of the symbiotic and aposymbiotic amoebae. The growth speed of R18DOX was decreased, although that of S13RFP was increased. A marked change in motility was observed only for R18DOX amoebae. There was no difference in phagocytic and pinocytic activities between the symbiotic and aposymbiotic amoebae. Meanwhile, we observed a significant change in the phalloidin staining pattern and morphological changes in R18DOX (but not S13RFP) aposymbiotic amoebae, indicating a change in actin accumulation upon removal of the Protochlamydia. Infection of C3 (a reference strain) or S13RFP amoebae with Protochlamydia had a harmful effect on the host amoebae, but R18DOX amoebae re-infected with Protochlamydia showed recovery in both growth speed and motility. Taken together, we conclude that endosymbiont environmental chlamydiae alter the growth speed and/or motility of their host Acanthamoeba, possibly implying an close mutual relationship between amoebae and environmental chlamydiae.

Lack of effective anti-apoptotic activities restricts growth of Parachlamydiaceae in insect cells

The fundamental role of programmed cell death in host defense is highlighted by the multitude of anti-apoptotic strategies evolved by various microbes, including the well-known obligate intracellular bacterial pathogens Chlamydia trachomatis and Chlamydia (Chlamydophila) pneumoniae. As inhibition of apoptosis is assumed to be essential for a successful infection of humans by these chlamydiae, we analyzed the anti-apoptotic capacity of close relatives that occur as symbionts of amoebae and might represent emerging pathogens. While Simkania negevensis was able to efficiently replicate within insect cells, which served as model for metazoan-derived host cells, the Parachlamydiaceae (Parachlamydia acanthamoebae and Protochlamydia amoebophila) displayed limited intracellular growth, yet these bacteria induced typical features of apoptotic cell death, including formation of apoptotic bodies, nuclear condensation, internucleosomal DNA fragmentation, and effector caspase activity. Induction of apoptosis was dependent on bacterial activity, but not bacterial de novo protein synthesis, and was detectable already at very early stages of infection. Experimental inhibition of host cell death greatly enhanced parachlamydial replication, suggesting that lack of potent anti-apoptotic activities in Parachlamydiaceae may represent an important factor compromising their ability to successfully infect non-protozoan hosts. These findings highlight the importance of the evolution of anti-apoptotic traits for the success of chlamydiae as pathogens of humans and animals.

Nucleotide parasitism by Simkania negevensis (Chlamydiae)

Intracellular bacteria live in an environment rich in most essential metabolites but need special mechanisms to access these substrates. Nucleotide transport proteins (NTTs) catalyze the import of ATP and other nucleotides from the eukaryotic host into the bacterial cell and render de novo synthesis of these compounds dispensable. The draft genome sequence of Simkania negevensis strain Z, a chlamydial organism considered a newly emerging pathogen, revealed four genes encoding putative nucleotide transport proteins (SnNTT1 to SnNTT4), all of which are transcribed during growth of S. negevensis in Acanthamoeba host cells, as confirmed by reverse transcription-PCR. Using heterologous expression in Escherichia coli, we could show that SnNTT1 functions as an ATP/ADP antiporter, SnNTT2 as a guanine nucleotide/ATP/H(+) symporter driven by the membrane potential, and SnNTT3 as a nucleotide triphosphate antiporter. In addition, SnNTT3 is able to transport dCTP, which has not been shown for a prokaryotic transport protein before. No substrate could be identified for SnNTT4. Taking these data together, S. negevensis employs a set of nucleotide transport proteins to efficiently tap its host's energy and nucleotide pools. Although similar to other chlamydiae, these transporters show distinct and unique adaptations with respect to substrate specificities and mode of transport.

Survival and transfer ability of phylogenetically diverse bacterial endosymbionts in environmental Acanthamoeba isolates

Obligate intracellular bacteria are commonly found as endosymbionts of acanthamoebae; however, their survival in and ability to transfer to amoebae are currently uncharacterized. In this study, six bacterial endosymbionts, found in five environmental Acanthamoeba isolates (S13, R18, S23, S31, S40) from different locations of Sapporo city, Japan, were characterized. Phylogenetic analysis revealed that three bacterial endosymbionts (eS23, eS31, eS40a) belonged to α- and β-Proteobacteria phyla and the remaining endosymbionts (eS13, eR18, eS40b) belonged to the order Chlamydiales. The Acanthamoeba isolate (S40) contained two phylogenetically different bacterial endosymbionts (eS40a, eS40b). Fluorescent in situ hybridization analysis showed that all bacterial endosymbionts were diffusely localized within amoebae. Transmission electron microscopy also showed that the endosymbionts were rod-shaped (eS23, eS31, eS40a) or sphere- or crescent-shaped (eS13, eR18, eS40b). No successful culture of these bacteria was achieved using conventional culture methods, but the viability of endosymbionts was confirmed by live/dead staining and RT-PCR methods. However, endosymbionts (except eR18) derived from original host cells lost the ability to be transferred to another Acanthamoebae strains [ATCC strain (C3), environmental strains (S14, R23, S24)]. Thus, our data demonstrate that phylogenetically diverse bacterial endosymbionts found in amoebae maintain a stable interaction with amoebae, but the transferability is limited.

Biodiversity of amoebae and amoeba-associated bacteria in water treatment plants

In this study, we enlarged our previous investigation focusing on the biodiversity of chlamydiae and amoebae in a drinking water treatment plant, by the inclusion of two additional plants and by searching also for the presence of legionellae and mycobacteria. Autochthonous amoebae were recovered onto non-nutritive agar, identified by 18S rRNA gene sequencing, and screened for the presence of bacterial endosymbionts. Bacteria were also searched for by Acanthamoeba co-culture. From a total of 125 samples, we recovered 38 amoebae, among which six harboured endosymbionts (three chlamydiae and three legionellae). In addition, we recovered by amoebal co-culture 11 chlamydiae, 36 legionellae (no L. pneumophila), and 24 mycobacteria (all rapid-growers). Two plants presented a similar percentage of samples positive for chlamydiae (11%), mycobacteria (20%) and amoebae (27%), whereas in the third plant the number of recovered bacteria was almost twice higher. Each plant exhibited a relatively high specific microbiota. Amoebae were mainly represented by various Naegleria species, Acanthamoeba species and Hartmannella vermiformis. Parachlamydiaceae were the most abundant chlamydiae (8 strains in total), and in this study we recovered a new genus-level strain, along with new chlamydiae previously reported. Similarly, about 66% of the recovered legionellae and 47% of the isolated mycobacteria could represent new species. Our work highlighted a high species diversity among legionellae and mycobacteria, dominated by putative new species, and it confirmed the presence of chlamydiae in these artificial water systems.

Detection of Chlamydiae from freshwater environments by PCR, amoeba coculture and mixed coculture

Water systems have been shown to be a potential source of Chlamydiae, intracellular symbionts of eukaryotes. However, their diversity is likely underestimated, and natural hosts remain undetermined in many cases. In this study, we combined PCR-based and cultivation approaches to search for chlamydiae in different freshwaters, including natural ponds, garden pots and fountains. From a total of 40 samples, we recovered 16 phylotypes, clustered into nine species-level taxa belonging to the Parachlamydiaceae, Simkaniaceae, Rhabdochlamydiaceae, cvE6 lineage and a novel lineage. Parachlamydiaceae (four species) were recovered by amoeba coculture, while the other chlamydiae were maintained in mixed eukaryotic cultures. This study confirms the widespread occurrence of novel chlamydiae in the environment and enlarges our knowledge of their biodiversity in freshwater habitats.

Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes

Background

Chlamydiae are obligate intracellular bacteria of protists, invertebrates and vertebrates, but have not been found to date in photosynthetic eukaryotes (algae and embryophytes). Genes of putative chlamydial origin, however, are present in significant numbers in sequenced genomes of photosynthetic eukaryotes. It has been suggested that such genes were acquired by an ancient horizontal gene transfer from Chlamydiae to the ancestor of photosynthetic eukaryotes. To further test this hypothesis, an extensive search for proteins of chlamydial origin was performed using several recently sequenced algal genomes and EST databases, and the proteins subjected to phylogenetic analyses.

Results

A total of 39 proteins of chlamydial origin were retrieved from the photosynthetic eukaryotes analyzed and their identity verified through phylogenetic analyses. The distribution of the chlamydial proteins among four groups of photosynthetic eukaryotes (Viridiplantae, Rhodoplantae, Glaucoplantae, Bacillariophyta) was complex suggesting multiple acquisitions and losses. Evidence is presented that all except one of the chlamydial genes originated from an ancient endosymbiosis of a chlamydial bacterium into the ancestor of the Plantae before their divergence into Viridiplantae, Rhodoplantae and Glaucoplantae, i.e. more than 1.1 BYA. The chlamydial proteins subsequently spread through secondary plastid endosymbioses to other eukaryotes. Of 20 chlamydial proteins recovered from the genomes of two Bacillariophyta, 10 were of rhodoplant, and 10 of viridiplant origin suggesting that they were acquired by two different secondary endosymbioses. Phylogenetic analyses of concatenated sequences demonstrated that the viridiplant secondary endosymbiosis likely occurred before the divergence of Chlorophyta and Streptophyta.

Conclusion

We identified 39 proteins of chlamydial origin in photosynthetic eukaryotes signaling an ancient invasion of the ancestor of the Plantae by a chlamydial bacterium accompanied by horizontal gene transfer. Subsequently, chlamydial proteins spread through secondary endosymbioses to other eukaryotes. We conclude that intracellular chlamydiae likely persisted throughout the early history of the Plantae donating genes to their hosts that replaced their cyanobacterial/plastid homologs thus shaping early algal/plant evolution before they eventually vanished.

Emerging role of Chlamydia and Chlamydia-like organisms in adverse pregnancy outcomes

PURPOSE OF THE REVIEW

This review considers the roles of Chlamydia spp. and newly identified Chlamydia-like organisms in miscarriage, stillbirths and preterm labour in both animals and humans.

RECENT FINDINGS

The cause of miscarriage, stillbirth and preterm labour often remains unexplained. Intracellular bacteria that grow either poorly or not at all on media used routinely to detect human pathogens could be the aetiological agents of these obstetrical conditions. There is growing evidence that Chlamydia trachomatis, Chlamydophila abortus, Chlamydophila psittaci and Chlamydophila pneumoniae infections may result in adverse pregnancy outcomes in humans and/or animals. Waddlia, a Chlamydia-like organism first isolated from an aborted bovine, has emerged as an agent of abortion in cattle. Recently, Waddlia was also implicated in human foetal death. Moreover, Parachlamydia acanthamoebae is also abortigenic in ruminants. Whether additional novel Chlamydia-like organisms, such as Protochlamydia amoebophila, Neochlamydia hartmanellae, Criblamydia sequanensis, Rhabdochlamydia crassificans and Simkania negevensis, are involved in foetal loss or premature delivery remains to be determined.

SUMMARY

This review provides an update on the consequences of chlamydial infection during pregnancy and summarizes current evidence suggesting that some Chlamydia-related organisms are probably emerging obstetrical pathogens.