Characteristics of chlamydia-like organisms pathogenic to fish

The Fish Pathogen "Candidatus Clavichlamydia salmonicola"-A Missing Link in the Evolution of Chlamydial Pathogens of Humans

Chlamydiae like Chlamydia trachomatis and Chlamydia psittaci are well-known human and animal pathogens. Yet, the chlamydiae are a much larger group of evolutionary ancient obligate intracellular bacteria that includes predominantly symbionts of protists and diverse animals. This makes them ideal model organisms to study evolutionary transitions from symbionts in microbial eukaryotes to pathogens of humans. To this end, comparative genome analysis has served as an important tool. Genome sequence data for many chlamydial lineages are, however, still lacking, hampering our understanding of their evolutionary history. Here, we determined the first high-quality draft genome sequence of the fish pathogen "Candidatus Clavichlamydia salmonicola", representing a separate genus within the human and animal pathogenic Chlamydiaceae. The "Ca. Clavichlamydia salmonicola" genome harbors genes that so far have been exclusively found in Chlamydia species suggesting that basic mechanisms important for the interaction with chordate hosts have evolved stepwise in the history of chlamydiae. Thus, the genome sequence of "Ca. Clavichlamydia salmonicola" allows to constrain candidate genes to further understand the evolution of chlamydial virulence mechanisms required to infect mammals.

Microbiome composition and autochthonous probiotics from contrasting probiosis/dysbiosis states in cobia (Rachycentron canadum) fish epitheliocystis

Microbiome components and bacterial isolates related to healthy and epitheliocystis states in aquaculture cycles of cobia fish were studied. We detected well-defined 16S rRNA amplicon gene sequence variants showing differential abundance in healthy or diseased cycles. Isolation trials were performed, and experimental tests were used to determine probiotic potential of the bacterial strains obtained from water, tissues or live food used in this aquaculture model. The taxonomic affiliation of these strains was cross-compared against microbiome components, finding that some of them had close or identical affiliation to the abundant types found in healthy cycles. Strains belonging to the groups already identified as predominant by culture-independent means were screened as potential probiotics based on desirable activities such as antagonism and antibiosis against marine pathogenic bacteria, quorum quenching, bile acid resistance, antibiotic sensitivity and enzymatic activities for improved nutrient digestion. We have also found that in the tracking of microbiome composition across different developmental stages of cobia, healthy cycles exhibited a consistent high relative abundance of a Mesobacillus sp., while in the diseased cycle the emergence of a Vibrio sp. was observed. Our study suggests that epithelocystis in cobia is associated with a displacement of a symbiotic microbiome community linked to the increase frequency of Vibrio species.

Co-infection of Candidatus Piscichlamydia Trichopodus (Order Chlamydiales) and Henneguya sp. (Myxosporea, Myxobolidae) in Snakeskin Gourami Trichopodus pectoralis (Regan 1910)

The present study describes a simultaneous infection of a novel Chlamydia-like organism (CLO) with a Myxozoa parasite, Henneguya sp. in snakeskin gourami Trichopodus pectoralis in Thailand. A new CLO is proposed “Candidatus Piscichlamydia trichopodus” (CPT) based on 16S rRNA phylogenetic analysis. Systemic intracellular CPT infection was confirmed by histological examination, in situ hybridization, PCR assay, and sequencing of 16S rRNA. This novel pathogen belongs to the order Chlamydiales but differs in certain aspects from other species. The histopathological changes associated with CPT infection were different from the typical pathological lesions of epitheliocystis caused by previously known CLO. Unlike other CLO, CPT localized in the connective tissue rather than in the epithelial cells and formed smaller clumps of intracellular bacteria that stained dark blue with hematoxylin. On the other hand, typical myxospores of the genus Henneguya with tails were observed in the gill sections. Infection with Henneguya sp. resulted in extensive destruction of the gill filaments, most likely leading to respiratory distress. Due to the frequency of co-infections and the unavailability of culture methods for CLO and Henneguya sp., it was difficult to determine which pathogens were directly responsible for the associated mortality. However, co-infections may increase the negative impact on the host and the severity of the disease. Given the commercial importance of the snakeskin gourami and its significant aquaculture potential, the findings of this study are important for further studies on disease prevention.

Presence of DNA from Chlamydia-like organisms in the nasal cavities of grey seal pups (Halichoerus grypus) and three different substrates present in a breeding colony

Background

Chlamydia-like organisms (CLO) have been found to be present in many environmental niches, including human sewage and agricultural run-off, as well as in a number of aquatic species worldwide. Therefore, monitoring their presence in sentinel wildlife species may be useful in assessing the wider health of marine food webs in response to habitat loss, pollution and disease. We used nasal swabs from live (n = 42) and dead (n = 50) pre-weaned grey seal pups and samples of differing natal substrates (n = 8) from an off-shore island devoid of livestock and permanent human habitation to determine if CLO DNA is present in these mammals and to identify possible sources.

Results

We recovered CLO DNA from 32/92 (34.7%) nasal swabs from both live (n = 17) and dead (n = 15) seal pups that clustered most closely with currently recognised species belonging to three chlamydial families: Parachlamydiaceae (n = 22), Rhabdochlamydiaceae (n = 6), and Simkaniaceae (n = 3). All DNA positive sediment samples (n = 7) clustered with the Rhabdochlamydiaceae. No difference was found in rates of recovery of CLO DNA in live versus dead pups suggesting the organisms are commensal but their potential as opportunistic secondary pathogens could not be determined.

Conclusion

This is the first report of CLO DNA being found in marine mammals. This identification warrants further investigation in other seal populations around the coast of the UK and in other areas of the world to determine if this finding is unique or more common than shown by this data. Further investigation would also be warranted to determine if they are present as purely commensal organisms or whether they could also be opportunistic pathogens in seals, as well as to investigate possible sources of origin, including whether they originated as a result of anthropogenic impacts, including human waste and agricultural run-off.

Wood and sulfur-based cyclic denitrification filters for treatment of saline wastewaters

This study investigated the performance and microbiome of cyclic denitrification filters (CDFs) for wood and sulfur heterotrophic-autotrophic denitrification (WSHAD) of saline wastewater. Wood-sulfur CDFs integrated into two pilot-scale marine recirculating aquaculture systems achieved high denitrification rates (103 ± 8.5 g N/(m³·d)). The combined use of pine wood and sulfur resulted in lower SO₄^2- accumulation compared with prior saline wastewater denitrification studies with sulfur alone. Although fish tank water quality parameters, including ammonia, nitrite, nitrate and sulfide, were below the inhibitory levels for marine fish production, lower survival rates of Poecilia sphenops were observed compared with prior studies. Heterotrophic denitrification was the dominant removal mechanism during the early operational stages, while sulfur autotrophic denitrification increased as readily biodegradable organic carbon released from wood chips decreased over time. 16S rRNA-based analysis of the CDF microbiome revealed that Sulfurimonas, Thioalbus, Defluviimonas, and Ornatilinea as notable genera that contributed to denitrification performance.

Comparative proteomic profiling of newly acquired, virulent and attenuated Neoparamoeba perurans proteins associated with amoebic gill disease

The causative agent of amoebic gill disease, Neoparamoeba perurans is reported to lose virulence during prolonged in vitro maintenance. In this study, the impact of prolonged culture on N. perurans virulence and its proteome was investigated. Two isolates, attenuated and virulent, had their virulence assessed in an experimental trial using Atlantic salmon smolts and their bacterial community composition was evaluated by 16S rRNA Illumina MiSeq sequencing. Soluble proteins were isolated from three isolates: a newly acquired, virulent and attenuated N. perurans culture. Proteins were analysed using two-dimensional electrophoresis coupled with liquid chromatography tandem mass spectrometry (LC-MS/MS). The challenge trial using naïve smolts confirmed a loss in virulence in the attenuated N. perurans culture. A greater diversity of bacterial communities was found in the microbiome of the virulent isolate in contrast to a reduction in microbial community richness in the attenuated microbiome. A collated proteome database of N. perurans, Amoebozoa and four bacterial genera resulted in 24 proteins differentially expressed between the three cultures. The present LC-MS/MS results indicate protein synthesis, oxidative stress and immunomodulation are upregulated in a newly acquired N. perurans culture and future studies may exploit these protein identifications for therapeutic purposes in infected farmed fish.

Enrichment of potential pathogens in marine microbiomes with different degrees of anthropogenic activity

Anthropogenic activities in coastal marine ecosystems can lead to an increase in the abundance of potentially harmful microorganisms in the marine environment. To understand anthropogenic impacts on the marine microbiome, we first used publicly available microbial phylogenetic and functional data to establish a dataset of bacterial genera potentially related to pathogens that cause diseases (BGPRD) in marine organisms. Representatives of low-, medium- and highly impacted marine coastal environments were selected, and the abundance and composition of their microbial communities were determined by quantitative PCR and 16 S rRNA gene sequencing. In total, 72 BGPRD were cataloged, and 11, 36 and 37 BGPRD were found in low-, medium- and highly human-impacted ecosystems, respectively. The absolute abundance of BGPRD and the co-occurrence of antibiotic resistance genes (AGR) increased with the degree of anthropogenic perturbation in these ecosystems. Anthropogenically impacted coastal microbiomes were compositionally and functionally distinct from those of less impacted sites, presenting features that may contribute to adverse outcomes for marine macrobiota in the Anthropocene era.

A molecular assessment of infectious agents carried by Atlantic salmon at sea and in three eastern Canadian rivers, including aquaculture escapees and North American and European origin wild stocks

Infectious agents are key components of animal ecology and drivers of host population dynamics. Knowledge of their diversity and transmission in the wild is necessary for the management and conservation of host species like Atlantic salmon ( Salmo salar). Although pathogen exchange can occur throughout the salmon life cycle, evidence is lacking to support transmission during population mixing at sea or between farmed and wild salmon due to aquaculture exposure. We tested these hypotheses using a molecular approach that identified infectious agents and transmission potential among sub-adult Atlantic salmon at marine feeding areas and adults in three eastern Canadian rivers with varying aquaculture influence. We used high-throughput qPCR to quantify infection profiles and next generation sequencing to measure genomic variation among viral isolates. We identified 14 agents, including five not yet described as occurring in Eastern Canada. Phylogenetic analysis of piscine orthoreovirus showed homology between isolates from European and North American origin fish at sea, supporting the hypothesis of intercontinental transmission. We found no evidence to support aquaculture influence on wild adult infections, which varied relative to environmental conditions, life stage, and host origin. Our findings identify research opportunities regarding pathogen transmission and biological significance for wild Atlantic salmon populations.

High carbohydrate diet partially protects Nile tilapia (Oreochromis niloticus) from oxytetracycline-induced side effects

Antibiotics used in global aquaculture production cause various side effects, which impair fish health. However, the use of dietary composition such as carbohydrate, which is one of the dominant components in fish diets to attenuate the side effects induced by antibiotics, remains unclear. We determined the ability of high carbohydrate diet to protect Nile tilapia (Oreochromis niloticus) from oxytetracycline-induced side effects. Triplicate groups of thirty O. niloticus (9.50 ± 0.08 g) were fed on medium carbohydrate (MC; 335 g/kg) and high carbohydrate (HC; 455 g/kg) diets without and with 2.00 g/kg diet of oxytetracycline (80 mg/kg body weight/day) hereafter, MCO and HCO for 35 days. Thereafter, we assessed growth performance, hepatic nutrients composition and metabolism, microbiota abundance, immunity, oxidative and cellular stress, hepatotoxicity, lipid peroxidation and apoptosis. To understand the possible mechanism of carbohydrate protection on oxytetracycline, we assessed the binding effects and efficiencies of mixtures of medium and high starch with oxytetracycline as well as the MCO and HCO diets. The O. niloticus fed on the MCO and HCO diets had lower growth rate, nutrients utilization and survival rate than those fed on the MC and HC diets, respectively. Dietary HCO increased hepatosomatic index and hepatic protein content of O. niloticus than MCO diet. The O. niloticus fed on the HCO diet had lower mRNA expression of genes related to protein, glycogen and lipid metabolism compared to those fed on the MCO diet. Feeding O. niloticus on the HCO diet increased innate immunity and reduced pathogenic bacteria, pro-inflammation, hepatotoxicity, cellular stress and apoptosis than the MCO diet. The high starch with oxytetracycline and HCO diet had higher-oxytetracycline binding effects and efficiencies than the medium starch with oxytetracyline and MCO diet, respectively. Our study demonstrates that, high carbohydrate partially protects O. niloticus from oxytetracycline-induced side effects by binding the antibiotic. Incorporating high carbohydrate in diet formulation for omnivorous fish species alleviates some of the side effects caused by antibiotics.

Epitheliocystis: Development of PCR assay for the monitoring among the commercially important aquaculture species of Ukraine

Epitheliocystis is an emerging disease of wild and cultured fish caused by a number of bacterial species, characterized by the presence of cytoplasmic bacterial inclusions in the epithelial cells of the gills, which contribute to the merging of the gill plates, and in some cases also spread to the skin of fish. This disease may manifest as hypertrophy and inflammation of the gills, white nodular lesions of epithelial tissue in the gills or skin, gasping on the surface of the water, lethargy, poor swimming and stunted growth. Among the commercially important aquaculture species of Ukraine, such as Atlantic salmon (Salmo salar), brown trout (S. trutta), grass carp (Ctenopharyngodon idella), common carp (Cyprinus carpio) and gibel carp (Carassius auratus), Candidatus Clavochlamydia salmonicola and Candidatus Piscichlamydia salmonis are associated with epitheliocystis. There are currently no tools at the disposal of ichthyologists and veterinary laboratories in Ukraine to identify Ca. C. salmonicola and Ca. Piscichlamydia salmonis. Our basic concern was to develop a PCR assay of epitheliocystis diagnosis. We suggest the use of general primers for simultaneous detection of Ca. C. salmonicola and Ca. Piscichlamydia salmonis. The developed PCR assay for identification of Ca. C. salmonicola and Ca. Piscichlamydia salmonis has shown its suitability for amplifying control DNA. Confirmation of the amplification products identity was performed using selective recognition of the sequence by the TasI restriction endonuclease (Thermo Fisher Scientific, US). Analytical specificity verification of the PCR assay performed by amplifying the control DNA of 10 species of the Chlamydiales order showed the absence of PCR products, but observed in one. The designed PCR assay, after approbation on clinical material, can be used by researchers for extensive monitoring of epitheliocystis, doctors of veterinary medicine for diagnosis clarification, in addition to introduction into the practice of veterinary medicine laboratories and implementation in fish farm improvement programmes. The amplicon size of 197 base pairs theoretically permits application of this oligonucleotide primers pair for real-time PCR.

Yersinia ruckeri Isolated from Common Mudpuppy Necturus maculosus

During a routine health inspection of apparently healthy wild-caught common mudpuppies Necturus maculosus, the bacteria Yersinia ruckeri was isolated and the identity confirmed using biochemical and molecular methods. This represents the first isolation of Y. ruckeri from an amphibian. This finding increases the known host range capable of harboring this important fish pathogen and could have serious management implications for aquaculture. Furthermore, addressing wild amphibians in fish hatchery biosecurity plans is discussed.

Epitheliocystis in fish: An emerging aquaculture disease with a global impact

Epitheliocystis is a skin and gill disease in fish caused by pathogenic intracellular bacteria. The disease has been reported in at least 90 species of marine and freshwater fish in both the southern and northern hemispheres. It affects a number of commercially important aquaculture species, including salmon, kingfish and bream. In infected fish, cysts typically develop in the gill epithelia, promoting the fusion of gill lamellae. Infections can lead to respiratory distress and death, particularly in cultured and juvenile fish with cases rarely reported in wild fish. Modern molecular techniques are challenging the conventional wisdoms regarding the epidemiology of epitheliocystis, showing now that a number of distinct bacterial pathogens from completely different phyla can cause this disease. Here, we review the state of knowledge, including updates on aetiology, host range, diagnosis and treatments. Traditionally, bacteria from the phylum Chlamydiae were the only known pathogenic agents of epitheliocystis, but aetiology is now recognized as being more complex, including a range of Proteobacteria. Notwithstanding recent advances in identifying the pathogens, the reservoirs and modes of transmission remain largely unknown. Recent genome sequencing of the growing number of epitheliocystis agents suggests that many bacteria causing this disease are unique to individual species of fish. Environmental conditions that approach or exceed animals' physiological tolerances (e.g. atypical temperature, salinity or pH levels) are thought to contribute to disease development and progression. Empirical data and evidence concerning epidemiology, aetiology and treatments are, however, in many cases limited, highlighting the need for more work to better characterize this disease across the different hosts and locales affected.

Detection of Chlamydiaceae and Chlamydia-like organisms on the ocular surface of children and adults from a trachoma-endemic region

Trachoma, the leading infectious cause of blindness, is caused by Chlamydia trachomatis (Ct), a bacterium of the phylum Chlamydiae. Recent investigations revealed the existence of additional families within the phylum Chlamydiae, also termed Chlamydia-like organisms (CLOs). In this study, the frequency of Ct and CLOs was examined in the eyes of healthy Sudanese (control) participants and those with trachoma (case). We tested 96 children (54 cases and 42 controls) and 93 adults (51 cases and 42 controls) using broad-range Chlamydiae and Ct-specific (omcB) real-time PCR. Samples positive by broad-range Chlamydiae testing were subjected to DNA sequencing. Overall Chlamydiae prevalence was 36%. Sequences corresponded to unclassified and classified Chlamydiae. Ct infection rate was significantly higher in children (31.5%) compared to adults (0%) with trachoma (p < 0.0001). In general, 21.5% of adults and 4.2% of children tested positive for CLOs (p = 0.0003). Our findings are consistent with previous investigations describing the central role of Ct in trachoma among children. This is the first study examining human eyes for the presence of CLOs. We found an age-dependent distribution of CLO DNA in human eyes with significantly higher positivity in adults. Further studies are needed to understand the impact of CLOs in trachoma pathogenicity and/or protection.

Genotyping of Candidatus Syngnamydia salmonis (chlamydiales; Simkaniaceae) co-cultured in Paramoeba perurans (amoebozoa; Paramoebidae)

Candidatus Syngnamydia salmonis (Chlamydiales, Simkaniaceae) was described as an epitheliocystis-causing bacterium from the gills of Atlantic salmon (Salmo salar) in Norway. A bacterium showing 99.2% 16S rRNA identity to Cand. S. salmonis is able to multiply in Paramoeba perurans and based on the classification criteria this bacterium could represent the same species as Cand. S. salmonis. Sequencing the genome of the cultured bacterium has made it possible to fulfill the minimal standards for genetic characterization of species within the order Chlamydiales. The complete rRNA genes, the amino acid sequences of SucA, PepF, Adk, HemL, DnaA, FtsK and FabI, are presented in addition to the morphology of the Chlamydia-like morphs in the cytoplasm of P. perurans.

Candidatus Actinochlamydia pangasiae sp. nov. (Chlamydiales, Actinochlamydiaceae), a bacterium associated with epitheliocystis in Pangasianodon hypophthalmus

Chlamydial infections are recognised as causative agent of epitheliocystis, reported from over 90 fish species. In the present study, the farmed striped catfish Pangasianodon hypophthalmus (14-15 cm, 70-90 g) with a history of cumulative mortality of about 23% during June and July 2015, were brought to the laboratory. The histopathological examination of gills from the affected fish revealed presence of granular basophilic intracellular inclusions, mostly at the base of the interlamellar region and in gill filaments. A concurrent infection with Trichodina spp., Ichthyobodo spp. and Dactylogyrus spp. was observed in the gills. The presence of chlamydial DNA in the gills of affected fish was confirmed by amplification and sequencing of 16S rRNA gene. BLAST-n analysis of these amplicons revealed maximum similarity (96%) with Candidatus Actinochlamydia clariae. On the basis of phylogenetic analysis, it was inferred that the epitheliocystis agents from striped catfish were novel and belonged to the taxon Ca. Actinochlamydia. It is proposed that epitheliocystis agents from striped catfish will be named as Ca. Actinochlamydia pangasiae. The 16S rRNA gene amplicons from novel chlamydiae were labelled and linked to inclusions by in situ hybridisation. This is the first report of epitheliocystis from India in a new fish host P. hypophthalmus.

Unexpected genomic features in widespread intracellular bacteria: evidence for motility of marine chlamydiae

Chlamydiae are obligate intracellular bacteria comprising important human pathogens and symbionts of protists. Molecular evidence indicates a tremendous diversity of chlamydiae particularly in marine environments, yet our current knowledge is based mainly on terrestrial representatives. Here we provide first insights into the biology of marine chlamydiae representing three divergent clades. Our analysis of single-cell amplified genomes revealed hallmarks of the chlamydial lifestyle, supporting the ancient origin of their characteristic developmental cycle and major virulence mechanisms. Surprisingly, these chlamydial genomes encode a complete flagellar apparatus, a previously unreported feature. We show that flagella are an ancient trait that was subject to differential gene loss among extant chlamydiae. Together with a chemotaxis system, these marine chlamydiae are likely motile, with flagella potentially playing a role during host cell infection. This study broadens our view on chlamydial biology and indicates a largely underestimated potential to adapt to different hosts and environments.

Response of gut health and microbiota to sulfide exposure in Pacific white shrimp Litopenaeus vannamei

Sulfide is a natural and widely distributed toxicant. It can be commonly found on the interface between water and sediment in the aquatic environment. The Pacific white shrimp Litopenaeus vannamei starts life in the benthic zone soon after the mysis stage, an early stage of post larvae. Therefore, L. vannamei is inevitably affected by exposure to sulfide released from pond sediment. This study explored the toxicant effect of different concentrations of sulfide on the intestinal health and microbiota of Pacific white shrimp by monitoring the change of expression of inflammatory, immune related cytokines, and the structure of the intestinal microbiota. The gut histology, expressions of inflammatory and immune related cytokines (tumor necrosis factor-alpha, C-type lectin 3, myostatin and heat shock transcription factor 1), and the microbiota were determined in L. vannamei after exposure to 0 (control), 425.5 (1/10 LC 50-96 h), and 851 μg/L (1/5 LC 50-96 h) of sulfide for 21 days. With the increase of sulfide concentration, intestinal injury was aggravated and the inflammatory and immune related cytokines generated a range of reactions. The expression of myostatin (MSTN) was significantly down-regulated by the concentration of sulfide exposure. No difference in the expression of heat shock transcription factor 1 (HSF1) was found between the control and shrimp exposed to 425.5 μg/L, but significantly higher HSF1 expression was found in shrimp exposed to 851 μg/L of sulfide. Significantly higher values of tumor necrosis factor-alpha (TNF-α) and C-type lectin 3 (CTL3) were found in the shrimp exposed to 425.5 μg/L of sulfide compared to the control, but a lower value was found in the shrimp exposed to 851 μg/L (P < 0.05). Sulfide also changed the intestinal microbial communities. The abundance of pathogenic bacteria, such as Cyanobacteria, Vibrio and Photobacterium, increased significantly with exposure to the increasing concentration of sulfide. The abundance of some anti-stress bacteria, such as Chlorobi and Fusobacterium, increased. Nitrospirae which can alleviate nitrite toxicity decreased. Microbacterium, Parachlamydia, and Shewanella were all commonly found and down-regulated in both sulfide groups, which is associated with an adaptation to sulfide stimulation. This study indicates that chronic exposure to sub-lethal levels of sulfide could lead to damage of the gut structure, stimulate the response of the inflammatory and immune systems, and shape the structure of the gut microbiota in L. vannamei.