Identification of new amoebae strains in rainbow trout (Oncorhynchus mykiss, Walbaum) farms affected by nodular gill disease (NGD) in Northeastern Italy

Nodular gill disease (NGD) is an emerging condition associated with amoeba trophozoites in freshwater salmonid farms. However, unambiguous identification of the pathogens still must be achieved. This study aimed to identify the amoeba species involved in periodic NGD outbreaks in two rainbow trout (Oncorhynchus mykiss) farms in Northeastern Italy. During four episodes (February-April 2023), 88 fish were euthanized, and their gills were evaluated by macroscopic, microscopic and histopathological examination. The macroscopic and microscopic severity of the lesions and the degree of amoebae infestation were scored and statistically evaluated. One gill arch from each animal was put on non-nutrient agar (NNA) Petri dishes for amoeba isolation, cultivation and subsequent identification with SSU rDNA sequencing. Histopathology confirmed moderate to severe lesions consistent with NGD and mild to moderate amoeba infestation. The presence of amoebae was significantly correlated with lesion severity. Light microscopy of cultured amoebae strains and SSU rDNA analysis revealed the presence of a previously characterized amoeba Naegleria sp. strain GERK and several new strains: two strains from Hartmannelidae, three vannelid amoebae from the genus Ripella and cercozoan amoeba Rosculus. Despite the uncertainty in NGD etiopathogenesis and amoebae pathogenic role, identifying known and new amoebae leans towards a possible multi-aetiological origin.

Living in the cracks: Two novel genera of Variosea (Amoebozoa) discovered on an urban sidewalk

Biological soil crusts represent a rich habitat for diverse and complex eukaryotic microbial communities. A unique but extremely common habitat is the urban sidewalk and its cracks that collect detritus. While these habitats are ubiquitous across the globe, little to no work has been conducted to characterize protists found there. Amoeboid protists are major predators of bacteria and other microbial eukaryotes in these microhabitats and therefore play a substantial ecological role. From sidewalk crack soil crusts, we have isolated three naked amoebae with finely tapered subpseudopodia, and a simple life cycle consisting of a trophic amoeba and a cyst stage. Using a holistic approach including light, electron, and fluorescence microscopy as well as phylogenetics using the ribosomal small subunit rRNA gene and phylogenomics using 230 nuclear genes, we find that these amoeboid organisms fail to match any previously described eukaryote genus. However, we determined the amoebae belong to the amoebozoan lineage Variosea based on phylogenetics. The molecular analyses place our isolates in two novel genera forming a grade at the base of the variosean group Protosteliida. These three novel varioseans among two novel genera and species are herein named "Kanabo kenzan" and "Parakanabo toge."

A comparison of the use of different swab materials for optimal diagnosis of amoebic gill disease (AGD) in Atlantic salmon (Salmo salar L.)

Routine gill swabbing is a non-destructive sampling method used for the downstream qPCR detection and quantitation of the pathogen Neoparamoeba perurans, a causative agent of amoebic gill disease (AGD). Three commercially available swabs were compared aiming their application for timelier AGD diagnosis (Calgiswab^® (calcium alginate fibre-tipped), Isohelix^® DNA buccal and cotton wool-tipped). Calcium alginate is soluble in most sodium salts, which potentially allows the total recovery of biological material, hence a better extraction of target organisms' DNA. Thus, this study consisted of (a) an in vitro assessment involving spiking of the swabs with known amounts of amoebae and additional assessment of retrieval efficiency of amoebae from agar plates; (b) in vivo testing by swabbing of gill arches (second, third and fourth) of AGD-infected fish. Both in vitro and in vivo experiments identified an enhanced amoeba retrieval with Calgiswab® and Isohelix® swabs in comparison with cotton swabs. Additionally, the third and fourth gill arches presented significantly higher amoebic loads compared to the second gill arch. Results suggest that limiting routine gill swabbing to one or two arches, instead of all, could likely lead to reduced stress-related effects incurred by handling and sampling and a timelier diagnosis of AGD.

Bog Microtopography and the Climatic Sensitivity of Testate Amoeba Communities: Implications for Transfer Function-Based Paleo-Water Table Reconstructions

Although the use of sub-fossil testate amoebae as a proxy for raised bog hydrology in Holocene paleoecological studies is well-established, some detailed aspects of species-environment relationships remain under-researched. One such issue is the effect of bog surface microtopography on the climatic sensitivity of testate amoeba communities. Although it has been suggested that some microforms-especially hummocks-may be less sensitive to climatic forcing than others, this has rarely been objectively tested. To investigate this, subfossil testate amoebae assemblages have been examined in a series of shallow cores collected along a hummock-lawn-hollow transect from a bog in central Ireland and the resulting reconstructed water table records, dated using ²¹⁰Pb, have been compared with instrumental weather data. Testate amoebae communities in the hollow microform were found to be significantly less diverse than those in the hummock and lawn, and both the hummock and lawn showed statistically significant correlations with instrumental temperature and precipitation data. Therefore, whilst the suggestion that paleoecological investigations should target intermediate bog microforms remains sound, the notion that hummock-based testate amoebae hydrological data are climatically-insensitive is challenged.

Non-lethal loop-mediated isothermal amplification assay as a point-of-care diagnostics tool for Neoparamoeba perurans, the causative agent of amoebic gill disease

Neoparamoeba perurans is the causative agent of amoebic gill disease (AGD). Two loop-mediated isothermal amplification (LAMP) assays targeting the parasite 18S rRNA and the Atlantic salmon EF1α, used as internal control, were designed. The N. perurans LAMP assay did not amplify close relatives N. pemaquidensis and N. branchiphila, or the host DNA. This assay detected 10⁶ copies of the parasite 18S rRNA gene under 13 min and 10³ copies under 35 min. Five "fast-and-dirty" DNA extraction methods were compared with a reference method and further validated by TaqMan™ qPCR. Of those, the QuickExtract buffer was selected for field tests. Seventy-one non-lethal gill swabs were analysed from AGD-clinically infected Atlantic salmon. The pathogen was detected under 23 min in fish of gill score >2 and under 39 min for lower gill scores. About 1.6% of the tests were invalid (no amplification of the internal control). 100% of positives were obtained from swabs taken from fish showing gill score ˃3, but only ~50% of positives for lower gill scores. The present LAMP assay could be implemented as a point-of-care test for the on-site identification of N. perurans; however, further work is required to improve its performance for lower scores.

Effect of heat shock on hot water plumbing microbiota and Legionella pneumophila control

BACKGROUND

Heat shock is a potential control strategy for Legionella pneumophila in hot water plumbing systems. However, it is not consistently effective, with little understanding of its influence on the broader plumbing microbiome. Here, we employed a lab-scale recirculating hot water plumbing rig to compare the pre- and post-"heat shock" (i.e., 40 → 60 → 40 °C) microbiota at distal taps. In addition, we used a second plumbing rig to represent a well-managed system at 60 °C and conducted a "control" sampling at 60 °C, subsequently reducing the temperature to 40 °C to observe the effects on Legionella and the microbiota under a simulated "thermal disruption" scenario.

RESULTS

According to 16S rRNA gene amplicon sequencing, in the heat shock scenario, there was no significant difference or statistically significant, but small, difference in the microbial community composition at the distal taps pre- versus post-heat shock (both biofilm and water; weighted and unweighted UniFrac distance matrices). While heat shock did lead to decreased total bacteria numbers at distal taps, it did not measurably alter the richness or evenness of the microbiota. Quantitative PCR measurements demonstrated that L. pneumophila relative abundance at distal taps also was not significantly different at 2-month post-heat shock relative to the pre-heat shock condition, while relative abundance of Vermamoeba vermiformis, a known Legionella host, did increase. In the thermal disruption scenario, relative abundance of planktonic L. pneumophila (quantitative PCR data) increased to levels comparable to those observed in the heat shock scenario within 2 months of switching long-term operation at 60 to 40 °C. Overall, water use frequency and water heater temperature set point exhibited a stronger effect than one-time heat shock on the microbial composition and Legionella levels at distal taps.

CONCLUSIONS

While heat shock may be effective for instantaneous Legionella control and reduction in total bacteria numbers, water heater temperature set point and water use frequency are more promising factors for long-term Legionella and microbial community control, illustrating the importance of maintaining consistent elevated temperatures in the system relative to short-term heat shock.

PCR survey for Paramoeba perurans in fauna, environmental samples and fish associated with marine farming sites for Atlantic salmon (Salmo salar L.)

Amoebic gill disease (AGD) caused by the amoeba Paramoeba perurans is an increasing problem in Atlantic salmon aquaculture. In the present PCR survey, the focus was to identify reservoir species or environmental samples where P. perurans could be present throughout the year, regardless of the infection status in farmed Atlantic salmon. A total of 1200 samples were collected at or in the proximity to farming sites with AGD, or with history of AGD, and analysed for the presence of P. perurans. No results supported biofouling organisms, salmon lice, biofilm or sediment to maintain P. perurans. However, during clinical AGD in Atlantic salmon, the amoeba were detected in several samples, including water, biofilm, plankton, several filter feeders and wild fish. It is likely that some of these samples were positive as a result of the continuous exposure through water. Positive wild fish may contribute to the spread of P. perurans. Cleaner fish tested positive for P. perurans when salmon tested negative, indicating that they may withhold the amoeba longer than salmon. The results demonstrate the high infection pressure produced from an AGD-afflicted Atlantic salmon population and thus the importance of early intervention to reduce infection pressure and horizontal spread of P. perurans within farms.

Environmental Free-Living Amoebae Isolated from Soil in Khon Kaen, Thailand, Antagonize Burkholderia pseudomallei

Presence of Burkholderia pseudomallei in soil and water is correlated with endemicity of melioidosis in Southeast Asia and northern Australia. Several biological and physico-chemical factors have been shown to influence persistence of B. pseudomallei in the environment of endemic areas. This study was the first to evaluate the interaction of B. pseudomallei with soil amoebae isolated from B. pseudomallei-positive soil site in Khon Kaen, Thailand. Four species of amoebae, Paravahlkampfia ustiana, Acanthamoeba sp., Naegleria pagei, and isolate A-ST39-E1, were isolated, cultured and identified based on morphology, movement and 18S rRNA gene sequence. Co-cultivation combined with a kanamycin-protection assay of B. pseudomallei with these amoebae at MOI 20 at 30°C were evaluated during 0–6 h using the plate count technique on Ashdown’s agar. The fate of intracellular B. pseudomallei in these amoebae was also monitored by confocal laser scanning microscopy (CLSM) observation of the CellTracker^™ Orange-B. pseudomallei stained cells. The results demonstrated the ability of P. ustiana, Acanthamoeba sp. and isolate A-ST39-E1 to graze B. pseudomallei. However, the number of internalized B. pseudomallei substantially decreased and the bacterial cells disappeared during the observation period, suggesting they had been digested. We found that B. pseudomallei promoted the growth of Acanthamoeba sp. and isolate A-ST39-E1 in co-cultures at MOI 100 at 30°C, 24 h. These findings indicated that P. ustiana, Acanthamoeba sp. and isolate A-ST39-E1 may prey upon B. pseudomallei rather than representing potential environmental reservoirs in which the bacteria can persist.

Isolation and molecular characterization of free-living amoebae from different water sources in Italy

Free-living amoebae (FLA) are protozoa ubiquitous in Nature, isolated from a variety of environments worldwide. In addition to their natural distribution, some species have been found to be pathogenic to humans. In the present study a survey was conducted in order to evaluate the presence and to characterize at molecular level the isolates of amoebic organisms collected from different water sources in Italy. A total of 160 water samples were analyzed by culture and microscopic examination. FLA were found in 46 (28.7%) of the investigated water samples. Groundwater, well waters, and ornamental fountain waters were the sources with higher prevalence rates (85.7%, 50.0%, and 45.9%, respectively). Identification of FLA species/genotypes, based on the 18S rDNA regions, allowed to identify 18 (39.1%) Acanthamoeba isolates (genotypes T4 and T15) and 21 (45.6%) Vermamoeba vermiformis isolates. Other FLA species, including Vahlkampfia sp. and Naegleria spp., previously reported in Italy, were not recovered. The occurrence of potentially pathogenic free-living amoebae in habitats related to human population, as reported in the present study, supports the relevance of FLA as a potential health threat to humans.

Detection of a parasitic amoeba (Order Dactylopodida) in the female gonads of oysters in Brazil

The impacts of oocyte parasites on the reproductive success of molluscs are largely unknown. In this study, we evaluated the presence of gonad parasites in 6 species of marine bivalve molluscs native to southern Brazil. Cultured bivalves included the mangrove oyster Crassostrea gasar (sometimes called C. brasiliana), the brown mussel Perna perna, the lion's paw scallop Nodipecten nodosus and the wing pearl oyster Pteria hirundo. Another species of mangrove oyster, C. rhizophorae, and the carib pointed venus clam Anomalocardia brasiliana (syn. A. flexuosa) were collected from the wild. Molluscs were collected in winter 2009 and summer 2010 for histopathological and molecular evaluation. An unknown ovarian parasite (UOP) was observed in histopathological sections of female gonads of C. gasar and C. rhizophorae. The UOP possessed features suggestive of amoebae, including an irregular outer membrane, frothy cytoplasm, a nucleus with a prominent central nucleolus and a closely associated basophilic parasome. PCR analysis was negative for Marteilioides chungmuensis, Perkinsus spp. and Paramoeba perurans. However, real-time PCR successfully amplified DNA from oyster gonads when using universal Paramoeba spp. primers. Also, conventional PCR amplified DNA using primers specific for Perkinsela amoebae-like organisms (syn. Perkinsiella), which are considered as endosymbionts of Parameoba spp., previously thought to be the parasome. Our results suggest that this UOP is a species of amoeba belonging to 1 of the 2 families of the order Dactylopodida, possibly related to Paramoeba spp. This study represents the first report of this type of organism in oysters. We found that C. gasar and C. rhizophorae were the most susceptible molluscs to these UOPs.

Biofouling of reverse osmosis membranes used in river water purification for drinking purposes: analysis of microbial populations

Biofouling in water treatment processes represents one of the most frequent causes of plant performance decline. Investigation of clogged membranes (reverse osmosis membranes, microfiltration membranes and ultrafiltration membranes) is generally performed on fresh membranes. In the present study, a multidisciplinary autopsy of a reverse osmosis membrane (ROM) was conducted. The membrane, which was used in sulfate-rich river water purification for drinking purposes, had become inoperative after 6 months because of biofouling and was later stored for 18 months in dry conditions before analysis. SSU rRNA gene library construction, clone sequencing, T-RFLP, light microscope, and scanning electron microscope (SEM) observations were used to identify the microorganisms present on the membrane and possibly responsible for biofouling at the time of removal. The microorganisms were mainly represented by bacteria belonging to the phylum Actinobacteria and by a single protozoan species belonging to the Lobosea group. The microbiological analysis was interpreted in the context of the treatment plant operations to hypothesize as to the possible mechanisms used by microorganisms to enter the plant and colonize the ROM surface.

Microhabitat and climatic preferences of protosteloid amoebae in a region with a Mediterranean climate

The role of microhabitat and climate variation in structuring protosteloid amoebae communities has been investigated for the first time in the Mediterranean Basin, a biodiversity hotspot for plants and animals and the largest of the world's five areas with a Mediterranean climate. Abundance data were obtained from natural substrates collected in 13 localities from central Spain, and a total of 1,504 colonies and 18 species were recorded. For this new area, it has been carried out an optimization of the culturing effort based on rarefaction analyses, thus making possible to adapt the protocol to the objectives in future research. Canonical correspondence analysis and generalized linear models showed that microhabitat type was the most important factor for differentiating the niches of the species studied, but climatic variables, especially minimum temperature of the coldest month, precipitation seasonality, and temperature range, had secondary but also important effects. Bark inhabitants tend to be more abundant in localities with high temperature range and low annual precipitation. Aerial litter was the microhabitat with the highest species richness, abundance, and evenness. Species typical of this microhabitat are more abundant when there is high precipitation, low temperature of the warmest month, and low minimum temperature of the coldest month.

Neoparamoeba branchiphila infections in moribund sea urchins Diadema aff. antillarum in Tenerife, Canary Islands, Spain

A total of 109 sea urchins from 3 species collected in 2 localities off the coast of Tenerife Island, Spain, were examined for the presence of free-living amoebae in their coelomic fluid. Amoeba trophozoites were isolated exclusively from moribund individuals of long-spined sea urchins Diadema aff. antillarum (Philippi) (Echinoidea, Echinodermata) that manifested lesions related to sea urchin bald disease on their tests (16 out of 56 examined). No amoebae were detected in Arbacia lixula (L.) and Paracentrotus lividus (Lamarck). From the former sea urchin species, 8 strains, established from 10 primary isolates, were identified as Neoparamoeba branchiphila Dyková et al., 2005 using morphological and molecular methods. Results of this study (limited to the screening for free-living amoebae) together with data on agents of sea urchin mortalities reported to date justify the hypothesis that free-living amoebae play an opportunistic role in D. aff. antillarum mortality. The enlargement of the dataset of SSU rDNA sequences brought new insight into the phylogeny of Neoparamoeba species.

Demographic and ecological effects on patterns of parasitism in eastern chimpanzees (Pan troglodytes schweinfurthii) in Gombe National Park, Tanzania

From January 2006 to January 2008, we collected 1,045 fecal samples from 90 individually-recognized, free-ranging, eastern chimpanzees (Pan troglodytes schweinfurthii) inhabiting Gombe National Park, Tanzania to determine how patterns of parasitism are affected by demographic and ecological covariates. Seventeen parasite species were recovered, including eight nematodes (Oesophagostomum sp., Necator sp., Probstmayria gombensis, Strongyloides fulleborni, Ascaris sp., Trichuris sp., Abbreviata caucasica, and an unidentified strongyle), 1 cestode (Bertiella sp.), 1 trematode (Dicrocoeliidae), and 7 protozoa (Entamoeba coli, Entamoeba histolytica/dispar, Iodamoeba bütschlii, Troglodytella abrassarti, Troglocorys cava, Balantidium coli, and an unidentified protozoa). Significant differences were observed in interannual infection prevalence and parasite richness between 2006 and 2007. Intercommunity comparisons demonstrated higher prevalence of parasites for the Mitumba compared with Kasekela chimpanzee community. Prevalence of several parasites was strongly correlated with monthly rainfall patterns for both 2006 and 2007. Subadult chimpanzees had lower prevalence for most parasite species compared with adults in both years and also yielded a lower average parasite species richness. No significant differences were observed between males and females in prevalence in 2006. However, in 2007 the prevalence of S. fulleborni and I. bütschlii were higher in males than in females. Parasite prevalence and richness were substantially higher in this multiyear study compared with previous short-term studies of the gastrointestinal parasites of Gombe chimpanzees. This coupled with the significant interannual and interseasonal variation, demonstrated in this study, emphasizes the importance of multiyear monitoring with adequate sample size to effectively determine patterns of parasitism in wild primate populations.

Centers for Disease Control and Prevention (CDC). Notes from the field: transplant-transmitted Balamuthia mandrillaris --- Arizona, 2010

On August 23, 2010, CDC was notified regarding two organ transplant recipients in Arizona who had encephalitis with multiple ring-enhancing lesions revealed by cerebral magnetic resonance imaging. The common organ donor, a Hispanic male landscaper aged 27 years, had died in Arizona from a presumed stroke on July 21. He had a large skin lesion for approximately 6 months on his back that he had attributed to an insect bite. The ill recipients, a male liver recipient aged 56 years, and a male recipient of a kidney and pancreas aged 24 years, received organ transplants on July 22. In addition, two other recipients received organs from this donor: an adult male heart recipient received his transplant in California on July 22, and an adult male kidney recipient received his transplant in Utah on July 23.

Centers for Disease Control and Prevention (CDC). Balamuthia mandrillaris transmitted through organ transplantation --- Mississippi, 2009

On December 14, 2009, a physician in Mississippi contacted CDC to report possible transplant-transmitted encephalitis in two kidney transplant recipients who shared the same organ donor. Histopathologic testing of donor autopsy brain tissue at CDC showed amebae, and subsequent testing of specimens from the donor and the two kidney recipients confirmed transmission by transplantation of Balamuthia granulomatous amebic encephalitis (GAE), a rare disease caused by Balamuthia mandrillaris, a free-living ameba found in soil. One kidney recipient, a woman aged 31 years, died; the other recipient, a man aged 27 years, survived with neurologic sequelae. Recipients of the heart and liver from the same donor received preemptive therapy and have shown no signs of infection. The donor, a previously healthy boy aged 4 years, was presumed to have died from acute disseminated encephalomyelitis (ADEM), an autoimmune neurologic disease, after infection with influenza A. An investigation was conducted by the state health departments in Mississippi, Kentucky, Florida, and Alabama and CDC to characterize the cases, elucidate possible exposures in the donor, and develop recommendations for early detection and prevention. This is the first reported transmission of Balamuthia by organ transplantation. Clinicians should be aware of Balamuthia infection as a potentially fatal cause of encephalitis. Organ procurement organizations (OPOs) and transplant centers should be aware of the potential for Balamuthia infection in donors with encephalitis of uncertain etiology, and OPOs should communicate this elevated risk for infection to transplant centers so they can make an informed risk assessment in the decision to accept an organ.

Screening of Swiss hot spring resorts for potentially pathogenic free-living amoebae

Free-living amoebae (FLA) belonging to Acanthamoeba spp., Naegleria fowleri, Balamuthia mandrillaris, and Sappinia pedata are known to cause infections in humans and animals leading to severe brain pathologies. Worldwide, warm aquatic environments have been found to be suitable habitats for pathogenic FLA. The present study reports on screening for potentially pathogenic FLA in four hot spring resorts in Switzerland. Water samples were taken from water filtration units and from the pools, respectively. Amoebae isolated from samples taken during, or before, the filtration process were demonstrated to be morphologically and phylogenetically related to Stenoamoeba sp., Hartmannella vermiformis, Echinamoeba exundans, and Acanthamoeba healyi. With regard to the swimming pools, FLA were isolated only in one resort, and the isolate was identified as non-pathogenic and as related to E. exundans. Further investigations showed that the isolates morphologically and phylogenetically related to A. healyi displayed a pronounced thermotolerance, and exhibited a marked in vitro cytotoxicity upon 5-day exposure to murine L929 fibroblasts. Experimental intranasal infection of Rag2-immunodeficient mice with these isolates led to severe brain pathologies, and viable trophozoites were isolated from the nasal mucosa, brain tissue, and lungs post mortem. In summary, isolates related to A. healyi were suggestive of being potentially pathogenic to immunocompromised persons. However, the presence of these isolates was limited to the filtration units, and an effective threat for health can therefore be excluded.