Use of subgenic 18S ribosomal DNA PCR and sequencing for genus and genotype identification of acanthamoebae from humans with keratitis and from sewage sludge

Real-Time PCR for the Diagnosis of Acanthamoeba Genotype T4

Acanthamoeba spp. are ubiquitous and opportunistic free-living amoebae (FLA) that can cause Acanthamoeba keratitis and other infections in the human host. A quick and efficient diagnosis is often challenging. Our study aimed to establish a qPCR assay to detect and, at the same time, quantify the predominant Acanthamoeba genotype T4. DNA from clinical corneal scrapings and Acanthamoeba reference strains, including genotypes T3, T4, T5, T6, T10, T11, and T12, were used to develop the new T4 assay and it was compared to published protocols and one commercial kit for evaluation. The T4 assay showed no amplification with Acanthamoeba genotypes T3, T5, T6, T10, T11, and T12. The efficiencies ranged from 92.01 to 97.59% (R² of 0.9768 to 0.9951). The calculated LOD range was 3.63 to 33.27 cells/µL. The protocol published by Qvarnstrom and colleagues was more sensitive compared to the other assays, and an overall good agreement was observed between the new T4 and the Qvarnstrom assays. We successfully developed and validated a genotype T4 assay that could be run in duplex with the Qvarnstrom assay to reliably and simultaneously diagnose Acanthamoeba genotype T4 and other genotypes from clinical samples.

Surveillance of Amoebic Keratitis-Causing Acanthamoebae for Potential Bacterial Endosymbionts in Ontario, Canada

Acanthamoeba spp. are the causative pathogens of several infections, including amoebic keratitis (AK), a vision-threatening infection. Acanthamoebae from corneal specimens of patients with AK harbor bacterial endosymbionts, which may increase virulence. We sought to understand the spectrum of bacterial endosymbionts present in clinical isolates of Acanthamoeba spp. identified in our reference parasitology laboratory. Isolates of Acanthamoeba spp. obtained from our biobank of anonymized corneal scrapings were screened for potential endosymbionts by PCR using primer pairs detecting bacteria belonging to orders Chlamydiales, Rickettsiales, or Legionellales and pan16S primers. Three primer pairs specific to the 18s rRNA gene of Acanthamoeba spp. were used for the amplification of Acanthamoeba DNA used for sequencing. Sanger sequencing of all PCR products was performed, followed by BLAST analysis for species identification. We screened 26 clinical isolates of Acanthamoeba spp. for potential endosymbionts. Five isolates (19%) were found to contain bacterial DNA belonging to Legionellales. Three (11%) contained members of the Rickettsiales and Pseudomonas genticulata was detected in a Rickettsia-positive sample. One strain (4%) contained Neochlamydia hartmannellae, a member of the Chlamydiales order. Bacterial endosymbionts are prevalent in clinical strains of Acanthamoeba causing AK isolated from corneal scrapings. The demonstration of these organisms in clinical Acanthamoeba isolates supports a potential exploration of anti-endosymbiont therapeutics as an adjuvant therapy in the treatment of AK.

Pathogenic free-living amoebae from water sources in Cape Verde

Free-living amoebae (FLA) are protozoa which have been reported in different countries worldwide from diverse sources (water, soil, dust, air), contributing to the environmental microbiological contamination. Most of the FLA species present a life cycle with two different phases: an active vegetative and physiologically form named trophozoite, and an extremely resistant phase called cyst. Acanthamoeba spp., Naegleria fowleri, Balamuthia mandrillaris, Sapinia pedata, Vahlkampfia spp., Paravahlkampfia spp. and Vermamoeba vermiformis have been reported not only as causal agents of several opportunistic diseases including fatal encephalitis or epithelial disorders, but also as capable to favour the intracellular survival of common pathogenic bacteria, which could avoid the typical water disinfection systems, non-effective against FLAs cysts. Even though Santiago Island possesses high levels of humidity compared to the rest of the archipelago of Cape Verde, the water resources are scarce. Therefore, it is important to carry out proper microbiological quality controls, which currently do not contemplate the FLA presence in most of the countries. In the present work, we have reported the presence of Acanthamoeba spp. (69.2%); Vannella spp. (15.4%); Vermamoeba vermiformis (7.7%) and the recently discovered Stenamoeba dejonckheerei (7.7%) in different water sources of Santiago Island.

Environmental water surveillance for free-living amoeba in North India

PURPOSE

Free-living amoebae (FLA) exist in various environmental sources and are the causative agents of many serious human diseases. We surveyed various natural and artificial water bodies in areas of north India to detect the presence of FLA species.

MATERIALS AND METHODS

Surface water samples were collected from 29 water bodies and subjected to microscopy, non-nutrient agar (NNA) culture, and various polymerase chain reaction (PCR) assays for the detection of FLA.

RESULTS

FLA were found in 62.1% (18/29) of the natural and artificial water bodies by NNA culture. Based on PCR based detection, Acanthamoeba spp. was identified in 41.4% (12/29), Vannella spp./Vahlkampfia ovis in 17.2% (5/29) and Naegleria spp. in 20.7% (6/29) of the samples from different locations. PCR-sequencing of Naegleria positive samples identified them as Naegleria australiensis and Naegleria species.

CONCLUSIONS

The present study reports widespread occurrence of medically important FLA species in various natural and artificial water bodies, and highlights the need for regular molecular surveillance of FLA in the environment for better control and prevention of the diseases caused by FLA.

Report of rare genotypes of Acanthamoeba from soil source of the Payeh Maga Highland forest, North-eastern Sarawak, Malaysia

Pathogenic Acanthamoeba species are the causative agents of Acanthamoeba keratitis and granulomatous amoebic encephalitis. Members of this amoeba genus are ubiquitous in the environments. In Malaysia, most environmental studies performed to date have targeted the detection and characterisation of Acanthamoeba sp. in different water sources, dust and soil samples collected near human habitats. However, no local study has yet to examine these amoebae in a forest, an isolated terrestrial environment, where human activity is relatively scarce. Further, there are also limited studies to investigate the same globally. The current study reported the isolation, morphological and genotypic characterisations of eleven Acanthamoeba sp. isolated from soils of the Payeh Maga Highland forest, Sarawak, Malaysia. Morphological analysis revealed that nine isolates belonged to Group II, whereas two isolates belonged to Group III as defined by the criteria of Pussard and Pons. The phylogenetic analysis based on complete 18S rRNA gene sequences showed that the isolates belonged to the rare T1 (six isolates), T6 (two isolates) and T13 (three isolates) genotypes. To the best of our knowledge, this is the first report about the detection of T6 Acanthamoeba sp. in this country. Overall, the current findings have enriched the knowledge pertaining to the occurrence, morphological and genotypic characteristics of Acanthamoeba sp. in an isolated terrestrial environment of Malaysia.

A Comparative Genomic Approach to Determine the Virulence Factors and Horizontal Gene Transfer Events of Clinical Acanthamoeba Isolates

Acanthamoeba species are among the most ubiquitous protists that are widespread in soil and water and act as both a replicative niche and vectors for dispersal. They are the most important human intracellular pathogens, causing Acanthamoeba keratitis (AK) and severely damaging the human cornea. The sympatric lifestyle within the host and amoeba-resisting microorganisms (ARMs) promotes horizontal gene transfer (HGT). However, the genomic diversity of only A. castellanii and A. polyphaga has been widely studied, and the pathogenic mechanisms remain unknown. Thus, we examined 7 clinically pathogenic strains by comparative genomic, phylogenetic, and rhizome gene mosaicism analyses to explore amoeba-symbiont interactions that possibly contribute to pathogenesis. Genetic characterization and phylogenetic analysis showed differences in functional characteristics between the "open" state of T3 and T4 isolates, which may contribute to the differences in virulence and pathogenicity. Through comparative genomic analysis, we identified potential genes related to virulence, such as metalloprotease, laminin-binding protein, and HSP, that were specific to the genus Acanthamoeba. Then, analysis of putative sequence trafficking between Acanthamoeba and Pandoraviruses or Acanthamoeba castellanii medusaviruses provided the best hits with viral genes; among bacteria, Pseudomonas had the most significant numbers. The most parsimonious evolutionary scenarios were between Acanthamoeba and endosymbionts; nevertheless, in most cases, the scenarios are more complex. In addition, the differences in exchanged genes were limited to the same family. In brief, this study provided extensive data to suggest the existence of HGT between Acanthamoeba and ARMs, explaining the occurrence of diseases and challenging Darwin's concept of eukaryotic evolution. IMPORTANCE Acanthamoeba has the ability to cause serious blinding keratitis. Although the prevalence of this phenomenon has increased in recent years, our knowledge of the underlying opportunistic pathogenic mechanism maybe remains incomplete. In this study, we highlighted the importance of Pseudomonas in the pathogenesis pathway using comprehensive a whole genomics approach of clinical isolates. The horizontal gene transfer events help to explain how endosymbionts contribute Acanthamoeba to act as an opportunistic pathogen. Our study opens up several potential avenues for future research on the differences in pathogenicity and interactions among clinical strains.

Isolation and identification of potentially pathogenic free-living amoeba in drinking, surface, and stagnant water sources from Alborz Province, Iran

Free-living amoebas (FLAs) can cause neurological and ocular complications in humans. Water supplies play a critical role in transmitting FLAs to humans. The aim of the present study was to investigate the presence of FLAs in various aquatic sources including drinking water, stagnant water, and surface water in Alborz province, northern Iran, using morphological and molecular techniques. A total of 70 water samples were collected from 34 drinking waters, 23 surface waters, and 13 stagnant waters. Filtration and cultivation were employed to isolate FLAs. PCR assay was applied by using the genus-specific primers on positive samples. Pathogenicity tests (osmo- and thermo-tolerance properties) were performed for Acanthamoeba spp., positive sample. Considering the morphological criteria, four positive samples of Acanthamoeba sp., three Vermamoeba sp., two mixed Vermamoeba sp. with Vahlkamfiids, and one mixed Acanthamoeba sp. with Vahlkamfiids were isolated. Five Acanthamoeba sp. isolates were amplified using the JDP primer pairs. Among them, two genotypes, T4 (three isolates) and T5 (two isolates) corresponding to A. lenticulata, were identified. Four V. vermiformis samples were confirmed using the sequencing. This study highlighted the occurrence of potentially pathogenic waterborne FLAs in water habitats associated with high human activity. The results of such research on the prevalence of FLAs, as a human hazard, should be communicated to health policymakers.

Clinical and molecular diagnosis of Acanthamoeba keratitis in contact lens wearers in southern Brazil reveals the presence of an endosymbiont

Acanthamoeba keratitis (AK) is an infection that is mostly observed in contact lens wearers. It is often misdiagnosed causing delays in the administration of the correct treatment. The aim of this study was to report the outcome of clinical and molecular diagnosis of AK cases during the summer of 2019 in the southern region of Brazil. Three suspected cases of AK were discovered after an ophthalmic examination at a public hospital in the city of Porto Alegre. These cases were then confirmed through laboratory diagnosis (cell culture and molecular analysis by PCR and sequencing). In each of the three clinical sample cell cultures of corneal scraping and molecular analysis confirmed the presence of Acanthamoeba spp., all belonging to the morphological group II and to the genotype T4, which is the most common genotype associated with AK. In addition, Acanthamoeba spp. isolated from one of the clinical samples was found to harbor the Candidatus Paracaedibacter acanthamoeba, a bacterial endosymbiont. The presence of Ca. Paracaedibacter acanthamoeba in clinical isolates requires further research to reveal its possible role in the pathogenicity of Acanthamoeba infections.

Molecular characterization and phylogenetic analysis of FLA from different water sources in Egypt

Free-living amoebae (FLA) are protozoa ubiquitously found in nature. In addition to their natural distribution, some species have been documented as pathogenic to humans. The main aim of the current study was the molecular identification, sequencing and phylogenetic analysis of morphologically detected FLA in water sources in El-Qalyubia, Egypt. A total of 96 water samples were collected from different water sources. Each water sample was filtrated and cultured on non-nutrient agar (NNA). Morphologically positive FLA were subjected to PCR, PCR products were sequenced and the obtained sequences were phylogenetically analysed. FLA were found in 41 water samples examined (42.7%). Nile water and groundwater were the sources with the highest prevalence rates (83.3 and 62.5%, respectively). Naegleria italica was first identified in Egypt from the waters of the Nile. In addition, Vahlkampfia spp. and Hartmannella spp. were also detected. However, other FLA species, including Acanthamoeba spp. and the pathogenic Naegleria fowleri, previously reported in Egypt, were not included in this study. The recent identification of these FLA in the Egyptian waters related to human populations indicates the need for more phylogenetic studies using larger sample sizes to investigate their potential threat to human health.

Survey and first report of Acanthamoeba T4 genotype in natural spring water resources in the Black Sea, Turkey

Infection with Acanthamoeba spp. may result in granulomatous amoebic encephalitis and Acanthamoeba keratitis. Water is an important habitat where Acanthamoeba species thrive. Therefore, studying the occurrence of this free-living amoeba in water sources will help understand the infection dynamics. The aim of the study was to survey and report on the presence of Acanthamoeba spp. in water resources from the Ordu and Giresun provinces in Black Sea. Acanthamoeba spp. was found in 1/17 natural spring water samples from Ordu and in 2/18 from Giresun. Acanthamoeba species were not detected in any of the investigated tap water samples. Sequencing of the (SSU) rDNA gene resulted in the identification of haplotype I (Acanthamoeba genotype: KJ094684). T4 (8.6%) was the only isolated genotype in both Ordu and Giresun provinces. This is the first report of Acanthamoeba T4 genotype in natural spring water resources in the Black Sea. The occurrence of Acanthamoeba species in natural spring water sources should be considered as a potential risk for human infection, especially to high-risk populations.

Acanthamoeba species isolated from marine water in Malaysia exhibit distinct genotypes and variable physiological properties

The present study identifies the Acanthamoeba genotypes and their pathogenic potential in five marine waters in Malaysia. Fifty water samples were collected between January and May 2019. Physical parameters of water quality were measured in situ, whereas chemical and microbiological analyses were conducted in the laboratory. All samples had undergone filtration using nitrocellulose membrane and were tested for Acanthamoeba using cultivation and polymerase chain reaction by targeting the 18S ribosomal RNA gene. The pathogenic potential of all positive isolates was identified using physiological tolerance tests. Thirty-six (72.0%) samples were positive for Acanthamoeba. Total coliforms (p = 0.013) and pH level (p = 0.023) displayed significant correlation with Acanthamoeba presence. Phylogenetic analysis showed that 27 samples belonged to genotype T4, four (T11), two (T18) and one from each genotype T5, T15 and T20. Thermo- and osmo-tolerance tests signified that three (8.3%) Acanthamoeba strains displayed highly pathogenic attributes. This study is the first investigation in Malaysia describing Acanthamoeba detection in marine water with molecular techniques and genotyping. The study outcomes revealed that the marine water in Malaysia could be an integral source of Acanthamoeba strains potentially pathogenic in humans. Thus, the potential risk of this water should be monitored routinely in each region.

Co-Existence of Free-Living Amoebae and Potential Human Pathogenic Bacteria Isolated from Rural Household Water Storage Containers

Simple Summary

In many households in rural communities, water needed for drinking and cooking is fetched from rivers, fountains, or boreholes shared by the community. The water is then stored in various storage containers for several days without treatment and exposed to several conditions that could potentially contaminate the water and cause diseases. If the storage containers are not regularly and properly cleaned, biofilms can form inside the containers. Several microorganisms can be found inside the biofilm that can potentially cause diseases in humans. One such group of organisms is called free-living amoebae, which graze on the bacteria found inside the biofilm. Several of these potentially harmful bacteria have adapted and can survive inside these free-living amoebae and potentially cause diseases when ingested by humans.

Abstract

This study investigated the co-existence of potential human pathogenic bacteria and free-living amoebae in samples collected from stored water in rural households in South Africa using borehole water as a primary water source. Over a period of 5 months, a total of 398 stored water and 392 biofilm samples were collected and assessed. Free-living amoebae were identified microscopically in 92.0% of the water samples and 89.8% of the biofilm samples. A further molecular identification using 18S rRNA sequencing identified Vermamoeba vermiformis, Entamoeba spp., Stenamoeba spp., Flamella spp., and Acanthamoeba spp. including Acanthamoeba genotype T4, which is known to be potentially harmful to humans. Targeted potential pathogenic bacteria were isolated from the water samples using standard culture methods and identified using 16S rRNA sequencing. Mycobacterium spp., Pseudomonas spp., Enterobacter spp., and other emerging opportunistic pathogens such as Stenotrophomonas maltophilia were identified. The results showed the importance of further studies to assess the health risk of free-living amoebae and potential human pathogenic bacteria to people living in rural communities who have no other option than to store water in their homes due to water shortages.

Contact lenses contamination by Acanthamoeba spp. in Upper Egypt

Background

Acanthamoeba spp. are one of the free-living amoeba that spread worldwide causing keratitis. Owing to the increase in the use of lenses, whether for medical or cosmetic purposes, the incidence of disease increases every year. Contamination of the lenses with the Acanthamoeba trophozoites or cysts may lead to eye infection and cause sight-threatening keratitis in human. We isolated Acanthamoeba spp. from new lenses, used lenses, and contact lens disinfecting solutions and identified them based on morphological characteristics and molecular test.

Methods

New and used lenses and contact lens disinfecting solutions were cultured on monogenic media. Light and scanning electron microscope was used to identify Acanthamoeba spp. morphological features. Genotype identification was also evaluated using PCR sequencing of 18S rRNA gene specific primer pair JDP1 and JDP2.

Results

A hundred samples were examined, 29 (29%) were infected with Acanthamoeba spp. That belonged to two strains of Acanthamoeba (Acanthamoeba 41 and Acanthamoeba 68). 18S rRNA of the Acanthamoeba 41 had 99.69% sequence identity to Acanthamoeba castellanii clone HDU-JUMS-2, whereas Acanthamoeba 68 had 99.74% similar pattern to that of Acanthamoeba sp. isolate T4 clone ac2t4 that are morphologically identified as Acanthamoeba polyphaga. The obtained data revealed that the isolated strains belong to T4 genotype that was evolutionarily similar to strains isolated in Iran.

Conclusions

Cosmetic lenses and disinfectant solutions are a major transmissible mode for infection. This genotype is common as the cause of Acanthamoeba keratitis. To avoid infection, care must be taken to clean the lenses and their preservative solutions and prevent contamination with the parasite.

Efficient nested-PCR-based method development for detection and genotype identification of Acanthamoeba from a small volume of aquatic environmental sample

Acanthamoeba spp. are opportunistic human pathogens that cause granulomatous amoebic encephalitis and keratitis, and their accurate detection and enumeration in environmental samples is a challenge. In addition, information regarding the genotyping of Acanthamoeba spp. using various PCR methods is equally critical. Therefore, considering the diverse niches of habitats, it is necessary to develop an even more efficient genotyping method for Acanthamoeba spp. detection. This study improved the sensitivity of detection to avoid underestimation of Acanthamoeba spp. occurrence in aquatic environmental samples, and to accurately define the pathogenic risk by developing an efficient PCR method. In this study, a new nested genotyping method was established and compared with various PCR-based methods using in silico, lab, and empirical tests. The in silico test showed that many PCR-based methods could not successfully align specific genotypes of Acanthamoeba, except for the newly designed nested PCR and real-time PCR method. Furthermore, 52 water samples from rivers, reservoirs, and a river basin in Taiwan were analysed by six different PCR methods and compared for genotyping and detection efficiency of Acanthamoeba. The newly developed nested-PCR-based method of genotyping was found to be significantly sensitive as it could effectively detect the occurrence of Acanthamoeba spp., which was underestimated by the JDP-PCR method. Additionally, the present results are consistent with previous studies indicating that the high prevalence of Acanthamoeba in the aquatic environment of Taiwan is attributed to the commonly found T4 genotype. Ultimately, we report the development of a small volume procedure, which is a combination of recent genotyping PCR and conventional real-time PCR for enumeration of aquatic Acanthamoeba and acquirement of biologically meaningful genotyping information. We anticipate that the newly developed detection method will contribute to the precise estimation, evaluation, and reduction of the contamination risk of pathogenic Acanthamoeba spp., which is regularly found in the water resources utilised for domestic purposes.

Acanthamoeba Keratitis: an update on amebicidal and cysticidal drug screening methodologies and potential treatment with azole drugs

Introduction: Acanthamoeba encompasses several species of free-living ameba encountered commonly throughout the environment. Unfortunately, these species of ameba can cause opportunistic infections that result in Acanthamoeba keratitis, granulomatous amebic encephalitis, and occasionally systemic infection.Areas covered: This review discusses relevant literature found through PubMed and Google scholar published as of January 2021. The review summarizes current common Acanthamoeba keratitis treatments, drug discovery methodologies available for screening potential anti-Acanthamoeba compounds, and the anti-Acanthamoeba activity of various azole antifungal agents.Expert opinion: While several biguanide and diamidine antimicrobial agents are available to clinicians to effectively treat Acanthamoeba keratitis, no singular treatment can effectively treat every Acanthamoeba keratitis case.Efforts to identify new anti-Acanthamoeba agents include trophozoite cell viability assays, which are amenable to high-throughput screening. Cysticidal assays remain largely manual and would benefit from further automation development. Additionally, the existing literature on the effectiveness of various azole antifungal agents for treating Acanthamoeba keratitis is incomplete or contradictory, suggesting the need for a systematic review of all azoles against different pathogenic Acanthamoeba strains.

Isolation and identification of potentially pathogenic free-living amoeba in dialysis fluid samples of hydraulic systems in hemodialysis units

BACKGROUND

Free-living amoeba (FLA), including Acanthamoeba, Naegleria, Balamuthia and Vermamoeba, have been isolated from water, sand, soil, dust and air. Numerous studies considered that FLA are a significant cause of neurological and ocular complications in high-risk groups, including immunocompromised individuals. The present study aimed to identify morphological and molecular characteristics of FLA isolates in dialysis fluid samples of hydraulic systems in hemodialysis units in Iran.

METHODS

A total of 328 dialysis fluid samples were collected from 16 dialysis machines, including 164 samples before hemodialysis sessions (after cleaning) and 164 samples after hemodialysis sessions (before cleaning). Filtration and cultivation were performed on non-nutrient agar medium. Also, PCR and sequencing were applied by using the genus-specific primers along with a common primer set on positive samples.

RESULTS

Both morphology and molecular investigations showed that 22.5% (74/328) of dialysis fluid samples were positive for FLA. There was a positive relationship between the high frequency of FLA after hemodialysis sessions (before cleaning) compared with before hemodialysis sessions (after cleaning) (OR=2.86; 95% CI 1.5 to 5.45). Considering the PCR assay, 16.46% (54/328) samples were identified as Acanthamoeba spp. (belonging to T3 and T4 genotypes), 5.18% (17/328) as Vermamoeba vermiformis and 0.91% (3/328) as Vahlkampfiidae family (Naegleria australiensis, Naegleria pagei and Allovahlkampfia).

CONCLUSION

The present results support a need to improve filtration and purification methods for dialysis fluid of hydraulic systems in hemodialysis units. They also highlight the relevance of periodic screenings for FLA-related diseases in hemodialysis patients.

High occurrence of Acanthamoeba spp. in the water samples of public swimming pools from Kerman Province, Iran

Acanthamoeba spp. is a free-living amoeba that can cause major infections in humans, including keratitis and granulomatous encephalitis. Thus, water resources play an important role in transmitting Acanthamoeba spp. infection to humans. The purpose of this study was to investigate the presence of Acanthamoeba spp. in public swimming pools from three cities of Kerman Province, southeastern Iran. Eighty water samples of 20 public indoor swimming pools were taken from Kerman, Jiroft, and Kahnauj cities. Water temperature (°C), pH, and free chlorine concentration (ppm) were measured. Filtration and cultivation were applied on non-nutrient agar medium. The polymerase chain reaction was applied by using the genus-specific primers (JDP1 and JDP2) on positive samples; these primers can amplify the 423-551 bp fragment. Eighteen of the 20 swimming pools (including 32/80; 40% samples) were contaminated with Acanthamoeba spp. All swimming pools of Jiroft and Kahnauj and 88.2% of swimming pools in Kerman were contaminated. As such, all 32 Acanthamoeba isolates were amplified using the JDP primer pairs. Two genotypes, T3 and T4, were also identified. The present research is the first to report Acanthamoeba spp. in public swimming pools from Kerman Province. Due to high occurrence of this protozoan, it is recommended to use warning signs around swimming pools to create awareness of this infection.

First Evidence for Colonizing of Acanthamoeba T4 Genotype in Urinary Tracts of Patients with Recurrent Urinary Tract Infections

BACKGROUND

Limited evidence about the presence of Acanthamoeba spp. in urine specimens collected from urinary catheters of the patients in the intensive care units persuaded our study. No evidence has been found about colonizing of Acanthamoeba spp., in urinary tracts of patients with recurrent urinary tract infections (UTIs) yet.

METHODS

In this study, 50 urine samples were collected from patients presenting with recurrent UTI. The type of bacteria causing UTI was determined by using bacteriological tests. To cultivate Acanthamoeba spp., in a sterile condition, 10 mL of urine was centrifuged and the sediment was cultivated on non-nutrient agar. Genotypes were determined by sequencing the DF3 region of the 18S rRNA gene.

RESULTS

The bacteriological test findings on the urine samples of the UTI patients (n = 30) demonstrated that those were found to be positive for Escherichia coli (n = 17), Staphylococcus aureus (n = 6), Pseudomonas aeruginosa (n = 4) and Klebsiella spp. (n = 3) respectively. Moreover, a total of 50 urine samples was examined; 6 (6/50; 12%) and 11 (11/50; 22%) were positive by using culture and the PCR test for Acanthamoeba spp., respectively. Sequencing analysis showed all isolates were T4 genotype.

CONCLUSIONS

Our data showed that the high relative prevalence of Acanthamoeba T4 genotype spp., in the urine of recurrent UTI patients. As well as, providing the first evidence for colonizing of the Acanthamoeba in the urinary tracts of patients with recurrent UTIs. These findings, warrant further investigation among those patients to fully appraise the role of Acanthamoeba spp., as possible latent carriers for resistant bacteria and biofilm formation in the future.

Evaluation of molecular characterization and phylogeny for quantification of Acanthamoeba and Naegleria fowleri in various water sources, Turkey

Free-living amoeba (FLA) is widely distributed in the natural environment. Since these amoebae are widely found in various waters, they pose an important public health problem. The aim of this study was to detect the presence of Acanthamoeba, B. mandrillaris, and N. fowleri in various water resources by qPCR in Izmir, Turkey. A total of (n = 27) 18.24% Acanthamoeba and (n = 4) 2.7% N. fowleri positives were detected in six different water sources using qPCR with ITS regions (ITS1) specific primers. The resulting concentrations varied in various water samples for Acanthamoeba in the range of 3.2x10⁵-1.4x10² plasmid copies/l and for N. fowleri in the range of 8x10³-11x10² plasmid copies/l. The highest concentration of Acanthamoeba and N. fowleri was found in seawater and damp samples respectively. All 27 Acanthamoeba isolates were identified in genotype level based on the 18S rRNA gene as T4 (51.85%), T5 (22.22%), T2 (14.81%) and T15 (11.11%). The four positive N. fowleri isolate was confirmed by sequencing the ITS1, ITS2 and 5.8S rRNA regions using specific primers. Four N. fowleri isolates were genotyped (three isolate as type 2 and one isolate as type 5) and detected for the first time from water sources in Turkey. Acanthamoeba and N. fowleri genotypes found in many natural environments are straightly related to human populations to have pathogenic potentials that may pose a risk to human health. Public health professionals should raise awareness on this issue, and public awareness education should be provided by the assistance of civil authorities. To the best of our knowledge, this is the first study on the quantitative detection and distribution of Acanthamoeba and N. fowleri genotypes in various water sources in Turkey.

Genotype distribution of Acanthamoeba in keratitis: a systematic review

Acanthamoeba spp. are among the most worldwide prevalent protozoa. It is the causative agent of a disease known as Acanthamoeba keratitis, a painful and severe sight-threatening corneal infection that can lead to blindness. In recent years, the prevalence of Acanthamoeba keratitis has rapidly increased, growing its importance to human health. This systematic review aims to assess the distribution of Acanthamoeba sp. genotypes causing keratitis around the world, considering the sample collected type and the used identification method. Most of the cases were found in Asia and Europe. Not surprisingly, the T4 genotype was the most prevalent worldwide, followed by T3, T15, T11, and T5. Furthermore, the T4 genotype contains a higher number of species. Given the differences in pathology, susceptibility to treatment, and clinical outcome between distinct genotypes, it is essential to genotype isolates from Acanthamoeba keratitis cases to help to establish a better correlation between in vitro and in vivo activities, resulting in better drug therapies and successful treatment in cases of this important ocular infection.

Free-Living Amoebae in Soil Samples from Santiago Island, Cape Verde

Free-Living Amoebae (FLA) are widely distributed protozoa, which contain some groups considered as pathogenic microorganisms. These members are able to produce several opportunistic diseases including epithelial disorders, such as keratitis and fatal encephalitis. Even though they have been reported in numerous sources, such as soils, dust and water, there is no legislation related to the presence of these protozoa in soil-related environments worldwide. Therefore, there are no established prevention or disinfection protocols to advise the population regarding FLA infections or eliminate these microorganisms from human-related environments to date. Acanthamoeba spp. are the most common FLA isolated in soil samples, which is also the most common genera found in clinical cases. Thus, the aim of the present study was to evaluate the presence of potentially pathogenic FLA in human-related soil samples of Santiago Island, Cabo Verde. A total of 26 soil samples were seeded in non-nutrient agar plates (2%), incubated at 26 °C, and monitored daily to evaluate the presence of FLA. DNA was extracted from those plates on which there was suspected FLA growth, and PCR amplification of the 18S rRNA gene was carried out. A total of 17 from the 26 analysed samples were positive for FLA, where Acanthamoeba is the most abundant isolated genus (14/17; 82.4%), with the T4 genotype being the most common (13/14; 92.9%), followed by the T5 genotype, A. lenticulata (1/14; 7.1%). Moreover, Vermamoeba vermiformis, Stenamoeba dejonckheerei and Vannella pentlandi were isolated in three other samples. To the best of our knowledge, this is the first report of FLA presence in Cape Verde and the first report of V. vermiformis in beach sand worldwide.

Detection of free-living amoebae in domestic cats with and without naturally-acquired keratitis

Pathogenic free-living amoebae, most notably Acanthamoeba spp., are important pathogens of the human cornea. The importance of infection with free-living amoebae in cats with keratitis is currently unclear. The aim of this study was to determine the frequency of amoeba detection in corneas of cats with naturally-acquired keratitis and in the ocular surface microflora of cats without ocular disease. Clinical ophthalmic and in vivo corneal confocal microscopic examinations were performed on 60 cats with keratitis. Corneal scrapings were analyzed by amoeba culture; cytological evaluation; and Acanthamoeba, Hartmannella, and Vahlkampfia PCR assays. Following ophthalmic examination, conjunctival specimens collected from 60 cats without clinically apparent ocular disease were analyzed similarly. In one cat with ulcerative keratitis, amoeba cysts and trophozoites were detected by in vivo corneal confocal microscopy; an Acanthamoeba sp. was isolated from corneal specimens and detected by Acanthamoeba PCR assay; and suppurative corneal inflammation was present cytologically. An Acanthamoeba sp. was isolated from conjunctival specimens from one cat without clinically apparent ocular disease, but with suppurative inflammation demonstrated cytologically. Both Acanthamoeba isolates belonged to the T4 genotype. Naegleria-like amoebae were isolated in samples from two cats with keratitis and seven cats without clinical ocular disease, but amoebae were not detected by the other assays in these samples. Amoeba detection by culture was significantly (P = 0.01) associated with cytologically diagnosed corneoconjunctival inflammation. This study identified naturally-acquired Acanthamoeba keratitis in cats. Detection of Naegleria-like amoebae in samples from cats with and without keratitis is of uncertain pathological significance.

PCR-based identification of thermotolerant free-living amoebae in Italian hot springs

Several thermal areas, also used for leisure purposes, may represent suitable habitats for free-living amoebae (FLAs), but few studies have been carried out in search for these organisms. The aim of this study was to assess the presence and distribution of FLAs by culture detection and molecular identification, over a one year-round sampling of two sites in Central Italy. Two geothermal springs (Site A and Site B) were investigated for a total of 36 water samples. Four sets of primers were used to amplify FLA DNA from all cultures positive for amoebic growth at both 37 °C and 45 °C. Overall, 33 (91.6%) water samples produced PCR amplification. Eleven taxa were identified. The array of identified species varied over the sampling period, and differed between the two hot springs, Site A harbouring 11 taxa compared to 5 of site B. However, both sites were characterized by the most common species Vermamoeba vermiformis and Naegleria australiensis. Acanthamoeba genotypes T4 and T15 were found at low frequency. Differences in the composition between the two sites could reflect environmental changes in biotic and chemical/physical parameters. From a public health perspective, the detection of potentially pathogenic amoebae could unveil a potential risk for humans.

On the diversity and clinical importance of Acanthamoeba spp. from Group 1

Group 1 acanthamoebae are morphologically and phylogenetically distinct from all other Acanthamoeba species. They include five species, each labelled by its genotype: A. astronyxis (T7), A. tubiashi (T8), A. comandoni (T9), unnamed Acanthamoeba sp. (T17), and A. byersi (T18). Thought only environmental, they have recently attracted attention due to their recovery in cases of human keratitis and encephalitis, the main diseases caused by Acanthamoeba, where the usual causative agents are mainly species of Groups 2 and 3. Analysis of the available data confirms the pathogenic importance of these species, although it is probably minor compared to that of the species in Groups 2 and 3. In addition, it should be noted that there are difficulties in identifying genotypes by widely used molecular methods, and some misidentifications are revealed.

Opportunistic Premise Plumbing Pathogens. A Potential Health Risk in Water Mist Systems Used as a Cooling Intervention

Water mist systems (WMS) are used for evaporative cooling in public areas. The health risks associated with their colonization by opportunistic premise plumbing pathogens (OPPPs) is not well understood. To advance the understanding of the potential health risk of OPPPs in WMS, biofilm, water and bioaerosol samples (n = 90) from ten (10) WMS in Australia were collected and analyzed by culture and polymerase chain reaction (PCR) methods to detect the occurrence of five representative OPPPs: Legionella pneumophila, Pseudomonas aeruginosa, Mycobacterium avium, Naegleria fowleri and Acanthamoeba. P. aeruginosa (44%, n = 90) occurred more frequently in samples, followed by L. pneumophila serogroup (Sg) 2–14 (18%, n = 90) and L. pneumophila Sg 1 (6%, n = 90). A negative correlation between OPPP occurrence and residual free chlorine was observed except with Acanthamoeba, rs (30) = 0.067, p > 0.05. All detected OPPPs were positively correlated with total dissolved solids (TDS) except with Acanthamoeba. Biofilms contained higher concentrations of L. pneumophila Sg 2–14 (1000–3000 CFU/mL) than water samples (0–100 CFU/mL). This study suggests that WMS can be colonized by OPPPs and are a potential health risk if OPPP contaminated aerosols get released into ambient atmospheres.

Detection of Free-Living Amoebae and Their Intracellular Bacteria in Borehole Water before and after a Ceramic Pot Filter Point-of-Use Intervention in Rural Communities in South Africa

Free-living amoebae (FLA) are ubiquitous in nature, whereas amoeba-resistant bacteria (ARB) have evolved virulent mechanisms that allow them to resist FLA digestion mechanisms and survive inside the amoeba during hostile environmental conditions. This study assessed the prevalence of FLA and ARB species in borehole water before and after a ceramic point-of-use intervention in rural households. A total of 529 water samples were collected over a five-month period from 82 households. All water samples were subjected to amoebal enrichment, bacterial isolation on selective media, and molecular identification using 16S PCR/sequencing to determine ARB species and 18S rRNA PCR/sequencing to determine FLA species present in the water samples before and after the ceramic pot intervention. Several FLA species including Acanthamoeba spp. and Mycobacterium spp. were isolated. The ceramic pot filter removed many of these microorganisms from the borehole water. However, design flaws could have been responsible for some FLA and ARB detected in the filtered water. FLA and their associated ARB are ubiquitous in borehole water, and some of these species might be potentially harmful and a health risk to vulnerable individuals. There is a need to do more investigations into the health risk of these organisms after point-of-use treatment.

Acanthamoeba sclerokeratitis in a cat

CASE DESCRIPTION

A 12-year-old neutered male domestic shorthair cat with chronic anterior uveitis and secondary glaucoma of the right eye was examined for persistent blepharospasm 2 weeks after corneal debridement and grid keratotomy for nonhealing superficial ulcerative keratitis.

CLINICAL FINDINGS

Examination of the right eye revealed a central superficial corneal ulcer associated with corneal epithelial and subepithelial infiltrates and mild aqueous flare. Structures consistent with amoeboid cysts and trophozoites were detected in the cornea by in vivo confocal microscopy. Suppurative keratitis was identified cytologically. An Acanthamoeba spp was isolated through culture and identified by a PCR assay of corneal specimens.

TREATMENT AND OUTCOME

Symptomatic and antiamoebic (polyhexamethylene biguanide 0.02% ophthalmic solution) treatments were instituted. Over the following 6 weeks, the cat lost vision in the affected eye and lesions progressed to nonulcerative stromal keratitis associated with a dense paracentral corneal stroma ring infiltrate and anterior lens luxation. The globe was enucleated, and lymphoplasmacytic sclerokeratitis, anterior uveitis, and retinal detachment were noted. Acanthamoeba organisms were detected within the corneal stroma and anterior sclera with histologic and immunohistochemical stains. The amoebae were classified to the Acanthamoeba T4 genotype by DNA sequencing. The cat had no medical problems attributed to Acanthamoeba infection over 36 months after enucleation, until the cat was lost to follow-up.

CLINICAL RELEVANCE

Naturally acquired Acanthamoeba sclerokeratitis is described in a cat for the first time. Acanthamoeba infection should be considered for cats with superficial corneal disease refractory to appropriate treatments and especially occurring after ocular trauma, including keratotomy.

Detection of potentially pathogenic free-living amoebae from the Caspian Sea and hospital ward dust of teaching hospitals in Guilan, Iran

Free-living amoebae (FLA) thrive in diverse environmental conditions. The present study aimed to define the FLA distribution from the Caspian Sea as well as from hospital ward dust from Guilan, Iran. Seawater (20) and hospital ward dust samples (100) were collected from May to June 2018. Seawater samples were vacuum filtered through a 0.45 μm pore-size membrane. Dust was collected using sterile gauze, washed with sterile distilled water, with washings collected thereafter. Washings were similarly filtered as seawater samples. FLA from the filtered material was cultivated in non-nutrient agar. Molecular analysis was performed by PCR and sequencing using specific primers for Acanthamoeba, Naegleria, and Vermamoeba/Hartmanella. Culture and PCR returned 50 and 65% positivity, respectively, for seawater samples where sequencing revealed Acanthamoeba T2, T5 and T6 genotypes and A. palestinensis and A. lenticulata, as well as N. dobsoni and N. clarki. In addition, 30% amoebic growth and 16% PCR detection were observed from hospital ward dust samples where sequencing revealed Acanthamoeba T2, T4 and T11 genotypes and A. castellanii, A. palestinensis and A. stevensoni as well as N. clarki. For both seawater and dust samples, Acanthamoeba was the dominant isolate. The detection of potentially pathogenic FLA from seawater may pose a threat to the public, while the presence of the same in dust spells threats to both hospital staff and patients, in particular, immunocompromised individuals. Public education, awareness, improved sanitation and hygiene, and the crafting of diagnostic strategies for the early detection of FLA in humans are necessary for the mitigation and management of potential human infection cases.

Diagnosis of Acanthamoeba keratitis in Mashhad, Northeastern Iran: A Gene-Based PCR Assay

Background:

The genus Acanthamoeba is a free-living opportunistic protozoan parasite, which widely distributed in soil and fresh water. Acanthamoeba keratitis, which causes a sight-threating infection of the cornea, is going to rise in Iran and worldwide. The aim of this study was to compare direct microscopy, culture and PCR for detection of Acanthamoeba spp. in clinical samples and to determine the genotypes of Acanthamoeba spp. by sequencing 18SrRNA gene.

Methods:

Among patients clinically suspected to AK referred to a tertiary ophthalmology center at Mashhad, northeastern Iran. During 2017-18, twenty corneal scrapes specimens obtained. The samples were divided into three parts, subjected to direct microscopic examination, culture onto non-nutrient agar and PCR technique. Sensitivity, specificity, accuracy and likelihood ratio were evaluated.

Results:

Among 20 persons clinically suspected to amoebic keratitis, 13(69.2%) patients definitely diagnosed as Acanthamoeba keratitis. Wearing contact lens, eye trauma due to foreign particle and swimming in fresh water were the main predisposing factors. Most of patients suffered from pain and photophobia. Corneal ring infiltration and epithelial defect were common clinical sings. Direct examination had the lowest sensitivity and sensitivity of both Nelson-PCR and JDP-PCR methods were equal and highest. In addition, the results of sequencing identified that all strains belonged to T4 genotype.

Conclusion:

Amoebic keratitis is a sporadic parasitic keratitis, which is mainly seen in contact lens user in Mashhad. PCR based on 18S ribosomal DNA with JDP primers is a reliable and highly sensitive method for diagnosis of Acanthamoeba keratitis in clinically suspected cases.

Distribution of amoebal endosymbiotic environmental chlamydia Neochlamydia S13 via amoebal cytokinesis

We previously isolated a symbiotic environmental amoeba, harboring an environmental chlamydia, Neochlamydia S13. Interestingly, this bacterium failed to survive outside of host cells and was immediately digested inside other amoebae, indicating bacterial distribution via cytokinesis. This may provide a model for understanding organelle development and chlamydial pathogenesis and evolution; therefore, we assessed our hypothesis of Neochlamydia S13 distribution via cytokinesis by comparative analysis with other environmental Chlamydiae (Protochlamydia R18 and Parachlamydia Bn₉ ). Dual staining with 4',6-diamidino-2-phenylindole and phalloidin revealed that the progeny of Neochlamydia S13 and Protochlamydia R18 existed in both daughter cells with a contractile ring on the verge of separation. However, in contrast to other environmental Chlamydiae, little Neochlamydia S13 16S ribosomal DNA was amplified from the culture supernatant. Interestingly, Neochlamydia S13 failed to infect aposymbiotic amoebae, indicating an intimate interaction with the host cells. Furthermore, its infectious rates in cultures expanded from a single amoeba were always maintained at 100%, indicating distribution via cytokinesis. We concluded that unlike other environmental Chlamydiae, Neochlamydia S13 has a unique ability to divide its progeny only via host amoebal cytokinesis. This may be a suitable model to elucidate the mechanism of cell organelle distribution and of chlamydial pathogenesis and evolution.

Microbiological diagnosis of Acanthamoebic keratitis: experience from tertiary care center of North India

Acanthamoeba keratitis (AK) is a painful vision-threatening infection caused by pathogenic free-living Acanthamoeba. Due to the non-specific clinical presentation, this condition tends to be misdiagnosed by clinicians. A timely diagnosis is crucial for favorable visual outcome. Three hundred patients with suspected microbial keratitis presenting to the Advanced Eye Center at our tertiary care center in North India during the period from 2014 to 2018 were included. Patient's corneal scrapings, contact lens, lens solution, lens case, and tears were processed for microscopic examination by Giemsa and Calcofluor staining, non-nutrient agar (NNA) culture and molecular diagnosis by conventional PCR (cPCR) and Real-time PCR (qPCR). 18S rDNA gene sequencing was done to assess phylogenetic relationship. AK was found in 3.6% (11/300) of non-bacterial non-fungal keratitis patients. Among microbiological techniques, microscopy for Acanthamoeba was positive in 7 cases, NNA culture was positive in 9 cases and 11 cases were detected both by cPCR and qPCR. The sensitivity of microscopy, culture, cPCR and qPCR was 63.64%, 81.82 %, 100%, and 100% respectively whereas specificity was 100% for all the tests. 18S rDNA sequencing revealed that A. castellanii was the predominant species and isolates were genetically distinct. AK should be considered in the differential diagnosis of infectious keratitis. Molecular tests are useful for rapid, sensitive and specific diagnosis and must be included in workup of keratitis.

Cluster of Post-Operative Endophthalmitis Caused by Acanthamoeba T10 Genotype - A First Report

PURPOSE

To report a cluster of postoperative Acanthamoeba endophthalmitis after routine cataract surgeries.

METHODS

A brief summary of sentinel events leading to the referral of 4 patients of postoperative endophthalmitis to our hospital is followed by clinical descriptions and the various diagnostic approaches and interventions used. Genotyping and phylogenetic analysis are also discussed.

RESULTS

Four cases of postoperative cluster endophthalmitis, presumed to be bacterial and treated as such, were referred to our hospital. The presence of an atypical ring infiltrate in the first case facilitated the diagnosis of Acanthamoeba endophthalmitis. All patients had vitritis, corneal involvement, and scleral inflammation. Multiple diagnostic methods, such as corneal scrapings, confocal microscopy, aqueous and vitreous taps, scleral abscess drainage, histopathological studies, polymerase chain reaction, and genotyping and phylogenetic analyses of isolated Acanthamoeba, were used to confirm the diagnosis of endophthalmitis and to establish the extent of ocular involvement. Various medical and therapeutic interventions used to control the infections were also documented. The isolated Acanthamoeba were confirmed as belonging to the T10 genotype, an environmentally and clinically rare variety.

CONCLUSIONS

This is the first report of a cluster of postoperative T10 genotype Acanthamoeba endophthalmitis, occurring after routine cataract surgery in immunocompetent individuals. Contrary to current perceptions, a rapidly evolving infection can occur with Acanthamoeba.

Evaluation of Acanthamoeba keratitis cases in a tertiary medical care centre over 21 years

To report on Acanthamoeba keratitis cases in a tertiary university eye-hospital in Graz, Austria, over a 21-year period. Retrospective study. Parameters included demographics, diagnostics, clinical courses, medical therapies, surgical interventions, secondary complications, and best spectacle-corrected visual acuity (BSCVA). Patient records for 44 eyes of 42 patients were analysed; 2 bilateral infections. Mean age at presentation was 31 ± 13 (16-65) years; contact lenses were used in 41 of 44 eyes (93.2%). Symptoms at initial presentation were mainly pain (41/43, 95.3%) and photophobia (16/43, 37.2%). Most frequent morphological findings were stromal infiltrates (30/44, 68.2%). Diagnosis was mainly confirmed by smears (40/42, 95.2%) and polymerase chain reaction (8/42, 19%). Antiamoebic treatment comprised biguanides and diamidines. Penetrating keratoplasty was performed in 10/44 (22.7%) eyes. Median time from symptom onset to initial visit was 2 (0-26) weeks; median follow-up was 30 (2-1008) weeks. BSCVA improved in 23/36 (63.9%) eyes, remained unchanged in 6/36 (16.7%) eyes and deteriorated in 7/36 (19.4%) eyes. Acanthamoeba keratitis predominantly occurs in young contact lens wearers. Diagnosis should be considered in patients with pain and stromal infiltrates. In the majority of cases, BSCVA can be improved. Early diagnosis and adequate treatment should be implemented to prevent complications.

Isolation and identification of free-living amoebae isolated from well water in Istanbul

Free-living amoebae (FLA) are ubiquitous protozoa commonly found in water and soil environments. FLA belonging to various genera, including Acanthamoeba, Balamuthia, Naegleria, and Vermamoeba, can cause opportunistic and non-opportunistic infections in humans and animals such as keratitis or meningoencephalitis. In addition, some of them serve as hosts for a large number of pathogenic bacteria, yeasts, and viruses. The purpose of the present study was to assess the prevalence and molecular characterization of FLA in well water samples in İstanbul. Ten well water samples were collected from the taps and the presence of FLA was monitored both by the culture and polymerase chain reaction methods. FLA were isolated in 8 out of the 10 samples (80%) included in this study. Morphological analysis and partial sequencing of the 18S rDNA revealed the presence of Acanthamoeba genotypes T3 and T4, and Vermamoeba vermiformis in the investigated well water samples. This study reports for the first time the detection of Acanthamoeba genotype T3 in well water samples in İstanbul. The presence of potentially pathogenic amoebae in habitats related to human activities supports the relevance of FLA as a potential public health concern.

PCR and culture for diagnosis of Acanthamoeba keratitis

Background/Aims

Acanthamoeba keratitis (AK) is a rare but sight-threatening infection. Molecular diagnosis of corneal scraping has improved the diagnosis of AK. Different molecular targets and conditions have been used in diagnosis thus far. In this study, we prospectively compared the performance of five PCR assays on corneal samples for the diagnosis of AK.

Methods

1217 corneal scraping samples were obtained from patients, for whom an AK was suspected. Sample processing involved both molecular diagnostics and culture. Acanthamoeba PCR assays detected different regions of the Acanthamoeba nuclear small-subunit rRNA gene: three final point PCR assays using Nelson, ACARNA and JDP1–JDP2 pairs of primers, and two real-time PCR assays using Acant primer-probe. Human DNA and internal control were co-amplified in the real-time PCR assay to ensure scraping quality and the absence of inhibitors. In the absence of a gold standard, the performance of each test was evaluated using latent class analysis. Genotypes of Acanthamoeba isolates were also characterised.

Results

Estimated prevalence of AK was 1.32%. The sensitivity of Acanthamoeba diagnostic PCRs (73.3% to 86.7%) did not differ significantly from that of culture (66.7%), or according to the target sequence or the technology. Sensitivity could be increased to 93.8% or 100% by combining two or three assays, respectively. PCR specificity (99.3% to 100%) differed between the assays. T4 was the predominant Acanthamoeba genotype (84.6%).

Conclusions

Culture and a single PCR assay could lead to misdiagnosing AK. A combination of different PCR assays and improved sample quality could increase diagnosis sensitivity.

Molecular detection of Acanthamoeba spp. in Seven Crater Lakes of Laguna, Philippines

Acanthamoeba spp. are ubiquitous free-living amoeba with genotypes that cause severe pathology of the eyes, central nervous systems, and rare reports of cutaneous infections. The Seven Crater Lakes are freshwater water resources in Laguna, Philippines primarily used for aquaculture and tourism. A total of 16 surface water samples were collected from different sampling areas per Crater Lake and placed in sterile plastic containers. Samples were filtered using 1.2 μm pore size, glass microfiber filter. Filtered sediments were placed on non-nutrient agar lawned with Escherichia coli and incubated aerobically at 35 °C for 14 days. Six out of 16 water samples exhibited amoebic growth. Cystic stages revealed circular to stellate morphology under light microscopy which were initially classified as Acanthamoeba spp. DNA from positive isolates were made to react with polymerase chain reaction using Acanthamoeba specific primers JDP1 5′-GGCCCAGATCGTTTACCGTGAA-3′ and JDP2 5′-TCTCACAAGCTGCTAGGGAGTCA-3′confirmed the presence of several Acanthamoeba species. Phylogenetic analysis revealed the presence of seven isolates belonging to Acanthamoeba genotypes T4, T5, and T9. The presence of potentially pathogenic Acanthamoeba genotypes in the Seven Crater Lakes of Laguna signifies risk to human health which necessitates the development of programs, policies, and guidelines on the understanding, prevention, and management of potential human infections.

Isolation and Identification of Pathogenic Acanthamoeba Species from Air Conditioning Systems, Egypt

Acanthamoeba are free-living amoebae that cause granulomatous amoebic encephalitis and keratitis. In this study, we aimed to isolate and identify Acanthamoeba from air conditioning systems using in vitro cell culture and polymerase chain reaction assays. We also estimated the pathogenicity of the isolates by measuring their thermotolerance and studying mice models inoculated with these isolates. Of the 80 dust samples acquired, 41 (51.25%) were found to be positive for Acanthamoeba spp. using in vitro cell culture and the results were validated using PCR. Out of these 41 samples, 27 (65.9%) were thermotolerant and 16 (39%) samples could infect mice and cause histopathological effects. Highly pathogenic Acanthamoeba isolates were characterized by their thermotolerance and the ability to disseminate in all organs after infection, causing early death of infected animals. Our study thus validated the presence of pathogenic isolates of Acanthamoeba in air conditioners that may be potentially infectious to humans.

Adaption of microbial communities to the hostile environment in the Doce River after the collapse of two iron ore tailing dams

In November 2015, two iron ore tailing dams collapsed in the city of Mariana, Brazil. The dams' collapse generated a wave of approximately 50 million m³ of a mixture of mining waste and water. It was a major environmental tragedy in Brazilian history, which damaged rivers, and cities 660 km away in the Doce River basin until it reached the ocean coast. Shortly after the incident, several reports informed that the concentration of metals in the water was above acceptable legal limits under Brazilian laws. Here the microbial communities in samples of water, mud, foam, and rhizosphere of Eichhornia from Doce River were analyzed for 16S and 18S rRNA-based amplicon sequencing, along with microbial isolation, chemical and mineralogical analyses. Samples were collected one month and thirteen months after the collapse. Prokaryotic communities from mud shifted drastically over time (33% Bray-Curtis similarity), while water samples were more similar (63% Bray-Curtis similarity) in the same period. After 12 months, mud samples remained with high levels of heavy metals and a reduction in the diversity of microeukaryotes was detected. Amoebozoans increased in mud samples, reaching 49% of microeukaryote abundance, with Discosea and Lobosa groups being the most abundant. The microbial communities’ structure in mud samples changed adapting to the new environment condition. The characterization of microbial communities and metal-tolerant organisms from such impacted environments is essential for understanding the ecological consequences of massive anthropogenic impacts and strategies for the restoration of contaminated sites such as the Doce River.

Species, Sequence Types and Alleles: Dissecting Genetic Variation in Acanthamoeba

Species designations within Acanthamoeba are problematic because of pleomorphic morphology. Molecular approaches, including DNA sequencing, hinted at a resolution that has yet to be fully achieved. Alternative approaches were required. In 1996, the Byers/Fuerst lab introduced the concept of sequence types. Differences between isolates of Acanthamoeba could be quantitatively assessed by comparing sequences of the nuclear 18S rRNA gene, ultimately producing 22 sequence types, designated T1 through T22. The concept of sequence types helps our understanding of Acanthamoeba evolution. Nevertheless, substantial variation in the 18S rRNA gene differentiates many isolates within each sequence type. Because the majority of isolates with sequences in the international DNA databases have been studied for only a small segment of the gene, designated ASA.S1, genetic variation within this hypervariable region of the 18S rRNA gene has been scrutinized. In 2002, we first categorized variation in this region in a sample of T3 and T4 isolates from Hong Kong, observing ten “alleles” within type T4 and five “alleles” within T3. Subsequently, confusion occurred when different labs applied redundant numerical labels to identify different alleles. A more unified approach was required. We have tabulated alleles occurring in the sequences submitted to the international DNA databases, and determined their frequencies. Over 150 alleles have occurred more than once within 3500+ isolates of sequence type T4. Results from smaller samples of other sequence types (T3, T5, T11 and T15, and supergroup T2/6) have also been obtained. Our results provide new insights into the evolutionary history of Acanthamoeba, further illuminating the degree of genetic separation between significant taxonomic units within the genus, perhaps eventually elucidating what constitutes a species of Acanthamoeba.

Presence and interaction of free-living amoebae and amoeba-resisting bacteria in water from drinking water treatment plants

Free-living amoebae (FLA) are ubiquitous and many isolates have been shown to be infected with amoeba-resisting bacteria, as the example of Acanthamoeba and Legionella interaction. Due to the high environmental prevalence of Acanthamoeba. in the Castilian Plateau (Spain), the aims of this work were to investigate the occurrence of Acanthamoeba and other FLA in water from several sampling points from four Drinking Water Treatment Plants (DWTP) and to investigate the presence of Legionella spp. and other amoeba-resisting bacteria in biofilms in raw and finished water, taking into account that no legislation exists for this protozoa control. Acanthamoeba was detected at different sampling points, and sand filters seemed to contribute to amoebic enrichment. After ozonation, a temporary decrease in viable amoebae was observed. The genotypes detected were T3, T4, and T5, revealing the first report of genotype T5 in waters from this region. Moreover, Balamuthia mandrillaris, Vermamoeba vermiformis and Paravahlkampfia sp. were detected. Regarding Legionella, PCR detection in raw and finished water was higher than by agar culture, but even higher after Acanthamoeba co-culture. Also, Legionella's presence was higher in raw water than in finished water. The decrease of free Legionella observed from raw (27.5%, by PCR) to finished water (3.4% by PCR) contrasted with the increase of Legionella-infected FLA from raw (30.7%) to finished water (52%). At biofilm, free Legionella was not detected, and the percentage of infected FLA was low (3.8%). Legionella species identified in these samples were L. drozanskii, L. donaldsonii and L. feeleii. Additionally, Acanthamoeba co-culture led to the isolation of Pseudomonas aeruginosa, P. stutzeri, P. fluorecens, Achromobacter xylosoxidans and Stenotrophomonas maltophilia. The highly disseminated presence of Acanthamoeba and the detection of amoeba-resisting bacteria inside amoebae highlight the importance of developing methods for controlling FLA in order to limit human pathogenic amoeba-resisting bacteria survival to the water purification processes.

18S rDNA sequencing aided diagnosis of Acanthamoeba jacobsi keratitis -A case report

Identification of Acanthamoeba cysts and trophozoites in cases of keratitis is traditionally done with microbiological techniques such as smear examination with 10% potassium hydroxide (KOH) and culture. Double walled cyst with hexagonal inner wall is characteristic of Acanthamoeba. We report a unique case of a 9 year old boy who presented with dense anterior corneal stromal infltration, which on smear examination showed atypical double walled spherical cysts, leading to a diagnostic dilemma. An 18S rRNA gene-based PCR done on the growth on culture, subsequently identifed a rarely reported species of Acanthamoeba. The patient was advised combination therapy with polyhexamethylene biguanide (PHMB 0.02%) and chlorhexidine (0.02%) eye drops. Three weeks post treatment, the keratitis resolved with scarring and vascularisation and visual acuity improved to 20/60. At 8 weeks follow up Best corrected visual acuity further improved to 20/30 with contact lens.

Identification of free-living amoebas and amoeba-resistant bacteria accumulated in Dreissena polymorpha

To identify the free-living amoeba (FLA) and amoeba-resistant bacteria (ARB) accumulated in zebra mussels and in the water in which they are found, mussels were collected at two locations in the Ebro river basin (North East Spain). FLAs and bacteria were isolated from mussel extracts and from natural water. PCR techniques were used to identify the FLAs and endosymbiont bacteria (Legionella, Mycobacterium, Pseudomonas and cyanobacteria), and to detect Giardia and Cryptosporidium. The most frequently found FLAs were Naegleria spp. The presence of Legionella, Mycobacterium and Pseudomonas inside the FLA was demonstrated, and in some cases both Legionella and Pseudomonas were found together. Differences between FLAs and ARB identified inside the mussels and in the water were detected. In addition, Escherichia coli, Clostridium perfringens, Salmonella spp. and Enterococcus spp. were accumulated in mussels in concentrations unconnected with those found in water. The results show the ability of the zebra mussel to act as a reservoir of potentially pathogenic FLAs, which are associated with potentially pathogenic ARB, although the lack of association between microorganisms inside the mussels and in the water suggests that they are not useful for monitoring microbiological contamination at a specific time.

Parasitic keratitis - An under-reported entity

Parasitic keratitis (PK) is unique entity among parasitic infections where corneal involvement could result from direct inoculation of the parasite via exogenous environment or spread via endogenous neighboring organs or as a result of immune-mediated damage secondary to a systemic parasitic infection. Most cases of PK are caused by Acanthamoeba spp. and Microsporidia spp. though few other parasitic agents can also lead to corneal involvement. Mimicking as other infectious and non-infectious causes of keratitis, PK often escapes detection. This review summarizes the predominant causes of PK along with the epidemiological, clinical and microbiological details of each. Though several gaps exist in our understanding of the prevalence of PK, the one thing for sure is that PK is on the rise. With advanced diagnostic modalities and enough literature on optimal management of cases of PK, it is now imperative that a strong clinical suspicion of PK is kept when examining a case of corneal pathology and adequate investigations are ordered.

Persistent Legionnaires' Disease and Associated Antibiotic Treatment Engender a Highly Disturbed Pulmonary Microbiome Enriched in Opportunistic Microorganisms

Despite the importance of pneumonia to public health, little is known about the composition of the lung microbiome during infectious diseases, such as pneumonia, and how it evolves during antibiotic therapy. To study the possible relation of the pulmonary microbiome to the severity and outcome of this respiratory disease, we analyzed the dynamics of the pathogen and the human lung microbiome during persistent infections caused by the bacterium Legionella pneumophila and their evolution during antimicrobial treatment. We collected 10 bronchoalveolar lavage fluid samples from three patients during long-term hospitalization due to pneumonia and performed a unique longitudinal study of the interkingdom microbiome, analyzing the samples for presence of bacteria, archaea, fungi, and protozoa by high-throughput Illumina sequencing of marker genes. The lung microbiome of the patients was characterized by a strong predominance of the pathogen, a low diversity of the bacterial fraction, and an increased presence of opportunistic microorganisms. The fungal fraction was more stable than the bacterial fraction. During long-term treatment, no genomic changes or antibiotic resistance-associated mutations that could explain the persistent infection occurred, according to whole-genome sequencing analyses of the pathogen. After antibiotic treatment, the microbiome did not recover rapidly but was mainly constituted of antibiotic-resistant species and enriched in bacteria, archaea, fungi, or protozoa associated with pathogenicity. The lung microbiome seems to contribute to nonresolving Legionella pneumonia, as it is strongly disturbed during infection and enriched in opportunistic and/or antibiotic-resistant bacteria and microorganisms, including fungi, archaea, and protozoa that are often associated with infections.IMPORTANCE The composition and dynamics of the lung microbiome during pneumonia are not known, although the lung microbiome might influence the severity and outcome of this infectious disease, similar to what was shown for the microbiome at other body sites. Here we report the findings of a comprehensive analysis of the lung microbiome composition of three patients with long-term pneumonia due to L. pneumophila and its evolution during antibiotic treatment. This work adds to our understanding of how the microbiome changes during disease and antibiotic treatment and points to microorganisms and their interactions that might be beneficial. In addition to bacteria and fungi, our analyses included archaea and eukaryotes (protozoa), showing that both are present in the pulmonary microbiota and that they might also play a role in the response to the microbiome disturbance.

Isolation and identification of free-living amoeba from the hot springs and beaches of the Caspian Sea

Free-living amoeba (FLA) such as Acanthamoeba, Naegleria, Balamuthia, and Vermamoeba have been identified from both natural and human-made environments such as Hot springs and spa. Naegleria fowleri causes Primary Amoebic Meningoencephalitis (PAM), while Acanthamoeba and Balamuthia cause chronic granulomatous encephalitis. Acanthamoeba also can cause cutaneous lesions and Amoebic Keratitis (AK) that is associated with contact lens use or corneal trauma. FLA are known to serve as host of and vehicles for diverse intracellular organisms. This study aimed was to identify the presence of FLA in the hot springs and beaches of the Caspian Sea in Ramsar tourist town located in the northern part of Iran. Water samples were collected in sterile bottles and were transferred to the laboratory. One litre of each sample passed through the nitrocellulose membrane filter. Each filter insert was then placed in non-nutrient agar plates already seeded with lawn culture of Escherichia coli. Positive samples were analyzed by morphological keys and Polymerase chain reaction (PCR) using 18S rDNA gene and ITS region to identify amoeba isolates. A total of 81 water sampled were tasted. After identified using the morphological key and PCR assay, 54 (66.6%) of the samples were positive for FLA. Ten of the samples were identified as Acanthamoeba (belong to T3, T4, and T5 genotypes), three as Vermamoeba vermiformis, four as Naegleria (3 N.australiensis and 1 N.grubery). Only one sample was positive Vahlkampfia. The presence of thermotolerant FLA in the Hot springs and beaches of the Caspian Sea as places for recreational purposes or wellness may be a potential health risk.

Acanthamoeba spp. in river water samples from the Black Sea region, Turkey

The present study aims to investigate the occurrence of free living amoeba (FLA) in water resources (rivers and tap water) in Samsun in the Black Sea. The presence of Acanthamoeba spp. was confirmed in 98 of 192 water samples collected from 32 sites of Samsun province (Samsun centre, Terme, Carsamba, Tekkekoy, Bafra) by PCR. Acanthamoeba spp. were found in 15/36 river samples from Samsun, in 58/90 from Terme, in 12/30 from Carsamba, in 7/18 from Tekkekoy and in 6/18 from Bafra. No Acanthamoeba species were detected in tap water samples. The highest rate in river waters contaminated with Acanthamoeba species was in Terme followed by Samsun centre (41.7%), Carsamba (40%), Tekkekoy (38.9%) and Bafra districts (33.3%), respectively. The result of the subsequent sequence analysis showed Haplotype I (A. triangularis) in 5%, Haplotype II (A. polyphaga) in 29.6%, Haplotype III (Acanthamoeba spp.) in 62% and Haplotype IV (A. lenticulata) in 3%. The most common genotype was Acanthamoeba T4 (Acanthamoeba spp., A. polyphaga, A. triangularis) and T5 genotype was also found in 3%. The T4 genotype is the most common genotype associated with Acanthamoeba keratitis (AK) worldwide; therefore, humans and animals living in the area are at risk after contact with such waters.

Free-living amoebae and their relationship to air quality in hospital environments: characterization of Acanthamoeba spp. obtained from air-conditioning systems

Free-living amoebae (FLA) are widely dispersed in the environment, can cause opportunistic and non-opportunistic infections in humans and other animals. The aim of the present study was characterize FLA obtained from air-conditioners of a public hospital in the city of Florianópolis, SC, Brazil. Fifty-four dust samples were collected of air conditioners, and were inoculated on 1.5% non-nutrient agar, overlaid with layers of Escherichia coli. Subsequently the isolates were axenised in PYG growth medium. The morphological and molecular characterization of the isolates was performed, as well as the tolerance (physiological) assays were used to evaluate the pathogenic potential. The results revealed the presence of FLA in 42 (77.8%) of the collected samples. Of these, 39 (92.9%) axenic isolates of FLA were obtained for morphological and genotypic studies. All the isolates characterized belong to the genus Acanthamoeba. Nineteen (48.7%) isolates belong to the genotype T4, 16 (41.0%) to the T5 genotype and 4 (10.3%) to genotype T11. Seven (18.0%) isolates were considered potentially pathogenic in tolerance assays. These findings require attention, considering the isolation environment and immunocompromised characteristics of many hospitalized patients.

Genotyping by Sequencing of Acanthamoeba and Naegleria Isolates from the Thermal Pool Distributed Throughout Turkey

PURPOSE

The main goal of this study was genotyping of free-living parasites and sub-grouping of pathogenic or non-pathogenic amebae obtained from Turkey's thermal springs. In so doing, distribution and abundance of possible pathogenic or causative strain for humans, which are caused by Acanthamoeba and Naegleria strains, would be elaborated. The number of extensive studies on the general occurrence and distribution of parasitic strains is very high worldwide, but there has been a paucity of information with regard to Turkey.

METHODS

From a total of 434 obtained thermal pool samples, free-living amebas were isolated from 148 water samples using the non-nutrient agar (NNA) culture method. Subsequently, the cultivated samples were used for DNA isolation; then 102 obtained DNA samples were subjected to PCR amplification using various primers for samples of genera Acanthamoeba and Naegleria. Ultimately, estimation of genotype or subtype was evaluated by sequencing.

RESULTS

About 29 samples that belong to Acanthamoeba and Naegleria were estimated from a total of 102 amplified PCR samples. These eukaryotic PCR products which have Acanthamoeba genus appearance, generated 26 subtypes and 3 Naegleria samples. Among the 26 Acanthamoeba genotypes, 22 aligned sequences were matched with various GenBank reference samples, while the 4 divergent genotypes were not elaborated and marked as ND. Most of the Acanthamoeba genera were determined as likely dominating groups and clustered as T form within totally eight groups. Eight, seven and three subtypes were found as T4A, T15 and T11 genotypes, respectively while the remainings were ultimately found in four groups. Results confirming the predominance of T4A, which is known the most causative form, the presence in the pools. Despite being uncommon, N. fowleri, lovaniensis and australiensis were also observed among the surveyed pools.

CONCLUSION

The present study is descriptive and is not unique. However, this is the most comprehensive study of the molecular distribution sampling of thermophilic Acanthamoeba and Naegleria that confirmed and demonstrated their ubiquitous presence throughout Turkey. By this estimation, in some spas, the most and likely causative form Acanthamoeba including T4 and Naegleria fowleri has also been confirmed.