Communities of culturable yeasts and yeast-like fungi in oligotrophic hypersaline coastal waters of the Arabian Gulf surrounding Qatar.

This report is the first investigation of yeast biodiversity from the oligotrophic hypersaline coastal waters of the Arabian Gulf surrounding Qatar. Yeasts and yeast-like fungi, were cultured from seawater sampled at 13 coastal areas surrounding Qatar over a period of 2 years (December 2013-September 2015). Eight hundred and forty-two isolates belonging to 82 species representing two phyla viz., Ascomycota (23 genera) and Basidiomycota (16 genera) were identified by molecular sequencing. The results indicated that the coastal waters of the Qatari oligotrophic marine environment harbor a diverse pool of yeast species, most of which have been reported from terrestrial, clinical and aquatic sources in various parts of the world. Five species, i.e., Candida albicans, C. parapsilosis, C. tropicalis, Pichia kudriavzevii and Meyerozyma guilliermondii (n = 252/842; 30% isolates) are known as major opportunistic human pathogens. Fifteen species belonging to nine genera (n = 498/842; 59%) and 12 species belonging to seven genera (n = 459/842; 55%) are hydrocarbon degrading yeast and pollution indicator yeast species, respectively. Ascomycetous yeasts were predominant (66.38%; 559/842) as compared to their basidiomycetous counterparts (33.6%; 283/842). The most isolated yeast genera were Candida (28%; 236/842) (e.g., C. aaseri, C. boidinii, C. glabrata, C. intermedia, C. oleophila, C. orthopsilosis, C. palmioleophila, C. parapsilosis, C. pseudointermedia, C. rugopelliculosa, C. sake, C. tropicalis and C. zeylanoides), Rhodotorula (12.7%; 107/842), Naganishia (8.4%; 71/842), Aureobasidium (7.4%; 62/842), Pichia (7.3%; 62/842), and Debaryomyces (6.4%; 54/842). A total of eleven yeast species ( n = 38) isolated in this study are reported for the first time from the marine environment. Chemical testing demonstrated that seven out of the 13 sites had levels of total petroleum hydrocarbons (TPH) ranging from 200 to 900 µg/L, whereas 6 sites showed higher TPH levels (> 1000-21000 µg/L). The results suggest that the yeast community structure and density are impacted by various physico-chemical factors, namely total organic carbon, dissolved organic carbon and sulphur.

Reclassification of Facklamia ignava, Facklamia sourekii and Facklamia tabacinasalis as Falseniella ignava gen. nov., comb. nov., Hutsoniella sourekii gen. nov., comb. nov., and Ruoffia tabacinasalis gen. nov., comb. nov., and description of Ruoffia halotolerans sp. nov., isolated from hypersaline Inland Sea of Qatar.

A Gram-stain-positive, non-pigmented, coccus-shaped, facultatively anaerobic and α-hemolytic bacterium designated as INB8T was isolated from a hypersaline marine water sample collected at the Inland Sea of Qatar. The isolate was able to grow at 25-40 °C (optimum, 30 °C), at pH 5-11 and with 2-8% NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain INB8T was placed within the family Aerococcaceae with the highest sequence similarity to Facklamia tabacinasalis CCUG 30090T (99.5%), followed by Facklamia hominis CCUG 36813T (93.9%), Facklamia sourekii Y17312T (93.8%), Facklamia ignava CCUG 37419T (93.6%), Facklamia miroungae CCUG 42728T (93.5%), Suicoccus acidiformans ZY16052T (93.5%), Facklamia languida CCUG 37842T (93.2%), Ignavigranum ruoffiae (93.1%), and Dolosicoccus paucivorans DSM 15742T (90.8%). Average nucleotide identity and digital DNA-DNA hybridization values between strain INB8T and F. tabacinasalis CCUG 30090T were determined to be 94.5% and 58.9% respectively, confirming strain INB8T represents a novel species. The major fatty acids were C14:0, C16:0, C18:0 and C18:1 ω9c. The G + C content of strain INB8T determined from the genome was 36.3 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic information, it is proposed that Facklamia tabacinasalis should be reclassified as Ruoffia tabacinasalis, Facklamia ignava be reclassified as Falseniella ignava, and Facklamia sourekii be reclassified Hutsoniella sourekii. It is further proposed that strain INB8T should be classified as a species of the genus Ruoffia for which the name Ruoffia halotolerans sp. nov. is proposed. The type strain is INB8T (= LMG 30291T = CCUG 70701T = QCC/B60/17T).

Ningiella ruwaisensis gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from marine water of the Arabian Gulf.

Strain B66T was isolated from a marine water sample collected at Al Ruwais, located on the northern tip of Qatar. Cells were Gram-stain-negative, strictly aerobic and short- rod-shaped with a polar flagellum. The isolate was able to grow at 15-45 °C (optimum, 30 °C), at pH 5-11 (optimum, pH 6.5-8) and with 0-6 % NaCl. 16S rRNA gene sequence analysis revealed that strain B66T was affiliated with the family Alteromonadaceae, sharing the highest sequence similarities to the genera Alteromonas (93.7-95.4 %), Aestuariibacter (94.0-95.1 %), Agaribacter (93.3-93.7 %), Glaciecola (92.0-93.7 %), Marisendiminitalea (93.2-93.3 %) and Planctobacterium (92.9 %). In the phylogenetic trees, strain B66T demonstrated the novel organism formed a distinct lineage closely associated with Aestuariibacter and Planctobacterium. Major fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c/iso-C15 : 0 2-OH and iso-C15 : 0 3-OH. The major respiratory quinone was ubiquinone-8 and the major polar lipids are phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content derived from the genome was 43.2 mol%. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic data, strain B66T is considered to represent a novel species and genus for which the name Ningiella ruwaisensis gen. nov., sp. nov., is proposed. The type strain is B66T (=QCC B003/17T=LMG 30288 T=CCUG 70703T).

Cystobasidium halotolerans sp. nov., a novel basidiomycetous yeast species isolated from the Arabian Gulf.

Two strains, 1Y129 and 3Y383, which represent a single novel anamorphic yeast species, were isolated from the Arabian Gulf surrounding Qatar. The two strains have identical sequences in the D1/D2 domains of the large subunit (LSU) and the internal transcribed spacer (ITS) regions of the rRNA gene. On the basis of this sequence analysis the two strains were found to be closely related to Cystobasidium slooffiae CBS5706T with 97. 3 % nucleotide substitutions (12 nt; four gaps) in D1/D2 regions of the LSU rRNA and 97.0 % nucleotide substitutions (14 nt; two gaps) in ITS regions. In contrast to Cystobasidium halotolerans sp. nov., the related species Cystobasidium slooffiae, Cystobasidium minutum and Cystobasidium fimetarium were unable to assimilate d-galactose, soluble starch, galactitol, methanol or nitrate, and grew at 37 °C. The name proposed for this undescribed species is Cystobasidium halotolerans sp. nov. The ex-type strain is QCC/Y31/17 (=MUCL057192=CGMCC2.5570).

Kondoa qatarensis f.a., sp. nov., a novel yeast species isolated from marine water in Qatar.

During a study of yeast diversity in marine waters of the Arabian Gulf surrounding Qatar, 30 strains were isolated that represent a novel species of Kondoa. The isolates were obtained from five locations along the Qatari coast. Species identifications were based on sequence analysis of the internal transcribed spacer (ITS) regions and D1/D2 domains of the large subunit (LSU) rRNA gene. Five strains were selected for further study. The novel species was closely related to Kondoa aeria (CBS 8352T) and Kondoa malvinella (CBS 6082T) but differed from the two species by 5.6 % sequence divergence (16 substitutions and 14 gaps) in the ITS region. On the basis of D1/D2 domains of the LSU rRNA gene, the novel species differed from K. aeria by only >0.35 % sequence divergence (2 substitutions and 0 gaps) and 1.5 % sequence divergence (9 substitutions and 1 gap) to that of K. malvinella. Although the novel species showed a close similarity in the D1/D2 domains to K. aeria (CBS 8352T), based on the significant differences (16 substitutions) in ITS regions and on the basis of physiological and biochemical tests, viz ability to grow at 35 °C, and inability to assimilate, sucrose, raffinose, d,l-lactate, succinate, citrate and nitrite, these strains are considered as novel species of Kondoa. The species name of Kondoa qatarensis f.a., sp. nov. is proposed with specimen 2Y109 as the holotype.

Toxicocladosporium aquimarinum sp. nov. and Toxicocladosporium qatarense sp. nov., isolated from marine waters of the Arabian Gulf surrounding Qatar.

The Arabian Gulf surrounding Qatar is distinct from other marine ecosystems due to its high salinity (35-75 PSU) and extreme water temperature fluctuations (11-40 °C). Furthermore, in the last decade, Qatar has been witnessing an industrial boom as well as extensive infrastructure construction activities. Marine micro-organisms, including fungi, remain largely unexplored in the Arabian Gulf. During a 3 year study, we investigated the diversity of marine fungi in coastal waters around Qatar. As a result, two new Toxicocladosporium species were isolated from the Qatari marine environment. Molecular and phylogenetic analyses of rRNA gene sequences of five loci, namely the internal transcribed spacer 1 and 2 regions and the D1/D2 domains of the large subunit rRNA, actin, RNA polymerase second largest subunit and beta-tubulin genes, were used to confirm the identity of the novel species for which we propose the names Toxicocladosporium aquimarinum sp. nov. and Toxicocladosporium qatarense sp. nov.

Naganishia qatarensis sp. nov., a novel basidiomycetous yeast species from a hypersaline marine environment in Qatar.

Two yeast strains (INY29 and INY13) representing a novel yeast species were isolated from the hypersaline marine environment of the Inland Sea, Qatar. Phylogenetic analysis based on the D1/D2 domains of the large subunit (LSU) regions and internal transcribed spacer (ITS1 and ITS2) regions showed that the two strains represent a single species in the genus Naganishia that is distinct from other species. These two strains were classified as members of the genus Naganishia and clustered in a strongly supported clade represented by Naganishia albidus in the Filobasidiales order in the phylogenetic tree drawn from ITS and D1/D2 sequences. The novel species was most closely related to the type strain of Naganishia cerealis but the two species differed by 1 % sequence divergence (four substitutions and one gap) in the D1/D2 domains and (five substitutions and one gap) in the ITS regions. In contrast to the closest relative, N. cerealis, the novel yeast species assimilated melibiose, glycerol, meso-erythritol, dl-lactate, methanol, propane 1-2-diol, butane 2-3-diol, and grew at 35 °C. The name Naganishia qatarensis sp. nov. is proposed to accommodate these strains, with INY29 as the holotype.

Description of the Halophile Euplotes qatarensis nov. spec. (Ciliophora, Spirotrichea, Euplotida) Isolated from the Hypersaline Khor Al-Adaid Lagoon in Qatar.

The morphology, ontogenesis, and phylogenetic relationships of a halophile euplotid ciliates, Euplotes qatarensis nov. spec., isolated from the Khor Al-Adaid Lagoon in Qatar were investigated based on live observation as well as protargol- and silver nitrate-impregnated methods. The new species is characterised by a combination of features: the halophile habitat, a cell size of 50-65 × 33-40 µm, seven dorsal ridges, 10 commonly sized frontoventral cirri, two widely spaced marginal cirri, 10 dorsolateral kineties, and a double silverline pattern. The morphogenesis is similar to that of its congeners: (i) the oral primordium develops hypoapokinetally and the parental oral apparatus is retained; (ii) the frontoventral-transverse field of five streaks gives rise to the frontal, ventral, and transverse cirri, but not to the cirri I/1 and the marginal cirri; (iii) the dorsal somatic ciliature develops by intrakinetal proliferation of basal bodies in two anlagen per kinety that are just anterior and posterior to the future division furrow; (iv) the caudal cirri are formed by the two rightmost dorsolateral kineties. The SSU rDNA sequence of E. qatarensis branches with full support in the Euplotopsis elegans-Euplotes nobilii-Euplotopsis raikovi clade. The closest related publicly available SSU rDNA sequence is the one of E. nobilii, with which E. qatarensis has 93.4% sequence similarity. Euplotes parawoodruffi Song & Bradbury, 1997 is transferred to the genus Euplotoides based on the absence of frontoventral cirrus VI/3.

Origin of fungal hybrids with pathogenic potential from warm seawater environments.

Hybridisation is a common event in yeasts often leading to genomic variability and adaptation. The yeast Candida orthopsilosis is a human-associated opportunistic pathogen belonging to the Candida parapsilosis species complex. Most C. orthopsilosis clinical isolates are hybrids resulting from at least four independent crosses between two parental lineages, of which only one has been identified. The rare presence or total absence of parentals amongst clinical isolates is hypothesised to be a consequence of a reduced pathogenicity with respect to their hybrids. Here, we sequence and analyse the genomes of environmental C. orthopsilosis strains isolated from warm marine ecosystems. We find that a majority of environmental isolates are hybrids, phylogenetically closely related to hybrid clinical isolates. Furthermore, we identify the missing parental lineage, thus providing a more complete overview of the genomic evolution of this species. Additionally, we discover phenotypic differences between the two parental lineages, as well as between parents and hybrids, under conditions relevant for pathogenesis. Our results suggest a marine origin of C. orthopsilosis hybrids, with intrinsic pathogenic potential, and pave the way to identify pre-existing environmental adaptations that rendered hybrids more prone than parental lineages to colonise and infect the mammalian host.

Draft Genome Sequences of Seven Vibrio cholerae Isolates from Adult Patients in Qatar.

We report the draft genome sequences of seven Vibrio cholerae isolates from patients. Four isolates were profiled as multilocus sequence type 69, serogroup O1, a subset of seventh-pandemic El Tor clonal isolates. Presented here are genome assemblies and evidence for major pathogenicity islands, virulence factors, and antimicrobial resistance genes.

Prevalence of enteric protozoa in human immunodeficiency virus (HIV)-positive and HIV-negative men who have sex with men from Sydney, Australia.

A prospective, comparative study of the prevalence of enteric protozoa was determined among human immunodeficiency virus (HIV)- positive and HIV-negative men who have sex with men (MSM) in Sydney, Australia. A total of 1,868 patients submitted stool specimens; 1,246 were from MSM (628 HIV positive and 618 HIV positive) and 622 from non-MSM were examined over a 36-month period. A total of 651 (52.2%) stool specimens from MSM were positive for protozoa compared with 85 (13%) from non-MSM. There was a significant difference in the prevalence of Blastocystis hominis, Endolimax nana, Entamoeba histolytica/dispar complex, Entamoeba hartmanni, Iodamoeba butschlii, and Enteromonas hominis detected between MSM and non-MSM (P<0.001). The only notable difference between HIV-negative and HIV-positive MSM was that HIV-infected MSM were found to more likely have a Cryptosporidium parvum infection. Entamoeba histolytica was found in 3 patients, E. dispar in 25, and E. moshkovskii in 17, all of whom were MSM. When compared with a control group, MSM were significantly more likely to harbor intestinal protozoa and have multiple parasites present. The results of this study show high rates of enteric parasites persist in MSM and highlight the importance of testing for intestinal parasites in MSM. This is the first report of E. moshkovskii from MSM.

Discrepancy in MALDI-TOF MS identification of uncommon Gram-negative bacteria from lower respiratory secretions in patients with cystic fibrosis.

INTRODUCTION: Early identification of microbial organisms from respiratory secretions of patients with cystic fibrosis (CF) is important to guide therapeutic decisions. The objective was to compare the accuracy of matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) relative to the conventional phenotypic method in identifying common bacterial isolates, including nonfermenting Gram-negative bacteria, in a cohort of patients with CF. METHODS: A total of 123 isolates from 50 patients with CF representing 14 bacterial species from respiratory specimens were identified using MALDI-TOF MS in parallel with conventional phenotypic methods. Discrepancies were confirmed by 16S ribosomal RNA (rRNA) gene sequencing in five Gram-negative isolates. RESULTS: The MALDI-TOF MS managed to identify 122/123 (99.2%) bacterial isolates to the genus level and 118/123 (95.9%) were identified to the species level. The MALDI-TOF MS results were 100% consistent to the species level with conventional phenotypic identification for isolates of Staphylococcus aureus, Pseudomonas aeruginosa, Haemophilus influenzae, Streptococcus pyogenes, Achromobacter xylosoxidans, Stenotrophomonas maltophilia, and other uncommon organisms such as Chryseobacterium gleum and Enterobacter cloacae. The 5/123 (4.6%) isolates misidentified were all Gram-negative bacteria. The isolation of E. cloacae and Haemophilus paraphrohaemolyticus may extend the potentially pathogenic list of organisms isolated from patients with CF. CONCLUSION: Although the technique provides an early identification and antimicrobial therapy approach in patients with CF, limitation in the diagnosis of uncommon Gram-negative bacteria may exist.

Amoebiasis: current status in Australia.

Entamoeba histolytica is one of the most common parasitic infections worldwide, infecting about 50 million people and resulting in 40,000-100,000 deaths a year. In Australia, people at risk of infection include immigrants, travellers returning from countries of high endemicity, Indigenous people, and men who have sex with men. Clinical manifestations range from asymptomatic carriage to invasive disease. Amoebic colitis and amoebic liver abscess are the most common invasive manifestations observed in Australia. Diagnosis depends on a high index of suspicion and laboratory investigations. Molecular methods (using the polymerase chain reaction) are the most sensitive for identifying and differentiating Entamoeba species. Treatment should always include a luminal agent to eradicate colonisation, prevent spread and/or reduce the risk of invasive disease. Medical therapy can successfully cure invasive disease, including amoebic liver abscesses.