Subunit Ribosomal Ribonucleic Acid Gene Research Articles

Increased risk of Pneumocystis jirovecii colonization in rheumatoid arthritis patients on biologics and Janus kinase inhibitor

BackgroundThe prevalence of Pneumocystis jirovecii (PJ) pneumonia among rheumatic patients is rising. PJ colonization serves as a reservoir for transmission and precedes the development of PJ pneumonia. We aim to clarify the association of PJ colonization in patients of rheumatoid arthritis (RA) treated with biologics or Janus kinase inhibitors (JAKi). MethodsA prospective cohort study was performed from March 2021 to July 2022 in the rheumatology outpatient department of National Cheng Kung University Hospital. We obtained oral-wash samples from asymptomatic RA patients treated with biologic disease-modifying antirheumatic drugs (bDMARDs) and JAKi. A real-time quantitative polymerase chain reaction assay focusing on the mitochondrial large subunit ribosomal ribonucleic acid gene of PJ was applied to detect colonization. ResultsOne hundred and ten RA patients were enrolled. Adjusted odds ratios (ORs) of PJ colonization were 6.40 (95% CI 1.34-30.57, p-value =0.02) in patients receiving bDMARDs or JAKi. Specifically, in patients treated with bDMARDs the adjusted OR was 8.08 (95% CI 1.57-41.51, p-value=0.012), and a trend toward developing PJ colonization was further identified in patients receiving JAKi (adjusted OR: 4.79, 95% CI 0.89-25.91, p=0.069). Among patients treated with bDMARDs or JAKi, medication duration >3 years and age >60 y/o are risk factors for PJ colonization. ConclusionRA patients on bDMARDs or JAK inhibitors have an approximately 6-fold higher risk of developing P. jirovecii colonization. Patients treated with bDMARDs had an 8-fold higher risk of P. jirovecii colonization. Risk factors of PJ colonization are medication duration >3 years and age > 60 y/o.

The Biodiversity of Epilithic Microalgal Communities Colonising a Central Mediterranean Coastline

Schembri, S. and Zammit, G., 2022. The biodiversity of epilithic microalgal communities colonising a central Mediterranean coastline. Journal of Coastal Research, 38(2), 249–260. Coconut Creek (Florida), ISSN 0749-0208. Microbial communities colonise the coastal ecosystem around the Maltese islands. However, such communities are understudied, both in Malta and in the central Mediterranean. This research aims to increase current knowledge about the biodiversity of phototrophic communities growing along a central Mediterranean rocky shoreline and is the first such study to be performed on microorganisms growing in epilithic biofilms and microbial mats along the coastline in the Maltese islands. Samples were obtained using techniques that were noninvasive to the underlying substratum. These were studied by direct observation using light and electron microscopy, by culturing in vitro, by molecular analysis via sequencing of the small subunit ribosomal ribonucleic acid genes and phylogenetic analyses. Microscopic analyses revealed highly diverse communities made of both photosynthetic and heterotrophic organisms. The predominant microorganisms were simple filamentous cyanobacteria including species of Leptolyngbya, Phormidesmis, Nodosilinea, Toxifilum, Phormidium, and Lyngbya, as well as heterocytous Calothrix and Nunduva spp. The coccal cyanobacteria included species of Aphanocapsa and Chroococcus, whereas coccal microalgae belonged to Chlorella, Chlamydomonas, and Coelastrella spp., accompanied by diatoms of Navicula sp. These results include first records of cyanobacterial and microalgal barcodes that were genetically sequenced from a coastline in the central Mediterranean. Germlings of the filamentous macroalga Cladophora were embedded in the rocky substrate that was preconditioned by biofilm growth and ciliated protozoans, micronematodes, and microcrustaceans interacted with the microbial communities. The isolation of new cyanobacterial and microalgal strains from these phototrophic communities highlights the importance of employing a combined multiphasic approach to supplement current knowledge about the biodiversity of microbial communities colonising rocky shores.

Gut microbiota profile in patients with nonalcoholic fatty liver disease and presumed nonalcoholic steatohepatitis.

Background:The main composition of intestinal microbiota in nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH) patients has not yet been elucidated. In this, case-control study, we identified differences of intestinal microbiota in male patients with NAFLD, presumed NASH, and healthy controls.Materials and Methods:We compared gut microbial composition of 25 patients with NAFLD, 13 patients with presumed NASH, and 12 healthy controls. Demographic information as well as clinical, nutritional, and physical activity data was gathered. Stool and blood samples were collected to perform the laboratory analysis. The taxonomic composition of gut microbiota was assessed using V4 regions of microbial small subunit ribosomal Ribonucleic acid genes sequencing of stool samples.Results:Firmicutes, Actinobacteria, and Bacteroidetes were the most frequently phyla in all groups. Our results revealed that Veillonella was the only genus with significantly different amounts in presumed NASH patients compared with patients with NAFLD (P = 2.76 × 10−6, q = 2.07 × 10−4, logFC = 5.52).Conclusion:This pilot study was the first study to compare gut microbial composition in patients with NAFLD and presumed NASH in the Middle East. Given the potential effects of gut microbiota on the management and prevention of NAFLD, larger, prospective studies are recommended to confirm this study's findings.

New morphological and molecular perspectives about Macracanthorhynchus hirudinaceus (Acanthocephala: Oligacanthorhynchidae) from wild boar, Sus scrofa Linn., in Ukraine.

We make new morphological observations not previously reported for the old acanthocephalan Macracanthorhynchus hirudinaceus (Pallas, 1781) Travassos, 1917, described for the first time about 240 years ago. Our specimens were collected from the wild boar, Sus scrofa Linn., in Ukraine in 2005. We provide comparative morphometrics with other populations from Ukraine, Union of Soviet Socialist Republics, Europe, Brazil and the United States of America. Our specimens from the Ukraine had the smallest trunk (110-120 mm long), longest and thickest hooks, with the third hook being the largest, largest eggs, and a proboscis wider than long. We document the morphology of the proboscis, apical organ, hooks, hook roots, sensory pores, micropores, and eggs with scanning electron microscopy for the first time. We also provide chemical analysis of hooks and eggs using energy-dispersive X-ray analysis, discuss its micropores, and provide a new molecular profile based on 18S rDNA from a European population for the first time. Edge of hook tips feature high levels of calcium and phosphorous but the high level of sulphur is mostly found in the cortical layer of eggs. One new partial 18S rDNA sequence (482 nt length) was generated from an adult specimen of M. hirudinaceus. We present the first 18S rDNA published sequence for this cosmopolitan acanthocephalan obtained from Europe. The amplified region corresponded to the approximate middle region of the small subunit ribosomal ribonucleic acid gene, which is ~1800 nt in length. This molecular contribution is especially valuable in light of the extreme scarcity of genetic information about species of Macracanthorhynchus and of the family Oligacanthorhynchidae as a whole.

Stenamoeba polymorpha, a New Species Isolated from Domesticated Horse Equus ferus caballus.

A new species of lobosean amoeba, Stenamoeba polymorpha n. sp., was isolated from the diarrheic stool of a domesticated horse in Great Falls Virginia, U.S. It shares characteristics with the five other described Stenamoeba species. However, electron microscopy revealed S.polymorpha has a substantially thickened cell surface lamina. Under light microscopy, the amoebae had a dynamic polymorphic appearance because hyaloplasm readily formed and resorbed subpseudopodia from any peripheral region of the cell. While in locomotion, the amoebae produced subpseudopodia that led and alternated the direction of movement with an apparent zigzag path. Sometimes, stationary amoebae had a vertical cell posture that was substantially taller than wide or long. The new species description is also supported by small subunit ribosomal ribonucleic acid gene analyses using phylogenies with both broad and narrow taxon sampling, pairwise nucleotide comparisons, and in-silico secondary structure predictions. The latter suggested Stenamoeba spp. discriminatory motifs in variable region eight. Stenamoeba polymorpha n. sp. is the first of its genus to be recovered from mammal feces, the first to yield a potential group one intron and the second described from North America. Here, the phylogenies suggest Stenamoeba limacina is this new species' nearest known relative.

Haemoabdomen secondary to granulomatous periarteritis due to parasitism withHalicephalobus gingivalisin a mare

SummaryA 22‐year‐oldQuarterHorse mare exhibited neurological signs consisting of head pressing, central blindness, minimal ataxia and dysphagia. Despite treatment, the mare collapsed and died shortly after onset of signs. On necropsy, there were approximately 15 l of free blood in the abdominal cavity. A 12 × 4 cm diameter, irregularly‐shaped, nodular, firm, tan/yellow mass was found adhered to the outer surface of the right lateral aspect of the caudal abdominal aorta. A similar mass also affected the caudal aspect of the right kidney. Histopathology of the aortic and renal masses revealed multiple coalescing granulomas containing intralesional nematodes compatible withHalicephalobus gingivalis. Inflammatory cells disrupted the aortictunica adventitiaas well as the outertunica media. Similar exudate also affected the cerebrum, cerebellum and brainstem. Polymerase chain reaction amplification and sequencing of a portion of the large subunit ribosomal ribonucleic acid gene were performed using previously published primers forH. gingivalisto confirm the identity of the nematode. Although rupture of a blood vessel could not be demonstrated grossly, the histological findings suggest that inflammation may have breached a small calibre artery and caused the haemoabdomen.

First record of Eimeria furonis infection in a ferret, Japan, with notes on the usefulness of partial small subunit ribosomal RNA gene sequencing analysis for discriminating among Eimeria species

Eimeria is a genus of apicomplexan parasites found in a variety of vertebrates including the weasel. At present, three species have been reported in members of the weasel family, but the presence of weasel Eimeria in Japan have been quite unclear. The identification of Eimeria species has been performed based on oocyst morphology, host species, and habitat in the host, but sometimes discriminating among morphologically similar species under light microscopy is impossible. The present study detected for the first time the weasel coccidium, E. furonis, in a ferret in Japan. Since molecular information for E. furonis has been quite unclear, this species was compared molecularly with other Eimeria species, and also the usefulness of sequencing analysis of the small subunit ribosomal ribonucleic acid gene (SSUrDNA) for discriminating among Eimeria species was examined. About the 350-bp sequence of SSUrDNA of all species including E. furonis compared differed from each other, and its differences found in Eimeria species were also reflected in the phylogram constructed using the partial nucleotide sequences. The sequencing analysis of partial SSUrDNA examined in the present study thus appears useful for discriminating among morphologically similar Eimeria species.

Plasmodium Juxtanucleare associated with mortality in black-footed penguins (Spheniscus demersus) admitted to a rehabilitation center.

Five black-footed penguins (Spheniscus demersus) admitted to the Southern African Foundation for the Conservation of Coastal Birds, in Cape Town, South Africa, died from malaria infection. Evidence for malaria as the cause of death included antemortem clinical signs, parasitemia, splenomegaly, pulmonary edema, and the presence of histologically visible schizonts in the reticuloendothelial system. A portion of the malarial small subunit ribosomal ribonucleic acid gene was detected by polymerase chain reaction from postmortem blood samples from all the birds. A species-specific variable region of this gene was compared with the same region on genes from other known avian malarial organisms, establishing that Plasmodium juxtanucleare was involved.

Molecular diagnosis of theileriosis and heartwater in bovines in Africa

The advent of the polymerase chain reaction (PCR) coupled with the specificity of deoxyribocucleic acid (DNA)-DNA hybridization has led to the development of specific and sensitive molecular diagnostic tests to detect and characterize the organisms that cause theileriosis and heartwater. Theileriosis is a widespread disease of wild and domestic ruminants caused by apicomplexan parasites of the genus Theileria. Species-specific variations in small subunit ribosomal ribonucleic acid genes ( SSUrRNA) have been used to develop probes that can distinguish between Theileria species such as T. parva, T. annulata, T. mutans, T. buffeli and T. taurotragi. Routine application of this test has led to the discovery of previously unknown species, such as Theileria sp. (buffalo) which is apparently apathogenic to both buffalo and cattle, and Theileria sp. (sable) which is pathogenic to sable and possibly also to roan antelope. In addition, characterization probes located in the internal transcribed spacer (ITS) can be used to distinguish between most isolates of the causative agents of East Coast fever ( T. p. parva) and Corridor disease ( T. p. lawrencei). Heartwater is an economically important disease of livestock and some wild ruminants, caused by the intracellular rickettsial parasite Ehrlichia (ex Cowdria) ruminantium. DNA probes used to detect and characterize E. ruminantium isolates include SSUrRNA (16S) probes, the pCS20 probe and map1 probes. A panel of eight 16S probes has been developed for the detection of E. ruminantium and related Ehrlichia species. There are probes for 5 different E. ruminantium genotypes, one which will detect all 5 of these genotypes, one to detect any Ehrlichia species other than E. ruminantium, and one for any Anaplasma species. The pCS20 probe is specific for E. ruminantium and is the most sensitive of the probes for E. ruminantium detection, but it is not able to distinguish among the different genotypes. The map1 gene has also been used for diagnosis, but the extensive polymorphism of this gene means that it is most useful for characterization of different genotypes of the parasite. Routine application of these tests has led to the discovery of new genotypes that are probably not E. ruminantium but are probably new species of Ehrlichia.

Phylogenetic relationships of the genus Frenkelia: a review of its history and new knowledge gained from comparison of large subunit ribosomal ribonucleic acid gene sequences

The different genera currently classified into the family Sarcocystidae include parasites which are of significant medical, veterinary and economic importance. The genus Sarcocystis is the largest within the family Sarcocystidae and consists of species which infect a broad range of animals including mammals, birds and reptiles. Frenkelia, another genus within this family, consists of parasites that use rodents as intermediate hosts and birds of prey as definitive hosts. Both genera follow an almost identical pattern of life cycle, and their life cycle stages are morphologically very similar. How ever, the relationship between the two genera remains unresolved because previous analyses of phenotypic characters and of small subunit ribosomal ribonucleic acid gene sequences have questioned the validity of the genus Frenkelia or the monophyly of the genus Sarcocystis if Frenkelia was recognised as a valid genus. We therefore subjected the large subunit ribosomal ribonucleic acid gene sequences of representative taxa in these genera to phylogenetic analyses to ascertain a definitive relationship between the two genera. The full length large subunit ribosomal ribonucleic acid gene sequences obtained were aligned using Clustal W and Dedicated Comparative Sequence Editor secondary structure alignments. The Dedicated Comparative Sequence Editor alignment was then split into two data sets, one including helical regions, and one including non-helical regions, in order to determine the more informative sites. Subsequently, all four alignment data sets were subjected to different tree-building algorithms. All of the analyses produced trees supporting the paraphyly of the genus Sarcocystis if Frenkelia was recognised as a valid genus and, thus, call for a revision of the current definition of these genera. However, an alternative, more parsimonious and more appropriate solution to the Sarcocystis/Frenkelia controversy is to synonymise the genus Frenkelia with the genus Sarcocystis.