scholarly journals New vectors in northern Sarawak, Malaysian Borneo, for the zoonotic malaria parasite, Plasmodium knowlesi

2020 ◽  
Author(s):  
Joshua Xin De Ang ◽  
Khamisah Abdul Kadir ◽  
Dayang Shuaisah Awang Mohamad ◽  
Asmad Matusop ◽  
Paul Cliff Simon Divis ◽  
...  
Keyword(s):  
Plasmodium Knowlesi ◽  
Plasmodium Species ◽  
Small Subunit ◽  
Malaria Vectors ◽  
Rrna Gene ◽  
Cox1 Gene ◽  
Ssu Rrna ◽  
Ssu Rrna Gene ◽  
Zoonotic Malaria ◽  
Malaysian Borneo

Abstract Background: Plasmodium knowlesi is a significant cause of human malaria in Sarawak, Malaysian Borneo. Only one study has been previously undertaken in Sarawak to identify vectors of P. knowlesi, where Anopheles latens was incriminated as the vector in Kapit, central Sarawak. A study was therefore undertaken to identify malaria vectors in a different location in Sarawak.Methods: Mosquitoes found landing on humans and resting on leaves over a 5-day period at two sites in the Lawas District of northern Sarawak were collected and identified. DNA samples extracted from salivary glands of Anopheles mosquitoes were subjected to nested PCR malaria-detection assays. The small subunit ribosomal RNA (SSU rRNA) gene of Plasmodium was sequenced, and the internal transcribed spacer 2 (ITS2) and mitochondrial cytochrome c oxidase subunit 1 (cox1) gene of the mosquitoes were sequenced from the Plasmodium-positive samples for phylogenetic analysis.Results: Totals of 65 anophelines and 127 culicines were collected. By PCR, 6 An. balabacensis and 5 An. donaldi were found to have single P. knowlesi infections while 3 other An. balabacensis had either single, double or triple infections with P. inui, P. fieldi, P. cynomolgi and P. knowlesi. Phylogenetic analysis of the Plasmodium SSU rRNA gene confirmed 3 An. donaldi and 3 An. balabacensis with single P. knowlesi infections, while 3 other An. balabacensis had two or more Plasmodium species of P. inui, P. knowlesi, P. cynomolgi and some species of Plasmodium that could not be conclusively identified. Phylogenies inferred from the ITS2 and/or cox1 sequences of An. balabacensis and An. donaldi indicate that they are genetically indistinguishable from An. balabacensis and An. donaldi, respectively, found in Sabah, Malaysian Borneo. Conclusions: Previously An. latens was identified as the vector for P. knowlesi in Kapit, central Sarawak, Malaysian Borneo, and now An. balabacensis and An. donaldi have been incriminated as vectors for zoonotic malaria in Lawas, northern Sarawak.

scholarly journals New vectors in northern Sarawak, Malaysian Borneo, for the zoonotic malaria parasite, Plasmodium knowlesi

2020 ◽  
Author(s):  
Joshua Ang Xin De ◽  
Khamisah Abdul Kadir ◽  
Dayang Shuaisah Awang Mohamad ◽  
Asmad Matusop ◽  
Paul Cliff Simon Divis ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Plasmodium Knowlesi ◽  
Plasmodium Species ◽  
Malaria Vectors ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Ssu Rrna Gene ◽  
Zoonotic Malaria ◽  
Cox 1 ◽  
Malaysian Borneo

Abstract Background: Plasmodium knowlesi is a significant cause of human malaria in Sarawak, Malaysian Borneo. Only one study has been previously undertaken in Sarawak to identify vectors of P. knowlesi , where Anopheles latens was incriminated as the vector in Kapit, central Sarawak. A study was therefore undertaken to identify malaria vectors in a different location in Sarawak. Methods: Mosquitoes found landing on humans and resting on leaves over a 5-day period at two sites in the Lawas District of northern Sarawak were collected and identified. DNA samples extracted from salivary glands of Anopheles mosquitoes were subjected to nested PCR malaria-detection assays. The small subunit ribosomal RNA ( SSU rRNA) gene of Plasmodium was sequenced, and the internal transcribed spacer 2 (ITS2) and mitochondrial cytochrome c oxidase subunit 1 ( cox 1) gene of the mosquitoes were sequenced from the Plasmodium -positive samples for phylogenetic analysis. Results: Totals of 65 anophelines and 127 culicines were collected. By PCR, 6 An. balabacensis and 5 An. donaldi were found to have single P. knowlesi infections while 3 other An. balabacensis had either single, double or triple infections with P. inui , P. fieldi , P. cynomolgi and P. knowlesi . Phylogenetic analysis of the Plasmodium SSU rRNA gene confirmed 3 An. donaldi and 3 An. balabacensis with single P. knowlesi infections, while 3 other An. balabacensis had two or more Plasmodium species of P. inui , P. knowlesi , P. cynomolgi and some species of Plasmodium that could not be conclusively identified. Phylogenies inferred from the ITS2 and/or cox 1 sequences of An. balabacensis and An. donaldi indicate that they are genetically indistinguishable from An. balabacensis and An. donaldi , respectively, found in Sabah, Malaysian Borneo. Conclusions: Previously An. latens was identified as the vector for P. knowlesi in Kapit, central Sarawak, Malaysian Borneo, and now An. balabacensis and An. donaldi have been incriminated as vectors for zoonotic malaria in Lawas, northern Sarawak.

scholarly journals New vectors in northern Sarawak, Malaysian Borneo, for the zoonotic malaria parasite, Plasmodium knowlesi

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Joshua X. D. Ang ◽  
Khamisah A. Kadir ◽  
Dayang S. A. Mohamad ◽  
Asmad Matusop ◽  
Paul C. S. Divis ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Rna ◽  
Internal Transcribed Spacer ◽  
Plasmodium Knowlesi ◽  
Small Subunit ◽  
Malaria Vectors ◽  
Rrna Gene ◽  
Zoonotic Malaria ◽  
Parasite Plasmodium ◽  
Malaysian Borneo

Abstract Background Plasmodium knowlesi is a significant cause of human malaria in Sarawak, Malaysian Borneo. Only one study has been previously undertaken in Sarawak to identify vectors of P. knowlesi, where Anopheles latens was incriminated as the vector in Kapit, central Sarawak. A study was therefore undertaken to identify malaria vectors in a different location in Sarawak. Methods Mosquitoes found landing on humans and resting on leaves over a 5-day period at two sites in the Lawas District of northern Sarawak were collected and identified. DNA samples extracted from salivary glands of Anopheles mosquitoes were subjected to nested PCR malaria-detection assays. The small subunit ribosomal RNA (SSU rRNA) gene of Plasmodium was sequenced, and the internal transcribed spacer 2 (ITS2) and mitochondrial cytochrome c oxidase subunit 1 (cox1) gene of the mosquitoes were sequenced from the Plasmodium-positive samples for phylogenetic analysis. Results Totals of 65 anophelines and 127 culicines were collected. By PCR, 6 An. balabacensis and 5 An. donaldi were found to have single P. knowlesi infections while 3 other An. balabacensis had either single, double or triple infections with P. inui, P. fieldi, P. cynomolgi and P. knowlesi. Phylogenetic analysis of the Plasmodium SSU rRNA gene confirmed 3 An. donaldi and 3 An. balabacensis with single P. knowlesi infections, while 3 other An. balabacensis had two or more Plasmodium species of P. inui, P. knowlesi, P. cynomolgi and some species of Plasmodium that could not be conclusively identified. Phylogenies inferred from the ITS2 and/or cox1 sequences of An. balabacensis and An. donaldi indicate that they are genetically indistinguishable from An. balabacensis and An. donaldi, respectively, found in Sabah, Malaysian Borneo. Conclusions Previously An. latens was identified as the vector for P. knowlesi in Kapit, central Sarawak, Malaysian Borneo, and now An. balabacensis and An. donaldi have been incriminated as vectors for zoonotic malaria in Lawas, northern Sarawak.

scholarly journals New vectors in northern Sarawak, Malaysian Borneo, for the zoonotic malaria parasite, Plasmodium knowlesi

2020 ◽  
Author(s):  
Joshua Ang Xin De ◽  
Khamisah Abdul Kadir ◽  
Dayang Shuaisah Awang Mohamad ◽  
Asmad Matusop ◽  
Paul Cliff Simon Divis ◽  
...  
Keyword(s):  
Plasmodium Knowlesi ◽  
Phylogenetic Analyses ◽  
Plasmodium Species ◽  
Malaria Vectors ◽  
Anopheles Mosquitoes ◽  
Zoonotic Malaria ◽  
Parasite Plasmodium ◽  
Coi Sequences ◽  
Anopheles Barbirostris ◽  
Malaysian Borneo

Abstract Background: The vectors for Plasmodium knowlesi, a significant cause of human malaria in Southeast Asia, identified previously in nature all belong to the Anopheles Leucosphyrus Group. Only one study has been previously undertaken in Sarawak, Malaysian Borneo, to identify vectors of P. knowlesi , where Anopheles latens was incriminated as the vector in Kapit, central Sarawak. A study was therefore undertaken to identify malaria vectors in a different location in Sarawak. Methods: Mosquitoes found landing on humans and resting on leaves over a 5-day period at two sites in the Lawas District of northern Sarawak were collected and identified. DNA samples extracted from salivary glands of Anopheles mosquitoes were subjected to nested PCR malaria-detection assays. The small sub-unit ribosomal RNA (SSUrRNA) genes of Plasmodium , and the internal transcribed spacer 2 (ITSII) and mitochondrial cytochrome c oxidase subunit 1 (COI) sequences of the mosquitoes were derived from the Plasmodium -positive samples for phylogenetic analyses. Results: A total of 65 anophelines and 127 culicines were collected. By PCR, six An. balabacensis and five An. barbirostris Clade VI were found to have single P. knowlesi infecions while three other An. balabacensis had either single, double or triple infections with P. inui, P. fieldi, P. cynomolgi and P. knowlesi . Phylogenetic analyses of the Plasmodium SSUrRNA genes confirmed 3 An. barbirostris Clade VI and 3 An. balabacensis with single P. knowlesi infections, while 3 other An. balabacensis had two or more Plasmodium species of P. inui, P. knowlesi, P. cynomolgi and possibly novel species of Plasmodium . Phylogenies inferred from the ITSII and COI sequences of An. balabacensis and An. barbirostris Clade VI indicate that the former is genetically indistinguishable from An. balabacensis in Borneo while the latter is a novel sibling species belonging to the Anopheles Barbirostris Subgroup. Conclusions: New vectors for P. knowlesi in Sarawak were identified, including An. barbirostris Clade VI , which is a species that does not belong to the Anopheles Leucosphyrus Group.

scholarly journals New vectors in northern Sarawak, Malaysian Borneo, for the zoonotic malaria parasite, Plasmodium knowlesi

2020 ◽  
Author(s):  
Joshua Ang Xin De ◽  
Khamisah Abdul Kadir ◽  
Dayang Shuaisah Awang Mohamad ◽  
Asmad Matusop ◽  
Paul Cliff Simon Divis ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Internal Transcribed Spacer ◽  
Plasmodium Knowlesi ◽  
Plasmodium Species ◽  
Malaria Vectors ◽  
Anopheles Mosquitoes ◽  
Zoonotic Malaria ◽  
Parasite Plasmodium ◽  
Coi Sequences ◽  
Malaysian Borneo

Abstract Background: Plasmodium knowlesi is a significant cause of human malaria in Sarawak, Malaysian Borneo. Only one study has been previously undertaken in Sarawak to identify vectors of P. knowlesi, where Anopheles latens was incriminated as the vector in Kapit, central Sarawak. A study was therefore undertaken to identify malaria vectors in a different location in Sarawak.Methods: Mosquitoes found landing on humans and resting on leaves over a 5-day period at two sites in the Lawas District of northern Sarawak were collected and identified. DNA samples extracted from salivary glands of Anopheles mosquitoes were subjected to nested PCR malaria-detection assays. The small sub-unit ribosomal RNA (SSUrRNA) genes of Plasmodium , and the internal transcribed spacer 2 (ITS2) and mitochondrial cytochrome c oxidase subunit 1 (COI) sequences of the mosquitoes were derived from the Plasmodium -positive samples for phylogenetic analysis.Results: A total of 65 anophelines and 127 culicines were collected. By PCR, six An. balabacensis and five An. donaldi were found to have single P. knowlesi infections while three other An. balabacensis had either single, double or triple infections with P. inui, P. fieldi, P. cynomolgi and P. knowlesi . Phylogenetic analysis of the Plasmodium SSUrRNA genes confirmed 3 An. donaldi and 3 An. balabacensis with single P. knowlesi infections, while 3 other An. balabacensis had two or more Plasmodium species of P. inui, P. knowlesi, P. cynomolgi and some species of Plasmodium that could not be conclusively identified. Phylogenies inferred from the ITS2 and/or COI sequences of An. balabacensis and An. donaldi indicate that they are genetically indistinguishable from An. balabacensis and An. donaldi, respectively, found in Sabah, Malaysian Borneo.Conclusions: Previously An. latens was identified as the vector for P. knowlesi in Kapit, central Sarawak, Malaysian Borneo, and now An. balabacensis and An. donaldi have been incriminated as vectors for zoonotic malaria in Lawas, northern Sarawak.

scholarly journals Evidence of independent acquisition and adaption of ultra-small bacteria to human hosts across the highly diverse yet reduced genomes of the phylum Saccharibacteria

2018 ◽  
Author(s):  
Jeffrey S. McLean ◽  
Batbileg Bor ◽  
Thao T. To ◽  
Quanhui Liu ◽  
Kristopher A. Kerns ◽  
...  
Keyword(s):  
Oral Cavity ◽  
De Novo ◽  
Gc Content ◽  
Single Copy ◽  
Small Subunit ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Ssu Rrna Gene ◽  
Human Oral Cavity

ABSTRACTRecently, we discovered that a member of the Saccharibacteria/TM7 phylum (strain TM7x) isolated from the human oral cavity, has an ultra-small cell size (200-300nm), a highly reduced genome (705 Kbp) with limited de novo biosynthetic capabilities, and a very novel lifestyle as an obligate epibiont on the surface of another bacterium 1. There has been considerable interest in uncultivated phyla, particularly those that are now classified as the proposed candidate phyla radiation (CPR) reported to include 35 or more phyla and are estimated to make up nearly 15% of the domain Bacteria. Most members of the larger CPR group share genomic properties with Saccharibacteria including reduced genomes (<1Mbp) and lack of biosynthetic capabilities, yet to date, strain TM7x represents the only member of the CPR that has been cultivated and is one of only three CPR routinely detected in the human body. Through small subunit ribosomal RNA (SSU rRNA) gene surveys, members of the Saccharibacteria phylum are reported in many environments as well as within a diversity of host species and have been shown to increase dramatically in human oral and gut diseases. With a single copy of the 16S rRNA gene resolved on a few limited genomes, their absolute abundance is most often underestimated and their potential role in disease pathogenesis is therefore underappreciated. Despite being an obligate parasite dependent on other bacteria, six groups (G1-G6) are recognized using SSU rRNA gene phylogeny in the oral cavity alone. At present, only genomes from the G1 group, which includes related and remarkably syntenic environmental and human oral associated representatives1, have been uncovered to date. In this study we systematically captured the spectrum of known diversity in this phylum by reconstructing completely novel Class level genomes belonging to groups G3, G6 and G5 through cultivation enrichment and/or metagenomic binning from humans and mammalian rumen. Additional genomes for representatives of G1 were also obtained from modern oral plaque and ancient dental calculus. Comparative analysis revealed remarkable divergence in the host-associated members across this phylum. Within the human oral cavity alone, variation in as much as 70% of the genes from nearest oral clade (AAI 50%) as well as wide GC content variation is evident in these newly captured divergent members (G3, G5 and G6) with no environmental relatives. Comparative analyses suggest independent episodes of transmission of these TM7 groups into humans and convergent evolution of several key functions during adaptation within hosts. In addition, we provide evidence from in vivo collected samples that each of these major groups are ultra-small in size and are found attached to larger cells.

Redescription and SSU rRNA gene-based phylogeny of an anaerobic ciliate, Plagiopyla ovata Kahl, 1931 (Ciliophora, Plagiopylea)

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Ran Li ◽  
Wenbao Zhuang ◽  
Congcong Wang ◽  
Hamed El-Serehy ◽  
Saleh A. Al-Farraj ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Gene Trees ◽  
Ssu Rrna Gene ◽  
Anaerobic Ciliate ◽  
Pr China

The morphology and molecular phylogeny of Plagiopyla ovata Kahl, 1931, a poorly known anaerobic ciliate, were investigated based on a population isolated from sand samples collected from the Yellow Sea coast at Qingdao, PR China. Details of the oral ciliature are documented for the first time to our knowledge and an improved species diagnosis is given. The small subunit ribosomal RNA (SSU rRNA) gene was newly sequenced and phylogenetic analyses revealed that P. ovata clusters within the monophyletic family Plagiopylidae. However, evolutionary relationships within both the family Plagiopylidae and the genus Plagiopyla remain obscure owing to undersampling, the lack of sequence data from known species and low nodal support or unstable topologies in gene trees. A key to the identification of the species of the genus Plagiopyla with validly published names is also supplied.

scholarly journals Telonema antarcticum sp. nov., a common marine phagotrophic flagellate

2005 ◽  
Vol 55 (6) ◽  
pp. 2595-2604 ◽  
Author(s):  
Dag Klaveness ◽  
Kamran Shalchian-Tabrizi ◽  
Helge Abildhauge Thomsen ◽  
Wenche Eikrem ◽  
Kjetill S. Jakobsen
Keyword(s):  
Molecular Phylogeny ◽  
Small Subunit ◽  
Food Vacuole ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Small Subunit Rrna ◽  
Ssu Rrna Gene ◽  
Structural Identity ◽  
Food Particles ◽  
Ssu Rrna Gene Sequence

Telonema is a widely distributed group of phagotrophic flagellates with two known members. In this study, the structural identity and molecular phylogeny of Telonema antarcticum was investigated and a valid description is proposed. Molecular phylogeny was studied using small-subunit rRNA (SSU rRNA) gene sequences. The pear-shaped cell had two subequal flagella that emerged laterally on the truncated antapical tail. One flagellum had tripartite hairs. The cell was naked, but had subsurface vesicles containing angular paracrystalline bodies of an unknown nature. A unique complex cytoskeletal structure, the subcortical lamina, was found to be an important functional and taxonomic feature of the genus. Telonema has an antero-ventral depression where food particles are ingested and then transferred to a conspicuous anterior food vacuole. The molecular phylogeny inferred from the SSU rRNA gene sequence suggested that Telonema represents an isolated and deep branch among the tubulocristate protists.

scholarly journals phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes

mSystems ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Harald R. Gruber-Vodicka ◽  
Brandon K. B. Seah ◽  
Elmar Pruesse
Keyword(s):  
High Throughput ◽  
Small Subunit ◽  
General Purpose ◽  
Reference Database ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Small Subunit Rrna ◽  
Ssu Rrna Gene ◽  
Domains Of Life ◽  
Environmental Microbes

ABSTRACT The small-subunit rRNA (SSU rRNA) gene is the key marker in molecular ecology for all domains of life, but it is largely absent from metagenome-assembled genomes that often are the only resource available for environmental microbes. Here, we present phyloFlash, a pipeline to overcome this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based binning of full metagenomic assemblies. We show that a cleanup of artifacts is pivotal even with a curated reference database. With such a filtered database, the general-purpose mapper BBmap extracts SSU rRNA reads five times faster than the rRNA-specialized tool SortMeRNA with similar sensitivity and higher selectivity on simulated metagenomes. Reference-based targeted assemblers yielded either highly fragmented assemblies or high levels of chimerism, so we employ the general-purpose genomic assembler SPAdes. Our optimized implementation is independent of reference database composition and has satisfactory levels of chimera formation. phyloFlash quickly processes Illumina (meta)genomic data, is straightforward to use, even as part of high-throughput quality control, and has user-friendly output reports. The software is available at https://github.com/HRGV/phyloFlash (GPL3 license) and is documented with an online manual. IMPORTANCE To track organisms across all domains of life, the SSU rRNA gene is the gold standard. Many environmental microbes are known only from high-throughput sequence data, but the SSU rRNA gene, the key to visualization by molecular probes and link to existing literature, is often missing from metagenome-assembled genomes (MAGs). The easy-to-use phyloFlash software suite tackles this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based linking to MAGs. Starting from a cleaned reference database, phyloFlash profiles the taxonomic diversity and assembles the sorted SSU rRNA reads. The phyloFlash design is domain agnostic and covers eukaryotes, archaea, and bacteria alike. phyloFlash also provides utilities to visualize multisample comparisons and to integrate the recovered SSU rRNAs in a metagenomics workflow by linking them to MAGs using assembly graph parsing.

scholarly journals Morphological and Genetic Evidence that the Cyanobacterium Lyngbya wollei (Farlow ex Gomont) Speziale and Dyck Encompasses at Least Two Species

2008 ◽  
Vol 74 (12) ◽  
pp. 3710-3717 ◽  
Author(s):  
Jennifer J. Joyner ◽  
R. Wayne Litaker ◽  
Hans W. Paerl
Keyword(s):  
Phylogenetic Analysis ◽  
Habitat Degradation ◽  
Sequence Similarity ◽  
Inorganic Nitrogen ◽  
Small Subunit ◽  
Morphological Data ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Lyngbya Wollei ◽  
Ssu Rrna Gene

ABSTRACT Dense blooms of the cyanobacterium Lyngbya wollei are increasingly responsible for declining water quality and habitat degradation in numerous springs, rivers, and reservoirs. This research represents the first molecular phylogenetic analysis of L. wollei in comparison with the traditional morphological characterization of this species. Specimens were collected from several springs in Florida and a reservoir in North Carolina. Segments of the small-subunit (SSU) rRNA and nifH genes were PCR amplified, cloned, and sequenced. The phylogenetic analysis of the SSU rRNA gene revealed sequences that fell into three distinct subclusters, each with >97% sequence similarity. These were designated operational taxonomic unit 1 (OTU1), OTU2, and OTU3. Similarly, the nifH sequences fell into three distinct subclusters named S1, S2, and S3. When either bulk samples or individual filaments were analyzed, we recovered OTU1 with S1, OTU2 with S2, and OTU3 with S3. The coherence between the three SSU rRNA gene and nifH subclusters was consistent with genetically distinct strains or species. Cells associated with subclusters OTU3 and S3 were significantly wider and longer than those associated with other subclusters. The combined molecular and morphological data indicate that the species commonly identified as L. wollei in the literature represents two or possibly more species. Springs containing OTU3 and S3 demonstrated lower ion concentrations than other collection sites. Geographical locations of Lyngbya subclusters did not correlate with residual dissolved inorganic nitrogen or phosphorus concentrations. This study emphasizes the need to complement traditional identification with molecular characterization to more definitively detect and characterize harmful cyanobacterial species or strains.

Phylogeny of Actinobacteria Small Subunit (SSU) rRNA Gene Clones Recovered From Marine Bacterioplankton

1999 ◽  
Vol 22 (1) ◽  
pp. 106-112 ◽  
Author(s):  
Michael S. Rappé ◽  
Douglas A. Gordon ◽  
Kevin L. Vergin ◽  
Stephen J. Giovannoni
Keyword(s):  
Small Subunit ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Ssu Rrna Gene ◽  
Marine Bacterioplankton
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