scholarly journals Molecular Detection and Phylogeny of Tick-Borne Pathogens in Ticks Collected from Dogs in the Republic of Korea

Pathogens ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 613
Author(s):  
A-Tai Truong ◽  
Jinhyeong Noh ◽  
Yeojin Park ◽  
Hyun-Ji Seo ◽  
Keun-Ho Kim ◽  
...  
Keyword(s):  
Disease Surveillance ◽  
Large Scale ◽  
Phylogenetic Analyses ◽  
Republic Of Korea ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Haemaphysalis Longicornis ◽  
Babesia Gibsoni ◽  
The Republic ◽  
And Control

Ticks are important vectors of various pathogens that result in clinical illnesses in humans and domestic and wild animals. Information regarding tick infestations and pathogens transmitted by ticks is important for the identification and prevention of disease. This study was a large-scale investigation of ticks collected from dogs and their associated environments in the Republic of Korea (ROK). It included detecting six prevalent tick-borne pathogens (Anaplasma spp., A. platys, Borrelia spp., Babesia gibsoni, Ehrlichia canis, and E. chaffeensis). A total of 2293 ticks (1110 pools) were collected. Haemaphysalis longicornis (98.60%) was the most frequently collected tick species, followed by Ixodes nipponensis (0.96%) and H. flava (0.44%). Anaplasma spp. (24/1110 tick pools; 2.16%) and Borrelia spp. (4/1110 tick pools; 0.36%) were detected. The phylogenetic analyses using 16S rRNA genes revealed that the Anaplasma spp. detected in this study were closely associated with A. phagocytophilum reported in humans and rodents in the ROK. Borrelia spp. showed phylogenetic relationships with B. theileri and B. miyamotoi in ticks and humans in Mali and Russia. These results demonstrate the importance of tick-borne disease surveillance and control in dogs in the ROK.

Tick surveillance of migratory birds during 2010–2011 on Hong and Heuksan Islands, Jeollanam Province, Republic of Korea 

2018 ◽  
Vol 23 (11) ◽  
pp. 2214 ◽  
Author(s):  
Sung-Tae Chong ◽  
Heung Chul Kim ◽  
Jong-Gil Park ◽  
Chang-Yong Choi ◽  
Chang-Uk Park ◽  
...  
Keyword(s):  
Disease Surveillance ◽  
National Park ◽  
Migratory Birds ◽  
Bird Species ◽  
Republic Of Korea ◽  
Surveillance Program ◽  
Haemaphysalis Longicornis ◽  
Haemaphysalis Concinna ◽  
Park Service ◽  
The Republic

Migratory birds were captured, examined, banded and then released in accordance with a bird banding protocol of the Bird Research Center, National Park Research Institute, Korea National Park Service, from January-December 2010–2011 on Hong and Heuksan Islands, Jeollanam (Jeonnam) Province, in the Republic of Korea (ROK). Concurrently, ticks were collected from captured birds as part of a tick-borne disease surveillance program. A total of 381 ticks belonging to three genera and eight species – Ixodes turdus (297 ticks), Ixodes nipponensis (16), Haemaphysalis flava (46), Haemaphysalis longicornis (9), Haemaphysalis formosensis (5), Haemaphysalis ornithophila (6), Haemaphysalis concinna (1), and Amblyomma testudinarium (1)—were collected from 32 bird species belonging to 3 families. This is the first host report of A. testudinarium (1 nymph) collected from White’s Thrush, Zoothera aurea (Aves: Passeriformes: Turdidae), in the ROK. Most ticks were collected from birds during the months of April (44.1%) and November (54.2%).

scholarly journals Tick surveillance in two southeastern provinces, including three metropolitan areas, of the Republic of Korea during 2014 

2017 ◽  
Vol 22 (2) ◽  
pp. 271 ◽  
Author(s):  
Jaree L. Johnson ◽  
Heung-chul Kim ◽  
Jordan M. Coburn ◽  
Sung-tae Chong ◽  
Nicholas W. Chang ◽  
...  
Keyword(s):  
Disease Surveillance ◽  
Metropolitan Areas ◽  
Republic Of Korea ◽  
Haemaphysalis Longicornis ◽  
Haemaphysalis Flava ◽  
Tick Borne Disease ◽  
Males And Females ◽  
The Mean ◽  
The Republic ◽  
Amblyomma Testudinarium

Tick-borne disease surveillance was conducted from March–October 2014 in two southeastern provinces, including three metropolitan areas, in the Republic of Korea (ROK). Three general habitats were surveyed: Grasses (grasses and herbaceous and crawling vegetation), Forests (pine, larch, deciduous, and mixed), and Forests+Grasses. A total of 40,048 ticks (1,480 adults; 24,201 nymphs; 14,367 larvae) belonging to three genera and six species were collected. Haemaphysalis longicornis (84.25%; 33,741) was the most commonly collected tick, followed by Haemaphysalis flava (14.52%; 5,816), Ixodes nipponensis (1.09%; 436), Amblyomma testudinarium (0.07%; 27), Haemaphysalis phasiana (0.06%; 23), and Ixodes turdus (0.01%; 5). Overall, adult ticks accounted for only 3.70% of all ticks collected, while nymphs and larvae accounted for 60.43% and 35.87%, respectively. The proportion of H. longicornis nymphs was highest beginning in March (99.51%), slowly declined through July (82.01%) and then rapidly declined to a low in October (6.45%). Large increases in the proportion of H. longicornis larvae were observed in August (42.05%), September (84.19%) and October (93.55%) following increased numbers of adults collected in June (4.20%), July (17.99%) and August (9.79%). Haemaphysalis flava adults and nymphs were commonly collected from April–May and October, while larvae were first collected from July, with peak numbers collected in August and low numbers collected during September–October. The proportion of I. nipponensis adults was highest in March (75.34%), declined to a low in July (0%), and then increased in September (60.00%) and October (90.32%). Larvae were collected only in August–September and accounted for 64.29% and 20.00% of all I. nipponensis collected during those months. Similar proportions of males and females of H. flava (51.47% and 48.53%, respectively) were collected from all habitats, while significantly more I. nipponensis males (62.20%) were collected than females (37.80%). Conversely, the proportion of H. longicornis females (80.00%) collected was significantly higher than for males (20.00%). Overall, the mean number of ticks collected/hr of collection for all habitats was 156.06/hr of collection. Similar numbers were collected/hr for Forests (172.61) and Grasses (168.64), while lower numbers were collected/hr for Forests+Grasses (128.12). 

Morphological abnormalities in ticks (Acari: Ixodidae) from the Republic of Korea

2020 ◽  
Vol 25 (11) ◽  
pp. 1994-2002
Author(s):  
Sung-Tae Chong ◽  
Heung-Chul Kim ◽  
Sang-Jae Suh ◽  
Terry A. Klein ◽  
Richard G. Robbins
Keyword(s):  
Disease Surveillance ◽  
Mixed Forest ◽  
Republic Of Korea ◽  
Haemaphysalis Longicornis ◽  
Herbaceous Vegetation ◽  
Us Army ◽  
Tick Borne Disease ◽  
The Republic ◽  
First Time ◽  
Forest Habitats

Tick-borne disease surveillance was conducted by tick drag among uncut grasses/herbaceous vegetation and mixed forest habitats from 2018–2020 at US Army Garrison Humphreys, Pyeongtaek, the Republic of Korea (ROK). While identifying ticks collected in the spring of 2020, teratological anomalies were observed in nymphs of Haemaphysalis longicornis (in one specimen, partial twinning of the posterior idiosoma, resulting in 2 anuses; in a second, asymmetry of the idiosoma) and Ixodes nipponensis (7 legs). These teratological observations in H. longicornis and I. nipponensis are reported for the first time in the ROK.

scholarly journals Molecular investigation of tick-borne pathogens in ticks removed from tick-bitten humans in the southwestern region of the Republic of Korea

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252992
Author(s):  
Mi Seon Bang ◽  
Choon-Mee Kim ◽  
Sang-Hyun Pyun ◽  
Dong-Min Kim ◽  
Na Ra Yun
Keyword(s):  
Tick Species ◽  
Spotted Fever ◽  
Common Species ◽  
Republic Of Korea ◽  
Spotted Fever Group ◽  
Haemaphysalis Longicornis ◽  
Babesia Gibsoni ◽  
Specific Pcr ◽  
Rickettsia Monacensis ◽  
The Republic

In this study, we investigated the presence of tick-borne pathogens in ticks removed from tick-bitten humans in the southwestern provinces of the Republic of Korea (ROK). We identified 33 ticks from three tick species, namely Amblyomma testudinarium (60.6%), Haemaphysalis longicornis (27.3%), and Ixodes nipponensis (12.1%) in order of occurrence via morphology and 16S rDNA-targeting polymerase chain reaction (PCR). Tick-borne pathogens were detected in 16 ticks using pathogen-specific PCR. From the results, 12 ticks (36.4%) tested positive for spotted fever group (SFG) Rickettsia: Rickettsia monacensis (1/12), R. tamurae (8/12), and Candidatus Rickettsia jingxinensis (3/12). Three ticks (9.1%) were positive for Anaplasma phagocytophilum. In addition, three ticks (9.1%) tested positive for Babesia gibsoni (1/3) and B. microti (2/3). In conclusion, we identified three tick species; the most common species was A. testudinarium, followed by H. longicornis and I. nipponensis. SFG Rickettsia, A. phagocytophilum, and Babesia spp. were the most frequently detected pathogens in ticks removed from tick-bitten humans. To our knowledge, this is the first report of R. tamurae and Ca. R. jingxinensis detection in Korea. The present results will contribute to the understanding of tick-borne infections in animals and humans in the ROK.

scholarly journals First report of the molecular detection of human pathogen Rickettsia raoultii in ticks from the Republic of Korea

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Misbah Tariq ◽  
Jun-Won Seo ◽  
Da Young Kim ◽  
Merlin Jayalal Lawrence Panchali ◽  
Na Ra Yun ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Citrate Synthase ◽  
Phylogenetic Analyses ◽  
Spotted Fever ◽  
Republic Of Korea ◽  
Spotted Fever Group ◽  
Haemaphysalis Longicornis ◽  
Rickettsia Raoultii ◽  
Rickettsial Infections ◽  
The Republic

Abstract Background Rickettsial diseases associated with the spotted fever group constitute a growing number of newly identified Rickettsia pathogens and their tick vectors in various parts of the world. At least 15 distinct tick species belonging to six genera have shown the presence of Rickettsia raoultii. Herein, we report the detection of R. raoultii in ticks from the Republic of Korea (ROK). Methods Thirty-five ticks were collected from 29 patients with tick bites in Gwangju Metropolitan City, Jeollanam Province, ROK. The ticks were identified using molecular, morphological, and taxonomic characteristics. All samples were screened for presence of Rickettsia species using nested polymerase chain reactions of their outer membrane protein (ompA) and citrate synthase (gltA) genes. The amplified products were sequenced for subsequent phylogenetic analyses. Results Sequencing data showed the DNA sequences of R. raoultii in three Haemaphysalis longicornis ticks. All three tick samples were 99.4–100% similar to previously reported partial sequences of ompA of R. raoultii strains CP019435 and MF002523, which formed a single clade with the reference strains. Conclusions We provide the first description and molecular identification of R. raoultii detected in H. longicornis ticks in the ROK. This observation extends the geographical distribution of R. raoultii. Screening of human samples for this pathogen will provide information about the prevalence of rickettsial infections in this region.

scholarly journals Cultivation of Dominant Freshwater Bacterioplankton Lineages Using a High-Throughput Dilution-to-Extinction Culturing Approach Over a 1-Year Period

2021 ◽  
Vol 12 ◽  
Author(s):  
Suhyun Kim ◽  
Md. Rashedul Islam ◽  
Ilnam Kang ◽  
Jang-Cheon Cho
Keyword(s):  
16S Rrna ◽  
High Throughput ◽  
Large Scale ◽  
Phylogenetic Analyses ◽  
Amplicon Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Taxonomic Groups ◽  
Bacterial Groups

Although many culture-independent molecular analyses have elucidated a great diversity of freshwater bacterioplankton, the ecophysiological characteristics of several abundant freshwater bacterial groups are largely unknown due to the scarcity of cultured representatives. Therefore, a high-throughput dilution-to-extinction culturing (HTC) approach was implemented herein to enable the culture of these bacterioplankton lineages using water samples collected at various seasons and depths from Lake Soyang, an oligotrophic reservoir located in South Korea. Some predominant freshwater bacteria have been isolated from Lake Soyang via HTC (e.g., the acI lineage); however, large-scale HTC studies encompassing different seasons and water depths have not been documented yet. In this HTC approach, bacterial growth was detected in 14% of 5,376 inoculated wells. Further, phylogenetic analyses of 16S rRNA genes from a total of 605 putatively axenic bacterial cultures indicated that the HTC isolates were largely composed of Actinobacteria, Bacteroidetes, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Verrucomicrobia. Importantly, the isolates were distributed across diverse taxa including phylogenetic lineages that are widely known cosmopolitan and representative freshwater bacterial groups such as the acI, acIV, LD28, FukuN57, MNG9, and TRA3–20 lineages. However, some abundant bacterial groups including the LD12 lineage, Chloroflexi, and Acidobacteria could not be domesticated. Among the 71 taxonomic groups in the HTC isolates, representative strains of 47 groups could either form colonies on agar plates or be revived from frozen glycerol stocks. Additionally, season and water depth significantly affected bacterial community structure, as demonstrated by 16S rRNA gene amplicon sequencing analyses. Therefore, our study successfully implemented a dilution-to-extinction cultivation strategy to cultivate previously uncultured or underrepresented freshwater bacterial groups, thus expanding the basis for future multi-omic studies.

scholarly journals Prevalence, complete genome and metabolic potentials of a phylogenetically novel cyanobacterial symbiont in the coral-killing sponge, Terpios hoshinota

2021 ◽  
Author(s):  
Yu-Hsiang Chen ◽  
Hsing-Ju Chen ◽  
Cheng-Yu Yang ◽  
Jia-Ho Shiu ◽  
Daphne Z. Hoh ◽  
...  
Keyword(s):  
16S Rrna ◽  
Complete Genome ◽  
Large Scale ◽  
Phylogenetic Analyses ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Core Microbiome ◽  
Pigment Analysis ◽  
Terpios Hoshinota

AbstractTerpios hoshinota is a ferocious, space-competing sponge that kills a variety of stony corals by overgrowth. Outbreaks of this species have led to intense coral reef damage and declines in living corals on the square kilometer scale in many geographical locations. Our large-scale 16S rRNA gene survey across three oceans revealed that the core microbiome of T. hoshinota included operational taxonomic units (OTUs) related to Prochloron, Endozoicomonas, Pseudospirillum, SAR116, Magnetospira, and Ruegeria. A Prochloron- related OTU was the most dominant cyanobacterium in T. hoshinota in the western Pacific Ocean, South China Sea, and Indian Ocean. The complete metagenome-assembled genome of the Prochloron-related cyanobacterium and our pigment analysis revealed that this bacterium had phycobiliproteins and phycobilins and lacked chlorophyll b, inconsistent with the iconic definition of Prochloron. Furthermore, the phylogenetic analyses based on 16S rRNA genes and 120 single-copy genes demonstrated that the bacterium was phylogenetically distinct to Prochloron, strongly suggesting that it should be a sister taxon to Prochloron; we therefore proposed this symbiotic cyanobacterium as a novel species under a new genus: Candidatus Paraprochloron terpiosii. With the recovery of the complete genome, we characterized the metabolic potentials of the novel cyanobacterium in carbon and nitrogen cycling and proposed a model for the interaction between Ca. Pp. terpiosi LD05 and T. hoshinota. In addition, comparative genomics analysis revealed that Ca. Paraprochloron and Prochloron showed distinct features in transporter systems and DNA replication.ImportanceThe finding that one species predominates cyanobacteria in T. hoshinota from different geographic locations indicates that this sponge and Ca. Pp. terpiosi LD05 share a tight relationship. This study builds the foundation for T. hoshinota’s microbiome and paves a way for understanding the ecosystem, invasion mechanism, and causes of outbreak of this coral-killing sponge. Also, the first Prochloron-related complete genome enables us to study this bacterium with molecular approaches in the future and broadens our knowledge of the evolution of symbiotic cyanobacteria.

scholarly journals Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

Science ◽  
2021 ◽  
pp. eabf2946
Author(s):  
Louis du Plessis ◽  
John T. McCrone ◽  
Alexander E. Zarebski ◽  
Verity Hill ◽  
Christopher Ruis ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenetic Analyses ◽  
Transmission Dynamics ◽  
Genetic Lineage ◽  
Size Dependent ◽  
Spatio Temporal ◽  
The Uk ◽  
Lineage Structure ◽  
And Control ◽  
Lineage Diversity

The UK’s COVID-19 epidemic during early 2020 was one of world’s largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 SARS-CoV-2 genomes, including 26,181 from the UK sampled throughout the country’s first wave of infection. Using large-scale phylogenetic analyses, combined with epidemiological and travel data, we quantify the size, spatio-temporal origins and persistence of genetically-distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, while lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

scholarly journals Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Matthew R. Olm ◽  
Alexander Crits-Christoph ◽  
Spencer Diamond ◽  
Adi Lavy ◽  
Paula B. Matheus Carnevali ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Ribosomal Proteins ◽  
Large Scale ◽  
Bacterial Species ◽  
Bacterial Genome ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Species Discrimination ◽  
Bacterial Genomes ◽  
Discrimination Power

ABSTRACT Longstanding questions relate to the existence of naturally distinct bacterial species and genetic approaches to distinguish them. Bacterial genomes in public databases form distinct groups, but these databases are subject to isolation and deposition biases. To avoid these biases, we compared 5,203 bacterial genomes from 1,457 environmental metagenomic samples to test for distinct clouds of diversity and evaluated metrics that could be used to define the species boundary. Bacterial genomes from the human gut, soil, and the ocean all exhibited gaps in whole-genome average nucleotide identities (ANI) near the previously suggested species threshold of 95% ANI. While genome-wide ratios of nonsynonymous and synonymous nucleotide differences (dN/dS) decrease until ANI values approach ∼98%, two methods for estimating homologous recombination approached zero at ∼95% ANI, supporting breakdown of recombination due to sequence divergence as a species-forming force. We evaluated 107 genome-based metrics for their ability to distinguish species when full genomes are not recovered. Full-length 16S rRNA genes were least useful, in part because they were underrecovered from metagenomes. However, many ribosomal proteins displayed both high metagenomic recoverability and species discrimination power. Taken together, our results verify the existence of sequence-discrete microbial species in metagenome-derived genomes and highlight the usefulness of ribosomal genes for gene-level species discrimination. IMPORTANCE There is controversy about whether bacterial diversity is clustered into distinct species groups or exists as a continuum. To address this issue, we analyzed bacterial genome databases and reports from several previous large-scale environment studies and identified clear discrete groups of species-level bacterial diversity in all cases. Genetic analysis further revealed that quasi-sexual reproduction via horizontal gene transfer is likely a key evolutionary force that maintains bacterial species integrity. We next benchmarked over 100 metrics to distinguish these bacterial species from each other and identified several genes encoding ribosomal proteins with high species discrimination power. Overall, the results from this study provide best practices for bacterial species delineation based on genome content and insight into the nature of bacterial species population genetics.

A description of the second species of the genus Bleptus Eaton, 1885 (Ephemeroptera: Heptageniidae) from Japan, and phylogenetic relationships of two Bleptus mayflies inferred from mitochondrial and nuclear gene sequences

Zootaxa ◽  
2021 ◽  
Vol 4974 (2) ◽  
pp. 333-360
Author(s):  
KOJI TOJO ◽  
KEN MIYAIRI ◽  
YUTO KATO ◽  
AYANA SAKANO ◽  
TOMOYA SUZUKI
Keyword(s):  
Phylogenetic Analyses ◽  
Ribosomal Subunit ◽  
Nuclear Gene ◽  
Taxonomic Status ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Gene Sequences ◽  
Molecular Phylogenetic ◽  
Black Band ◽  
Relationship Of

A new mayfly species, Bleptus michinokuensis sp. nov. (Ephemeroptera: Heptageniidae) is described on the basis of specimens of male and female adults and mature nymphs collected at a seepage zone of a small freshwater branch of the ‘Tachiya-zawa-gawa’ River located amongst the northern foothills of Mt. Gassan (Shonai-machi Town, Yamagata Prefecture, Japan). This new Bleptus species is characterized by its clear fore and hind wings. That is, they neither exhibit the distinct black band on the fore wings, nor the characteristic darkened margins along the edges of both the fore and hind wings. Rather it has a blackish colored terminal half of its fore legs (i.e., tibial, tarsal and pretarsal segments). These features differ clearly when comparing them to the other known species, Bleptus fasciatus Eaton. The information and data describing the habitat and distribution range of this new species are also noted. We also examined and discussed the genetic relationship of two Bleptus mayflies to settle the taxonomic status, inferred from the partially sequenced cytochrome c oxidase subunit I (COI) and large mitochondrial ribosomal subunit (16S rRNA) genes, and also the nuclear internal transcribed spacer 2 (ITS2) gene sequences. Consequently, phenetic and molecular phylogenetic analyses agreed well in terms of clustering. 

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