scholarly journals Comparative genomics of Mycoplasma pneumoniae isolated from children with pneumonia: South Korea, 2010–2016

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Joon Kee Lee ◽  
Moon-Woo Seong ◽  
Dongjin Shin ◽  
Jong-Il Kim ◽  
Mi Seon Han ◽  
...  
Keyword(s):  
South Korea ◽  
Mycoplasma Pneumoniae ◽  
Gc Content ◽  
Structural Diversity ◽  
Whole Genome ◽  
Base Pairs ◽  
Tract Infections ◽  
Phylogenetic Associations

Abstract Background Mycoplasma pneumoniae is a common cause of respiratory tract infections in children and adults. This study applied high-throughput whole genome sequencing (WGS) technologies to analyze the genomes of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during the two epidemics from 2010 to 2016 in comparison with a global collection of 48 M. pneumoniae strains which includes seven countries ranging from 1944 to 2017. Results The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to > 99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific insertions (three in P1 type 1 and one in P1 type 2), of which were all hypothetical proteins except one tRNA insertion in all P1 type 1 strains. The phylogenetic associations of 30 strains were generally consistent with the multilocus sequence typing results. The phylogenetic tree constructed with 78 genomes including 30 genomes from Korea formed two clusters and further divided into two sub-clusters. eBURST analysis revealed two clonal complexes according to P1 typing results showing higher diversity among P1 type 2 strains. Conclusions The comparative whole genome approach was able to define high genetic identity, unique structural diversity, and phylogenetic associations among the 78 M. pneumoniae strains isolated worldwide.

scholarly journals Comparative Genomics of Mycoplasma pneumoniae isolated from Children with Pneumonia: South Korea, 2010-2016

2019 ◽  
Author(s):  
Joon Kee Lee ◽  
Moon-Woo Seong ◽  
Dongjin Shin ◽  
Jong-Il Kim ◽  
Mi Seon Han ◽  
...  
Keyword(s):  
South Korea ◽  
Mycoplasma Pneumoniae ◽  
Gc Content ◽  
Structural Diversity ◽  
Base Pairs ◽  
Tract Infections ◽  
Type 3 ◽  
Phylogenetic Associations

Abstract Background Mycoplasma pneumoniae is a common cause of respiratory tract infections in children and adults. This study applied high-throughput whole genome sequencing (WGS) technologies to analyze the genomes of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during the two epidemics from 2010 to 2016 in comparison with a global collection of 48 M. pneumoniae strains which includes seven countries ranging from 1944 to 2017. Results The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to > 99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific insertions (three in P1 type 1 and one in P1 type 2), of which were all hypothetical proteins except for one tRNA insertion in all P1 type 1 strains. The phylogenetic associations of 30 strains were generally consistent with the multilocus sequence typing results. eBURST analysis demonstrated two clonal complexes which are accordant with the known P1 typing, with higher diversity among P1 type 2 strains. The phylogenetic tree constructed with 78 genomes including 48 genomes outside Korea formed three clusters, in which the sequence type 3 strains from Korea were divided into two P1 type 1 clusters. Conclusions The comparative genome analysis of the 78 M. pneumoniae strains including 30 strains from Korea by WGS reveals structural diversity and phylogenetic associations, even though the similarity across the strains was very high.

scholarly journals Comparative Genomics of Mycoplasma pneumoniae isolated from Children with Pneumonia: South Korea, 2010-2016

2019 ◽  
Author(s):  
Joon Kee Lee ◽  
Eun Hwa Choi ◽  
Moon-Woo Seong ◽  
Youbin Yeon ◽  
Sung Im Cho ◽  
...  
Keyword(s):  
South Korea ◽  
Mycoplasma Pneumoniae ◽  
Gc Content ◽  
Structural Diversity ◽  
Base Pairs ◽  
Tract Infections ◽  
Type 3 ◽  
Phylogenetic Associations

Abstract Background Mycoplasma pneumoniae is a common cause of respiratory tract infections in children and adults. This study applied high-throughput whole genome sequencing (WGS) technologies to analyze the genomes of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during the two epidemics from 2010 to 2016 in comparison with a global collection of 48 M. pneumoniae strains which includes seven countries ranging from 1944 to 2017. Results The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to > 99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific insertions (three in P1 type 1 and one in P1 type 2), of which were all hypothetical proteins except for one tRNA insertion in all P1 type 1 strains. The phylogenetic associations of 30 strains were generally consistent with the multilocus sequence typing results. eBURST analysis demonstrated two clonal complexes which are accordant with the known P1 typing, with higher diversity among P1 type 2 strains. The phylogenetic tree constructed with 78 genomes including 48 genomes outside Korea formed three clusters, in which the sequence type 3 strains from Korea were divided into two P1 type 1 clusters. Conclusions The comparative genome analysis of the 78 M. pneumoniae strains including 30 strains from Korea by WGS reveals structural diversity and phylogenetic associations, even though the similarity across the strains was very high.

scholarly journals Comparative Genomics of Mycoplasma pneumoniae isolated from Children with Pneumonia: South Korea, 2010-2016

2019 ◽  
Author(s):  
Joon Kee Lee ◽  
Moon-Woo Seong ◽  
Dongjin Shin ◽  
Jong-Il Kim ◽  
Mi Seon Han ◽  
...  
Keyword(s):  
South Korea ◽  
Mycoplasma Pneumoniae ◽  
Gc Content ◽  
Structural Diversity ◽  
Base Pairs ◽  
Tract Infections ◽  
Type 3 ◽  
Phylogenetic Associations

Abstract Background Mycoplasma pneumoniae is a common cause of respiratory tract infections in children and adults. This study applied high-throughput whole genome sequencing (WGS) technologies to analyze the genomes of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during the two epidemics from 2010 to 2016 in comparison with a global collection of 48 M. pneumoniae strains which includes seven countries ranging from 1944 to 2017. Results The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to > 99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific insertions (three in P1 type 1 and one in P1 type 2), of which were all hypothetical proteins except for one tRNA insertion in all P1 type 1 strains. The phylogenetic associations of 30 strains were generally consistent with the multilocus sequence typing results. eBURST analysis demonstrated two clonal complexes which are accordant with the known P1 typing, with higher diversity among P1 type 2 strains. The phylogenetic tree constructed with 78 genomes including 48 genomes outside Korea formed three clusters, in which the sequence type 3 strains from Korea were divided into two P1 type 1 clusters. Conclusions The comparative genome analysis of the 78 M. pneumoniae strains including 30 strains from Korea by WGS reveals structural diversity and phylogenetic associations, even though the similarity across the strains was very high.

scholarly journals Comparative Genomics of Mycoplasma pneumoniae isolated from Children with Pneumonia: South Korea, 2010-2016

2019 ◽  
Author(s):  
Joon Kee Lee ◽  
Moon-Woo Seong ◽  
Dongjin Shin ◽  
Jong-Il Kim ◽  
Mi Seon Han ◽  
...  
Keyword(s):  
South Korea ◽  
Mycoplasma Pneumoniae ◽  
Gc Content ◽  
Structural Diversity ◽  
Base Pairs ◽  
Tract Infections ◽  
Type 3 ◽  
Phylogenetic Associations

Abstract Background Mycoplasma pneumoniae is a common cause of respiratory tract infections in children and adults. This study applied high-throughput whole genome sequencing (WGS) technologies to analyze the genomes of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during the two epidemics from 2010 to 2016 in comparison with a global collection of 48 M. pneumoniae strains which includes seven countries ranging from 1944 to 2017. Results The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to > 99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific insertions (three in P1 type 1 and one in P1 type 2), of which were all hypothetical proteins except for one tRNA insertion in all P1 type 1 strains. The phylogenetic associations of 30 strains were generally consistent with the multilocus sequence typing results. eBURST analysis demonstrated two clonal complexes which are accordant with the known P1 typing, with higher diversity among P1 type 2 strains. The phylogenetic tree constructed with 78 genomes including 48 genomes outside Korea formed three clusters, in which the sequence type 3 strains from Korea were divided into two P1 type 1 clusters. Conclusions The comparative genome analysis of the 78 M. pneumoniae strains including 30 strains from Korea by WGS reveals structural diversity and phylogenetic associations, even though the similarity across the strains was very high.

scholarly journals 638. Comparative Genomics of Mycoplasma pneumoniae Isolated From Children with Pneumonia: South Korea, 2010–2016

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S295-S295
Author(s):  
Hoan J Lee ◽  
Joon Kee Lee ◽  
Yun Young Choi ◽  
Ji Young Park ◽  
Moon-Woo Seong ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
South Korea ◽  
Mycoplasma Pneumoniae ◽  
Gc Content ◽  
Genomic Analysis ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Whole Genome

Abstract Background This study applied high-throughput whole-genome sequencing (WGS) technologies to investigate the comparative genomics of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during two epidemics from 2010 to 2016 in comparison with a global collection of 48 Mycoplasma pneumoniae strains which includes seven countries ranging from 1944 to 2017. Methods A total number of 30 M. pneumoniae strains were selected for whole-genome sequence analysis from two epidemics, 2010–2012 and 2014–2016. Next-generation sequencing (NGS) of all M. pneumoniae strains was performed using the Illumina MiSeq desktop sequencer. Comparative genomic analysis was performed using BLAST Ring Image Generator (BRIG), MAUVE, MAFFT, CLC Phylogeny Module, SnpEff, and Pathosystems Resource Integration Center (PATRIC). Results The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to>99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific of which were all hypothetical proteins except for one tRNA insertion in all P1 type 1 strains. eBURST analysis demonstrated two clonal complexes which are accordant with the known P1 typing, with higher diversity among P1 type 2 strains. The phylogenetic tree constructed with 78 genomes including 48 genomes outside Korea, formed three clusters, in which the sequence type 3 strains from Korea were divided into two P1 type 1 clusters. Conclusion The comparative genomics of the 78 M. pneumoniae strains including 30 strains from Korea by WGS reveals structural diversity and phylogenetic associations, even though the similarity across the strains was very high. Disclosures All authors: No reported disclosures.

Sick day advice for people with diabetes

2021 ◽  
Vol 32 (Sup3) ◽  
pp. S10-S13
Author(s):  
Martha Stewart
Keyword(s):  
Type 2 Diabetes ◽  
Diabetes Management ◽  
Glucose Levels ◽  
Emergency Hospital Admission ◽  
Intercurrent Illness ◽  
Martha Stewart ◽  
The Common ◽  
Tract Infections

In this article Martha Stewart discusses how illness affects diabetes management and outlines the ‘sick-day advice’ that should be shared with people living with type 1 and type 2 diabetes Intercurrent illness can cause glucose levels to rise in people with diabetes mellitus. These illnesses include the common cold, diarrhoea and vomiting, urinary tract infections and COVID-19. If diabetes is not managed well during illness it can escalate and result in more serious conditions, such as diabetic ketoacidosis (DKA) and hyperosmolar hyperglycaemic state (HHS), which would require emergency hospital admission. This article discusses how illness affects diabetes management and outlines the ‘sick-day advice’ that should be shared with people living with type 1 and type 2 diabetes.

scholarly journals Debris Flow Damage Assessment by Considering Debris Flow Direction and Direction Angle of Structure in South Korea

Water ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 328 ◽  
Author(s):  
Dong Nam ◽  
Man-Il Kim ◽  
Dong Kang ◽  
Byung Kim
Keyword(s):  
South Korea ◽  
Debris Flow ◽  
Debris Flows ◽  
Impact Force ◽  
Mountainous Areas ◽  
Mountainous Regions ◽  
Impact Forces ◽  
The Impact

Recently, human and property damages have often occurred due to various reasons—such as landslides, debris flow, and other sediment-related disasters—which are also caused by regional torrential rain resulting from climate change and reckless development of mountainous areas. Debris flows mainly occur in mountainous areas near urban living communities and often cause direct damages. In general, debris flows containing soil, rock fragments, and driftwood temporarily travel down to lower parts along with a mountain torrent. However, debris flows are also often reported to stream down from the point where a slope failure or a landslide occurs in a mountain directly to its lower parts. The impact of those debris flows is one of the main factors that cause serious damage to structures. To mitigate such damage of debris flows, a quantitative assessment of the impact force is thus required. Moreover, technologies to evaluate disaster prevention facilities and structures at disaster-prone regions are needed. This study developed two models to quantitatively analyze the damages caused by debris flows on structures: Type-1 model for calculating the impact force, which reflected the flow characteristics of debris flows and the Type-2 model, which calculated the impact force based on the topographical characteristics of mountainous regions. Using RAMMS a debris flow runoff model, the impact forces assessed through Type-1 and Type-2 models were compared to check reliability. Using the assessed impact forces, the damage ratio of the structures was calculated and the amount of damage caused by debris flows on the structures was ultimately assessed. The results showed that the Type-1 model overestimated the impact force by 10% and the Type-2 model by 4% for Mt. Umyeon in Seoul, compared to the RAMMS model. In addition, the Type-1 model overestimated the impact force by 3% and Type-2 by 2% for Mt. Majeok in Chuncheon, South Korea.

scholarly journals Draft Genome Sequence of Aspergillus oryzae BP2-1, Isolated from Traditional Malted Rice in South Korea

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Jongbum Jeon ◽  
Jung A Kim ◽  
Sook-Young Park ◽  
Gye-Won Kim ◽  
Cheon-Seok Park ◽  
...  
Keyword(s):  
South Korea ◽  
Aspergillus Oryzae ◽  
Genome Sequence ◽  
Draft Genome ◽  
Starter Culture ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type

The fungus Aspergillus oryzae strain BP2-1 was isolated from the traditional malted starter culture nuruk. We report here the draft whole-genome sequence of A. oryzae BP2-1, which is comprised of 14 scaffolds with a total length of 39,455,382 bp and a GC content of 47.13%.

scholarly journals Mycoplasma pneumoniae P1 Type 1- and Type 2-Specific Sequences within the P1 Cytadhesin Gene of Individual Strains

2001 ◽  
Vol 69 (9) ◽  
pp. 5612-5618 ◽  
Author(s):  
J. Wendelien Dorigo-Zetsma ◽  
Berry Wilbrink ◽  
Jacob Dankert ◽  
Sebastian A. J. Zaat
Keyword(s):  
Mycoplasma Pneumoniae ◽  
Direct Sequencing ◽  
Variable Region ◽  
Polymorphism Analysis ◽  
Nucleotide Polymorphisms ◽  
Gene Sequences ◽  
Gene Variation ◽  
Individual Strain

ABSTRACT Mycoplasma pneumoniae strains traditionally are divided into two types, based on sequence variation in the P1 gene. Recently, however, we have identified 8 P1 subtypes by restriction fragment length polymorphism analysis. In the present study the P1 gene sequences of three P1 type 1 and two P1 type 2 M. pneumoniae strains were analyzed. A new P1 gene sequence in a type 1 strain with partial similarity to a recently reported variable region in the P1 gene of an M. pneumoniae type 2 strain (T. Kenri, R. Taniguchi, Y. Sasaki, N. Okazaki, M. Narita, K. Izumikawa, M. Umetsu, and T.Sasaki, Infect. Immun. 67:4557–4562, 1999) was identified. In addition, the P1 gene of the type 1 strain contained another region with nucleotide polymorphisms identical to a stretch in the P1 gene of one of our type 2 strains. These findings indicate that recombination between sequences specific for P1 type 1 and type 2 had occurred and that P1 type 1 and type 2 hybrid sequences can be present within the P1 gene of an individual strain. Identical or nearly identical variable P1 gene sequences were present in several repetitive regions outside the P1 gene locus in the genome of M. pneumoniae strain M129, implying recombination as a mechanism for generation of the P1 gene variation. Additionally, in the P1 gene sequences of four of the five strains studied, single-nucleotide polymorphisms different from the previously reported P1 type 1 and 2 characteristic sequences were identified. The polymorphic sites are candidate targets for genotyping of M. pneumoniae by direct sequencing of amplicons from clinical specimens.

Effectiveness of Decitabine in Chronic Myelomonocytic Leukemia Patients. International Cooperative Multi-Center Study.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 3809-3809
Author(s):  
Marcelo Iastrebner ◽  
Jun Ho Jang ◽  
Isolda Fernandez ◽  
Kihyun Kim ◽  
Guy Garay ◽  
...  
Keyword(s):  
Overall Survival ◽  
South Korea ◽  
Complete Response ◽  
Chronic Myelomonocytic Leukemia ◽  
First Year ◽  
Cell Transplant ◽  
Myelomonocytic Leukemia

Abstract Abstract 3809 Poster Board III-745 Background Epigenetic therapy with hypomethylating agents has recently been approved for the treatment of myelodysplastic syndromes (MDS) in South Korea and Argentina. Chronic Myelomonocytic Leukemia (CMML) is a hybrid disorder characterized by myeloid proliferation and erythroid-megakaryocytic dysplasia. Subgroups analysis (Steensma D et al. JCO.2008.19) and open-label studies (Aribi A, Cancer 2007;109:713-7) have reported that decitabine (DACOGEN, Janssen Cilag Farmaceutica S.A. and Eisai Inc.) is effective in the management of CMML. Study objective To describe the clinical and hematological improvement with decitabine among patients with CMML on a “real world program”. Methods We enrolled patients with CMML, who received decitabine at different centers of South Korea and Argentina, between July 2007 and June 2009. A report prepared ad hoc was completed. We took into account WHO classification, as well as performance status by ECOG, co-morbidities, previous treatments and IWG 2006 criteria. Efficacy was evaluated with at least 2 cycles. Inclusion criteria were ≥18 years of age and confirmed diagnosis of CMML type 1 or type 2. Exclusion criteria were diagnosis of acute myeloid leukemia (AML) or other progressive malignant disease. Patients with prior therapy were not excluded. All patients received decitabine 20 mg/m2 IV over 1 hour once daily for 5 consecutive days repeating every 4 weeks. We evaluated the overall improvement rate (complete response + marrow complete response + partial response + hematologic improvement) and rate of stable disease or better. Results We analyzed 26 CMML patients, Type-1: 65% and Type-2: 35%, median age 61 (R 23-82), male: 81%, all patients were BCR/ABL negative, and 23% had proliferative features with WBC >13000/mm3 and splenomegaly at the time of diagnosis. Karyotype was normal (n=19), isolated -7/7q- (n=2), +8 (n=1), del3q/der3 (n=1), tY/1 (n=1), complex (n=1) and no metaphases (n=1). The median interval from diagnosis to treatment was 8 months (R 0-35); Eight patients received previous chemotherapy: low dose (n=4), high dose (n=2) or bone marrow transplant (n=2); and the median number of cycles received was 5 (R 1-13). Clinical and Hematological response are summarized in Table. Most of the patients remained alive during the first year of follow-up. The accumulated overall survival curve showed a plateau that lasted until the end of the first year; afterwards it progressively decreased (Graphic). Two patients received allogeneic stem cell transplant without additional toxicity. Conclusion Decitabine demonstrated a remarkable activity (58%) in CMML with an accumulated overall survival of 37% at 2 years of follow-up. This treatment allowed patients to be transplanted in a better condition. Disclosures: No relevant conflicts of interest to declare.

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