scholarly journals Optical DNA Mapping of Plasmids Reveals Clonal Spread of Carbapenem-Resistant Klebsiella pneumoniae in a Large Thai Hospital

Antibiotics ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1029
Author(s):  
Sriram KK ◽  
Tsegaye Sewunet ◽  
Walaiporn Wangchinda ◽  
Teerawit Tangkoskul ◽  
Visanu Thamlikitkul ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Surrogate Marker ◽  
Bacterial Strains ◽  
Dna Mapping ◽  
Carbapenem Resistant ◽  
Different Types ◽  
Siriraj Hospital ◽  
Clonal Spread ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Carbapenem-resistant Klebsiella pneumoniae (CR-KP) in patients admitted to hospitals pose a great challenge to treatment. The genes causing resistance to carbapenems are mostly found in plasmids, mobile genetic elements that can spread easily to other bacterial strains, thus exacerbating the problem. Here, we studied 27 CR-KP isolates collected from different types of samples from 16 patients admitted to the medical ward at Siriraj Hospital in Bangkok, Thailand, using next generation sequencing (NGS) and optical DNA mapping (ODM). The majority of the isolates belonged to sequence type (ST) 16 and are described in detail herein. Using ODM, we identified the plasmid carrying the blaNDM-1 gene in the ST16 isolates and the plasmids were very similar, highlighting the possibility of using ODM of plasmids as a surrogate marker of nosocomial spread of bacteria. We also demonstrated that ODM could identify that the blaCTX-M-15 and blaOXA-232 genes in the ST16 isolates were encoded on separate plasmids from the blaNDM-1 gene and from each other. The other three isolates belonged to ST147 and each of them had distinct plasmids encoding blaNDM-1.

scholarly journals Evaluation of Ion Torrent next-generation sequencing for thalassemia diagnosis

2020 ◽  
Vol 48 (12) ◽  
pp. 030006052096777
Author(s):  
Peisong Chen ◽  
Xuegao Yu ◽  
Hao Huang ◽  
Wentao Zeng ◽  
Xiaohong He ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Ion Torrent ◽  
Next Generation ◽  
Large Deletions ◽  
Different Types ◽  
Variant Detection ◽  
Polymerase Chain ◽  
Next Generation Sequencing Ngs ◽  
Accuracy And Repeatability ◽  
Generation Sequencing

Introduction To evaluate a next-generation sequencing (NGS) workflow in the screening and diagnosis of thalassemia. Methods In this prospective study, blood samples were obtained from people undergoing genetic screening for thalassemia at our centre in Guangzhou, China. Genomic DNA was polymerase chain reaction (PCR)-amplified and sequenced using the Ion Torrent system and results compared with traditional genetic analyses. Results Of the 359 subjects, 148 (41%) were confirmed to have thalassemia. Variant detection identified 35 different types including the most common. Identification of the mutational sites by NGS were consistent with those identified by Sanger sequencing and Gap-PCR. The sensitivity and specificities of the Ion Torrent NGS were 100%. In a separate test of 16 samples, results were consistent when repeated ten times. Conclusion Our NGS workflow based on the Ion Torrent sequencer was successful in the detection of large deletions and non-deletional defects in thalassemia with high accuracy and repeatability.

scholarly journals Use of Next Generation Sequencing and Synergy Susceptibility Testing in Diagnosis and Treatment of Carbapenem-Resistant Klebsiella pneumoniae Blood Stream Infection

2018 ◽  
Vol 2018 ◽  
pp. 1-4
Author(s):  
Yuetian Yu ◽  
Fupin Hu ◽  
Cheng Zhu ◽  
Erzhen Chen ◽  
Liangjing Lu ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Klebsiella Pneumoniae ◽  
Lupus Erythematosus ◽  
Susceptibility Testing ◽  
Blood Stream Infection ◽  
Blood Stream ◽  
Next Generation ◽  
Carbapenem Resistant ◽  
Appropriate Treatment ◽  
Generation Sequencing

Early diagnosis and appropriate treatment for carbapenem-resistant Klebsiella pneumoniae (CR-Kp) infection is a big challenge for clinicians due to its high mortality. Every effort has been made to improve its clinical outcomes. However, treatment according to synergy susceptibility testing has never been reported in the literature. We reported a 29-year-old systemic lupus erythematosus female with CR-Kp blood stream infection. We highlighted the identification by next generation sequencing and treatment according to synergy susceptibility testing in the case.

PLAG1 Immunohistochemical Staining Is a Surrogate Marker for PLAG1 Fusions in Lipoblastomas

2021 ◽  
pp. 109352662110433
Author(s):  
Mikako Warren ◽  
Nishant Tiwari ◽  
Sabrina Sy ◽  
Gordana Raca ◽  
Ryan J Schmidt ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Gold Standard ◽  
Immunohistochemical Staining ◽  
Surrogate Marker ◽  
Molecular Testing ◽  
Protein Overexpression ◽  
Conventional Cytogenetics ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Lipomatous Tumors

Background The hallmark of lipoblastoma is a PLAG1 fusion. PLAG1 protein overexpression has been reported in sporadic PLAG1-rearranged lipoblastomas. Methods We evaluated the utility of PLAG1 immunohistochemical staining (IHC) in 34 pediatric lipomatous tumors, correlating the results with histology and conventional cytogenetics, FISH and/or next generation sequencing (NGS) results. Results The study included 24 lipoblastomas, divided into 2 groups designated as “Lipoblastoma 1” with both lipoblastoma histology and PLAG1 rearrangement (n = 16) and “Lipoblastoma 2” with lipoblastoma histology but without PLAG1 cytogenetic rearrangement (n = 8), and 10 lipomas with neither lipoblastoma histology nor a PLAG1 rearrangement. Using the presence of a fusion as the “gold standard” for diagnosing lipoblastoma (Lipoblastoma 1), the sensitivity of PLAG1 IHC was 94%. Using histologic features alone (Lipoblastoma 1 + 2), the sensitivity was 96%. Specificity, as defined by the ability to distinguish lipoma from lipoblastoma, was 100%, as there were no false positives in the lipoma group. Conclusions Cytogenetics/molecular testing is expensive and may not be ideal for detecting PLAG1 fusions because PLAG1 fusions are often cytogenetically cryptic and NGS panels may not include all partner genes. PLAG1 IHC is an inexpensive surrogate marker of PLAG1 fusions and may be useful in distinguishing lipoblastomas from lipomas.

scholarly journals Draft Genome Sequence of Carbapenem-Resistant Klebsiella pneumoniae XPY20 Collected from a Bloodstream Infection Patient

2018 ◽  
Vol 6 (21) ◽  
Author(s):  
Qiong Chen ◽  
Jia-wei Zhou ◽  
Sheng-hai Wu ◽  
Xiao-hua Meng ◽  
Dao-jun Yu ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Draft Genome ◽  
Bloodstream Infections ◽  
Mortality Rates ◽  
Resistance Mechanisms ◽  
Severe Problem ◽  
Content Type ◽  
Carbapenem Resistant ◽  
Infection Patient ◽  
Generation Sequencing

ABSTRACT Bloodstream infections caused by carbapenem-resistant Klebsiella pneumoniae (CRKP) strains have been a severe problem with high clinical costs and high mortality rates. The bla KPC-2-producing CRKP strain XPY20 was collected from the blood of a patient. The genome characteristics and antimicrobial resistance mechanisms were determined using next-generation sequencing.

scholarly journals Effect of Different Saudi Honey Types Mixed with Natural Substances on Some Bacterial Strains

2017 ◽  
Vol 24 (1) ◽  
pp. 23-31 ◽  
Author(s):  
Fatimah A. Nashawi ◽  
Hani Y. Abdullah ◽  
Nahlaa A. Khalifa ◽  
Ibrahim A. Alzahrani ◽  
Ahmed A. Al-Ghamdi
Keyword(s):  
Staphylococcus Aureus ◽  
Klebsiella Pneumoniae ◽  
Antibacterial Effect ◽  
Synergistic Effects ◽  
Bacterial Species ◽  
Bacterial Strains ◽  
Natural Substances ◽  
Different Types ◽  
And Staphylococcus Aureus ◽  
Natural Honey

To evaluate the antibacterial eff ects of three types of Saudi honey (Feghra, Sider and Natural honey) alone and mixed with ginger or lemon in comparison to Manuka honey as a potential natural antibacterial agent. Saudi honeys were evaluated against five types of bacterial strains; Klebsiella pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa, Haemophilus influenzae and Streptococcus pneumoniae. Chocolate agars were prepared first with different concentrations of each type of honey, and then with specific concentrations either of ginger or lemon added to honey. Bacterial species were inoculated on each agar and incubated at 37oC in a CO2 incubator overnight. Significant differences were found between diff erent types of honey and different concentrations of the same honey on bacterial growth. There are no significant differences and synergistic effects when adding ginger to diff erent honey types. Addition of lemon show significant differences and good synergistic effects against all tested bacterial species except Klebsiella pneumoniae and Staphylococcus aureus at 15 and 20% honey concentration. In conclusion, antibacterial effects of different types of honey are type and concentration dependent. Adding lemon to the different types of honey changes the pH and acidity and increases the honey’s antibacterial effect.

Mutational landscape of AKT1/2/3 in Chinese patients with solid tumors.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e15566-e15566
Author(s):  
Hui Kong ◽  
Weijia Fang ◽  
Haibo Mou ◽  
Feng Xiao Chen ◽  
Lingxiang Liu ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Solid Tumors ◽  
Chinese Patients ◽  
Great Promise ◽  
Central Component ◽  
Next Generation ◽  
Gene Panel Testing ◽  
Different Types ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

e15566 Background: As a central component of PI3K/AKT pathway, AKT serves as an attractive target of anti-cancer strategy with various AKT inhibitors, which show great promise in phase I/II clinical trials. This study aimed to investigate AKT1/2/3 status in different types of cancers by using next generation sequencing (NGS). Methods: Formalin-fixed, paraffin-embedded (FFPE) tumor samples were collected from 10,010 Chinese patients with solid tumors and subjected to next-generation sequencing (NGS)-based 450 gene panel testing carried out by a College of American Pathologists (CAP) accredited and Clinical Laboratory Improvement Amendments (CLIA) certified laboratory. Genomic alterations, tumor mutational burden (TMB) values, and microsatellite instability (MSI) status were assessed with a mean coverage of 1000X, including single base substitutions, short and long insertion/deletions, copy number variations, gene fusions, and rearrangements. Genomic data and immune checkpoint inhibitors (ICIs) treatment outcome of a cohort of 1610 patients with solid tumors were derived from cBioPortal (MSKCC, Nat Genet. 2019). Results: AKT1/2/3 were found to be mutually exclusive with each other and accounted for 3.4% in this cohort. The frequencies of AKT1/2/3 variations were 1.1%, 1.6%, and 0.8%, respectively. The most common co-altered genes associated with AKT1/2/3 variations were TP53 (69.4%), PIK3CA (19.3%), KRAS (19%), CCNE1 (18.4%), CDKN2A (16.6%), and 11q13 (6.5%). AKT1/2/3 variations were significantly associated with higher TMB, and independent of MSI status. Outcome data from the MSKCC cohort showed that patients with AKT1/2/3 variations had a remarkable clinical benefit to ICIs treatment compared to patients with wild-type AKT1/2/3 in overall survival (OS) (NA vs 18 months, p = 0.009). Furthermore, AKT1/2/3 variations were independent risk factors of OS (HR: 0.55, 95%CI: 0.34-0.87, p = 0.012). Conclusions: The prevalence of AKT1/2/3 somatic alterations across different types of solid tumors in China was 3.4%. AKT1/2/3 variations were associated with an increased TMB and favorable response to ICIs, suggesting that A KT1/2/3 variations may be biomarkers for guiding anti-AKT agents and ICI treatment.

scholarly journals Molecular Epidemiology, Sequence Types, and Plasmid Analyses of KPC-Producing Klebsiella pneumoniae Strains in Israel

2010 ◽  
Vol 54 (7) ◽  
pp. 3002-3006 ◽  
Author(s):  
Azita Leavitt ◽  
Yehuda Carmeli ◽  
Inna Chmelnitsky ◽  
Moran G. Goren ◽  
Itzhak Ofek ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Molecular Epidemiology ◽  
Medical Center ◽  
Sequence Type ◽  
Beta Lactamase ◽  
Drug Resistant ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Clonal Spread ◽  
Sequence Types

ABSTRACT Sporadic isolates of carbapenem-resistant KPC-2-producing Klebsiella pneumoniae were isolated in Tel Aviv Medical Center during 2005 and 2006, parallel to the emergence of the KPC-3-producing K. pneumoniae sequence type 258 (ST 258). We aimed to study the molecular epidemiology of these isolates and to characterize their bla KPC-carrying plasmids and their origin. Ten isolates (8 KPC-2 and 2 KPC-3 producing) were studied. All isolates were extremely drug resistant. They possessed the bla KPC gene and varied in their additional beta-lactamase contents. The KPC-2-producing strains belonged to three different sequence types: ST 340 (n = 2), ST 277 (n = 2), and a novel sequence type, ST 376 (n = 4). Among KPC-3-producing strains, a single isolate (ST 327) different from ST 258 was identified, but both strains carried the same plasmid (pKpQIL). The KPC-2-encoding plasmids varied in size (45 to 95 kb) and differed among each of the STs. Two of the Klebsiella bla KPC-2-carrying plasmids were identical to plasmids from Escherichia coli, suggesting a common origin of these plasmids. These data indicate that KPC evolution in K. pneumoniae is related to rare events of interspecies spread of bla KPC-2-carrying plasmids from E. coli followed by limited clonal spread, whereas KPC-3 carriage in this species is related almost strictly to clonal expansion of ST 258 carrying pKpQIL.

scholarly journals Prevalence of pharmacogenomic variants in 100 pharmacogenes among Southeast Asian populations under the collaboration of the Southeast Asian Pharmacogenomics Research Network (SEAPharm)

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Chakkaphan Runcharoen ◽  
Koya Fukunaga ◽  
Insee Sensorn ◽  
Nareenart Iemwimangsa ◽  
Sommon Klumsathian ◽  
...  
Keyword(s):  
Drug Efficacy ◽  
Cost Effective ◽  
Southeast Asian ◽  
Research Network ◽  
Serious Adverse Events ◽  
Asian Populations ◽  
Effective Technology ◽  
Different Types ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AbstractPharmacogenomics can enhance the outcome of treatment by adopting pharmacogenomic testing to maximize drug efficacy and lower the risk of serious adverse events. Next-generation sequencing (NGS) is a cost-effective technology for genotyping several pharmacogenomic loci at once, thereby increasing publicly available data. A panel of 100 pharmacogenes among Southeast Asian (SEA) populations was resequenced using the NGS platform under the collaboration of the Southeast Asian Pharmacogenomics Research Network (SEAPharm). Here, we present the frequencies of pharmacogenomic variants and the comparison of these pharmacogenomic variants among different SEA populations and other populations used as controls. We investigated the different types of pharmacogenomic variants, especially those that may have a functional impact. Our results provide substantial genetic variations at 100 pharmacogenomic loci among SEA populations that may contribute to interpopulation variability in drug response phenotypes. Correspondingly, this study provides basic information for further pharmacogenomic investigations in SEA populations.

scholarly journals An integrated overview of the bacterial flora composition of Hyalomma anatolicum, the main vector of CCHF

2021 ◽  
Vol 15 (6) ◽  
pp. e0009480
Author(s):  
Nayyereh Choubdar ◽  
Fateh Karimian ◽  
Mona Koosha ◽  
Mohammad Ali Oshaghi
Keyword(s):  
Bacterial Flora ◽  
Hyalomma Anatolicum ◽  
Bacterial Strains ◽  
Bacillus Velezensis ◽  
Bacterial Phyla ◽  
Control Intervention ◽  
Vector Control Intervention ◽  
Integrated Methods ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

The microbial flora associated with Hyalomma anatolicum ticks was investigated using culture-dependent (CD) and independent (next generation sequencing, NGS) methods. The bacterial profiles of different organs, development stages, sexes, and of host cattle skins were analyzed using the CD method. The egg and female gut microbiota were investigated using NGS. Fourteen distinct bacterial strains were identified using the CD method, of which Bacillus subtilis predominated in eggs, larval guts and in adult female and male guts, suggesting probable transovarial transmission. Bacillus velezensis and B. subtilis were identified in cattle skin and tick samples, suggesting that skin is the origin of tick bacteria. H.anatolicum males harbour lower bacterial diversity and composition than females. The NGS analysis revealed five different bacterial phyla across all samples, Proteobacteria contributing to >95% of the bacteria. In all, 56611sequences were generated representing 6,023 OTUs per female gut and 421 OTUs per egg. Francisellaceae family and Francisella make up the vast majority of the OTUs. Our findings are consistent with interference between Francisella and Rickettsia. The CD method identified bacteria, such B. subtilis that are candidates for vector control intervention approaches such paratransgenesis whereas NGS revealed high Francisella spp. prevalence, indicating that integrated methods are more accurate to characterize microbial community and diversity.

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