scholarly journals Heme is crucial for medium-dependent metronidazole resistance in clinical isolates of C. difficile

2020 ◽  
Author(s):  
Ilse M. Boekhoud ◽  
Igor Sidorov ◽  
Sam Nooij ◽  
Céline Harmanus ◽  
Ingrid M.J.G. Bos-Sanders ◽  
...  
Keyword(s):  
Inhibitory Concentration ◽  
Sequence Type ◽  
Clinical Isolates ◽  
Whole Genome Sequence ◽  
Nucleotide Polymorphism ◽  
First Line ◽  
Single Nucleotide ◽  
Clostridioides Difficile ◽  
Metronidazole Resistance ◽  
First Line Treatment

AbstractUntil recently, metronidazole was the first-line treatment for Clostridioides difficile infection and it is still commonly used. Though resistance has been reported due to the plasmid pCD-METRO, this does not explain all cases. Here, we investigate resistance to metronidazole in a collection of clinical isolates of C. difficile. We find that nearly all isolates demonstrate a heme-dependent increase in the minimal inhibitory concentration for metronidazole, which in some cases leads to isolates being qualified as resistant (MIC > 2 mg/L). Moreover, whole genome sequence analysis reveals a single nucleotide polymorphism in the heme responsive gene hsmA, which defines a metronidazole resistant lineage of PCR ribotype 010 / multilocus sequence type 15 isolates that also includes pCD-METRO containing strains. Together our data demonstrate that heme is crucial for medium-dependent metronidazole resistance in C. difficile.

Survey of a cDNA library from the turkey (Meleagris gallopavo)

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 12-17 ◽  
Author(s):  
L D Chaves ◽  
J A Rowe ◽  
K M Reed
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Expressed Sequence Tags ◽  
Expressed Sequence Tag ◽  
Meleagris Gallopavo ◽  
Whole Genome Sequence ◽  
Snp Discovery ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Important Species ◽  
Expressed Sequence

Genome characterization and analysis is an imperative step in identifying and selectively breeding for improved traits of agriculturally important species. Expressed sequence tags (ESTs) represent a transcribed portion of the genome and are an effective way to identify genes within a species. Downstream applications of EST projects include DNA microarray construction and interspecies comparisons. In this study, 694 ESTs were sequenced and analyzed from a library derived from a 24-day-old turkey embryo. The 437 unique sequences identified were divided into 76 assembled contigs and 361 singletons. The majority of significant comparative matches occurred between the turkey sequences and sequences reported from the chicken. Whole genome sequence from the chicken was used to identify potential exon–intron boundaries for selected turkey clones and intron-amplifying primers were developed for sequence analysis and single nucleotide polymorphism (SNP) discovery. Identified SNPs were genotyped for linkage analysis on two turkey reference populations. This study significantly increases the number of EST sequences available for the turkey.Key words: turkey, cDNA, expressed sequence tag, single nucleotide polymorphism.

A snapshot of the predominant single nucleotide polymorphism cluster groups of Mycobacterium tuberculosis clinical isolates in Delhi, India

Tuberculosis ◽  
2016 ◽  
Vol 100 ◽  
pp. 72-81 ◽  
Author(s):  
Mandira Varma-Basil ◽  
Anshika Narang ◽  
Soumitesh Chakravorty ◽  
Kushal Garima ◽  
Shraddha Gupta ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Mycobacterium Tuberculosis ◽  
Clinical Isolates ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

scholarly journals Spread of TEM, VIM, SHV, and CTX-Mβ-Lactamases in Imipenem-Resistant Gram-Negative Bacilli Isolated from Egyptian Hospitals

2016 ◽  
Vol 2016 ◽  
pp. 1-15 ◽  
Author(s):  
El sayed Hamdy Mohammed ◽  
Ahmed Elsadek Fakhr ◽  
Hanan Mohammed El sayed ◽  
Said abd Elmohsen Al Johery ◽  
Wesam Abdel Ghani Hassanein
Keyword(s):  
Direct Sequencing ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Gram Negative ◽  
Carbapenem Resistant ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Therapeutic Problem

Carbapenem-resistant Gram-negative bacilli resulting fromβ-lactamases have been reported to be an important cause of nosocomial infections and are a critical therapeutic problem worldwide. This study aimed to describe the prevalence of imipenem-resistant Gram-negative bacilli isolates and detection ofblaVIM,blaTEM,blaSHV,blaCTX-M-1, andblaCTX-M-9genes in these clinical isolates in Egyptian hospitals. The isolates were collected from various clinical samples, identified by conventional methods and confirmed by API 20E. Antibiotic susceptibility testing was determined by Kirby-Bauer technique and interpreted according to CLSI. Production ofblaVIM,blaTEM,blaSHV, andblaCTX-Mgenes was done by polymerase chain reaction (PCR). Direct sequencing from PCR products was subsequently carried out to identify and confirm theseβ-lactamases genes. Out of 65 isolates, (46.1%) Escherichia coli, (26.2%) Klebsiella pneumoniae, and (10.7%) Pseudomonas aeruginosa were identified as the commonest Gram-negative bacilli. 33(50.8%) were imipenem-resistant isolates. 22 isolates (66.7%) carriedblaVIM, 24(72.7%) hadblaTEM, and 5(15%) showedblaSHV, while 12(36%), 6(18.2%), and 0(0.00%) harboredblaCTX-M-1,blaCTX-M-9, andblaCTX-M-8/25, respectively. There is a high occurrence ofβ-lactamase genes in clinical isolates and sequence analysis of amplified genes showed differences between multiple SNPs (single nucleotide polymorphism) sites in the same gene among local isolates in relation to published sequences.

scholarly journals Multidrug-Resistant Sequence Type 235 Pseudomonas aeruginosa Clinical Isolates Producing IMP-26 with Increased Carbapenem-Hydrolyzing Activities in Vietnam

2016 ◽  
Vol 60 (11) ◽  
pp. 6853-6858 ◽  
Author(s):  
Tatsuya Tada ◽  
Pham Hong Nhung ◽  
Tohru Miyoshi-Akiyama ◽  
Kayo Shimada ◽  
Mitsuhiro Tsuchiya ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Multidrug Resistant ◽  
Sequence Type ◽  
Clinical Isolates ◽  
Medical Setting ◽  
Single Nucleotide ◽  
Content Type ◽  
E Coli ◽  
Whole Genomes ◽  
Encoding Genes

ABSTRACTForty clinical isolates of multidrug-resistantPseudomonas aeruginosawere obtained in a medical setting in Hanoi, Vietnam. Whole genomes of all 40 isolates were sequenced by MiSeq (Illumina), and phylogenic trees were constructed from the single nucleotide polymorphism concatemers. Of these 40 isolates, 24 (60.0%) harbored metallo-β-lactamase-encoding genes, includingblaIMP-15,blaIMP-26,blaIMP-51, and/orblaNDM-1. Of these 24 isolates, 12 harboredblaIMP-26and belonged to sequence type 235 (ST235).Escherichia coliexpressingblaIMP-26was significantly more resistant to doripenem and meropenem thanE. coliexpressingblaIMP-1andblaIMP-15. IMP-26 showed higher catalytic activity against doripenem and meropenem than IMP-1 and against all carbapenems tested, including doripenem, imipenem, meropenem, and panipenem, than did IMP-15. These data suggest that clinical isolates of multidrug-resistant ST235P. aeruginosaproducing IMP-26 with increased carbapenem-hydrolyzing activities are spreading in medical settings in Vietnam.

scholarly journals Genomic Prediction Using LD-Based Haplotypes Inferred From High-Density Chip and Imputed Sequence Variants in Chinese Simmental Beef Cattle

2021 ◽  
Vol 12 ◽  
Author(s):  
Hongwei Li ◽  
Bo Zhu ◽  
Ling Xu ◽  
Zezhao Wang ◽  
Lei Xu ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Genomic Prediction ◽  
Whole Genome Sequence ◽  
Data Sets ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Individual Single Nucleotide Polymorphism ◽  
Improve Accuracy ◽  
The Individual

A haplotype is defined as a combination of alleles at adjacent loci belonging to the same chromosome that can be transmitted as a unit. In this study, we used both the Illumina BovineHD chip (HD chip) and imputed whole-genome sequence (WGS) data to explore haploblocks and assess haplotype effects, and the haploblocks were defined based on the different LD thresholds. The accuracies of genomic prediction (GP) for dressing percentage (DP), meat percentage (MP), and rib eye roll weight (RERW) based on haplotype were investigated and compared for both data sets in Chinese Simmental beef cattle. The accuracies of GP using the entire imputed WGS data were lower than those using the HD chip data in all cases. For DP and MP, the accuracy of GP using haploblock approaches outperformed the individual single nucleotide polymorphism (SNP) approach (GBLUP_In_Block) at specific LD levels. Hotelling’s test confirmed that GP using LD-based haplotypes from WGS data can significantly increase the accuracies of GP for RERW, compared with the individual SNP approach (∼1.4 and 1.9% for GHBLUP and GHBLUP+GBLUP, respectively). We found that the accuracies using haploblock approach varied with different LD thresholds. The LD thresholds (r2 ≥ 0.5) were optimal for most scenarios. Our results suggested that LD-based haploblock approach can improve accuracy of genomic prediction for carcass traits using both HD chip and imputed WGS data under the optimal LD thresholds in Chinese Simmental beef cattle.

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