scholarly journals Fitness Trade-Offs in blaTEM Evolution

2008 ◽  
Vol 52 (7) ◽  
pp. 2340-2345 ◽  
Author(s):  
Joanna E. Mroczkowska ◽  
Miriam Barlow
Keyword(s):  
Microbial Populations ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Bacterial Populations ◽  
Real Time Quantitative Pcr ◽  
Fitness Effects ◽  
Fitness Advantage ◽  
Extended Spectrum ◽  
Trade Offs ◽  
Pcr Method

ABSTRACT bla TEM-1 expression results in penicillin resistance, whereas expression of many bla TEM-1 descendants, called extended-spectrum β-lactamases (ESBLs), results simultaneously in resistance to penicillins and extended-spectrum cephalosporins. Despite the expanded resistance phenotypes conferred by many ESBLs, bla TEM-1 is still the most abundant bla TEM allele in many microbial populations. This study examines the fitness effects of the two amino acid substitutions, R164S and E240K, that have occurred repeatedly among ESBL bla TEM-1 descendants. Using a single-nucleotide polymorphism-specific real-time quantitative PCR method, we analyzed the fitness of strains expressing bla TEM-1, bla TEM-10, and bla TEM-12. Our results show that bacteria expressing the ancestral bla TEM-1 allele have a fitness advantage over those expressing either bla TEM-10 or bla TEM-12 when exposed to ampicillin. This observation, combined with the fact that penicillins are the most prevalent antimicrobials prescribed worldwide, may explain why bla TEM-1 has persisted as the most frequently encountered bla TEM allele in bacterial populations.

scholarly journals Genomic Investigation Reveals Contaminated Detergent as the Source of an Extended-Spectrum-β-Lactamase-Producing Klebsiella michiganensis Outbreak in a Neonatal Unit

2020 ◽  
Vol 58 (5) ◽  
Author(s):  
Paul Chapman ◽  
Brian M. Forde ◽  
Leah W. Roberts ◽  
Haakon Bergh ◽  
Debra Vesey ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Klebsiella Oxytoca ◽  
Multidrug Resistant ◽  
Hospital Environment ◽  
Nucleotide Polymorphism ◽  
Taxonomic Assignment ◽  
Single Nucleotide ◽  
Content Type ◽  
Extended Spectrum ◽  
Antimicrobial Resistance Genes

ABSTRACT Klebsiella species are problematic pathogens in neonatal units and may cause outbreaks, for which the sources of transmission may be challenging to elucidate. We describe the use of whole-genome sequencing (WGS) to investigate environmental sources of transmission during an outbreak of extended-spectrum-β-lactamase (ESBL)-producing Klebsiella michiganensis colonizing neonates. Ceftriaxone-resistant Klebsiella spp. isolated from neonates (or their mothers) and the hospital environment were included. Short-read sequencing (Illumina) and long-read sequencing (MinION; Oxford Nanopore Technologies) were used to confirm species taxonomy, to identify antimicrobial resistance genes, and to determine phylogenetic relationships using single-nucleotide polymorphism profiling. A total of 21 organisms (10 patient-derived isolates and 11 environmental isolates) were sequenced. Standard laboratory methods identified the outbreak strain as an ESBL-producing Klebsiella oxytoca, but taxonomic assignment from WGS data suggested closer identity to Klebsiella michiganensis. Strains isolated from multiple detergent-dispensing bottles were either identical or closely related by single-nucleotide polymorphism comparison. Detergent bottles contaminated by K. michiganensis had been used for washing milk expression equipment. No new cases were identified once the detergent bottles were removed. Environmental reservoirs may be an important source in outbreaks of multidrug-resistant organisms. WGS, in conjunction with traditional epidemiological investigation, can be instrumental in revealing routes of transmission and guiding infection control responses.

scholarly journals A modified simple RFLP-PCR method for single nucleotide polymorphism (SNP) typing

2006 ◽  
Vol 29 (3) ◽  
pp. 562-565 ◽  
Author(s):  
Junhua Xiao ◽  
Xiujuan Xin ◽  
Xiaohui Luan ◽  
Wei Dongzhi ◽  
Yang Shengli
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Snp Typing ◽  
Pcr Method

scholarly journals Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Thomas Sakoparnig ◽  
Chris Field ◽  
Erik van Nimwegen
Keyword(s):  
Bacterial Species ◽  
Genome Alignment ◽  
Whole Genome ◽  
Allele Sharing ◽  
Nucleotide Polymorphism ◽  
Recombination Rates ◽  
Single Nucleotide ◽  
Bacterial Populations ◽  
New Methods ◽  
Alignment Analysis

Although recombination is accepted to be common in bacteria, for many species robust phylogenies with well-resolved branches can be reconstructed from whole genome alignments of strains, and these are generally interpreted to reflect clonal relationships. Using new methods based on the statistics of single-nucleotide polymorphism (SNP) splits, we show that this interpretation is incorrect. For many species, each locus has recombined many times along its line of descent, and instead of many loci supporting a common phylogeny, the phylogeny changes many thousands of times along the genome alignment. Analysis of the patterns of allele sharing among strains shows that bacterial populations cannot be approximated as either clonal or freely recombining, but are structured such that recombination rates between lineages vary over several orders of magnitude, with a unique pattern of rates for each lineage. Thus, rather than reflecting clonal ancestry, whole genome phylogenies reflect distributions of recombination rates.

scholarly journals Pyrosequencing Using the Single-Nucleotide Polymorphism Protocol for Rapid Determination of TEM- and SHV-Type Extended-Spectrum β-Lactamases in Clinical Isolates and Identification of the Novel β-Lactamase Genes blaSHV-48, blaSHV-105, and blaTEM-155

2008 ◽  
Vol 53 (3) ◽  
pp. 977-986 ◽  
Author(s):  
C. Hal Jones ◽  
Alexey Ruzin ◽  
Margareta Tuckman ◽  
Melissa A. Visalli ◽  
Peter J. Petersen ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Amino Acid ◽  
Sequence Data ◽  
Rapid Determination ◽  
The United States ◽  
Amino Acid Substitutions ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Extended Spectrum ◽  
Rapid Sequence

ABSTRACT TEM- and SHV-type extended-spectrum β-lactamases (ESBLs) are the most common ESBLs found in the United States and are prevalent throughout the world. Amino acid substitutions at a number of positions in TEM-1 lead to the ESBL phenotype, although substitutions at residues 104 (E to K), 164 (R to S or H), 238 (G to S), and 240 (E to K) appear to be particularly important in modifying the spectrum of activity of the enzyme. The SHV-1-derived ESBLs are a less diverse collection of enzymes; however, the majority of amino acid substitutions resulting in an ESBL mirror those seen in the TEM-1-derived enzymes. Pyrosequencing by use of the single-nucleotide polymorphism (SNP) protocol was applied to provide sequence data at positions critical for the ESBL phenotype spanning the bla TEM and bla SHV genes. Three novel β-lactamases are described: the ESBLs TEM-155 (Q39K, R164S, E240K) and SHV-105 (I8F, R43S, G156D, G238S, E240K) and a non-ESBL, SHV-48 (V119I). The ceftazidime, ceftriaxone, and aztreonam MICs for an Escherichia coli isolate expressing bla SHV-105 were >128, 128, and >128 μg/ml, respectively. Likewise, the ceftazidime, ceftriaxone, and aztreonam MICs for an E. coli isolate expressing bla TEM-155 were >128, 64, and > 128 μg/ml, respectively. Pyrosequence analysis determined the true identity of the β-lactamase on plasmid R1010 to be SHV-11 rather than SHV-1, as previously reported. Pyrosequencing is a real-time sequencing-by-synthesis approach that was applied to SNP detection for TEM- and SHV-type ESBL identification and represents a robust tool for rapid sequence determination that may have a place in the clinical setting.

scholarly journals OsDREB2A Gene Polymorphism Does Not Affect Salinity Tolerance Potency of Local Rice Varieties from Banten

2021 ◽  
Vol 28 (2) ◽  
pp. 123
Author(s):  
‘Ainun Sayyidah Zakiyah ◽  
Elhah Nailul Khasna ◽  
I Kade Karisma Gita Ardana ◽  
Choirun Nita Fikriani ◽  
Nina Bunga Anggraini ◽  
...  
Keyword(s):  
Salinity Tolerance ◽  
Agricultural Land ◽  
High Salinity ◽  
Salt Tolerant ◽  
Nucleotide Polymorphism ◽  
Analysis Software ◽  
Specific Primers ◽  
Rice Varieties ◽  
Single Nucleotide ◽  
Pcr Method

Indonesia possesses vast coastal agricultural land areas with high salinity. This high salinity is a threat to rice productivity which may decrease to 79.8%. Banten province of Indonesia houses many local rice varieties which have salinity tolerance potency based on its agronomical characters. The adaptability of rice plant in high salinity soil can be affected by OsDREB2A gene, which encodes transcription factors from several salt-tolerant signaling pathway genes. The aims of this study were to find out the possible polymorphism of OsDREB2A gene from Banten local rice varieties. The polymorphism of OsDREB2A analyzed by Single Nucleotide Polymorphism (SNP) and possible molecular structure. OsDREB2A gene was amplified using DNA from Tambleng, Bulu Putih, and Pare Caok varieties as templates through PCR method with a pair of specific primers. DNA fragments obtained were analyzed by means of series of analysis software. From those analysis we obtained 840 bp, 836 bp, and 850 bp gene fragments from Tambleng, Bulu Putih, and Pare Caok varieties, respectively. There is polymorphism of OsDREB2A due to some mutation yet does not massively alter its protein structure. From this study, we suggest that Tambleng, Bulu Putih, and Pare Caok varieties potential for salinity stress resistance genetically.

scholarly journals Investigating the Association of Orosomucoid 1-like 3 (ORMDL3) Gene Polymorphism (rs12603332) with Susceptibility to Allergic Asthma in Iranian Northwestern Azeri Population

2019 ◽  
Author(s):  
Ilghar Zeinaly ◽  
Naghmeh Vossoughi ◽  
Daniel Elieh Ali Komi ◽  
Tohid Kazemi ◽  
Zohreh Babaloo ◽  
...  
Keyword(s):  
Allergic Asthma ◽  
Fragment Length Polymorphism ◽  
Airway Remodeling ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Asthmatic Patients ◽  
Normal Individuals ◽  
Significant Difference ◽  
Pcr Method ◽  
Polymerase Chain

Orosomucoid 1-like 3 (ORMDL3) gene, located on chromosome 17q21, is an asthma candidate gene that encodes ORMDL3. This molecule has been reported to play a role in airway remodeling and bronchial hyper-responsiveness. In this study, we aimed to investigate the possible association of ORMDL3 single nucleotide polymorphism (SNP) (rs12603332) with susceptibility to allergic asthma in Iranian Northwestern Azeri population. 193 asthmatic patients and 185 normal individuals were included. Genomic DNA was extracted and genotyping was performed by standard restriction fragment length polymorphism-polymerase chain reaction RFLP-PCR method using BstUI restriction enzyme. Our results showed dominant presence of TC genotype and C allele in both patients (49.2% and 59.8%, respectively) and controls (48.6% and 60%, respectively). Frequency of genotypes and alleles showed no significant difference between two groups (p=0.994 and p=1.00, respectively). None of alleles could be defined as risk allele for allergic asthma (OR=0.99, 0.88-1.12, 95% CI). We failed to show significant association between ORMDL3 rs12603332 with predisposition to allergic asthma in Iranian Northwestern Azeri population. More studies with larger number of participants should be done to find more reliable results for such association.  

scholarly journals The association of codon 392 polymorphism in ESR2 gene with breast cancer in Iran

2019 ◽  
pp. 243-248
Author(s):  
Sakineh Abbasi ◽  
Samira Kalbasi
Keyword(s):  
Breast Cancer ◽  
Epidemiological Studies ◽  
Nucleotide Polymorphism ◽  
Presurgical Evaluation ◽  
Single Nucleotide ◽  
East Region ◽  
Direct Association ◽  
Pcr Method ◽  
Middle East Region ◽  
Esr2 Gene

Epidemiological studies revealed that the pattern of age onset of breast cancer in the Middle East region differ from those in Caucasians. Therefore, genomic data for ESR2 (ER-β) is of the value in the clinical setting for that ethnic group and the aim of the current investigation is investigated whether polymorphisms in the ER-β gene are associated with breast cancer risk among Iranian women. The coding sequence in Exon 7 at ESR2 gene was looking for any variation among the Iranian breast cancer women by SSCP-PCR method. In codon 392 of exon 7, showed a silent SNP (silent single nucleotide polymorphism). The frequency of allele G in codon 392 (CTC → CTG was found only in cases (5.7%). We also found that allele G in codon 392 (C1176G) had direct association with development of lymph node metastasis in breast cancer. The current results suggest that ESR2 SNP in exon 7, codon 392 is associated with various aspects of breast cancer in Iran. ESR2 gene structure determination, in presurgical evaluation, might be a useful marker in predicting familial breast cancer and metastasis in LN.

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