Analysis of single nucleotide polymorphisms (SNPs) associated with antibiotic resistance genes in Chilean Piscirickettsia salmonis strains

2019 ◽  
Vol 42 (12) ◽  
pp. 1645-1655 ◽  
Author(s):  
Jaime Figueroa ◽  
Diana Castro ◽  
Fernando Lagos ◽  
Carlos Cartes ◽  
Adolfo Isla ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Single Nucleotide Polymorphisms ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Piscirickettsia Salmonis

scholarly journals Phylogeographical Analyses and Antibiotic Resistance Genes of Acinetobacter johnsonii Highlight Its Clinical Relevance

mSphere ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Santiago Castillo-Ramírez ◽  
Valeria Mateo-Estrada ◽  
Gerardo Gonzalez-Rocha ◽  
Andrés Opazo-Capurro
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Clinical Importance ◽  
Antibiotic Resistance Genes ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Content Type ◽  
Acinetobacter Johnsonii ◽  
Well Differentiated

ABSTRACT Acinetobacter johnsonii has been severely understudied and its population structure and the presence of antibiotic resistance genes (ARGs) are very much uncertain. Our phylogeographical analysis shows that intercontinental transmission has occurred frequently and that different lineages are circulating within single countries; notably, clinical and nonclinical strains are not well differentiated from one another. Importantly, in this species recombination is a significant source of single nucleotide polymorphisms. Furthermore, our results show this species could be an important reservoir of ARGs since it has a significant amount of ARGs, and many of them show signals of horizontal gene transfer. Thus, this study clearly points out the clinical importance of A. johnsonii and the urgent need to better appreciate its genomic diversity.

Complex integrons containing qnrB4-ampC (blaDHA-1) in plasmids of multidrug-resistant Citrobacter freundii from wastewater

2013 ◽  
Vol 59 (2) ◽  
pp. 110-116 ◽  
Author(s):  
Grace Yim ◽  
Waldan Kwong ◽  
Julian Davies ◽  
Vivian Miao
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Wastewater Treatment Plants ◽  
Antibiotic Resistance Genes ◽  
Multidrug Resistant ◽  
Microbial Populations ◽  
Citrobacter Freundii ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Encoding Genes

Microbial populations in wastewater treatment plants (WWTPs) are increasingly being recognized as environmental reservoirs of antibiotic resistance genes. PCR amplicons for plasmid-mediated quinolone resistance determinants qnrA, qnrB, and qnrS were recorded in samples from a WWTP in Vancouver, British Columbia. Six strains of ciprofloxacin-resistant Citrobacter freundii were isolated and found to carry mutations in gyrA and parC, as well as multiple plasmid-borne resistance genes, collectively including qnrB; aac(6′)-Ib-cr; β-lactamase-encoding genes from molecular classes A (blaTEM-1), C (ampC), D (blaOXA-1, blaOXA-10); and genes for resistance to 5 other types of antibiotics. In 3 strains, large (>60 kb) plasmids carried qnrB4 and ampC as part of a complex integron in a 14 kb arrangement that has been reported worldwide but, until recently, only among pathogenic strains of Klebsiella. Analysis of single-nucleotide polymorphisms in the qnrB4-ampC regions infers 2 introductions into the WWTP environment. These results suggest recent passage of plasmid-borne fluoroquinolone and β-lactam resistance genes from pathogens to bacteria that may be indigenous inhabitants of WWTPs, thus contributing to an environmental pool of antibiotic resistance.

scholarly journals Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome

GigaScience ◽  
2019 ◽  
Vol 8 (10) ◽  
Author(s):  
Bo Song ◽  
Yue Song ◽  
Yuan Fu ◽  
Elizabeth Balyejusa Kizito ◽  
Sandra Ndagire Kamenya ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Single Nucleotide Polymorphisms ◽  
Drought Tolerance ◽  
Resistance Genes ◽  
Draft Genome ◽  
Disease Resistance Genes ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Protein Coding ◽  
Protein Coding Genes

Abstract Background The African eggplant (Solanum aethiopicum) is a nutritious traditional vegetable used in many African countries, including Uganda and Nigeria. It is thought to have been domesticated in Africa from its wild relative, Solanum anguivi. S. aethiopicum has been routinely used as a source of disease resistance genes for several Solanaceae crops, including Solanum melongena. A lack of genomic resources has meant that breeding of S. aethiopicum has lagged behind other vegetable crops. Results We assembled a 1.02-Gb draft genome of S. aethiopicum, which contained predominantly repetitive sequences (78.9%). We annotated 37,681 gene models, including 34,906 protein-coding genes. Expansion of disease resistance genes was observed via 2 rounds of amplification of long terminal repeat retrotransposons, which may have occurred ∼1.25 and 3.5 million years ago, respectively. By resequencing 65 S. aethiopicum and S. anguivi genotypes, 18,614,838 single-nucleotide polymorphisms were identified, of which 34,171 were located within disease resistance genes. Analysis of domestication and demographic history revealed active selection for genes involved in drought tolerance in both “Gilo” and “Shum” groups. A pan-genome of S. aethiopicum was assembled, containing 51,351 protein-coding genes; 7,069 of these genes were missing from the reference genome. Conclusions The genome sequence of S. aethiopicum enhances our understanding of its biotic and abiotic resistance. The single-nucleotide polymorphisms identified are immediately available for use by breeders. The information provided here will accelerate selection and breeding of the African eggplant, as well as other crops within the Solanaceae family.

Development of a simple method for the determination of single nucleotide polymorphisms

2010 ◽  
Vol 34 (8) ◽  
pp. S75-S75
Author(s):  
Weifeng Zhu ◽  
Zhuoqi Liu ◽  
Daya Luo ◽  
Xinyao Wu ◽  
Fusheng Wan
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Simple Method ◽  
Single Nucleotide
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