scholarly journals Identification and Characterization of a Novel Chromosomal Aminoglycoside 2′-N-Acetyltransferase, AAC(2′)-If, From an Isolate of a Novel Providencia Species, Providencia wenzhouensis R33

2021 ◽  
Vol 12 ◽  
Author(s):  
Kexin Zhou ◽  
Jialei Liang ◽  
Xu Dong ◽  
Peiyao Zhang ◽  
Chunlin Feng ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Resistance Gene ◽  
Genome Sequencing ◽  
Resistance Mechanisms ◽  
Parameter Analysis ◽  
Resistant Bacteria ◽  
Comparative Genomic ◽  
Molecular Characteristics ◽  
Whole Genome ◽  
Aminoglycoside Resistance

Multidrug-resistant bacteria from different sources have been steadily emerging, and an increasing number of resistance mechanisms are being uncovered. In this work, we characterized a novel resistance gene named aac(2′)-If from an isolate of a novel Providencia species, Providencia wenzhouensis R33 (CCTCC AB 2021339). Susceptibility testing and enzyme kinetic parameter analysis were conducted to determine the function of the aminoglycoside 2′-N-acetyltransferase. Whole-genome sequencing and comparative genomic analysis were performed to elucidate the molecular characteristics of the genome and the genetic context of the resistance gene-related sequences. Among the functionally characterized resistance genes, AAC(2′)-If shares the highest amino acid sequence identity of 70.79% with AAC(2′)-Ia. AAC(2′)-If confers resistance to several aminoglycoside antibiotics, showing the highest resistance activity against ribostamycin and neomycin. The recombinant strain harboring aac(2′)-If (pUCP20-aac(2′)-If/DH5α) showed 256- and 128-fold increases in the minimum inhibitory concentration (MIC) levels to ribostamycin and neomycin, respectively, compared with those of the control strains (DH5α and pUCP20/DH5α). The results of the kinetic analysis of AAC(2′)-If were consistent with the MIC results of the cloned aac(2′)-If with the highest catalytic efficiency for ribostamycin (kcat/Km ratio = [3.72 ± 0.52] × 104 M–1⋅s–1). Whole-genome sequencing demonstrated that the aac(2′)-If gene was located on the chromosome with a relatively unique genetic environment. Identification of a novel aminoglycoside resistance gene in a strain of a novel Providencia species will help us find ways to elucidate the complexity of resistance mechanisms in the microbial population.

scholarly journals Expected Plazomicin Susceptibility in India Based on the Prevailing Aminoglycoside Resistance Mechanisms in Gram-Negative Organisms Derived from Whole-Genome Sequencing

2020 ◽  
Vol 38 (3-4) ◽  
pp. 313-318
Author(s):  
Agila Kumari Pragasam ◽  
S.Lydia Jennifer ◽  
Dhanalakshmi Solaimalai ◽  
Dhiviya Prabaa Muthuirulandi Sethuvel ◽  
Tanya Rachel ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Mechanisms ◽  
Whole Genome ◽  
Aminoglycoside Resistance ◽  
Gram Negative ◽  
Gram Negative Organisms

scholarly journals Enterobacter cloacae Complex Sequence Type 171 Isolates Expressing KPC-4 Carbapenemase Recovered from Canine Patients in Ohio

2018 ◽  
Vol 62 (12) ◽  
Author(s):  
Joshua B. Daniels ◽  
Liang Chen ◽  
Susan V. Grooters ◽  
Dixie F. Mollenkopf ◽  
Dimitria A. Mathys ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Companion Animals ◽  
Enterobacter Cloacae ◽  
Sequence Type ◽  
Resistant Bacteria ◽  
Whole Genome ◽  
Content Type ◽  
Complex Sequence ◽  
Enterobacter Cloacae Complex

ABSTRACT Companion animals are likely relevant in the transmission of antimicrobial-resistant bacteria. Enterobacter xiangfangensis sequence type 171 (ST171), a clone that has been implicated in clusters of infections in humans, was isolated from two dogs with clinical disease in Ohio. The canine isolates contained IncHI2 plasmids encoding blaKPC-4. Whole-genome sequencing was used to put the canine isolates in phylogenetic context with available human ST171 sequences, as well as to characterize their blaKPC-4 plasmids.

scholarly journals Whole Genome Sequencing and Comparative Genomic Analyses of Lysinibacillus pakistanensis LZH-9, a Halotolerant Strain with Excellent COD Removal Capability

2020 ◽  
Vol 8 (5) ◽  
pp. 716
Author(s):  
Xueling Wu ◽  
Han Zhou ◽  
Liangzhi Li ◽  
Enhui Wang ◽  
Xiangyu Zhou ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Industrial Wastewater ◽  
Treatment Plant ◽  
Cod Removal ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Toxic Compound ◽  
Adaptive Mutations ◽  
Metabolic Versatility

Halotolerant microorganisms are promising in bio-treatment of hypersaline industrial wastewater. Four halotolerant bacteria strains were isolated from wastewater treatment plant, of which a strain LZH-9 could grow in the presence of up to 14% (w/v) NaCl, and it removed 81.9% chemical oxygen demand (COD) at 96 h after optimization. Whole genome sequencing of Lysinibacillus pakistanensis LZH-9 and comparative genomic analysis revealed metabolic versatility of different species of Lysinibacillus, and abundant genes involved in xenobiotics biodegradation, resistance to toxic compound, and salinity were found in all tested species of Lysinibacillus, in which Horizontal Gene Transfer (HGT) contributed to the acquisition of many important properties of Lysinibacillus spp. such as toxic compound resistance and osmotic stress resistance as revealed by phylogenetic analyses. Besides, genome wide positive selection analyses revealed seven genes that contained adaptive mutations in Lysinibacillus spp., most of which were multifunctional. Further expression assessment with Codon Adaption Index (CAI) also reflected the high metabolic rate of L. pakistanensis to digest potential carbon or nitrogen sources in organic contaminants, which was closely linked with efficient COD removal ability of strain LZH-9. The high COD removal efficiency and halotolerance as well as genomic evidences suggested that L. pakistanensis LZH-9 was promising in treating hypersaline industrial wastewater.

scholarly journals Streptococcus gallolyticus subsp. gallolyticus from Human and Animal Origins: Genetic Diversity, Antimicrobial Susceptibility, and Characterization of a Vancomycin-Resistant Calf Isolate Carrying avanA-Tn1546-Like Element

2015 ◽  
Vol 59 (4) ◽  
pp. 2006-2015 ◽  
Author(s):  
Beatriz Romero-Hernández ◽  
Ana P. Tedim ◽  
José Francisco Sánchez-Herrero ◽  
Pablo Librado ◽  
Julio Rozas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Antibiotic Susceptibility ◽  
Resistant Isolate ◽  
Comparative Genomic ◽  
Gene Gain ◽  
Whole Genome ◽  
Content Type ◽  
Streptococcus Gallolyticus

ABSTRACTThe aim of this work was to characterize the antibiotic susceptibility and genetic diversity of 41Streptococcus gallolyticussubsp.gallolyticusisolates: 18 isolates obtained from animals and 23 human clinical isolates. Antibiotic susceptibility was determined by the semiautomatic Wider system and genetic diversity by pulsed-field gel electrophoresis (PFGE) with SmaI. Animal isolates grouped separately in the PFGE analysis, but no statistical differences in antimicrobial resistance were found between the two groups. The LMG 17956 sequence type 28 (ST28) strain recovered from the feces of a calf exhibited high levels of resistance to vancomycin and teicoplanin (MIC, ≥256 mg/liter). Its glycopeptide resistance mechanism was characterized by Southern blot hybridization and a primer-walking strategy, and finally its genome, determined by whole-genome sequencing, was compared with four closely relatedS. gallolyticussubsp.gallolyticusgenomes. Hybridization experiments demonstrated that a Tn1546-like element was integrated into the bacterial chromosome. In agreement with this finding, whole-genome sequencing confirmed a partial deletion of thevanY-vanZregion and partial duplication of thevanHgene. The comparative genomic analyses revealed that the LMG 17956 ST28 strain had acquired an unusually high number of transposable elements and had experienced extensive chromosomal rearrangements, as well as gene gain and loss events. In conclusion,S. gallolyticussubsp.gallolyticusisolates from animals seem to belong to lineages separate from those infecting humans. In addition, we report a glycopeptide-resistant isolate from a calf carrying a Tn1546-like element integrated into its chromosome.

The use of whole-genome sequencing for molecular epidemiology and antimicrobial surveillance: identifying the role of IncX3 plasmids and the spread of blaNDM-4-like genes in the Enterobacteriaceae

2015 ◽  
Vol 68 (10) ◽  
pp. 835-838 ◽  
Author(s):  
Björn A Espedido ◽  
Borce Dimitrijovski ◽  
Sebastiaan J van Hal ◽  
Slade O Jensen
Keyword(s):  
Antibiotic Resistance ◽  
Whole Genome Sequencing ◽  
Resistance Gene ◽  
Genome Sequencing ◽  
De Novo ◽  
Antibiotic Resistance Genes ◽  
Whole Genome ◽  
Antimicrobial Surveillance ◽  
Metropolitan Hospital ◽  
Genetic Context

AimsTo characterise the resistome of a multi-drug resistant Klebsiella pneumoniae (Kp0003) isolated from an Australian traveller who was repatriated to a Sydney Metropolitan Hospital from Myanmar with possible prosthetic aortic valve infective endocarditis.MethodsKp0003 was recovered from a blood culture of the patient and whole genome sequencing was performed. Read mapping and de novo assembly of reads facilitated in silico multi-locus sequence and plasmid replicon typing as well as the characterisation of antibiotic resistance genes and their genetic context. Conjugation experiments were also performed to assess the plasmid (and resistance gene) transferability and the effect on the antibiotic resistance phenotype.ResultsImportantly, and of particular concern, the carbapenem-hydrolysing β-lactamase gene blaNDM-4 was identified on a conjugative IncX3 plasmid (pJEG027). In this respect, the blaNDM-4 genetic context is similar (at least to some extent) to what has previously been identified for blaNDM-1 and blaNDM-4-like variants.ConclusionsThis study highlights the potential role that IncX3 plasmids have played in the emergence and dissemination of blaNDM-4-like variants worldwide and emphasises the importance of resistance gene surveillance.

scholarly journals Combining callers improves the detection of copy number variants from whole-genome sequencing

2021 ◽  
Author(s):  
Marie Coutelier ◽  
Manuel Holtgrewe ◽  
Marten Jäger ◽  
Ricarda Flöttman ◽  
Martin A. Mensah ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Copy Number ◽  
Copy Number Variants ◽  
Computation Time ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Base Pairs ◽  
Whole Exome ◽  
Human Pathology

AbstractCopy Number Variants (CNVs) are deletions, duplications or insertions larger than 50 base pairs. They account for a large percentage of the normal genome variation and play major roles in human pathology. While array-based approaches have long been used to detect them in clinical practice, whole-genome sequencing (WGS) bears the promise to allow concomitant exploration of CNVs and smaller variants. However, accurately calling CNVs from WGS remains a difficult computational task, for which a consensus is still lacking. In this paper, we explore practical calling options to reach the best compromise between sensitivity and sensibility. We show that callers based on different signal (paired-end reads, split reads, coverage depth) yield complementary results. We suggest approaches combining four selected callers (Manta, Delly, ERDS, CNVnator) and a regenotyping tool (SV2), and show that this is applicable in everyday practice in terms of computation time and further interpretation. We demonstrate the superiority of these approaches over array-based Comparative Genomic Hybridization (aCGH), specifically regarding the lack of resolution in breakpoint definition and the detection of potentially relevant CNVs. Finally, we confirm our results on the NA12878 benchmark genome, as well as one clinically validated sample. In conclusion, we suggest that WGS constitutes a timely and economically valid alternative to the combination of aCGH and whole-exome sequencing.

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