scholarly journals Limited genetic diversity of blaCMY-2-containing IncI1-pST12 plasmids from Enterobacteriaceae of human and broiler chicken origin in the Netherlands

2020 ◽  
Author(s):  
Evert den Drijver ◽  
Joep J.J.M. Stohr ◽  
Jaco J. Verweij ◽  
Carlo Verhulst ◽  
Francisca C. Velkers ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Pan Genome ◽  
Long Read ◽  
Short Read Sequence ◽  
High Degree ◽  
Limited Genetic Diversity

AbstractDistinguishing epidemiologically related and unrelated plasmids is essential to confirm plasmid transmission. We compared IncI1-pST12 plasmids from both human and livestock origin and explored the degree of sequence similarity between plasmids from Enterobacteriaceae with different epidemiological links. Short-read sequence data of Enterobacteriaceae cultured from humans and broilers were screened for the presence of both a blaCMY-2 gene and an IncI1-pST12 replicon. Isolates were long-read sequenced on a MinION sequencer (OxfordNanopore Technologies). After plasmid reconstruction using hybrid assembly, pairwise single nucleotide polymorphisms (SNP) were determined. The plasmids were annotated, and a pan-genome was constructed to compare genes variably present between the different plasmids. Nine Escherichia coli sequences of broiler origin, four Escherichia coli sequences and one Salmonella enterica sequence of human origin were selected for the current analysis. A circular contig with the IncI1-pST12 replicon and blaCMY-2 gene was extracted from the assembly graph of all fourteen isolates. Analysis of the IncI1-pST12 plasmids revealed a low number of SNP differences (range of 0-9 SNPs). The range of SNP differences overlapped in isolates with different epidemiological links. One-hundred and twelve from a total of 113 genes of the pan-genome were present in all plasmid constructs. NGS-analysis of blaCMY--2-containing IncI1-pST12 plasmids isolated from Enterobacteriaceae with different epidemiological links show a high degree of sequence similarity in terms of SNP differences and the number of shared genes. Therefore, statements on the horizontal transfer of these plasmids based on genetic identity should be made with caution.

scholarly journals Limited Genetic Diversity of blaCMY-2-Containing IncI1-pST12 Plasmids from Enterobacteriaceae of Human and Broiler Chicken Origin in The Netherlands

2020 ◽  
Vol 8 (11) ◽  
pp. 1755
Author(s):  
Evert Drijver ◽  
Joep Stohr ◽  
Jaco Verweij ◽  
Carlo Verhulst ◽  
Francisca Velkers ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Sequencing Analysis ◽  
Nucleotide Polymorphisms ◽  
Pan Genome ◽  
Next Generation Sequencing Analysis ◽  
Long Read ◽  
Short Read Sequence ◽  
High Degree

Distinguishing epidemiologically related and unrelated plasmids is essential to confirm plasmid transmission. We compared IncI1–pST12 plasmids from both human and livestock origin and explored the degree of sequence similarity between plasmids from Enterobacteriaceae with different epidemiological links. Short-read sequence data of Enterobacteriaceae cultured from humans and broilers were screened for the presence of both a blaCMY-2 gene and an IncI1–pST12 replicon. Isolates were long-read sequenced on a MinION sequencer (OxfordNanopore Technologies). After plasmid reconstruction using hybrid assembly, pairwise single nucleotide polymorphisms (SNPs) were determined. The plasmids were annotated, and a pan-genome was constructed to compare genes variably present between the different plasmids. Nine Escherichia coli sequences of broiler origin, four Escherichia coli sequences, and one Salmonella enterica sequence of human origin were selected for the current analysis. A circular contig with the IncI1–pST12 replicon and blaCMY-2 gene was extracted from the assembly graph of all fourteen isolates. Analysis of the IncI1–pST12 plasmids revealed a low number of SNP differences (range of 0–9 SNPs). The range of SNP differences overlapped in isolates with different epidemiological links. One-hundred and twelve from a total of 113 genes of the pan-genome were present in all plasmid constructs. Next generation sequencing analysis of blaCMY-2-containing IncI1–pST12 plasmids isolated from Enterobacteriaceae with different epidemiological links show a high degree of sequence similarity in terms of SNP differences and the number of shared genes. Therefore, statements on the horizontal transfer of these plasmids based on genetic identity should be made with caution.

scholarly journals Genetic diversity of blaKPC-gene-containing IncF plasmids from epidemiologically related and unrelated Enterobacteriaceae

2020 ◽  
Author(s):  
Joep J.J.M. Stohr ◽  
Marjolein F. Q. Kluytmans-van den Bergh ◽  
Veronica A.T.C. Weterings ◽  
John W. A. Rossen ◽  
Jan A. J. W. Kluytmans
Keyword(s):  
Genetic Similarity ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Similarity Index ◽  
Pairwise Comparisons ◽  
Phylogenetic Distance ◽  
Limited Information ◽  
Hospital Outbreak ◽  
Long Read ◽  
High Degree

AbstractBackgroundLimited information is available on whether blaKPC-containing plasmids from isolates in a hospital outbreak can be differentiated from epidemiologically unrelated blaKPC-containing plasmids based on sequence data.ObjectiveThis study aimed to evaluate the performance of three approaches to distinguish epidemiologically related from unrelated blaKPC-containing IncF plasmids.MethodEpidemiologically related isolates, were short- and long-read whole genome sequenced on an Illumina MiSeq and MinION sequencer. A hybrid assembly was performed and plasmid sequences were extracted from the assembly graph. Epidemiologically unrelated plasmid sequences were extracted from the GenBank. Pairwise comparisons were performed of epidemiologically related and unrelated plasmids based on SNP differences using snippy, phylogenetic distance using Roary and using a similarity index that penalizes size differences between plasmids (Stoesser-index). The percentage of pairwise comparisons misclassified as genetically related or as clonally unrelated was determined using different genetic thresholds for genetic relatedness for all three comparison methods.ResultsDespite the median number of SNP differences, Roary phylogenetic distance, and Stoesser-index differed between the epidemiologically related and unrelated plasmids, the range of differences overlapped between the two comparison groups for all three comparison methods. When using a genetic similarity threshold that classified 100% of epidemiologically related plasmid pairs as genetically related, the percentages of plasmids misclassified as epidemiologically related ranged from 6.7% (Roary) to 20.8% (Stoesser-index).DiscussionAlthough epidemiologically related plasmids can be distinguished from unrelated plasmids based on genetic similarity, epidemiologically related and unrelated blaKPC-containing IncF plasmids show a high degree of sequence similarity. The phylogenetic distance as determined using Roary showed the highest degree of discriminatory power between the epidemiologically related and unrelated plasmids.Impact statementAccurately distinguishing epidemiologically related from unrelated plasmids is essential to detect nosocomial plasmid transmission in outbreaks. However, limited information is available on whether blaKPC-containing plasmids from isolates in a hospital outbreak can be differentiated from epidemiologically unrelated blaKPC-containing plasmids based on sequence data. This study aimed to evaluate the performance of three approaches to distinguish epidemiologically related from unrelated blaKPC-containing IncF plasmids. Pairwise comparisons were performed of epidemiologically related and unrelated plasmids based on SNP differences using snippy, phylogenetic distance using Roary and using a similarity index that penalizes size differences between plasmids (Stoesser-index). Based on our results, epidemiologically related plasmids can be distinguished from unrelated plasmids based on genetic similarity. Despite this, epidemiologically related and unrelated blaKPC-containing IncF plasmids show a high degree of sequence similarity and judgements on the horizontal transfer of these plasmids during hospital outbreaks based on genetic identity should be made with caution. The phylogenetic distance determined using Roary showed the highest discriminatory power between the epidemiologically related and unrelated plasmids.Data summaryShort-and long-read sequence data of the epidemiologically related Enterobacteriaceae isolates included in this study are available from the publicly available European Nucleotide Archive of the European Bioinformatics Institute under study accession number: PRJEB41009. The authors confirm that all supporting data have been provided within the article and through the supplementary data files.

Detection of the antimicrobial peptide gene in different Amaranthus species

Biologia ◽  
2008 ◽  
Vol 63 (2) ◽  
Author(s):  
Radka Pribylova ◽  
Petr Kralik ◽  
Bohumila Pisarikova ◽  
Ivo Pavlik
Keyword(s):  
Antimicrobial Peptide ◽  
Amino Acid Change ◽  
Sequence Similarity ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Amaranthus Caudatus ◽  
Amaranth Species ◽  
Pcr Products ◽  
Peptide Gene ◽  
High Degree

AbstractUsing primers to amplify the gene AMP2 in Amaranthus caudatus, we found the gene to be present in seven other species of the Amaranthus genus (A. albus, A. cruentus, A. blitum, A. hybridus, A. hypochondriacus, A. retroflexus and A. tricolor), in which it had not been described previously. The PCR products were sequenced and it was established that all the sequences were identical, except for two polymorphisms. These single nucleotide polymorphisms occurred at nucleotide positions 45 and 246. This exchange of one nucleotide for another was manifested in an amino acid change in both cases. Due to the fact that both polymorphisms lay outside the region encoding the chitin-binding peptide domain, which is crucial for antimicrobial peptide function, they will not likely affect the proper functioning of the peptide. With the exception of the above-mentioned polymorphisms, all sequences were identical to the sequence of the AMP2 gene that codes for the A. caudatus Ac-AMP2 (antimicrobial peptide isolated from Amaranthus caudatus seeds). The detection of sequences with high degree of sequence similarity to A. caudatus AMP2 gene leads us to the assumption that an antimicrobial peptide could also be produced by other amaranth species.

scholarly journals Distinguishing blaKPC -gene-containing IncF plasmids from epidemiologically related and unrelated Enterobacteriaceae based on short- and long-read sequence data

2021 ◽  
Author(s):  
Joep J.J.M. Stohr ◽  
Marjolein F. Q. Kluytmans-van den Bergh ◽  
Veronica A.T.C. Weterings ◽  
John W. A. Rossen ◽  
Jan A. J. W. Kluytmans
Keyword(s):  
Genetic Relatedness ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Similarity Index ◽  
Pairwise Comparisons ◽  
Phylogenetic Distance ◽  
Limited Information ◽  
Hospital Outbreak ◽  
Long Read ◽  
High Degree

Background: Limited information is available on whether blaKPC -containing plasmids from isolates in a hospital outbreak can be differentiated from epidemiologically unrelated blaKPC-containing plasmids based on sequence data. This study aimed to evaluate the performance of three approaches to distinguish epidemiologically related from unrelated blaKPC-containing pKpQiL-like IncFII(k2)-IncFIB(pQiL) plasmids. Method: Epidemiologically related isolates, were short- and long-read whole genome sequenced. A hybrid assembly was performed and plasmid sequences were extracted from the assembly graph. Epidemiologically unrelated plasmid sequences were extracted from the GenBank. Pairwise comparisons were performed of epidemiologically related and unrelated plasmids based on SNP differences using snippy, phylogenetic distance using Roary and using a similarity index that penalizes size differences between plasmids (Stoesser-index). The percentage of pairwise comparisons misclassified as genetically related or as clonally unrelated was determined using different genetic thresholds for genetic relatedness. Results: The ranges in number of SNP differences, Roary phylogenetic distance, and Stoesser-index overlapped between the epidemiologically related and unrelated plasmids. When using a genetic similarity threshold that classified 100% of epidemiologically related plasmid pairs as genetically related, the percentages of plasmids misclassified as epidemiologically related ranged from 6.7% (Roary) to 20.8% (Stoesser-index). Discussion: Although epidemiologically related plasmids can be distinguished from unrelated plasmids based on genetic differences, blaKPC-containing pKpQiL-like IncFII(k2)-IncFIB(pQiL) plasmids show a high degree of sequence similarity. The phylogenetic distance as determined using Roary showed the highest degree of discriminatory power between the epidemiologically related and unrelated plasmids.

scholarly journals Worldwide tracing of mutations and the evolutionary dynamics of SARS-CoV-2

2020 ◽  
Author(s):  
Zhong-Yin Zhou ◽  
Hang Liu ◽  
Yue-Dong Zhang ◽  
Yin-Qiao Wu ◽  
Min-Sheng Peng ◽  
...  
Keyword(s):  
Substitution Rate ◽  
Evolutionary Dynamics ◽  
Vaccine Development ◽  
Sequence Data ◽  
Immune Recognition ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Protein Coding ◽  
Theoretical Support ◽  
Recurrent Mutations

AbstractUnderstanding the mutational and evolutionary dynamics of SARS-CoV-2 is essential for treating COVID-19 and the development of a vaccine. Here, we analyzed publicly available 15,818 assembled SARS-CoV-2 genome sequences, along with 2,350 raw sequence datasets sampled worldwide. We investigated the distribution of inter-host single nucleotide polymorphisms (inter-host SNPs) and intra-host single nucleotide variations (iSNVs). Mutations have been observed at 35.6% (10,649/29,903) of the bases in the genome. The substitution rate in some protein coding regions is higher than the average in SARS-CoV-2 viruses, and the high substitution rate in some regions might be driven to escape immune recognition by diversifying selection. Both recurrent mutations and human-to-human transmission are mechanisms that generate fitness advantageous mutations. Furthermore, the frequency of three mutations (S protein, F400L; ORF3a protein, T164I; and ORF1a protein, Q6383H) has gradual increased over time on lineages, which provides new clues for the early detection of fitness advantageous mutations. Our study provides theoretical support for vaccine development and the optimization of treatment for COVID-19. We call researchers to submit raw sequence data to public databases.

scholarly journals Strain-Specific Genotyping of Bifidobacterium animalis subsp. lactis by Using Single-Nucleotide Polymorphisms, Insertions, and Deletions

2009 ◽  
Vol 75 (23) ◽  
pp. 7501-7508 ◽  
Author(s):  
Elizabeth P. Briczinski ◽  
Joseph R. Loquasto ◽  
Rodolphe Barrangou ◽  
Edward G. Dudley ◽  
Anastasia M. Roberts ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Sequence Similarity ◽  
Nucleotide Polymorphisms ◽  
Strain Specificity ◽  
Typing Method ◽  
Single Nucleotide ◽  
Bifidobacterium Animalis ◽  
Molecular Approaches ◽  
Commercial Applications ◽  
High Level

ABSTRACT Several probiotic strains of Bifidobacterium animalis subsp. lactis are widely supplemented into food products and dietary supplements due to their documented health benefits and ability to survive within the mammalian gastrointestinal tract and acidified dairy products. The strain specificity of these characteristics demands techniques with high discriminatory power to differentiate among strains. However, to date, molecular approaches, such as pulsed-field gel electrophoresis and randomly amplified polymorphic DNA-PCR, have been ineffective at achieving strain separation due to the monomorphic nature of this subspecies. Previously, sequencing and comparison of two B. animalis subsp. lactis genomes (DSMZ 10140 and Bl-04) confirmed this high level of sequence similarity, identifying only 47 single-nucleotide polymorphisms (SNPs) and four insertions and/or deletions (INDELs) between them. In this study, we hypothesized that a sequence-based typing method targeting these loci would permit greater discrimination between strains than previously attempted methods. Sequencing 50 of these loci in 24 strains of B. animalis subsp. lactis revealed that a combination of nine SNPs/INDELs could be used to differentiate strains into 14 distinct genotypic groups. In addition, the presence of a nonsynonymous SNP within the gene encoding a putative glucose uptake protein was found to correlate with the ability of certain strains to transport glucose and to grow rapidly in a medium containing glucose as the sole carbon source. The method reported here can be used in clinical, regulatory, and commercial applications requiring identification of B. animalis subsp. lactis at the strain level.

scholarly journals 1202. Multimodal Sequencing of a Clonal Case Cluster of Carbapenem-Resistant Citrobacter Reveals Unexpectedly Rapid Dynamics of KPC3-Containing Plasmids

2018 ◽  
Vol 5 (suppl_1) ◽  
pp. S364-S364
Author(s):  
Roby Bhattacharyya ◽  
Alejandro Pironti ◽  
Bruce J Walker ◽  
Abigail Manson ◽  
Virginia Pierce ◽  
...  
Keyword(s):  
Point Mutations ◽  
Illumina Miseq ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
Carbapenem Resistant ◽  
Oxford Nanopore ◽  
Close Relationship ◽  
Long Read ◽  
Carbapenem Resistant Enterobacteriaceae

Abstract Background Carbapenem-resistant Enterobacteriaceae (CRE) are a major public health threat. We report four clonally related Citrobacter freundii isolates harboring the blaKPC-3 carbapenemase in April–May 2017 that are nearly identical to a strain from 2014 at the same institution. Despite differing by ≤5 single nucleotide polymorphisms (SNPs), these isolates exhibited dramatic differences in carbapenemase plasmid architecture. Methods We sequenced four carbapenem-resistant C. freundii isolates from 2017 and compared them with an ongoing CRE surveillance project at our institution. SNPs were identified from Illumina MiSeq data aligned to a reference genome using the variant caller Pilon. Plasmids were assembled from Illumina and Oxford Nanopore sequencing data using Unicycler. Results The four 2017 isolates differed from one another by 0–5 chromosomal SNPs; two were identical. With one exception, these isolates differed by >38,000 SNPs from 25 C. freundii isolates sequenced from 2013 to 2017 at the same institution for CRE surveillance. The exception was a 2014 isolate that differed by 13–16 SNPs from each 2017 isolate, with 13 SNPs common to all four. Each C. freundii isolate harbored wild-type blaKPC-3. Despite the close relationship among the 2017 cluster, the plasmids harboring the blaKPC-3 genes differed dramatically: the carbapenemase occurred in one of the two different plasmids, with rearrangements between these plasmids across isolates. The related 2014 isolate harbored both plasmids, each with a separate copy of blaKPC-3. No transmission chains were found between any of the affected patients. Conclusion WGS confirmed clonality among four contemporaneous blaKPC-3-containing C. freundii isolates, and marked similarity with a 2014 isolate, within an institution. That only 13–16 SNPs varied between the 2014 and 2017 isolates suggests durable persistence of the blaKPC-3 gene within this lineage in a hospital ecosystem. The plasmids harboring these carbapenemase genes proved remarkably plastic, with plasmid loss and rearrangements occurring on the same time scale as two to three chromosomal point mutations. Combining short and long-read sequencing in a case cluster uniquely revealed unexpectedly rapid dynamics of carbapenemase plasmids, providing critical insight into their manner of spread. Disclosures M. J. Ferraro, SeLux Diagnostics: Scientific Advisor and Shareholder, Consulting fee. D. C. Hooper, SeLux Diagnostics: Scientific Advisor, Consulting fee.

scholarly journals High Degree of Single Nucleotide Polymorphisms in California Culex pipiens (Diptera: Culicidae) sensu lato

2012 ◽  
Vol 49 (2) ◽  
pp. 299-306 ◽  
Author(s):  
Yoosook Lee ◽  
Stephanie N. Seifert ◽  
Catelyn C. Nieman ◽  
Rory D. McAbee ◽  
Parker Goodell ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Culex Pipiens ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
High Degree
Sign in / Sign up

Export Citation Format

Share Document