scholarly journals Phylogeny and Historical-Geographical Analysis of Yersinia pestis Strains from Vietnam

2020 ◽  
pp. 98-107
Author(s):  
K. A. Nikiforov ◽  
L. M. Kukleva ◽  
Zh. V. Al’khova ◽  
E. G. Oglodin ◽  
M. A. Makashova ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Yersinia Pestis ◽  
Genome Sequencing ◽  
Yunnan Province ◽  
Molecular Genetic ◽  
Snp Analysis ◽  
Whole Genome ◽  
Separate Branch ◽  
Second Wave

Objective of the work was to identify molecular-genetic peculiarities, to conduct whole genome sequencing and phylogenetic analysis of Yersinia pestis strains isolated inVietnam between 1962 and 1989.Materials and methods. We have studied the properties of 50 Y. pestis strains, carried out whole genome sequencing of 18 and fragment sequencing of 32 strains from Vietnam. Phylogenetic analysis was performed on the basis of whole genome SNPanalysis by 1391 identified SNPs. Whole genome SNP-analysis and search for marker SNPs were conducted applying Wombac 2.0 software package. Phylogenetic diagram construction was done using Maximum Likelihood algorithm.Results and discussion. Several phylogenetic branches and Y. pestis populations coinciding with geographical and historical dissemination of the strains have been distinguished. The major part of the strains from Vietnam falls under the branch designated by us as 1.ORI2v. Two strains form a separate branch together with the strain from India belonging to 1.ORI2 line, one more strain, 55-801 Saigon, is set among the strains of 1.ORI1 line. Based on the data obtained and evidence from the literature sources it can be assumed that introduction of plague into Vietnam occurred through several waves: Nha Trang city in 1898, by sea; north provinces of the country – 1908. The second wave of Y. pestis dissemination across the territory of Vietnam began in 1960s with the emergence of the strains from the natural plague focus in Yunnan province, China.

scholarly journals Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1803
Author(s):  
Jitendra Singh ◽  
Anvita Gupta Malhotra ◽  
Debasis Biswas ◽  
Prem Shankar ◽  
Leena Lokhande ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Spike Protein ◽  
Whole Genome ◽  
The Novel ◽  
Genome Sequences ◽  
Second Wave ◽  
Insight Into

India experienced a tragic second wave after the end of March 2021, which was far more massive than the first wave and was driven by the emergence of the novel delta variant (B.1.617.2) of the SARS-CoV-2 virus. In this study, we explored the local and national landscape of the viral variants in the period immediately preceding the second wave to gain insight into the mechanism of emergence of the delta variant and thus improve our understanding of the causation of the second wave. We randomly selected 20 SARS-CoV-2 positive samples diagnosed in our lab between 3 February and 8 March 2021 and subjected them to whole genome sequencing. Nine of the 20 sequenced genomes were classified as kappa variant (B.1.617.1). The phylogenetic analysis of pan-India SARS-CoV-2 genome sequences also suggested the gradual replacement of the α variant with the kappa variant during this period. This relative consolidation of the kappa variant was significant, since it shared 3 of the 4 signature mutations (L452R, E484Q and P681R) observed in the spike protein of delta variant and thus was likely to be the precursor in its evolution. This study demonstrates the predominance of the kappa variant in the period immediately prior to the second wave and underscores its role as the “bridging variant” between the α and delta variants that drove the first and second waves of COVID-19 in India, respectively.

scholarly journals Phylogenetic Analysis of Yersinia pestis Strains of Medieval Biovar, Isolated in Precaspian North-Western Steppe Plague Focus in the XX Century

2019 ◽  
pp. 55-61 ◽  
Author(s):  
G. A. Eroshenko ◽  
N. V. Popov ◽  
Zh. V. Al’khova ◽  
A. N. Balykova ◽  
L. M. Kukleva ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Yersinia Pestis ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Natural Focus ◽  
Phylogenetic Relations ◽  
Ion Pgm ◽  
System Life ◽  
North Western

Objective of the study – comparative phylogenetic analysis of Yersinia pestis strains, isolated in Precaspian North-Western steppe focus in 1924–1926, 1972, and 1986–1990 to understand the causes of focal reactivation during different time periods of the XX century.Materials and methods. The work included 30 strains of Yersinia pestis from Precaspian North-Western steppe natural focus and adjacent plague foci. Whole genome sequencing of eight Y. pestis strains from the former was carried out. Also whole-genome sequences of 16 strains from neighboring natural foci were used. Whole-genome sequencing of Y. pestis strains was conducted in Ion PGM system (Life technologies). SNPs search across the core genome was performed using software package Wombac 2.0. Tree diagram Maximum Likelihood, HKU85 model, was constructed to analyze phylogenetic relations.Results and discussion. It is established that in early XX century (1924–1926), strains of phylogenetic branches 2.MED4 and 2.MED1, belonging to medieval biovar, main subspecies, circulated on Ergenin Upland in the Precaspian North-Western steppe natural focus. Later on they became extinct in the territory. It is shown that the strains, isolated on Ergenin Upland in 1972, constituted a common subcluster on the dendrogram with the strains from low-mountain and piedmont plague foci of Caucasus and Transcaucasia, dated the same time period. It was inferred that epizootic manifestations on Ergenin upland in 1972, after a long recess since 1938, were caused by importation of Y. pestis strains from low-mountain natural plague foci of Caucasus and Transcaucasia. It was noted that expansion of Caucasian strains was of short-term character, and plague infected animals have not been found on Ergenin Upland since 1974 (including modern period). It is established that Y. pestis strains isolated in the eastern part of Precaspian North-Western steppe focus between 1986 and 1990, do not have close genetic relation to the strains that circulated on Ergenin Upland in 1924–1926 and 1972. It is determined that each epizootic period (1913–1938 and 1972–1973) in Precaspian North-Western steppe natural focus culminated in the elimination of the circulating Y. pestis strains and rehabilitation of the focal territory. 

scholarly journals Whole-Genome Sequencing for Investigating a Health Care-Associated Outbreak of Carbapenem-Resistant Acinetobacter baumannii

Diagnostics ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 201
Author(s):  
Sang Mee Hwang ◽  
Hee Won Cho ◽  
Tae Yeul Kim ◽  
Jeong Su Park ◽  
Jongtak Jung ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Snp Analysis ◽  
Whole Genome ◽  
Phylogenetic Tree Analysis ◽  
Web Based ◽  
Hospital Outbreak ◽  
Carbapenem Resistant ◽  
Bioinformatics Tools

Carbapenem-resistant Acinetobacter baumannii (CRAB) outbreaks in hospital settings challenge the treatment of patients and infection control. Understanding the relatedness of clinical isolates is important in distinguishing outbreak isolates from sporadic cases. This study investigated 11 CRAB isolates from a hospital outbreak by whole-genome sequencing (WGS), utilizing various bioinformatics tools for outbreak analysis. The results of multilocus sequence typing (MLST), single nucleotide polymorphism (SNP) analysis, and phylogenetic tree analysis by WGS through web-based tools were compared, and repetitive element polymerase chain reaction (rep-PCR) typing was performed. Through the WGS of 11 A. baumannii isolates, three clonal lineages were identified from the outbreak. The coexistence of blaOXA-23, blaOXA-66, blaADC-25, and armA with additional aminoglycoside-inactivating enzymes, predicted to confer multidrug resistance, was identified in all isolates. The MLST Oxford scheme identified three types (ST191, ST369, and ST451), and, through whole-genome MLST and whole-genome SNP analyses, different clones were found to exist within the MLST types. wgSNP showed the highest discriminatory power with the lowest similarities among the isolates. Using the various bioinformatics tools for WGS, CRAB outbreak analysis was applicable and identified three discrete clusters differentiating the separate epidemiologic relationships among the isolates.

Whole Genome Sequencing and Phylogenetic Analysis of the Rabies Virus Strain Moscow 3253 Adapted to a Vero Cell Line

2020 ◽  
Vol 35 (4) ◽  
pp. 237-242
Author(s):  
Ya. M. Krasnov ◽  
Zh. V. Alkhova ◽  
S. V. Generalov ◽  
I. V. Tuchkov ◽  
E. A. Naryshkina ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Vero Cell ◽  
Whole Genome Sequencing ◽  
Cell Line ◽  
Rabies Virus ◽  
Genome Sequencing ◽  
Virus Strain ◽  
Whole Genome ◽  
Vero Cell Line ◽  
Rabies Virus Strain

Identification of multiple species and subpopulations among Australian clinical Sporothrix isolates using whole genome sequencing

2018 ◽  
Vol 57 (7) ◽  
pp. 905-908 ◽  
Author(s):  
David New ◽  
Alicia G Beukers ◽  
Sarah E Kidd ◽  
Adam J Merritt ◽  
Kerry Weeks ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Sporothrix Schenckii ◽  
Sensu Stricto ◽  
Northern Territory ◽  
Whole Genome ◽  
Phylogenetic Resolution ◽  
Genetic Clustering ◽  
Multiple Species

AbstractWhole genome sequencing (WGS) was used to demonstrate the wide genetic variability within Sporothrix schenckii sensu lato and establish that there are two main species of Sporothrix within Australian clinical isolates—S. schenckii sensu stricto and Sporothrix globosa. We also demonstrated southwest Western Australia contained genetically similar S. schenckii ss strains that are distinct from strains isolated in the eastern and northern states of Australia. Some genetic clustering by region was also noted for northern NSW, Queensland, and Northern Territory. Phylogenetic analysis of WGS data provided greater phylogenetic resolution compared to analysis of the calmodulin gene alone.

scholarly journals Putative Integrative Mobile Elements That Exploit the Xer Recombination Machinery Carrying blaIMI-Type Carbapenemase Genes in Enterobacter cloacae Complex Isolates in Singapore

2017 ◽  
Vol 62 (1) ◽  
Author(s):  
Tse H. Koh ◽  
Nurdyana Binte Abdul Rahman ◽  
Jeanette W. P. Teo ◽  
My-Van La ◽  
Balamurugan Periaswamy ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Multilocus Sequence Typing ◽  
Enterobacter Cloacae ◽  
Mobile Elements ◽  
Whole Genome ◽  
Content Type ◽  
Flanking Regions ◽  
Enterobacter Cloacae Complex

ABSTRACT Whole-genome sequencing was performed on 16 isolates of the carbapenemase-producing Enterobacter cloacae complex to determine the flanking regions of bla IMI-type genes. Phylogenetic analysis of multilocus sequence typing (MLST) targets separated the isolates into 4 clusters. The bla IMI-type genes were all found on Xer-dependent integrative mobile elements (IMEX). The IMEX elements of 5 isolates were similar to those described in Canada, while the remainder were novel. Five isolates had IMEX elements lacking a resolvase and recombinase.

scholarly journals Evaluating whole-genome sequencing quality metrics for enteric pathogen outbreaks

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12446
Author(s):  
Darlene D. Wagner ◽  
Heather A. Carleton ◽  
Eija Trees ◽  
Lee S. Katz
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Assembly ◽  
Enteric Bacteria ◽  
Quality Metrics ◽  
Read Length ◽  
Snp Analysis ◽  
Whole Genome ◽  
Insert Size ◽  
E Coli

Background Whole genome sequencing (WGS) has gained increasing importance in responses to enteric bacterial outbreaks. Common analysis procedures for WGS, single nucleotide polymorphisms (SNPs) and genome assembly, are highly dependent upon WGS data quality. Methods Raw, unprocessed WGS reads from Escherichia coli, Salmonella enterica, and Shigella sonnei outbreak clusters were characterized for four quality metrics: PHRED score, read length, library insert size, and ambiguous nucleotide composition. PHRED scores were strongly correlated with improved SNPs analysis results in E. coli and S. enterica clusters. Results Assembly quality showed only moderate correlations with PHRED scores and library insert size, and then only for Salmonella. To improve SNP analyses and assemblies, we compared seven read-healing pipelines to improve these four quality metrics and to see how well they improved SNP analysis and genome assembly. The most effective read healing pipelines for SNPs analysis incorporated quality-based trimming, fixed-width trimming, or both. The Lyve-SET SNPs pipeline showed a more marked improvement than the CFSAN SNP Pipeline, but the latter performed better on raw, unhealed reads. For genome assembly, SPAdes enabled significant improvements in healed E. coli reads only, while Skesa yielded no significant improvements on healed reads. Conclusions PHRED scores will continue to be a crucial quality metric albeit not of equal impact across all types of analyses for all enteric bacteria. While trimming-based read healing performed well for SNPs analyses, different read healing approaches are likely needed for genome assembly or other, emerging WGS analysis methodologies.

scholarly journals Comparison of whole genome sequencing to restriction endonuclease analysis and gel diffusion precipitin-based serotyping of Pasteurella multocida

2017 ◽  
Vol 30 (1) ◽  
pp. 42-55 ◽  
Author(s):  
Karen J. LeCount ◽  
Linda K. Schlater ◽  
Tod Stuber ◽  
Suelee Robbe Austerman ◽  
Timothy S. Frana ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Restriction Endonuclease ◽  
Genome Sequencing ◽  
Pasteurella Multocida ◽  
Restriction Endonuclease Analysis ◽  
The United States ◽  
Snp Analysis ◽  
Whole Genome ◽  
Gel Diffusion ◽  
Endonuclease Analysis

The gel diffusion precipitin test (GDPT) and restriction endonuclease analysis (REA) have commonly been used in the serotyping and genotyping of Pasteurella multocida. Whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) analysis has become the gold standard for other organisms, offering higher resolution than previously available methods. We compared WGS to REA and GDPT on 163 isolates of P. multocida to determine if WGS produced more precise results. The isolates used represented the 16 reference serovars, isolates with REA profiles matching an attenuated fowl cholera vaccine strain, and isolates from 10 different animal species. Isolates originated from across the United States and from Chile. Identical REA profiles clustered together in the phylogenetic tree. REA profiles that differed by only a few bands had fewer SNP differences than REA profiles with more differences, as expected. The GDPT results were diverse but it was common to see a single serovar show up repeatedly within clusters. Several errors were found when examining the REA profiles. WGS was able to confirm these errors and compensate for the subjectivity in analysis of REA. Also, results of WGS and SNP analysis correlated more closely with the epidemiologic data than GDPT. In silico results were also compared to a lipopolysaccharide rapid multiplex PCR test. From the data produced in our study, WGS and SNP analysis was superior to REA and GDPT and highlighted some of the issues with the older tests.

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