scholarly journals Fast forward evolution in real time: the rapid spread of SARS-CoV-2 variant of concern lineage B.1.1.7 in Saxony-Anhalt over a period of 5 months

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Markus Glaß ◽  
Danny Misiak ◽  
Claudia Misiak ◽  
Simon Müller ◽  
Alexander Rausch ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Immune Escape ◽  
Point Mutations ◽  
Clinical Signs ◽  
Relevant Information ◽  
University Hospital ◽  
Surveillance Program ◽  
Binding Motif ◽  
Whole Genome

Abstract Objectives Random mutations and recombinations are the main sources for the genetic diversity in SARS-CoV-2, with mutations in the SARS-CoV-2 spike (S) receptor binding motif (RBM) representing a high potential for the emergence of new putative variants under investigation (VUI) or variants of concern (VOC). It is of importance, to measure the different circulating SARS-CoV-2 lineages in order to establish a regional SARS-CoV-2 surveillance program. We established whole genome sequencing (WGS) of circulating SARS-CoV-2 lineages in order to establish a regional SARS-CoV-2 surveillance program. Methods We established a surveillance program for circulating SARS-CoV-2 lineages by performing whole genome sequencing (WGS) in SARS-CoV-2 isolates. Specimens were collected over a period of 5 months from three different sites. Specimens were collected from both patients suffering from COVID-19 and from outpatients without any clinical signs or symptoms; both in a tertiary university hospital, and two private laboratories within an urban area of eastern part Germany. Results Viral WGS from the 364 respiratory specimens with positive SARS-CoV-2 RT-PCR comprised 16 different SARS-CoV-2 lineages. The majority of the obtained sequences (252/364=69%) was assigned to the variant of concern (VOC) Alpha (B.1.1.7). This variant first appeared in February in our samples and quickly became the dominant virus variant. All SNP PCR results could be verified using WGS. Other VOCs found in our cohort were Beta (B.1.351, n=2) and Delta (B.1.617.2, n=1). Conclusions Lineage analysis revealed 16 different virus variants among 364 respiratory samples analyzed by WGS. The number of distinct lineages dramatically decreased over time in leaving only few variants, in particular, the VOC Alpha or B.1.1.7. By closer inspection of point mutations, we found several distinct mutations of the viral spike protein that were reported to increase affinity or enable immune escape. Within a study period of only 5 months, SARS-CoV-2 lineage B.1.1.7 became the dominant lineage in our study population. This study emphasizes the benefit of SARS-CoV-2 testing by WGS. The increasing use of WGS to sequence the entire SARS-CoV-2 genome will reveal additional VUIs and VOCs with the potential to evade the immune system and, thus, will be a promising tool for data mining of relevant information for epidemiological studies. SARS-CoV-2 lineage monitoring using WGS is an important surveillance tool for early detection of upcoming new lineages of concern.

scholarly journals A Retrospective Whole-Genome Sequencing Analysis of Carbapenem and Colistin-Resistant Klebsiella pneumoniae Nosocomial Strains Isolated during an MDR Surveillance Program

Antibiotics ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 246 ◽  
Author(s):  
Bernardina Gentile ◽  
Antonella Grottola ◽  
Gabriella Orlando ◽  
Giulia Fregni Serpini ◽  
Claudia Venturelli ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Capsular Polysaccharide ◽  
University Hospital ◽  
Surveillance Program ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Nucleotide Polymorphisms ◽  
Colistin Resistance

Multidrug-resistant Klebsiella pneumoniae (MDR Kp), in particular carbapenem-resistant Kp (CR-Kp), has become endemic in Italy, where alarming data have been reported on the spread of colistin-resistant CR-Kp (CRCR-Kp). During the period 2013–2014, 27 CRCR-Kp nosocomial strains were isolated within the Modena University Hospital Policlinico (MUHP) multidrug resistance surveillance program. We retrospectively investigated these isolates by whole-genome sequencing (WGS) analysis of the resistome, virulome, plasmid content, and core single nucleotide polymorphisms (cSNPs) in order to gain insights into their molecular epidemiology. The in silico WGS analysis of the resistome revealed the presence of genes, such as blaKPC, related to the phenotypically detected resistances to carbapenems. Concerning colistin resistance, the plasmidic genes mcr 1–9 were not detected, while known and new genetic variations in mgrB, phoQ, and pmrB were found. The virulome profile revealed the presence of type-3 fimbriae, capsular polysaccharide, and iron acquisition system genes. The detected plasmid replicons were classified as IncFIB(pQil), IncFIB(K), ColRNAI, IncX3, and IncFII(K) types. The cSNPs genotyping was consistent with the multi locus sequence typing (MLST) and with the distribution of mutations related to colistin resistance genes. In a nosocomial drug resistance surveillance program, WGS proved to be a useful tool for elucidating the spread dynamics of CRCR-Kp nosocomial strains and could help to limit their diffusion.

scholarly journals Transmission of ESBL-producing Enterobacteriaceae and their mobile genetic elements—identification of sources by whole genome sequencing: study protocol for an observational study in Switzerland

BMJ Open ◽  
2018 ◽  
Vol 8 (2) ◽  
pp. e021823 ◽  
Author(s):  
Tanja Stadler ◽  
Dominik Meinel ◽  
Lisandra Aguilar-Bultet ◽  
Jana S Huisman ◽  
Ruth Schindler ◽  
...  
Keyword(s):  
Observational Study ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bacterial Species ◽  
Mobile Genetic Elements ◽  
University Hospital ◽  
Whole Genome ◽  
Hospital Acquired Infections ◽  
Genetic Elements ◽  
Hospital Acquired

IntroductionExtended-spectrum beta-lactamases (ESBL)-producing Enterobacteriaceae were first described in relation with hospital-acquired infections. In the 2000s, the epidemiology of ESBL-producing organisms changed as especially ESBL-producingEscherichia coliwas increasingly described as an important cause of community-acquired infections, supporting the hypothesis that in more recent years ESBL-producing Enterobacteriaceae have probably been imported into hospitals rather than vice versa. Transmission of ESBL-producing Enterobacteriaceae is complicated by ESBL genes being encoded on self-transmissible plasmids, which can be exchanged among the same and different bacterial species. The aim of this research project is to quantify hospital-wide transmission of ESBL-producing Enterobacteriaceae on both the level of bacterial species and the mobile genetic elements and to determine if hospital-acquired infections caused by ESBL producers are related to strains and mobile genetic elements predominantly circulating in the community or in the healthcare setting. This distinction is critical in prevention since the former emphasises the urgent need to establish or reinforce antibiotic stewardship programmes, and the latter would call for more rigorous infection control.Methods and analysisThis protocol presents an observational study that will be performed at the University Hospital Basel and in the city of Basel, Switzerland. ESBL-producing Enterobacteriaceae will be collected from any specimens obtained by routine clinical practice or by active screening in both inpatient and outpatient settings, as well as from wastewater samples and foodstuffs, both collected monthly over a 12-month period for analyses by whole genome sequencing. Bacterial chromosomal, plasmid and ESBL-gene sequences will be compared within the cohort to determine genetic relatedness and migration between humans and their environment.Ethics and disseminationThis study has been approved by the local ethics committee (Ethikkommission Nordwest-und Zentralschweiz) as a quality control project (Project-ID 2017–00100). The results of this study will be published in peer-reviewed medical journals, communicated to participants, the general public and all relevant stakeholders.

scholarly journals Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Silvia Argimón ◽  
Melissa A. L. Masim ◽  
June M. Gayeta ◽  
Marietta L. Lagrada ◽  
Polle K. V. Macaranas ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
The Philippines ◽  
Surveillance Program ◽  
Whole Genome ◽  
Antimicrobial Resistance Surveillance

scholarly journals RARE-26. WHOLE GENOME SEQUENCING OF AN OSSEOUS METASTASIS DURING CHECKPOINT-CONTROLLED INTRACRANIAL GLIOBLASTOMA REVEALS NEW INSIGHTS INTO POTENTIAL MECHANISMS OF IMMUNE ESCAPE

2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi227-vi227
Author(s):  
Malte Mohme ◽  
Cecile Maire ◽  
Simon Schliffke ◽  
Simon Joosse ◽  
Malik Alawi ◽  
...  
Keyword(s):  
T Cell ◽  
Bone Metastasis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Cell Response ◽  
Immune Escape ◽  
T Cell Response ◽  
Molecular Profile ◽  
Whole Genome ◽  
Checkpoint Inhibition

Abstract Glioblastoma (GBM) has a devastating prognosis and recent advances in the treatment of a variety of cancer entities, e.g. through checkpoint inhibition, could so far not be translated into improved outcome in newly-diagnosed GBM. Characterizing rare cases of peripheral metastases which succeeded in overcoming immune control, can help to understand the mechanisms of immune escape. Here we describe the first reported case of a detailed genetic and immunological characterization of a peripheral bone metastasis from a GBM which was controlled intracranially by anti-PD1 checkpoint inhibition We performed whole genome sequencing (WGS) of the primary- and recurrent tumor, as well as the bone metastasis. Genomic data was analyzed for copy number variations and mutational profiles. In addition, immune monitoring with flow cytometric phenotyping and next-generation sequencing of the peripheral T-cell repertoire was used. A 70-year old patient developed multiple osseous metastases in the spine, while his IDHwt GBM recurrence was immunologically controlled with checkpoint inhibition. Biopsy confirmed peripheral GBM metastases. Immunophenotyping reflected the effective activation of the peripheral T-cell response, with, however, simultaneous upregulation of regulatory T-cells during disease progression. WGS sequencing demonstrated a distinct molecular profile of the GBM metastasis, with amplifications in chromosome 3 and 9, as well as genomic loss on chromosomes 4, 10 and 11. The peripheral metastasis was distinguished by mutations in mismatch repair genes, such as MSH4 and MLH1, associated with a hypermutated phenotype. Among the mutated genes we found potential candidates involved in immune escape of circulating tumor cells. This case represents a unique opportunity to analyze potential mechanisms of GBM-mediated immune escape during immune activation with anti-PD1 checkpoint therapy. It highlights the fact, that although an effective, disinhibited immune response can control the cranial GBM disease, hypermutated tumor clones can evade the tumor-specific T-cell response and disseminate to distant organs.

scholarly journals A fully automated approach for quality control of cancer mutations in the era of high-resolution whole genome sequencing

2021 ◽  
Author(s):  
Jacob Househam ◽  
William CH Cross ◽  
Giulio Caravagna
Keyword(s):  
Quality Control ◽  
Data Quality ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Large Scale ◽  
Control Method ◽  
Point Mutations ◽  
Basic Research ◽  
Whole Genome ◽  
Colorectal Cancer Patients

AbstractCancer is a global health issue that places enormous demands on healthcare systems. Basic research, the development of targeted treatments, and the utility of DNA sequencing in clinical settings, have been significantly improved with the introduction of whole genome sequencing. However the broad applications of this technology come with complications. To date there has been very little standardisation in how data quality is assessed, leading to inconsistencies in analyses and disparate conclusions. Manual checking and complex consensus calling strategies often do not scale to large sample numbers, which leads to procedural bottlenecks. To address this issue, we present a quality control method that integrates point mutations, copy numbers, and other metrics into a single quantitative score. We demonstrate its power on 1,065 whole-genomes from a large-scale pan-cancer cohort, and on multi-region data of two colorectal cancer patients. We highlight how our approach significantly improves the generation of cancer mutation data, providing visualisations for cross-referencing with other analyses. Our approach is fully automated, designed to work downstream of any bioinformatic pipeline, and can automatise tool parameterization paving the way for fast computational assessment of data quality in the era of whole genome sequencing.

scholarly journals Whole genome sequencing for revealing the point mutations of SARS-CoV-2 genome in Bangladeshi isolates and their structural effects on viral proteins

RSC Advances ◽  
2021 ◽  
Vol 11 (61) ◽  
pp. 38868-38879
Author(s):  
Mohammad Uzzal Hossain ◽  
Ishtiaque Ahammad ◽  
Arittra Bhattacharjee ◽  
Zeshan Mahmud Chowdhury ◽  
Md. Tabassum Hossain Emon ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Impact Analysis ◽  
Point Mutations ◽  
Viral Proteins ◽  
Whole Genome ◽  
Structural Effects

SARS-CoV-2 mutational impact analysis.

scholarly journals Agrobacterium spp. nosocomial outbreak assessment using rapid MALDI-TOF MS based typing, confirmed by whole genome sequencing

2019 ◽  
Vol 8 (1) ◽  
Author(s):  
Carlo Casanova ◽  
Elia Lo Priore ◽  
Adrian Egli ◽  
Helena M. B. Seth-Smith ◽  
Lorenz Räber ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Point Sources ◽  
University Hospital ◽  
Outbreak Investigation ◽  
Whole Genome ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Epidemiological Characteristics ◽  
Tof Ms

Abstract Background A number of episodes of nosocomial Agrobacterium spp. bacteremia (two cases per year) were observed at Bern University Hospital, Switzerland, from 2015 to 2017. This triggered an outbreak investigation. Methods Cases of Agrobacterium spp. bacteremias that occurred between August 2011 and February 2017 were investigated employing line lists, environmental sampling, rapid protein- (MALDI-TOF MS), and genome-based typing (pulsed field gel electrophoresis and whole genome sequencing) of the clinical isolates. Results We describe a total of eight bacteremia episodes due to A. radiobacter (n = 2), Agrobacterium genomovar G3 (n = 5) and A. pusense (n = 1). Two tight clusters were observed by WGS typing, representing the two A. radiobacter isolates (cluster I, isolated in 2015) and four of the Agrobacterium genomovar G3 isolates (cluster II, isolated in 2016 and 2017), suggesting two different point sources. The epidemiological investigations revealed two computer tomography (CT) rooms as common patient locations, which correlated with the two outbreak clusters. MALDI-TOF MS permitted faster evaluation of strain relatedness than DNA-based methods. High resolution WGS-based typing confirmed the MALDI-TOF MS clustering. Conclusions We report clinical and epidemiological characteristics of two outbreak clusters with Agrobacterium. spp. bacteremia likely acquired during CT contrast medium injection and highlight the use of MALDI-TOF MS as a rapid tool to assess relatedness of rare gram-negative pathogens in an outbreak investigation.

scholarly journals Whole genome sequencing of a clinical drug resistant Candida albicans isolate reveals known and novel mutations in genes involved in resistance acquisition mechanisms

2021 ◽  
Vol 70 (4) ◽  
Author(s):  
Roy A. Khalaf ◽  
Nour Fattouh ◽  
Matej Medvecky ◽  
Jaroslav Hrabak
Keyword(s):  
Candida Albicans ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Point Mutations ◽  
Antifungal Resistance ◽  
Antifungal Drugs ◽  
Resistant Isolate ◽  
Whole Genome ◽  
Ergosterol Content ◽  
Virulence Potential

Candida albicans is an opportunistic pathogen accounting for the majority of cases of Candida infections. Currently, C. albicans are developing resistance towards different classes of antifungal drugs and this has become a global health burden that does not spare Lebanon. This study aims at determining point mutations in genes known to be involved in resistance acquisition and correlating resistance to virulence and ergosterol content in the azole resistant C. albicans isolate CA77 from Lebanon. This pilot study is the first of its kind to be implemented in Lebanon. We carried out whole genome sequencing of the azole resistant C. albicans isolate CA77 and examined 18 genes involved in antifungal resistance. To correlate genotype to phenotype, we evaluated the virulence potential of this isolate by injecting it into BALB/c mice and we quantified membrane ergosterol. Whole genome sequencing revealed that eight out of 18 genes involved in antifungal resistance were mutated in previously reported and novel residues. These genotypic changes were associated with an increase in ergosterol content but no discrepancy in virulence potential was observed between our isolate and the susceptible C. albicans control strain SC5314. This suggests that antifungal resistance and virulence potential in this antifungal resistant isolate are not correlated and that resistance is a result of an increase in membrane ergosterol content and the occurrence of point mutations in genes involved in the ergosterol biosynthesis pathway.

scholarly journals The Role of Whole Genome Sequencing in the Surveillance of Antimicrobial Resistant Enterococcus spp.: A Scoping Review

2021 ◽  
Vol 9 ◽  
Author(s):  
Lindsay A. Rogers ◽  
Kayla Strong ◽  
Susan C. Cork ◽  
Tim A. McAllister ◽  
Karen Liljebjelke ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Scoping Review ◽  
Companion Animals ◽  
Surveillance Program ◽  
Whole Genome ◽  
Antimicrobial Resistance Genes ◽  
Wide Range ◽  
Scoping Reviews

Enterococcus spp. have arisen as important nosocomial pathogens and are ubiquitous in the gastrointestinal tracts of animals and the environment. They carry many intrinsic and acquired antimicrobial resistance genes. Because of this, surveillance of Enterococcus spp. has become important with whole genome sequencing emerging as the preferred method for the characterization of enterococci. A scoping review was designed to determine how the use of whole genome sequencing in the surveillance of Enterococcus spp. adds to our knowledge of antimicrobial resistance in Enterococcus spp. Scoping review design was guided by the PRISMA extension and checklist and JBI Reviewer's Guide for scoping reviews. A total of 72 articles were included in the review. Of the 72 articles included, 48.6% did not state an association with a surveillance program and 87.5% of articles identified Enterococcus faecium. The majority of articles included isolates from human clinical or screening samples. Significant findings from the articles included novel sequence types, the increasing prevalence of vancomycin-resistant enterococci in hospitals, and the importance of surveillance or screening for enterococci. The ability of enterococci to adapt and persist within a wide range of environments was also a key finding. These studies emphasize the importance of ongoing surveillance of enterococci from a One Health perspective. More studies are needed to compare the whole genome sequences of human enterococcal isolates to those from food animals, food products, the environment, and companion animals.

scholarly journals 2165. Helicobacter pylori Infections in the Bronx, New York: Whole-Genome Sequencing for Rapid Genotypic Susceptibility Testing

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S734-S735
Author(s):  
Saranathan Rajagopalan ◽  
Wendy Szymczak ◽  
William Jacobs ◽  
Daniel Behin ◽  
Debra Pan ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Active Form ◽  
Point Mutations ◽  
Illumina Miseq ◽  
23S Rrna ◽  
Whole Genome ◽  
Resistance Mutations ◽  
Clinical Value ◽  
H Pylori

Abstract Background Susceptibility-guided treatment of H. pylori is superior to empiric therapy. We determined the accuracy of whole-genome sequencing (WGS) compared with phenotypic testing using CLSI/EUCAST breakpoints. Methods Thirty-three clinical isolates of H. pylori cultured from gastric biopsies were sequenced with a coverage range between 40x and 80x using Illumina Miseq platform and the reads were assembled and annotated with PATRIC. Phenotypic susceptibility tests were performed using E-test strips under microaerophilic conditions for 72 hours. Mutations associated with amoxicillin, tetracycline, clarithromycin, levofloxacin, metronidazole and rifampin resistance were examined. Results Of the 33 isolates, two were phenotypically resistant to amoxicillin: one carried a β-lactamase gene (blaTEM-116) and the other exhibited a point mutation pbp2 (A541T). All isolates were tetracycline susceptible phenotypically, but three isolates had point mutations in 16S rRNA that are associated with resistance (A926G). Clarithromycin results showed a good correlation between methods. Nine clarithromycin-resistant isolates demonstrated point mutations in 23S rRNA (A2142G/A2143G). Fifteen isolates were phenotypically resistant to levofloxacin, but resistance mutations were found in only 14 strains (N87I/N87K/D91Y/D91N/D91G/D99N in gyrA). We analyzed our strains for the presence of intact genes rdxA and frxA, either of which convert the prodrug form of metronidazole into the active form. Twenty-four of 33 isolates were tested phenotypically. We found 3 isolates with truncations in both genes. These isolates had metronidazole MICs >256. The presence of one or both intact genes did not always result in low MICs, indicating that there may be significant point mutations that contribute to resistance. Rifampin was not tested phenotypically, but no mutations in rpoB were found. In summary, the correlation of WGS and phenotypic testing was 100% for amoxicillin and clarithromycin, 97% for levofloxacin, 91% for tetracycline (n = 33), and 67% for metronidazole (n = 24). Conclusion WGS provides a detailed analysis of H. pylori resistance and a broader analysis of antimicrobials that may be of clinical value. Additional studies are needed for genotypic prediction of metronidazole resistance. Disclosures All authors: No reported disclosures.

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