scholarly journals Two multi-fragment recombination events resulted in the β-lactam-resistant serotype 11A-ST6521 related to Spain9V-ST156 pneumococcal clone spreading in south-western Europe, 2008 to 2016

2020 ◽  
Vol 25 (16) ◽  
Author(s):  
Aida González-Díaz ◽  
Miguel P Machado ◽  
Jordi Càmara ◽  
José Yuste ◽  
Emmanuelle Varon ◽  
...  
Keyword(s):  
Multicentre Study ◽  
Genome Sequencing ◽  
Pneumococcal Disease ◽  
Western Europe ◽  
Whole Genome ◽  
Recombinant Clone ◽  
Prospective Multicentre Study ◽  
European Nucleotide Archive ◽  
Depth Analysis ◽  
Vaccine Effect

Background The successful pneumococcal clone Spain9V-ST156 (PMEN3) is usually associated with vaccine serotypes 9V and 14. Aim Our objective was to analyse the increase of a serotype 11A variant of PMEN3 as cause of invasive pneumococcal disease (IPD) in Spain and its spread in south-western Europe. Methods We conducted a prospective multicentre study of adult IPD in Spain (2008–16). Furthermore, a subset of 61 penicillin-resistant serotype 11A isolates from France, Italy, Portugal and Spain were subjected to whole genome sequencing (WGS) and compared with 238 genomes from the European Nucleotide Archive (ENA). Results Although the incidence of serotype 11A in IPD was stable, a clonal shift was detected from CC62 (penicillin-susceptible) to CC156 (penicillin-resistant). By WGS, three major 11A-CC156 lineages were identified, linked to ST156 (n = 5 isolates; France, Italy and Portugal), ST166 (n = 4 isolates; France and Portugal) and ST838/6521 (n = 52 isolates; France, Portugal and Spain). Acquisition of the 11A capsule allowed to escape vaccine effect. AP200 (11A-ST62) was the donor for ST156 and ST838/6521 but not for ST166. In-depth analysis of ST838/6521 lineage showed two multi-fragment recombination events including four and seven fragments from an 11A-ST62 and an NT-ST344 representative, respectively. Conclusion The increase in penicillin-resistant serotype 11A IPD in Spain was linked to the spread of a vaccine escape PMEN3 recombinant clone. Several recombination events were observed in PMEN3 acquiring an 11A capsule. The most successful 11A-PMEN3 lineage spreading in south-western Europe appeared after two multi-fragment recombination events with representatives of two major pneumococcal clones (11A-ST62 and NT-ST344).

scholarly journals Five-year Microevolution of a Multidrug-Resistant Mycobacterium Tuberculosis Strain within a Patient with Inadequate Compliance to Treatment.

2021 ◽  
Author(s):  
Dario Fernández Do Porto ◽  
Johana Monteserin ◽  
Josefina Campos ◽  
Ezequiel J Sosa ◽  
Mario Matteo ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Sequence ◽  
Treatment Compliance ◽  
Whole Genome Sequence ◽  
Intermittent Therapy ◽  
Whole Genome ◽  
Short Term ◽  
Depth Analysis

Abstract BackgroundWhole-genome sequencing has shown that the Mycobacterium tuberculosis infection process can be more heterogeneous than previously thought. Compartmentalized infections, exogenous reinfections, and microevolution are manifestations of this clonal complexity. The analysis of the mechanisms causing the microevolution —the genetic variability of M. tuberculosis at short time scales— of a parental strain into clonal variants with a patient is a relevant issue that has not been yet completely addressed. To our knowledge, a whole genome sequence microevolution analysis in a single patient with inadequate adherence to treatment has not been previously reported.Case Presentations In this work, we applied whole genome sequencing for a more in-depth analysis of the microevolution of a parental Mycobacterium tuberculosis strain into clonal variants within a patient with poor treatment compliance in Argentina. We analyzed the whole-genome sequence of 8 consecutive Mycobacterium. tuberculosis isolates obtained from a patient within 57-month of intermittent therapy. Nineteen mutations (9 short-term, 10 fixed variants) emerged, most of them associated with drug resistance. The first isolate was already resistant to isoniazid, rifampicin, and streptomycin, thereafter the strain developed resistance to fluoroquinolones and pyrazinamide. Surprisingly, isolates remained susceptible to the pro-drug ethionamide after acquiring a frameshift mutation in ethA, a gene required for its activation. We also found a novel variant, (T-54G), in the 5' untranslated region of whiB7 (T-54G), a region allegedly related to kanamycin resistance. Notably, discrepancies between canonical and phage-based susceptibility testing to kanamycin were previously found for the isolate harboring this mutation. In our patience, microevolution was mainly driven by drug selective pressure. Rare short-term mutations fixed together with resistance-conferring mutations during therapy.ConclusionsThis report highlights the relevance of whole-genome sequencing in the clinic for characterization of pre-XDR and MDR resistance profile, particularly in patients with incomplete and/or intermittent treatment.

scholarly journals Overlapping of independent SARS-CoV-2 nosocomial transmissions in a complex outbreak

2021 ◽  
Author(s):  
Laura Pérez-Lago ◽  
Helena Martinez Lozano ◽  
Jose Antonio pajares Diaz ◽  
Arantxa Diaz Gomez ◽  
Marina Machado ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Healthcare Workers ◽  
Virulent Strain ◽  
Control Measures ◽  
Protective Equipment ◽  
Whole Genome ◽  
Single Patient ◽  
High Fatality Rate ◽  
Depth Analysis

Abstract SARS-CoV-2 nosocomial outbreaks in the first COVID-19 wave were likely associated to a shortage of personal protective equipment and scare indications on control measures. Having covered these limitations, updates on current SARS-CoV-2 nosocomial outbreaks are required. We carried out an in-depth analysis of a 27-day nosocomial outbreak in a gastroenterology ward in our hospital, potentially involving 15 patients and three healthcare workers. Patients had stayed in one of three neighbouring rooms in the ward. The severity of the infections in six of the cases and a high fatality rate suggested the possible involvement of a single virulent strain persisting in those rooms. Whole genome sequencing of the strains from 12 patients and one healthcare worker revealed an unexpected complexity. Five different SARS-CoV-2 strains were identified, two infecting a single patient each, ruling out their relationship with the outbreak; the remaining three strains were involved in three independent overlapping limited transmission clusters with three, three, and five cases. Whole genome sequencing was key to understand the complexity of this outbreak.

scholarly journals 1470. Epidemiology of Invasive Pneumococcal Disease (IPD) Following 18 years of Pneumococcal Conjugate Vaccine (PCV) Use in the United States

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S736-S737
Author(s):  
Tamara Pilishvili ◽  
Ryan Gierke ◽  
Monica M Farley ◽  
William Schaffner ◽  
Ann Thomas ◽  
...  
Keyword(s):  
United States ◽  
Older Adults ◽  
Genome Sequencing ◽  
Invasive Pneumococcal Disease ◽  
Pneumococcal Disease ◽  
The United States ◽  
Census Bureau ◽  
Incidence Rates ◽  
Whole Genome ◽  
Vaccine Type

Abstract Background PCVs have been recommended for U.S. children since 2000. A 7-valent vaccine (PCV7) was introduced in 2000. This was replaced by a 13-valent vaccine (PCV13) in 2010. PCV13 was also recommended for adults aged ≥ 65 years in August 2014. We evaluated PCV impact on IPD. Methods IPD cases (isolation of pneumococcus from sterile sites) were identified through CDC’s Active Bacterial Core surveillance during 1998-2018. Isolates were serotyped by Quellung or whole genome sequencing and classified as PCV13-type and non-vaccine-type (NVT). Incidence rates (cases/100,000) were calculated using U.S. Census Bureau population denominators. Results From 1998 through 2018, overall IPD rates among children aged < 5 years decreased by 93% (from 95 to 7 cases/100,000). PCV13-type IPD decreased by 98% (from 88 to 2 cases/100,000). Among adults aged ≥ 65 years, overall IPD rates decreased by 60% (from 61 to 25 cases/100,000). PCV13-type IPD rates declined 86% (from 46 to 7 cases/100,000). Declines were most dramatic in the years following PCV7 introduction, with additional declines after PCV13 introduction in children (Figures 1 and 2). Serotypes 3, 19A, and 19F caused most of the remaining PCV13-type IPD. NVT IPD rates did not change significantly among children. Among adults aged 50-64 years, NVT IPD increased by 83% (from 6 to 12 cases/100,000) (p< 0.01). Among adults aged ≥ 65 years, NVT IPD increased by 22% (from 15 to 18 cases/100,000) (p< 0.01). The most common NVTs in 2018 were 22F (10% of all IPD), 9N (7%) and 15A (5%). Among children, the proportion of cases with meningitis increased from 5% to 14% (p< 0.01), and the proportion with pneumonia/empyema increased from 17% to 31% (p< 0.01). Among adults, the proportion of cases with meningitis did not change (3%), while the proportion with pneumonia/empyema increased from 72% to 76% (p=0.01). Figure 1: Incidence of invasive pneumococcal disease among children aged < 5 years, 1998-2018 Figure 2: Incidence of invasive pneumococcal disease among adults aged ≥ 65 years, 1998-2018 Conclusion Overall IPD incidence among children and adults decreased following PCV introduction for children, driven primarily by reductions in PCV-type IPD. NVT IPD increased in older adults, but these increases did not eliminate reductions from PCV13-type IPD. Disclosures Lee Harrison, MD, GSK (Consultant)Merck (Consultant)Pfizer (Consultant)Sanofi Pasteur (Consultant)

The largest prison outbreak of TB in Western Europe investigated using whole-genome sequencing

2021 ◽  
Vol 25 (6) ◽  
pp. 491-497
Author(s):  
E. Roycroft ◽  
M. M. Fitzgibbon ◽  
D. M. Kelly ◽  
M. Scully ◽  
A. M. McLaughlin ◽  
...  
Keyword(s):  
Public Health ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Western Europe ◽  
Education Programme ◽  
Multidrug Resistant ◽  
Case Finding ◽  
Contact Tracing ◽  
Whole Genome ◽  
Nucleotide Polymorphisms

BACKGROUND: In March 2011, the Department of Public Health East in Ireland were notified of two cases of TB in two prisoners sharing a cell. We define the resulting outbreak and highlight the role of public health and laboratory-based molecular epidemiology in mapping and control of a prison outbreak.METHODS: Cases were identified through clinical presentation, contact tracing, case-finding exercise or enhanced laboratory surveillance. Mycobacterium tuberculosis isolates were genotyped and underwent whole-genome sequencing (WGS).RESULTS: Of the 34 cases of TB linked to the outbreak, 27 were prisoners (79%), 4 prison officers (12%) and 3 community cases (9%). M. tuberculosis was isolated from 31 cases (culture positivity: 91%). A maximum of six single-nucleotide polymorphisms separated the isolates, with 22 being identical, suggestive of a highly infectious ‘super-spreader´ within the prison. Isolates belonged to the Beijing sub-lineage, and were susceptible to first-line anti-TB agents. A case-finding exercise incidentally detected a prisoner with multidrug-resistant TB. Of the 143 prison officers screened, 52% had latent TB infection. Litigation costs exceeded five million euros.CONCLUSION: This constitutes the largest prison outbreak of TB in Western Europe investigated using WGS. A robust prison entry TB screening and education programme is required to effect better TB control, and prevent future outbreaks and attendant litigation.

scholarly journals Five-year microevolution of a multidrug-resistant Mycobacterium tuberculosis strain within a patient with inadequate compliance to treatment

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Darío A. Fernandez Do Porto ◽  
Johana Monteserin ◽  
Josefina Campos ◽  
Ezequiel J. Sosa ◽  
Mario Matteo ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Intermittent Therapy ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Short Term ◽  
Depth Analysis

Abstract Background Whole-genome sequencing has shown that the Mycobacterium tuberculosis infection process can be more heterogeneous than previously thought. Compartmentalized infections, exogenous reinfections, and microevolution are manifestations of this clonal complexity. The analysis of the mechanisms causing the microevolution —the genetic variability of M. tuberculosis at short time scales— of a parental strain into clonal variants with a patient is a relevant issue that has not been yet completely addressed. To our knowledge, a whole genome sequence microevolution analysis in a single patient with inadequate adherence to treatment has not been previously reported. Case presentation In this work, we applied whole genome sequencing analysis for a more in-depth analysis of the microevolution of a parental Mycobacterium tuberculosis strain into clonal variants within a patient with poor treatment compliance in Argentina. We analyzed the whole-genome sequence of 8 consecutive Mycobacterium tuberculosis isolates obtained from a patient within 57-months of intermittent therapy. Nineteen mutations (9 short-term, 10 fixed variants) emerged, most of them associated with drug resistance. The first isolate was already resistant to isoniazid, rifampicin, and streptomycin, thereafter the strain developed resistance to fluoroquinolones and pyrazinamide. Surprisingly, isolates remained susceptible to the pro-drug ethionamide after acquiring a frameshift mutation in ethA, a gene required for its activation. We also found a novel variant, (T-54G), in the 5′ untranslated region of whiB7 (T-54G), a region allegedly related to kanamycin resistance. Notably, discrepancies between canonical and phage-based susceptibility testing to kanamycin were previously found for the isolate harboring this mutation. In our patient, microevolution was mainly driven by drug selective pressure. Rare short-term mutations fixed together with resistance-conferring mutations during therapy. Conclusions This report highlights the relevance of whole-genome sequencing analysis in the clinic for characterization of pre-XDR and MDR resistance profile, particularly in patients with incomplete and/or intermittent treatment.

scholarly journals Anin silicosurvey ofClostridioides difficileextrachromosomal elements

2019 ◽  
Author(s):  
Bastian Hornung ◽  
Ed J. Kuijper ◽  
Wiep Klaas Smits
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
In Silico ◽  
Sequence Data ◽  
Whole Genome ◽  
Clostridioides Difficile ◽  
Extrachromosomal Elements ◽  
European Nucleotide Archive ◽  
Healthcare Associated ◽  
Systematic Identification

AbstractThe gram-positive enteropathogenClostridioides difficileis the major cause of healthcare associated diarrhoea and is also an important cause of community-acquired infectious diarrhoea. Considering the burden of the disease, many studies have employed whole genome sequencing to identify factors that contribute to virulence and pathogenesis. Though extrachromosomal elements such as plasmids are important for these processes in other bacteria, the few characterized plasmids ofC. difficilehave no relevant functions assigned and no systematic identification of plasmids has been carried out to date. Here, we perform anin silicoanalysis of publicly available sequence data, to show that ∼13% of allC. difficilestrains contain extrachromosomal elements, with 1-6 elements per strain. Our approach identifies known plasmids (e.g. pCD6, pCD630 and cloning plasmids) and 6 novel putative plasmid families. Our study shows that plasmids are abundant and may encode functions that are relevant forC. difficilephysiology. The newly identified plasmids may also form the basis for the construction of novel cloning plasmids forC. difficilethat are compatible with existing tools.RepositoriesThe assembled circular type plasmids have been deposited at the European Nucleotide Archive (ENA) under accession numbers ERZ940801 and ERZ940803-ERZ940808.

scholarly journals Whole-genome sequencing reveals recent and frequent genetic recombination between clonal lineages of Cryphonectria parasitica in western Europe

2019 ◽  
Vol 130 ◽  
pp. 122-133 ◽  
Author(s):  
Arthur Demené ◽  
Ludovic Legrand ◽  
Jérôme Gouzy ◽  
Robert Debuchy ◽  
Gilles Saint-Jean ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Western Europe ◽  
Genetic Recombination ◽  
Cryphonectria Parasitica ◽  
Whole Genome

scholarly journals Whole Genome Sequencing Characterization of HEV3-e and HEV3-f Subtypes among the Wild Boar Population in the Abruzzo Region, Italy: First Report

2020 ◽  
Vol 8 (9) ◽  
pp. 1393
Author(s):  
Giuseppe Aprea ◽  
Silvia Scattolini ◽  
Daniela D’Angelantonio ◽  
Alexandra Chiaverini ◽  
Valeria Di Lollo ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Wild Boar ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Wild Animals ◽  
Wild Boar Population ◽  
Wild Boars ◽  
First Report ◽  
Depth Analysis ◽  
Human Infections

Hepatitis E virus (HEV) is an emergent zoonotic pathogen, causing worldwide acute and chronic hepatitis in humans. HEV comprises eight genotypes and several subtypes. HEV genotypes 3 and 4 (HEV3 and HEV4) are zoonotic. In Italy, the most part of HEV infections (80%) is due to autochthonous HEV3 circulation of the virus, and the key role played by wild animals is generally accepted. Abruzzo is an Italian region officially considered an HEV “hot spot”, with subtype HEV3-c being up to now the only one reported among wild boars. During the year 2018–2019, a group of wild boars in Abruzzo were screened for HEV; positive RNA liver samples were subjected to HEV characterization by using the whole genome sequencing (WGS) approach methodology. This represents the first report about the detection of HEV-3 subtypes e and f in the wild boar population in this area. Since in Italy human infections from HEV 3-e and f have been associated with pork meat consumption, our findings deserve more in-depth analysis with the aim of evaluating any potential correlation between wild animals, the pork chain production and HEV human infections.

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