Clinical Genomics Örebro

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SciLifeLab Infrastructure Unit Since 2019.

Primary: Shown in the list of current labels, if end date is not specified.

Started: 2019

Ended: Current

Year 2024

PubMed DOI Crossref
Sensitive and Specific Droplet Digital PCR Assays for Circulating Tumor HPV DNA: Development, Validation, and Clinical Application in HPV-Associated Cancers.
Qvick A, Andersson E, Oldaeus Almerén A, ..., Karlsson MG, Helenius G
Mol Diagn Ther 28 (6) 835-845 [2024-11-00; online 2024-09-26]
Clinical Genomics Örebro [Technology development]
PubMed DOI Crossref
The power of hybridization capture - Illustrated using an expanded gene panel on 100 post mortem samples, focusing on sudden unexplained death.
Kling D, Adolfsson E, Gréen H, Gréen A
Forensic Sci Int Genet 74 (-) 103160 [2024-10-11; online 2024-10-11]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Early unrecognised SARS-CoV-2 introductions shaped the first pandemic wave, Sweden, 2020.
Dyrdak R, Hodcroft EB, Broddesson S, ..., Neher RA, Albert J
Euro Surveill. 29 (41) - [2024-10-00; online 2024-10-11]
Clinical Genomics Stockholm [Service] Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
In silico gepotidacin target mining among 33 213 global Neisseria gonorrhoeae genomes from 1928 to 2023 combined with gepotidacin MIC testing of 22 gonococcal isolates with different GyrA and ParC substitutions.
David A, Golparian D, Jacobsson S, ..., Davies C, Unemo M
J. Antimicrob. Chemother. 79 (9) 2221-2226 [2024-09-03; online 2024-07-15]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Conference report: the first bacterial genome sequencing pan-European network conference.
Germuskova Z, Sosa E, Lagos AC, ..., Mölling P, Egli A
Microbes Infect - (-) 105410 [2024-08-30; online 2024-08-30]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
The novel 2024 WHO Neisseria gonorrhoeae reference strains for global quality assurance of laboratory investigations and superseded WHO N. gonorrhoeae reference strains-phenotypic, genetic and reference genome characterization.
Unemo M, Sánchez-Busó L, Golparian D, ..., Wi T, Lahra MM
J. Antimicrob. Chemother. 79 (8) 1885-1899 [2024-08-01; online 2024-06-18]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
The WHO Enhanced Gonococcal Antimicrobial Surveillance Programme (EGASP) identifies high levels of ceftriaxone resistance across Vietnam, 2023.
Lan PT, Nguyen HT, Golparian D, ..., Unemo M, EGASP-Vietnam WGS study group
Lancet Reg Health West Pac 48 (-) 101125 [2024-07-00; online 2024-06-27]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Diagnosis of external ventricular drainage related infections with real-time 16S PCR and third-generation 16S sequencing.
Widén J, Morén J, Mölling P, ..., Sundqvist M, Westman G
Infect Dis (Lond) 56 (7) 521-530 [2024-07-00; online 2024-03-26]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
A laboratory-based predictive pathway for the development of Neisseria gonorrhoeae high-level resistance to corallopyronin A, an inhibitor of bacterial RNA polymerase.
Balthazar JT, Golparian D, Unemo M, ..., Vassylyev DG, Shafer WM
Microbiol Spectr 12 (6) e0056024 [2024-06-04; online 2024-04-22]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Recent dynamics in Neisseria gonorrhoeae genomic epidemiology in Brazil: antimicrobial resistance and genomic lineages in 2017-20 compared to 2015-16.
Golparian D, Bazzo ML, Ahlstrand J, ..., Unemo M, Brazilian-GASP Network
J. Antimicrob. Chemother. 79 (5) 1081-1092 [2024-05-02; online 2024-03-22]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Pharmacodynamic evaluation of ceftriaxone single-dose therapy (0.125-1 g) to eradicate ceftriaxone-susceptible and ceftriaxone-resistant Neisseria gonorrhoeae strains in a hollow fibre infection model for gonorrhoea.
Unemo M, Golparian D, Oxelbark J, ..., Drusano G, Jacobsson S
J. Antimicrob. Chemother. 79 (5) 1006-1013 [2024-05-02; online 2024-03-18]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Antimicrobial-resistant Neisseria gonorrhoeae in Europe in 2020 compared with in 2013 and 2018: a retrospective genomic surveillance study.
Golparian D, Cole MJ, Sánchez-Busó L, ..., Unemo M, Euro-GASP study group
Lancet Microbe 5 (5) e478-e488 [2024-05-00; online 2024-04-10]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Complete reference genomes of two ceftriaxone-resistant Neisseria gonorrhoeae strains identified in routine surveillance in Bangkok, Thailand, using Nanopore Q20+ chemistry, VolTRAX V2b, and Illumina sequencing.
Sangprasert P, Golparian D, Paopang P, ..., Kittiyaowanarn R, Unemo M
Microbiol Resour Announc 13 (3) e0123123 [2024-03-12; online 2024-02-01]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
pyngoST: fast, simultaneous and accurate multiple sequence typing of Neisseria gonorrhoeae genome collections.
Sánchez-Busó L, Sánchez-Serrano A, Golparian D, Unemo M
Microb Genom 10 (1) - [2024-01-00; online 2024-01-30]
Clinical Genomics Örebro [Collaborative]

Year 2023

PubMed DOI Crossref
Trends in invasive bacterial diseases during the first 2 years of the COVID-19 pandemic: analyses of prospective surveillance data from 30 countries and territories in the IRIS Consortium.
Shaw D, Abad R, Amin-Chowdhury Z, ..., Zhou F, Brueggemann AB
Lancet Digit Health 5 (9) e582-e593 [2023-09-00; online 2023-07-27]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Sustained Transmission of Neisseria gonorrhoeae Strains with High-Level Azithromycin Resistance (MIC ≥ 256 μg/mL) in Argentina, 2018 to 2022.
Gianecini RA, Poklepovich T, Golparian D, ..., Campos J, Galarza P
Microbiol Spectr 11 (4) e0097023 [2023-08-17; online 2023-06-20]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Genomic surveillance and antimicrobial resistance determinants in Neisseria gonorrhoeae isolates from Uganda, Malawi and South Africa, 2015-20.
Kakooza F, Golparian D, Matoga M, ..., Wi T, Unemo M
J. Antimicrob. Chemother. 78 (8) 1982-1991 [2023-08-02; online 2023-06-23]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
High-level in vitro resistance to gentamicin acquired in a stepwise manner in Neisseria gonorrhoeae.
Golparian D, Jacobsson S, Holley CL, Shafer WM, Unemo M
J. Antimicrob. Chemother. 78 (7) 1769-1778 [2023-07-05; online 2023-05-30]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Whole exome sequencing of FFPE samples-expanding the horizon of forensic molecular autopsies.
Adolfsson E, Kling D, Gunnarsson C, ..., Gréen H, Gréen A
Int J Legal Med 137 (4) 1215-1234 [2023-07-00; online 2022-11-08]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization.
Koskela von Sydow A, Lindqvist CM, Asghar N, ..., Mölling P, Stenmark B
Sci Rep 13 (1) 6461 [2023-04-20; online 2023-04-20]
Clinical Genomics Örebro [Technology development]
PubMed DOI Crossref
Complete Reference Genome Sequence of the Clinical Neisseria gonorrhoeae Strain H035, with Resistance to the Novel Antimicrobial Zoliflodacin, Identified in Japan in 2000.
Golparian D, Jacobsson S, Ohnishi M, Unemo M
Microbiol Resour Announc 12 (3) e0113022 [2023-03-16; online 2023-02-28]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Multidrug-resistant Neisseria gonorrhoeae isolate SE690: mosaic penA-60.001 gene causing ceftriaxone resistance internationally has spread to the more antimicrobial-susceptible genomic lineage, Sweden, September 2022.
Golparian D, Vestberg N, Södersten W, ..., Bhattarai KH, Unemo M
Euro Surveill. 28 (10) - [2023-03-00; online 2023-03-10]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Prevalence and persistence of Neisseria meningitidis carriage in Swedish university students.
Olof S, Lorraine E, Berhane A I, ..., Paula M, Susanne J
Epidemiol. Infect. 151 (-) e25 [2023-02-13; online 2023-02-13]
Clinical Genomics Örebro [Collaborative]

Year 2022

PubMed DOI Crossref
GyrB in silico mining in 27 151 global gonococcal genomes from 1928-2021 combined with zoliflodacin in vitro testing of 71 international gonococcal isolates with different GyrB, ParC and ParE substitutions confirms high susceptibility.
Golparian D, Jacobsson S, Sánchez-Busó L, ..., Ohnishi M, Unemo M
J. Antimicrob. Chemother. - (-) - [2022-10-29; online 2022-10-29]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Complete Reference Genome Sequence of the Extensively Drug-Resistant Strain Neisseria gonorrhoeae AT159, with Ceftriaxone Resistance and High-Level Azithromycin Resistance, Using Nanopore Q20+ Chemistry and Illumina Sequencing.
Golparian D, Pleininger S, Jacobsson S, Indra A, Unemo M
Microbiol Resour Announc 11 (9) e0074422 [2022-09-15; online 2022-08-25]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Genomic surveillance and antimicrobial resistance in Neisseria gonorrhoeae isolates in Bangkok, Thailand in 2018.
Golparian D, Kittiyaowamarn R, Paopang P, ..., Wi T, Unemo M
J. Antimicrob. Chemother. 77 (8) 2171-2182 [2022-07-28; online 2022-05-12]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Evaluation of within-host evolution of methicillin-resistant Staphylococcus aureus (MRSA) by comparing cgMLST and SNP analysis approaches.
Lagos AC, Sundqvist M, Dyrkell F, ..., Söderquist B, Mölling P
Sci Rep 12 (1) 10541 [2022-06-22; online 2022-06-22]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Extensively drug-resistant (XDR) Neisseria gonorrhoeae causing possible gonorrhoea treatment failure with ceftriaxone plus azithromycin in Austria, April 2022.
Pleininger S, Indra A, Golparian D, ..., Heidler S, Unemo M
Euro Surveill. 27 (24) - [2022-06-00; online 2022-06-18]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Pharmacodynamic Evaluation of Zoliflodacin Treatment of Neisseria gonorrhoeae Strains With Amino Acid Substitutions in the Zoliflodacin Target GyrB Using a Dynamic Hollow Fiber Infection Model.
Jacobsson S, Golparian D, Oxelbark J, ..., Drusano G, Unemo M
Front Pharmacol 13 (-) 874176 [2022-04-14; online 2022-04-14]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
First National Genomic Epidemiological Study of Neisseria gonorrhoeae Strains Spreading Across Sweden in 2016.
Hadad R, Golparian D, Velicko I, ..., Engstrand L, Unemo M
Front Microbiol 12 (-) 820998 [2022-01-13; online 2022-01-13]
Bioinformatics Support for Computational Resources [Service] Clinical Genomics Örebro [Collaborative]

Year 2021

PubMed DOI Crossref
Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis.
Beale MA, Marks M, Cole MJ, ..., Fifer H, Thomson NR
Nat Microbiol 6 (12) 1549-1560 [2021-12-00; online 2021-11-24]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Genomic Epidemiology of Azithromycin-Nonsusceptible Neisseria gonorrhoeae, Argentina, 2005-2019.
Gianecini RA, Poklepovich T, Golparian D, ..., Galarza P, Gonococcal Antimicrobial Susceptibility Surveillance Programme—Argentina1
Emerg. Infect. Dis. 27 (9) 2369-2378 [2021-08-24; online 2021-08-24]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Optimization of droplet digital PCR assays for the type-specific detection and quantification of five HPV genotypes, including additional data on viral loads of nine different HPV genotypes in cervical carcinomas.
Malin K, Louise BM, Gisela H, Mats KG, Gabriella L
J Virol Methods 294 (-) 114193 [2021-08-00; online 2021-05-19]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Liquid biopsy as an option for predictive testing and prognosis in patients with lung cancer.
Qvick A, Stenmark B, Carlsson J, ..., Karlsson C, Helenius G
Mol. Med. 27 (1) 68 [2021-07-03; online 2021-07-03]
Clinical Genomics Örebro [Technology development]
PubMed DOI Crossref
Technical in-depth comparison of two massive parallel DNA-sequencing methods for formalin-fixed paraffin-embedded tissue from victims of sudden cardiac death.
Adolfsson E, Qvick A, Gréen H, ..., Jonasson J, Gréen A
Forensic Sci Int Genet 53 (-) 102522 [2021-07-00; online 2021-04-26]
Clinical Genomics Örebro [Technology development]
PubMed DOI Crossref
Lack of diagnostic-escape mutants of group B streptococcus in Slovenia.
Perme T, Golparian D, Unemo M, Jeverica S
Clin. Microbiol. Infect. 27 (7) 1054-1055 [2021-07-00; online 2021-02-02]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Pharmacodynamic Evaluation of Dosing, Bacterial Kill, and Resistance Suppression for Zoliflodacin Against Neisseria gonorrhoeae in a Dynamic Hollow Fiber Infection Model.
Jacobsson S, Golparian D, Oxelbark J, ..., Drusano G, Unemo M
Front Pharmacol 12 (-) 682135 [2021-05-21; online 2021-05-21]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Atypical presentation of Neisseria meningitidis serogroup W disease is associated with the introduction of the 2013 strain.
Säll O, Stenmark B, Jacobsson S, ..., Sundqvist M, Mölling P
Epidemiol. Infect. 149 (-) e126 [2021-04-29; online 2021-04-29]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch.
Sánchez-Busó L, Yeats CA, Taylor B, ..., Unemo M, Aanensen DM
Genome Med 13 (1) 61 [2021-04-19; online 2021-04-19]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Genome-wide methylome analysis of two strains belonging to the hypervirulent Neisseria meningitidis serogroup W ST-11 clonal complex.
Stenmark B, Eriksson L, Thulin Hedberg S, ..., Roberts RJ, Mölling P
Sci Rep 11 (1) 6239 [2021-03-18; online 2021-03-18]
Clinical Genomics Örebro [Technology development]
PubMed DOI Crossref
Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR) clonal complexes are consistent with genomic phylogeny and provide simple nomenclature, rapid visualization and antimicrobial resistance (AMR) lineage predictions.
Golparian D, Sánchez-Busó L, Cole M, Unemo M
J. Antimicrob. Chemother. 76 (4) 940-944 [2021-03-12; online 2021-01-08]
Clinical Genomics Örebro [Technology development]

Year 2020

PubMed DOI Crossref
Genomic epidemiology of Neisseria gonorrhoeae elucidating the gonococcal antimicrobial resistance and lineages/sublineages across Brazil, 2015-16.
Golparian D, Bazzo ML, Golfetto L, ..., Unemo M, Brazilian-GASP Network
J. Antimicrob. Chemother. 75 (11) 3163-3172 [2020-11-01; online 2020-08-14]
Clinical Genomics Örebro [Technology development]
PubMed DOI Crossref
Geographically widespread invasive meningococcal disease caused by a ciprofloxacin resistant non-groupable strain of the ST-175 clonal complex.
Willerton L, Lucidarme J, Campbell H, ..., Vogel U, Borrow R
J Infect 81 (4) 575-584 [2020-10-00; online 2020-08-25]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Genomic epidemiology and antimicrobial resistance determinants of Neisseria gonorrhoeae isolates from Ukraine, 2013-2018.
Boiko I, Golparian D, Jacobsson S, ..., Shevchenko T, Unemo M
APMIS 128 (7) 465-475 [2020-07-00; online 2020-05-23]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
High genomic-based predicted strain coverage among invasive meningococcal isolates when combining Bexsero and Trumenba vaccines.
Säll O, Olofsson E, Jacobsson S
Vaccine 38 (28) 4374-4378 [2020-06-09; online 2020-05-12]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Genomic analysis and antimicrobial resistance of Neisseria gonorrhoeae isolates from Vietnam in 2011 and 2015-16.
Lan PT, Golparian D, Ringlander J, ..., Van Thuong N, Unemo M
J. Antimicrob. Chemother. 75 (6) 1432-1438 [2020-06-01; online 2020-02-19]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Staphylococcus argenteus as an etiological agent of prosthetic hip joint infection: a case presentation.
Söderquist B, Wildeman P, Stenmark B, Stegger M
J Bone Jt Infect 5 (4) 172-175 [2020-05-25; online 2020-05-25]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Difference in virulence between Neisseria meningitidis serogroups W and Y in transgenic mice.
Eriksson L, Stenmark B, Deghmane A, ..., Mölling P, Taha M
BMC Microbiol. 20 (1) 92 [2020-04-15; online 2020-04-15]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Genomic characterization and outcome of prosthetic joint infections caused by Staphylococcus aureus.
Wildeman P, Tevell S, Eriksson C, ..., Söderquist B, Stenmark B
Sci Rep 10 (1) 5938 [2020-04-03; online 2020-04-03]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Complete genome and methylome analysis of Neisseria meningitidis associated with increased serogroup Y disease.
Stenmark B, Harrison OB, Eriksson L, ..., Maiden MCJ, Mölling P
Sci Rep 10 (1) 3644 [2020-02-27; online 2020-02-27]
Clinical Genomics Örebro [Technology development]

Year 2019

PubMed DOI Crossref
Comparative distribution of extended-spectrum beta-lactamase-producing Escherichia coli from urine infections and environmental waters.
Fagerström A, Mölling P, Khan FA, ..., Jass J, Söderquist B
PLoS ONE 14 (11) e0224861 [2019-11-07; online 2019-11-07]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Genomic analysis of Staphylococcus capitis isolated from blood cultures in neonates at a neonatal intensive care unit in Sweden.
Stenmark B, Hellmark B, Söderquist B
Eur. J. Clin. Microbiol. Infect. Dis. 38 (11) 2069-2075 [2019-11-00; online 2019-08-09]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Genome-based epidemiology and antimicrobial resistance determinants of Neisseria gonorrhoeae isolates with decreased susceptibility and resistance to extended-spectrum cephalosporins in Argentina in 2011-16.
Gianecini RA, Golparian D, Zittermann S, ..., Galarza P, Gonococcal Antimicrobial Susceptibility Surveillance Programme-Argentina (GASSP-AR) Working Group
J. Antimicrob. Chemother. 74 (6) 1551-1559 [2019-06-01; online 2019-03-02]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Staphylococcus aureus isolates from nares of orthopaedic patients in Sweden are mupirocin susceptible.
Magnusson C, Stegger M, Hellmark B, Stenmark B, Söderquist B
Infect Dis (Lond) 51 (6) 475-478 [2019-06-00; online 2019-04-15]
Clinical Genomics Örebro [Collaborative]
PubMed DOI Crossref
Increase of invasive meningococcal serogroup W disease in Europe, 2013 to 2017.
Krone M, Gray S, Abad R, ..., Vogel U, Borrow R
Euro Surveill. 24 (14) - [2019-04-00; online 2019-04-11]
Clinical Genomics Örebro [Collaborative]
SciLifeLab Data Centre
Publications 9.5.1