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3. Whole genomes from bacteria collected at diagnostic units around the world 2020

Author

Nag, S, Larsen, G, Szarvas, J, Birkedahl, L, Gulyas, G, Ciok, W, Lagermann, T, Tafaj, S, Bradbury, S, Collignon, P, Daley, D, Dougnon, V, Fabiyi, K, Coulibaly, B, Dembele, R, Nikiema, G, Magloire, N, Ouindgueta, I, Hossain, Z, Begum, A, Donchev, D, Diggle, M, Turnbull, L, Levesque, S, Berlinger, L, Sogaard, K, Guevara, P, Valderrama, C, Maikanti, P, Amlerova, J, Drevinek, P, Tkadlec, J, Dilas, M, Kaasch, A, Westh, H, Bachtarzi, M, Amhis, W, Salazar, C, Villacis, J, Luzon, M, Palau, D, Duployez, C, Paluche, M, Asante-Sefa, S, Moller, M, Ip, M, Marekovic, I, Pal-Sonnevend, A, Cocuzza, C, Dambrauskiene, A, Macanze, A, Cossa, A, Mandomando, I, Nwajiobi-Princewill, P, Okeke, I, Kehinde, A, Adebiyi, I, Akintayo, I, Popoola, O, Onipede, A, Blomfeldt, A, Nyquist, N, Bocker, K, Ussher, J, Ali, A, Ullah, N, Khan, H, Gustafson, N, Jarrar, I, Al-Hamad, A, Luvira, V, Paveenkittiporn, W, Baran, I, Mwansa, J, Sikakwa, L, Yamba, K, Hendriksen, R, Aarestrup, F, Nag S., Larsen G., Szarvas J., Birkedahl L. E. K., Gulyas G. M., Ciok W. J., Lagermann T. M., Tafaj S., Bradbury S., Collignon P., Daley D., Dougnon V., Fabiyi K., Coulibaly B., Dembele R., Nikiema G., Magloire N., Ouindgueta I. J., Hossain Z. Z., Begum A., Donchev D., Diggle M., Turnbull L. A., Levesque S., Berlinger L., Sogaard K. K., Guevara P. D., Valderrama C. D., Maikanti P., Amlerova J., Drevinek P., Tkadlec J., Dilas M., Kaasch A., Westh H. T., Bachtarzi M. A., Amhis W., Salazar C. E. S., Villacis J. E., Luzon M. A. D., Palau D. B., Duployez C., Paluche M., Asante-Sefa S., Moller M., Ip M., Marekovic I., Pal-Sonnevend A., Cocuzza C. E., Dambrauskiene A., Macanze A., Cossa A., Mandomando I., Nwajiobi-Princewill P., Okeke I. N., Kehinde A. O., Adebiyi I., Akintayo I., Popoola O., Onipede A., Blomfeldt A., Nyquist N. E., Bocker K., Ussher J., Ali A., Ullah N., Khan H., Gustafson N. W., Jarrar I., Al-Hamad A., Luvira V., Paveenkittiporn W., Baran I., Mwansa J. C. L., Sikakwa L., Yamba K., Hendriksen R. S., Aarestrup F. M., Nag, S, Larsen, G, Szarvas, J, Birkedahl, L, Gulyas, G, Ciok, W, Lagermann, T, Tafaj, S, Bradbury, S, Collignon, P, Daley, D, Dougnon, V, Fabiyi, K, Coulibaly, B, Dembele, R, Nikiema, G, Magloire, N, Ouindgueta, I, Hossain, Z, Begum, A, Donchev, D, Diggle, M, Turnbull, L, Levesque, S, Berlinger, L, Sogaard, K, Guevara, P, Valderrama, C, Maikanti, P, Amlerova, J, Drevinek, P, Tkadlec, J, Dilas, M, Kaasch, A, Westh, H, Bachtarzi, M, Amhis, W, Salazar, C, Villacis, J, Luzon, M, Palau, D, Duployez, C, Paluche, M, Asante-Sefa, S, Moller, M, Ip, M, Marekovic, I, Pal-Sonnevend, A, Cocuzza, C, Dambrauskiene, A, Macanze, A, Cossa, A, Mandomando, I, Nwajiobi-Princewill, P, Okeke, I, Kehinde, A, Adebiyi, I, Akintayo, I, Popoola, O, Onipede, A, Blomfeldt, A, Nyquist, N, Bocker, K, Ussher, J, Ali, A, Ullah, N, Khan, H, Gustafson, N, Jarrar, I, Al-Hamad, A, Luvira, V, Paveenkittiporn, W, Baran, I, Mwansa, J, Sikakwa, L, Yamba, K, Hendriksen, R, Aarestrup, F, Nag S., Larsen G., Szarvas J., Birkedahl L. E. K., Gulyas G. M., Ciok W. J., Lagermann T. M., Tafaj S., Bradbury S., Collignon P., Daley D., Dougnon V., Fabiyi K., Coulibaly B., Dembele R., Nikiema G., Magloire N., Ouindgueta I. J., Hossain Z. Z., Begum A., Donchev D., Diggle M., Turnbull L. A., Levesque S., Berlinger L., Sogaard K. K., Guevara P. D., Valderrama C. D., Maikanti P., Amlerova J., Drevinek P., Tkadlec J., Dilas M., Kaasch A., Westh H. T., Bachtarzi M. A., Amhis W., Salazar C. E. S., Villacis J. E., Luzon M. A. D., Palau D. B., Duployez C., Paluche M., Asante-Sefa S., Moller M., Ip M., Marekovic I., Pal-Sonnevend A., Cocuzza C. E., Dambrauskiene A., Macanze A., Cossa A., Mandomando I., Nwajiobi-Princewill P., Okeke I. N., Kehinde A. O., Adebiyi I., Akintayo I., Popoola O., Onipede A., Blomfeldt A., Nyquist N. E., Bocker K., Ussher J., Ali A., Ullah N., Khan H., Gustafson N. W., Jarrar I., Al-Hamad A., Luvira V., Paveenkittiporn W., Baran I., Mwansa J. C. L., Sikakwa L., Yamba K., Hendriksen R. S., and Aarestrup F. M.

Abstract

The Two Weeks in the World research project has resulted in a dataset of 3087 clinically relevant bacterial genomes with pertaining metadata, collected from 59 diagnostic units in 35 countries around the world during 2020. A relational database is available with metadata and summary data from selected bioinformatic analysis, such as species prediction and identification of acquired resistance genes.

Published
2023

13. Attributable mortality of vancomycin resistance in ampicillin-resistant Enterococcus faecium bacteremia in Denmark and the Netherlands: A matched cohort study

Author

Rottier, W.C., Pinholt, M., A.K. van der bij, Arpi, M., Blank, S.N., Nabuurs-Franssen, M.H., Ruijs, G.J.H.M., Tersmette, M., Ossewaarde, J.M., Groenwold, R.H., Westh, H., Bonten, M.J.M., Dutch VRE Bacteremia Investigators, and the Danish Collaborative Bacteraemia Network (DACOBAN)

Subjects
Microbiology (medical), Vancomycin resistance, 0303 health sciences, medicine.medical_specialty, biology, 030306 microbiology, Epidemiology, business.industry, biology.organism_classification, medicine.disease, 03 medical and health sciences, 0302 clinical medicine, Infectious Diseases, Matched cohort, Internal medicine, Ampicillin, Bacteremia, Attributable mortality, Medicine, 030212 general & internal medicine, business, Enterococcus faecium, medicine.drug
Abstract

Objective:To study whether replacement of nosocomial ampicillin-resistant Enterococcus faecium (ARE) clones by vancomycin-resistant E. faecium (VRE), belonging to the same genetic lineages, increases mortality in patients with E. faecium bacteremia, and to evaluate whether any such increase is mediated by a delay in appropriate antibiotic therapy.Design:Retrospective, matched-cohort study.Setting:The study included 20 Dutch and Danish hospitals from 2009 to 2014.Patients:Within the study period, 63 patients with VRE bacteremia (36 Dutch and 27 Danish) were identified and subsequently matched to 234 patients with ARE bacteremia (130 Dutch and 104 Danish) for hospital, ward, length of hospital stay prior to bacteremia, and age. For all patients, 30-day mortality after bacteremia onset was assessed.Methods:The risk ratio (RR) reflecting the impact of vancomycin resistance on 30-day mortality was estimated using Cox regression with further analytic control for confounding factors.Results:The 30-day mortality rates were 27% and 38% for ARE in the Netherlands and Denmark, respectively, and the 30-day mortality rates were 33% and 48% for VRE in these respective countries. The adjusted RR for 30-day mortality for VRE was 1.54 (95% confidence interval, 1.06–2.25). Although appropriate antibiotic therapy was initiated later for VRE than for ARE bacteremia, further analysis did not reveal mediation of the increased mortality risk.Conclusions:Compared to ARE bacteremia, VRE bacteremia was associated with higher 30-day mortality. One explanation for this association would be increased virulence of VRE, although both phenotypes belong to the same well-characterized core genomic lineage. Alternatively, it may be the result of unmeasured confounding.

Published
2021
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18. SARS-CoV-2 in First Trimester Pregnancy:A Cohort Study

Author

La Cour Freiesleben, N., Egerup, P., Hviid, K. V.R., Severinsen, E. R., Kolte, A. M., Westergaard, D., Olsen, L. Fich, Prætorius, L., Zedeler, A., Christiansen, A. M.H., Nielsen, J. R., Bang, D., Berntsen, S., Ollé-López, J., Ingham, A., Bello-Rodríguez, J., Storm, D. M., Ethelberg-Findsen, J., Hoffmann, E. R., Wilken-Jensen, C., Jørgensen, Finn Steener, Westh, H., Jørgensen, H. L., Nielsen, H. S., La Cour Freiesleben, N., Egerup, P., Hviid, K. V.R., Severinsen, E. R., Kolte, A. M., Westergaard, D., Olsen, L. Fich, Prætorius, L., Zedeler, A., Christiansen, A. M.H., Nielsen, J. R., Bang, D., Berntsen, S., Ollé-López, J., Ingham, A., Bello-Rodríguez, J., Storm, D. M., Ethelberg-Findsen, J., Hoffmann, E. R., Wilken-Jensen, C., Jørgensen, Finn Steener, Westh, H., Jørgensen, H. L., and Nielsen, H. S.

Published
2021

19. SARS-CoV-2 in first trimester pregnancy:a cohort study

Author

la Cour Freiesleben, N, Egerup, P, Vauvert Römmelmayer Hviid, K, Rosenbek Severinsen, E, Kolte, A M, Westergaard, D, Fich Olsen, L, Prætorius, L, Zedeler, A, Hellerung Christiansen, A-M, Reinhardt Nielsen, J, Bang, D, Berntsen, S, Ollé-López, J, Ingham, A, Bello-Rodríguez, J, Marie Storm, D, Ethelberg-Findsen, J, Hoffmann, E R, Wilken-Jensen, C, Stener Jørgensen, F, Westh, H, Løvendahl Jørgensen, H, Nielsen, H S, la Cour Freiesleben, N, Egerup, P, Vauvert Römmelmayer Hviid, K, Rosenbek Severinsen, E, Kolte, A M, Westergaard, D, Fich Olsen, L, Prætorius, L, Zedeler, A, Hellerung Christiansen, A-M, Reinhardt Nielsen, J, Bang, D, Berntsen, S, Ollé-López, J, Ingham, A, Bello-Rodríguez, J, Marie Storm, D, Ethelberg-Findsen, J, Hoffmann, E R, Wilken-Jensen, C, Stener Jørgensen, F, Westh, H, Løvendahl Jørgensen, H, and Nielsen, H S

Abstract

STUDY QUESTION: Does maternal infection with SARS-CoV-2 in first trimester pregnancy have an impact on the fetal development as measured by nuchal translucency thickness and pregnancy loss?SUMMARY ANSWER: Nuchal translucency thickness at the first trimester scan was not significantly different in pregnant women with versus without SARS-CoV-2 infection in early pregnancy and there was no significant increased risk of pregnancy loss in women with SARS-CoV-2 infection in the first trimester.WHAT IS KNOWN ALREADY: Pregnant women are more vulnerable to viral infections. Previous coronavirus epidemics have been associated with increased maternal morbidity, mortality and adverse obstetric outcomes. Currently, no evidence exists regarding possible effects of SARS-CoV-2 in first trimester pregnancies.STUDY DESIGN, SIZE, DURATION: Cohort study of 1,019 women with a double test taken between Feb. 17 and Apr. 23, 2020, as a part of the combined first trimester risk assessment, and 36 women with a first trimester pregnancy loss between Apr. 14 and May 21, 2020, prior to the double test. The study period was during the first SARS-CoV-2 epidemic wave in Denmark.PARTICIPANTS/MATERIALS, SETTING, METHODS: Cohort 1 included pregnant women with a double test taken within the study period. The excess serum from each double test was analyzed for SARS-CoV-2 antibodies. Results were correlated to the nuchal translucency thickness and the number of pregnancy losses before or at the time of the first trimester scan. Cohort 2 included women with a pregnancy loss before the gestational age for double test sample. Serum from a blood test taken the day the pregnancy loss was identified was analyzed for SARS-CoV-2 antibodies. The study was conducted at a public university hospital serving approximately 12% of pregnant women and births in Denmark. All participants in the study provided written informed consent.MAIN RESULTS AND THE ROLE OF CHANCE: Eighteen (1.8

Published
2021

20. Repeated introduction and spread of the MRSA clone t304/ST6 in northern Europe

Author

Bartels, M. D., Worning, P., Andersen, L. P., Bes, M., Enger, H., Ås, C. G., Hansen, T. A., Holzknecht, B. J., Larssen, K. W., Laurent, F., Mäkitalo, B., Pichon, B., Svartström, O., Westh, H., Bartels, M. D., Worning, P., Andersen, L. P., Bes, M., Enger, H., Ås, C. G., Hansen, T. A., Holzknecht, B. J., Larssen, K. W., Laurent, F., Mäkitalo, B., Pichon, B., Svartström, O., and Westh, H.

Abstract

Objectives: During the last decades several methicillin-resistant Staphylococcus aureus (MRSA) clones with the capability of global spread have emerged in the community. Here, we have investigated a large collection of clinical isolates belonging to MRSA clone t304/ST6, which has emerged in many European countries over the last years, in order to retrace its phylogeny and its spread. Methods: We characterized 466 ST6 isolates from Denmark (n = 354), France (n = 10), Norway (n = 24), Sweden (n = 27) and the UK (n = 51). All had spa-type t304 (n = 454) or t304-related spa-types (n = 12) and whole genome sequencing (WGS) was carried out on Illumina Miseq or Hiseq with 100–300 bp reads. cgMLST was performed using Ridom SeqSphere. Results: A minimum spanning tree (MST) of all 466 isolates showed one large cluster including 182 isolates collected only from Denmark and related to a long-term neonatal outbreak in Copenhagen. This cluster contrasted with numerous small clusters, including the remaining Danish isolates and isolates from the other countries that interspersed throughout the tree. Most isolates were Panton-Valentine leukocidin (PVL) negative (95%) and harboured SCCmec IVa. One genome was closed using Oxford Nanopore technology and Illumina MiSeq. It contained a plasmid of 19.769 bp including the blaZ gene. A similar plasmid was found in 78% of all isolates. Discussion: t304/ST6 is a successful emerging clone and the fact that isolates from five countries are interspersed throughout the MST indicates a common origin. This clone is commonly described in the Middle East and its emergence in Europe coincides with influx of refugees from the Syrian Civil War.

Published
2021

23. SARS-CoV-2 in First Trimester Pregnancy: A Cohort Study

Author

la Cour Freiesleben, N., primary, Egerup, P., additional, Hviid, K. V. R., additional, Severinsen, E. R., additional, Kolte, A. M., additional, Westergaard, D., additional, Olsen, L. Fich, additional, Prætorius, L., additional, Zedeler, A., additional, Christiansen, A.-M. H., additional, Nielsen, J. R., additional, Bang, D., additional, Berntsen, S., additional, Ollé-López, J., additional, Ingham, A., additional, Bello-Rodríguez, J., additional, Storm, D. M., additional, Ethelberg-Findsen, J., additional, Hoffmann, E. R., additional, Wilken-Jensen, C., additional, Jørgensen, F. S., additional, Westh, H., additional, Jørgensen, H. L., additional, and Nielsen, H. S., additional

Published
2021
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27. SARS-CoV-2 in first trimester pregnancy: a cohort study

Author

la Cour Freiesleben, N, primary, Egerup, P, additional, Hviid, K V R, additional, Severinsen, E R, additional, Kolte, A M, additional, Westergaard, D, additional, Fich Olsen, L, additional, Prætorius, L, additional, Zedeler, A, additional, Christiansen, A -M H, additional, Nielsen, J R, additional, Bang, D, additional, Berntsen, S, additional, Ollé-López, J, additional, Ingham, A, additional, Bello-Rodríguez, J, additional, Storm, D M, additional, Ethelberg-Findsen, J, additional, Hoffmann, E R, additional, Wilken-Jensen, C, additional, Jørgensen, F S, additional, Westh, H, additional, Jørgensen, H L, additional, and Nielsen, H S, additional

Published
2020
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30. Impact of SARS-CoV-2 antibodies at delivery in women, partners and newborns

Author

Egerup, P., Olsen, L.F., Christiansen, A.-M.H., Westergaard, D., Severinsen, E.R., Hviid, K.V.R., Kolte, A.M., Boje, A.D., Bertelsen, M.-L.M.F., Prætorius, L., Zedeler, A., Nielsen, J.R., Bang, D., Berntsen, S., Ethelberg-Findsen, J., Storm, D.M., Bello-Rodríguez, J., Ingham, A., Ollé-López, J., Hoffmann, E.R., Wilken-Jensen, C., Krebs, L., Jørgensen, F.S., Westh, H., Jørgensen, H.L., la Cour Freiesleben, N., and Nielsen, H.S.

Abstract

ackground Only few studies have focused on serological testing for SARS-CoV-2 in pregnant women and no previous study has investigated the frequency in partners. The aim was to investigate the frequency and impact of SARS-CoV-2 in parturient women, their partners and newborns.Methods From April 4th to July 3rd, 2020, all parturient women, their partners and newborns were invited to participate in the study. Participating women and partners had a pharyngeal swab and a blood sample taken at admission and immediately after delivery a blood sample was drawn from the umbilical cord. The swabs were analyzed for SARS-CoV-2 RNA by PCR and the blood samples were analyzed for SARS-CoV-2 antibodies. Full medical history, obstetric- and neonatal information were available.Results A total of 1,361 parturient women, 1,236 partners and 1,342 newborns participated in the study. No associations between previous COVID-19 disease and obstetric- or neonatal complications were found. The adjusted serological prevalence was 2.9% in women and 3.8% in partners. The frequency of blood type A was significantly higher in women with antibodies compared to women without antibodies. 17 newborns had SARS-CoV-2 IgG antibodies, and none had IgM antibodies. Full serological data from 1,052 families showed an absolute risk of infection of 0.37 if the partner had antibodies. Only 55% of individuals with antibodies reported symptoms.Conclusion This large prospective cohort study reports no association between COVID-19 and obstetric- or neonatal complications. The family pattern showed a substantial increase in absolute risk for women living with a partner with antibodies.

Published
2020
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35. Core genome multi-locus sequence typing as an essential tool in a high-cost livestock-associated meticillin-resistant Staphylococcus aureus CC398 hospital outbreak

Author

Slott Jensen, M. L., Nielsine Skov, M., Pries Kristiansen, H., Toft, A., Lundgaard, H., Gumpert, H., Westh, H., Holm, A., Kolmos, H. J., Kemp, M., Slott Jensen, M. L., Nielsine Skov, M., Pries Kristiansen, H., Toft, A., Lundgaard, H., Gumpert, H., Westh, H., Holm, A., Kolmos, H. J., and Kemp, M.

Abstract

Background: Livestock-associated meticillin-resistant Staphylococcus aureus (LA-MRSA) clonal complex (CC) 398 may be transmitted and cause morbidity and mortality in hospitals. The economic cost of stopping hospital transmission of LA-MRSA CC398 is poorly described. Early detection of transmission may limit the extent of the intervention. Aim: To evaluate core genome multi-locus sequence typing (cgMLST) for detecting transmission chains and to estimate the costs for interventions to prevent further spread after discovery of hospital transmission of LA-MRSA CC398. Methods: Five patients were involved in two episodes of transmission of LA-MRSA CC398 in a hospital. Standard interventions including MRSA screening of patients and healthcare workers were initiated. Whole genome sequences of the five isolates and 17 epidemiologically unrelated MRSA CC398 isolates from other hospitalized patients were analysed by single nucleotide polymorphism (SNP) comparisons and cgMLST. The economic costs of constraining transmission were calculated from relevant sources. Findings: The five isolates suspected to be involved in hospital transmission clustered with ≤2 SNPs in the draft genome sequences with some distance to other isolates. cgMLST allocated the five isolates to the same type, which was different from all but two of the sporadic isolates. Furthermore, cgMLST separated the five transmission isolates from all other isolates. The economic costs of the outbreak interventions exceeded €11,000 per patient. Conclusion: LA-MRSA CC398 is transmittable in hospitals, and intervention against transmission may reach considerable costs. cgMLST is useful in surveillance of hospital transmission of LA-MRSA.

Published
2020

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