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9. A multinational study of colonization with extended spectrum β-lactamase-producing Enterobacteriaceae in healthcare personnel and family members of carrier patients hospitalized in rehabilitation centres

Author

Adler, A., Baraniak, A., Izdebski, R., Fiett, J., Salvia, A., Samso, J.V., Lawrence, C., Solomon, J., Paul, M., Lerman, Y., Schwartzberg, Y., Mordechai, E., Rossini, A., Fierro, J., Lammens, C., Malhotra-Kumar, S., Goossens, H., Hryniewicz, W., Brun-Buisson, C., Gniadkowski, M., Carmeli, Y., and for MOSAR team

Published
2014
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10. Remarkable geographical variations between India and Europe in carriage of the staphylococcal surface protein-encoding sasX/sesI and in the population structure of methicillin-resistant Staphylococcus aureus belonging to clonal complex 8

Author

De Backer, S., Xavier, B.B., Vanjari, L., Coppens, J., Lammens, C., Vemu, L., Carevic, B., Hryniewicz, W., Jorens, P., Kumar-Singh, S., Lee, A., Harbarth, S., Schrenzel, J., Tacconelli, E., Goossens, H., and Malhotra-Kumar, S.

Published
2019
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18. International links between Streptococcus pneumoniae vaccine serotype 4 sequence type (ST) 801 in Northern European shipyard outbreaks of invasive pneumococcal disease

Author

Gladstone, R.A., Siira, L., Brynildsrud, O.B., Vestrheim, D.F., Turner, P., Clarke, S.C., Srifuengfung, S., Ford, R., Lehmann, D., Egorova, E., Voropaeva, E., Haraldsson, G., Kristinsson, K.G., McGee, L., Breiman, R.F., Bentley, S.D., Sheppard, C.L., Fry, N.K., Corander, J., Toropainen, M., Steens, A., Akpaka, P.E., Ampofo, K., Antonio, M., Balaji, V., Beall, B.W., Belabbès, H., Benisty, R., Bigogo, G., Brooks, A.W., Carter, P.E., Cornick, J.E., Corso, A., Cristina de Cunto Brandileone, M., Cristine Grassi Almeida, S., Croucher, N.J., Dagan, R., Davydov, A., Diawara, I., Doiphode, S., du Plessis, M., Elmdaghri, N., Köseoglu Eser, Ö., Everett, D.B., Faccone, D., Gagetti, P., Givon-Lavi, N., Hasanuzzaman, M., Hawkins, P.A., Hryniewicz, W., Hulten, K.G., Ip, M., Kapusta, A., Kandasamy, R., Kastrin, T., Keenan, J., Klugman, K.P., Kwambana-Adams, B., Law, P.Y., Lees, J.A., Leung Ho, P., Li, Y., Lo, S.W., Ochoa Woodell, Theresa Jean, Madhi, S.A., Metcalf, B.J., Moïsi, J., Mucavele Fundação Manhiça, H., Ndlangisa, K.M., Nurse-Lucas, M., Nzenze, S.A., Obaro, S.K., Paragi, M., Pollard, A.J., Ravikumar, K.L., Sadowy, E., Saha, S.K., Sampane-Donkor, E., Devi Sekaran, S., Shakoor, S., Shrestha, S., Sigauque, B., Skoczynska, A., Soo ko, K., Tientcheu, P.-E., Titov, L., Urban, Y., Verani, J., van Tonder, A.J., von Gottberg, A., Wolter, N., The Global Pneumococcal Sequencing Consortium, and Consortium, The Global Pneumococcal Sequencing

Subjects
Northern Ireland, Serogroup, Polymorphism, Single Nucleotide, Pneumococcal Infections, Disease Outbreaks, Occupational Exposure, PPV23, Humans, Serotyping, Finland, Phylogeny, Ships, General Veterinary, General Immunology and Microbiology, Norway, Public Health, Environmental and Occupational Health, Outbreak, ST801, PCVs, Infectious Diseases, Streptococcus pneumoniae, Serotype 4, Whole genome sequencing, Molecular epidemiology, Molecular Medicine, Pneumococcal, Genome, Bacterial
Abstract

Background Pneumococcal disease outbreaks of vaccine preventable serotype 4 sequence type (ST)801 in shipyards have been reported in several countries. We aimed to use genomics to establish any international links between them. Methods Sequence data from ST801-related outbreak isolates from Norway (n = 17), Finland (n = 11) and Northern Ireland (n = 2) were combined with invasive pneumococcal disease surveillance from the respective countries, and ST801-related genomes from an international collection (n = 41 of > 40,000), totalling 106 genomes. Raw data were mapped and recombination excluded before phylogenetic dating. Results Outbreak isolates were relatively diverse, with up to 100 SNPs (single nucleotide polymorphisms) and a common ancestor estimated around the year 2000. However, 19 Norwegian and Finnish isolates were nearly indistinguishable (0–2 SNPs) with the common ancestor dated around 2017. Conclusion The total diversity of ST801 within the outbreaks could not be explained by recent transmission alone, suggesting that harsh environmental and associated living conditions reported in the shipyards may facilitate invasion of colonising pneumococci. However, near identical strains in the Norwegian and Finnish outbreaks does suggest that transmission between international shipyards also contributed to those outbreaks. This indicates the need for improved preventative measures in this working population including pneumococcal vaccination.

Published
2022

19. Molecular epidemiology of MRSA in 13 ICUs from eight European countries

Author

Hetem, D. J., Derde, L. P. G., Empel, J., Mroczkowska, A., Orczykowska-Kotyna, M., Kozińska, A., Hryniewicz, W., Goossens, H., Bonten, M. J. M., Cooper, B., Malhotra-Kumar, S., Willems, R., Gniadkowski, M., Dautzenberg, M., Annane, D., Aragão, I., Chalfine, A., Dumpis, U., Esteves, F., Giamarellou, H., Muzlovic, I., Nardi, G., Petrikkos, G., Tomic, V., Martí, A. Torres, Stammet, P., Brun-Buisson, C., Aires, E., Antoniadou, A., Armaganidis, A., Blairon, F., Carneiro, J., Chaskou, D., Coppadoro, P., Dias, A.-P., Drinovec, I., Elia, M., Exarchou, V., Flet, A., Fournier, J., Gillet, N., Jaklič, A., Jereb, M., Kane, A., Karkali, E., Kieffer, J., Kirpach, P., Landelle, C., Landercy, F., Lawrence, C., Legrand, P., Lopes, V., Magira, E., Marco, F., Martínez, J. A., Melbārde-Kelmere, A., Misset, B., Monte, R., Moreno, E., Nguyen, J. C., Novak, M., Orazi, D., Papadomichelakis, E., Papaparaskevas, J., Paris, M., Pavleas, J., Pimenta, F., Piñer, R., Radouan, A., Ramunno, M.-G., Reis, M., Rinaldi, I., Ronco, E., Jose, A. San, Seme, K., Skiada, A., Trapassi, S., Tronci, M., Verachten, M., Vila, J., Vrankar, K., Winkler, M., Zagavierou, S., Hopman, M., Leus, F., Schotsman, J., and Zwerver, J.

Published
2016
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21. Phylogenetic lineages, clones and β-lactamases in an international collection of Klebsiella oxytoca isolates non-susceptible to expanded-spectrum cephalosporins

Author

Izdebski, R., Fiett, J., Urbanowicz, P., Baraniak, A., Derde, L. P. G., Bonten, M. J. M., Carmeli, Y., Goossens, H., Hryniewicz, W., Brun-Buisson, C., Brisse, S., Gniadkowski, M., Herda, M., Dautzenberg, M. J., Adler, A., Kazma, M., Navon-Venezia, S., Malhotra-Kumar, S., Lammens, C., Legrand, P., Chalfine, A., Giamarellou, H., Petrikkos, G. L., Balode, A., Dumpis, U., Stammet, P., Aragăo, I., Esteves, F., Martí, A. Torres, Lawrence, C., Salomon, J., Paul, M., Lerman, Y., Rossini, A., Salvia, A., Samso, J. Vidal, and Fierro, J.

Published
2015
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22. Survey of metallo-β-lactamase-producing Enterobacteriaceae colonizing patients in European ICUs and rehabilitation units, 2008–11

Author

Papagiannitsis, C. C., Izdebski, R., Baraniak, A., Fiett, J., Herda, M., Hrabák, J., Derde, L. P. G., Bonten, M. J. M., Carmeli, Y., Goossens, H., Hryniewicz, W., Brun-Buisson, C., Gniadkowski, M., Grabowska, A., Nikonorow, E., Dautzenberg, M. J., Adler, A., Kazma, M., Navon-Venezia, S., Malhotra-Kumar, S., Lammens, C., Legrand, P., Annane, D., Chalfine, A., Giamarellou, H., Petrikkos, G. L., Nardi, G., Balode, A., Dumpis, U., Stammet, P., Arag, I., Esteves, F., Muzlovic, I., Tomic, V., Mart, A. Torres, Lawrence, C., Salomon, J., Paul, M., Lerman, Y., Rossini, A., Salvia, A., Samso, J. Vidal, and Fierro, J.

Published
2015
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23. MLST reveals potentially high-risk international clones of Enterobacter cloacae

Author

Izdebski, R., Baraniak, A., Herda, M., Fiett, J., Bonten, M. J. M., Carmeli, Y., Goossens, H., Hryniewicz, W., Brun-Buisson, C., Gniadkowski, M., Grabowska, A., Nikonorow, E., Derde, L. P. G., Dautzenberg, M. J., Adler, A., Kazma, M., Navon-Venezia, S., Malhotra-Kumar, S., Lammens, C., Dumpis, U., Giamarellou, H., Muzlovic, I., Nardi, G., Petrikkos, G. L., Stammet, P., Salomon, J., Lawrence, C., Legrand, P., Rossini, A., Salvia, A., Samso, J. Vidal, Fierro, J., Paul, M., and Lerman, Y.

Published
2015
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30. A mosaic tetracycline resistance gene tet(S/M) detected in an MDR pneumococcal CC230 lineage that underwent capsular switching in South Africa

Author

Lo, SW, Gladstone, RA, Van Tonder, AJ, Du Plessis, M, Cornick, JE, Hawkins, PA, Madhi, SA, Nzenze, SA, Kandasamy, R, Ravikumar, KL, Elmdaghri, N, Kwambana-Adams, B, Almeida, SCG, Skoczynska, A, Egorova, E, Titov, L, Saha, SK, Paragi, M, Everett, DB, Antonio, M, Klugman, KP, Li, Y, Metcalf, BJ, Beall, B, McGee, L, Breiman, RF, Bentley, SD, Von Gottberg, A, Brooks, AW, Corso, A, Davydov, A, Maguire, A, Pollard, AJ, Kiran, A, Moiane, B, Sigauque, B, Aanensen, D, Lehmann, D, Faccone, D, Foster-Nyarko, E, Bojang, E, Voropaeva, E, Sampane-Donkor, E, Sadowy, E, Nagaraj, G, Bigogo, G, Mucavele, H, Belabbès, H, Diawara, I, Moïsi, J, Verani, J, Keenan, J, Nair Thulasee Bhai, JN, Ndlangisa, KM, Zerouali, K, De Gouveia, L, Alaerts, M, De Cunto Brandileone, MC, Ip, M, Hasanuzzaman, M, Ali, M, Croucher, N, Wolter, N, Givon-Lavi, N, Eser, ÖK, Ho, PL, Akpaka, PE, Turner, P, Gagetti, P, Tientcheu, PE, Carter, PE, Law, P, Benisty, R, Mostowy, R, Ford, R, Henderson, R, Malaker, R, Dagan, R, Shakoor, S, Doiphode, S, Sekaran, SD, Srifuengfung, S, Obaro, S, Clarke, SC, Kastrin, T, Ochoa, TJ, Hryniewicz, W, Balaji, V, Urban, Y, Lo, SW, Gladstone, RA, Van Tonder, AJ, Du Plessis, M, Cornick, JE, Hawkins, PA, Madhi, SA, Nzenze, SA, Kandasamy, R, Ravikumar, KL, Elmdaghri, N, Kwambana-Adams, B, Almeida, SCG, Skoczynska, A, Egorova, E, Titov, L, Saha, SK, Paragi, M, Everett, DB, Antonio, M, Klugman, KP, Li, Y, Metcalf, BJ, Beall, B, McGee, L, Breiman, RF, Bentley, SD, Von Gottberg, A, Brooks, AW, Corso, A, Davydov, A, Maguire, A, Pollard, AJ, Kiran, A, Moiane, B, Sigauque, B, Aanensen, D, Lehmann, D, Faccone, D, Foster-Nyarko, E, Bojang, E, Voropaeva, E, Sampane-Donkor, E, Sadowy, E, Nagaraj, G, Bigogo, G, Mucavele, H, Belabbès, H, Diawara, I, Moïsi, J, Verani, J, Keenan, J, Nair Thulasee Bhai, JN, Ndlangisa, KM, Zerouali, K, De Gouveia, L, Alaerts, M, De Cunto Brandileone, MC, Ip, M, Hasanuzzaman, M, Ali, M, Croucher, N, Wolter, N, Givon-Lavi, N, Eser, ÖK, Ho, PL, Akpaka, PE, Turner, P, Gagetti, P, Tientcheu, PE, Carter, PE, Law, P, Benisty, R, Mostowy, R, Ford, R, Henderson, R, Malaker, R, Dagan, R, Shakoor, S, Doiphode, S, Sekaran, SD, Srifuengfung, S, Obaro, S, Clarke, SC, Kastrin, T, Ochoa, TJ, Hryniewicz, W, Balaji, V, and Urban, Y

Abstract

Objectives: We reported tet(S/M) in Streptococcus pneumoniae and investigated its temporal spread in relation to nationwide clinical interventions. Methods: We whole-genome sequenced 12 254 pneumococcal isolates from 29 countries on an Illumina HiSeq sequencer. Serotype, multilocus ST and antibiotic resistance were inferred from genomes. An SNP tree was built using Gubbins. Temporal spread was reconstructed using a birth-death model. Results: We identified tet(S/M) in 131 pneumococcal isolates and none carried other known tet genes. Tetracycline susceptibility testing results were available for 121 tet(S/M)-positive isolates and all were resistant. A majority (74%) of tet(S/M)-positive isolates were from South Africa and caused invasive diseases among young children (59% HIV positive, where HIV status was available). All but two tet(S/M)-positive isolates belonged to clonal complex (CC) 230. A global phylogeny of CC230 (n=389) revealed that tet(S/M)-positive isolates formed a sublineage predicted to exhibit resistance to penicillin, co-trimoxazole, erythromycin and tetracycline. The birth-death model detected an unrecognized outbreak of this sublineage in South Africa between 2000 and 2004 with expected secondary infections (effective reproductive number, R) of ∼2.5. R declined to ∼1.0 in 2005 and <1.0 in 2012. The declining epidemic could be related to improved access to ART in 2004 and introduction of pneumococcal conjugate vaccine (PCV) in 2009. Capsular switching from vaccine serotype 14 to non-vaccine serotype 23A was observed within the sublineage. Conclusions: The prevalence of tet(S/M) in pneumococci was low and its dissemination was due to an unrecognized outbreak of CC230 in South Africa. Capsular switching in this MDR sublineage highlighted its potential to continue to cause disease in the post-PCV13 era.

Published
2020

31. Visualizing variation within global pneumococcal sequence clusters (GPSCS) and country population snapshots to contextualize pneumococcal isolates

Author

Gladstone, RA, Lo, SW, Goater, R, Yeats, C, Taylor, B, Hadfield, J, Lees, JA, Croucher, NJ, van Tonder, AJ, Bentley, LJ, Quah, FX, Blaschke, AJ, Pershing, NL, Byington, CL, Balaji, V, Hryniewicz, W, Sigauque, B, Ravikumar, KL, Almeida, SCG, Ochoa, TJ, Ho, PL, Plessis, MD, Ndlangisa, KM, Cornick, JE, Kwambana-Adams, B, Benisty, R, Nzenze, SA, Madhi, SA, Hawkins, PA, Pollard, AJ, Everett, DB, Antonio, M, Dagan, R, Klugman, KP, von Gottberg, A, Metcalf, BJ, Li, Y, Beall, BW, McGee, L, Breiman, RF, Aanensen, DM, Bentley, SD, Akpaka, PE, Ampofo, K, Belabbès, H, Bigogo, G, Brooks, AW, Carter, PE, Clarke, SC, Corso, A, de Cunto Brandileone, MC, Davydov, A, Diawara, I, Doiphode, S, Egorova, E, Elmdaghri, N, Eser, ÖK, Faccone, D, Ford, R, Gagetti, P, Givon-Lavi, N, Hasanuzzaman, M, Hulten, KG, Ip, M, Kapusta, A, Kandasamy, R, Kastrin, T, Keenan, J, Law, PY, Lehmann, D, Moïsi, J, Mucavele, H, Nurse-Lucas, M, Obaro, SK, Paragi, M, Sadowy, E, Saha, SK, Sampane-Donkor, E, Sekaran, SD, Shakoor, S, Shrestha, S, Skoczynska, A, Ko, S, Srifuengfung, S, Tientcheu, PE, Titov, L, Turner, P, Urban, Y, Verani, J, Voropaeva, E, Wolter, N, Gladstone, RA, Lo, SW, Goater, R, Yeats, C, Taylor, B, Hadfield, J, Lees, JA, Croucher, NJ, van Tonder, AJ, Bentley, LJ, Quah, FX, Blaschke, AJ, Pershing, NL, Byington, CL, Balaji, V, Hryniewicz, W, Sigauque, B, Ravikumar, KL, Almeida, SCG, Ochoa, TJ, Ho, PL, Plessis, MD, Ndlangisa, KM, Cornick, JE, Kwambana-Adams, B, Benisty, R, Nzenze, SA, Madhi, SA, Hawkins, PA, Pollard, AJ, Everett, DB, Antonio, M, Dagan, R, Klugman, KP, von Gottberg, A, Metcalf, BJ, Li, Y, Beall, BW, McGee, L, Breiman, RF, Aanensen, DM, Bentley, SD, Akpaka, PE, Ampofo, K, Belabbès, H, Bigogo, G, Brooks, AW, Carter, PE, Clarke, SC, Corso, A, de Cunto Brandileone, MC, Davydov, A, Diawara, I, Doiphode, S, Egorova, E, Elmdaghri, N, Eser, ÖK, Faccone, D, Ford, R, Gagetti, P, Givon-Lavi, N, Hasanuzzaman, M, Hulten, KG, Ip, M, Kapusta, A, Kandasamy, R, Kastrin, T, Keenan, J, Law, PY, Lehmann, D, Moïsi, J, Mucavele, H, Nurse-Lucas, M, Obaro, SK, Paragi, M, Sadowy, E, Saha, SK, Sampane-Donkor, E, Sekaran, SD, Shakoor, S, Shrestha, S, Skoczynska, A, Ko, S, Srifuengfung, S, Tientcheu, PE, Titov, L, Turner, P, Urban, Y, Verani, J, Voropaeva, E, and Wolter, N

Abstract

Knowledge of pneumococcal lineages, their geographic distribution and antibiotic resistance patterns, can give insights into global pneumococcal disease. We provide interactive bioinformatic outputs to explore such topics, aiming to increase dissemi-nation of genomic insights to the wider community, without the need for specialist training. We prepared 12 country-specific phylogenetic snapshots, and international phylogenetic snapshots of 73 common Global Pneumococcal Sequence Clusters (GPSCs) previously defined using PopPUNK, and present them in Microreact. Gene presence and absence defined using Roary, and recombination profiles derived from Gubbins are presented in Phandango for each GPSC. Temporal phylogenetic signal was assessed for each GPSC using BactDating. We provide examples of how such resources can be used. In our example use of a country-specific phylogenetic snapshot we determined that serotype 14 was observed in nine unrelated genetic backgrounds in South Africa. The international phylogenetic snapshot of GPSC9, in which most serotype 14 isolates from South Africa were observed, highlights that there were three independent sub-clusters represented by South African serotype 14 isolates. We estimated from the GPSC9-dated tree that the sub-clusters were each established in South Africa during the 1980s. We show how recombination plots allowed the identification of a 20 kb recombination spanning the capsular polysaccharide locus within GPSC97. This was consistent with a switch from serotype 6A to 19A estimated to have occured in the 1990s from the GPSC97-dated tree. Plots of gene presence/absence of resistance genes (tet, erm, cat) across the GPSC23 phylogeny were consistent with acquisition of a composite transposon. We estimated from the GPSC23-dated tree that the acquisition occurred between 1953 and 1975. Finally, we demonstrate the assignment of GPSC31 to 17 externally generated pneumococcal serotype 1 assemblies from Utah via Pathogenwatch. Most of

Published
2020

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