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1. Monitoring meticillin resistant Staphylococcus aureus and its spread in Copenhagen, Denmark, 2013, through routine whole genome sequencing

Author

Bartels, M D, Larner-Svensson, H, Meiniche, H, Kristoffersen, K, Schonning, K, Nielsen, J B, Rohde, S M, Christensen, L B, Skibsted, A W, Jarlov, J O, Johansen, H K, Andersen, L P, Petersen, I S, Crook, D W, Bowden, R, Boye, K, Worning, P, Westh, H, Bartels, M D, Larner-Svensson, H, Meiniche, H, Kristoffersen, K, Schonning, K, Nielsen, J B, Rohde, S M, Christensen, L B, Skibsted, A W, Jarlov, J O, Johansen, H K, Andersen, L P, Petersen, I S, Crook, D W, Bowden, R, Boye, K, Worning, P, and Westh, H

Abstract

Typing of meticillin resistant Staphylococcus aureus (MRSA) by whole genome sequencing (WGS) is performed routinely in Copenhagen since January 2013. We describe the relatedness, based on WGS data and epidemiological data, of 341 MRSA isolates. These comprised all MRSA (n = 300) identified in Copenhagen in the first five months of 2013. Moreover, because MRSA of staphylococcal protein A (spa)-type 304 (t304), sequence type (ST) 6 had been associated with a continuous neonatal ward outbreak in Copenhagen starting in 2011, 41 t304 isolates collected in the city between 2010 and 2012 were also included. Isolates from 2013 found to be of t304, ST6 (n=14) were compared to the 41 earlier isolates. In the study, isolates of clonal complex (CC) 22 were examined in detail, as this CC has been shown to include the hospitalacquired epidemic MRSA (EMRSA-15) clone. Finally, all MRSA ST80 were also further analysed, as representatives of an important community-acquired MRSA in Europe. Overall the analysis identified 85 spa-types and 35 STs from 17 CCs. WGS confirmed the relatedness of epidemiologically linked t304 neonatal outbreak isolates. Several non-outbreak related patients had isolates closely related to the neonatal isolates suggesting unrecognised community chains of transmission and insufficient epidemiological data. Only four CC22 isolates were related to EMRSA-15. No community spread was observed among the 13 ST80 isolates. WGS successfully replaced conventional typing and added information to epidemiological surveillance. Creation of a MRSA database allows clustering of isolates based on single nucleotide polymorphism (SNP) calling and has improved our understanding of MRSA transmission., Typing of meticillin resistant Staphylococcus aureus (MRSA) by whole genome sequencing (WGS) is performed routinely in Copenhagen since January 2013. We describe the relatedness, based on WGS data and epidemiological data, of 341 MRSA isolates. These comprised all MRSA (n = 300) identified in Copenhagen in the first five months of 2013. Moreover, because MRSA of staphylococcal protein A (spa)-type 304 (t304), sequence type (ST) 6 had been associated with a continuous neonatal ward outbreak in Copenhagen starting in 2011, 41 t304 isolates collected in the city between 2010 and 2012 were also included. Isolates from 2013 found to be of t304, ST6 (n=14) were compared to the 41 earlier isolates. In the study, isolates of clonal complex (CC) 22 were examined in detail, as this CC has been shown to include the hospital-acquired epidemic MRSA (EMRSA-15) clone. Finally, all MRSA ST80 were also further analysed, as representatives of an important community-acquired MRSA in Europe. Overall the analysis identified 85 spa-types and 35 STs from 17 CCs. WGS confirmed the relatedness of epidemiologically linked t304 neonatal outbreak isolates. Several non-outbreak related patients had isolates closely related to the neonatal isolates suggesting unrecognised community chains of transmission and insufficient epidemiological data. Only four CC22 isolates were related to EMRSA-15. No community spread was observed among the 13 ST80 isolates. WGS successfully replaced conventional typing and added information to epidemiological surveillance. Creation of a MRSA database allows clustering of isolates based on single nucleotide polymorphism (SNP) calling and has improved our understanding of MRSA transmission.

Published
2015

2. Monitoring meticillin resistant Staphylococcus aureus and its spread in Copenhagen, Denmark, 2013, through routine whole genome sequencing

Author

Bartels, M D, primary, Larner-Svensson, H, additional, Meiniche, H, additional, Kristoffersen, K, additional, Schønning, K, additional, Nielsen, J B, additional, Rohde, S M, additional, Christensen, L B, additional, Skibsted, A W, additional, Jarløv, J O, additional, Johansen, H K, additional, Andersen, L P, additional, Petersen, I S, additional, Crook, D W, additional, Bowden, R, additional, Boye, K, additional, Worning, P, additional, and Westh, H, additional

Published
2015
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3. Monitoring meticillin resistant Staphylococcus aureus and its spread in Copenhagen, Denmark, 2013, through routine whole genome sequencing

Author

Mette Damkjær Bartels, Larner-Svensson, H., Meiniche, H., Kristoffersen, K., Schonning, K., Nielsen, J. B., Rohde, S. M., Christensen, L. B., Skibsted, A. W., Jarlov, J. O., Johansen, H. K., Andersen, L. P., Petersen, I. S., Crook, D. W., Bowden, R., Boye, K., Worning, P., and Westh, H.

Subjects
Methicillin-Resistant Staphylococcus aureus, Molecular Typing, Molecular Epidemiology, Leukocidins, Denmark, Bacterial Toxins, Exotoxins, Humans, Sequence Analysis, DNA, Staphylococcal Infections, Staphylococcal Protein A, Polymorphism, Single Nucleotide, Genome, Bacterial
Abstract

Typing of meticillin resistant Staphylococcus aureus(MRSA) by whole genome sequencing (WGS) is performedroutinely in Copenhagen since January 2013.We describe the relatedness, based on WGS data andepidemiological data, of 341 MRSA isolates. Thesecomprised all MRSA (n = 300) identified in Copenhagenin the first five months of 2013. Moreover, becauseMRSA of staphylococcal protein A (spa)-type 304(t304), sequence type (ST) 6 had been associated witha continuous neonatal ward outbreak in Copenhagenstarting in 2011, 41 t304 isolates collected in the citybetween 2010 and 2012 were also included. Isolatesfrom 2013 found to be of t304, ST6 (n=14) were comparedto the 41 earlier isolates. In the study, isolatesof clonal complex (CC) 22 were examined in detail,as this CC has been shown to include the hospitalacquiredepidemic MRSA (EMRSA-15) clone. Finally,all MRSA ST80 were also further analysed, as representativesof an important community-acquired MRSAin Europe. Overall the analysis identified 85 spa-typesand 35 STs from 17 CCs. WGS confirmed the relatednessof epidemiologically linked t304 neonatal outbreakisolates. Several non-outbreak related patientshad isolates closely related to the neonatal isolatessuggesting unrecognised community chains of transmissionand insufficient epidemiological data. Onlyfour CC22 isolates were related to EMRSA-15. No communityspread was observed among the 13 ST80 isolates.WGS successfully replaced conventional typingand added information to epidemiological surveillance.Creation of a MRSA database allows clusteringof isolates based on single nucleotide polymorphism(SNP) calling and has improved our understanding ofMRSA transmission. Typing of meticillin resistant Staphylococcus aureus (MRSA) by whole genome sequencing (WGS) is performed routinely in Copenhagen since January 2013. We describe the relatedness, based on WGS data and epidemiological data, of 341 MRSA isolates. These comprised all MRSA (n = 300) identified in Copenhagen in the first five months of 2013. Moreover, because MRSA of staphylococcal protein A (spa)-type 304 (t304), sequence type (ST) 6 had been associated with a continuous neonatal ward outbreak in Copenhagen starting in 2011, 41 t304 isolates collected in the city between 2010 and 2012 were also included. Isolates from 2013 found to be of t304, ST6 (n=14) were compared to the 41 earlier isolates. In the study, isolates of clonal complex (CC) 22 were examined in detail, as this CC has been shown to include the hospital-acquired epidemic MRSA (EMRSA-15) clone. Finally, all MRSA ST80 were also further analysed, as representatives of an important community-acquired MRSA in Europe. Overall the analysis identified 85 spa-types and 35 STs from 17 CCs. WGS confirmed the relatedness of epidemiologically linked t304 neonatal outbreak isolates. Several non-outbreak related patients had isolates closely related to the neonatal isolates suggesting unrecognised community chains of transmission and insufficient epidemiological data. Only four CC22 isolates were related to EMRSA-15. No community spread was observed among the 13 ST80 isolates. WGS successfully replaced conventional typing and added information to epidemiological surveillance. Creation of a MRSA database allows clustering of isolates based on single nucleotide polymorphism (SNP) calling and has improved our understanding of MRSA transmission.

4. The added value of perineal swabs when screening for asymptomatic methicillin-resistant Staphylococcus aureus colonization and risk factors for perineal carriage.

Author

Smidt-Nielsen IG, Boel JB, Meiniche H, Petersen A, Salgård C, Damkjær Bartels M, and Holzknecht BJ

Subjects
Humans, Risk Factors, Female, Adult, Middle Aged, Male, Aged, Young Adult, Adolescent, Mass Screening methods, Child, Child, Preschool, Aged, 80 and over, Pharynx microbiology, Infant, Nose microbiology, Methicillin-Resistant Staphylococcus aureus isolation & purification, Perineum microbiology, Carrier State microbiology, Carrier State diagnosis, Staphylococcal Infections diagnosis, Staphylococcal Infections microbiology
Abstract

We examined the added value of perineal swabs in addition to nose and throat swabs when screening for Methicillin-resistant Staphylococcus aureus colonization, and risk factors for perineal carriage in 6,642 patients. In our mainly primary care setting, the added value was 9.3%. Patients <3 or ≥80 had the highest risk., Competing Interests: Declaration of competing interest The authors declare that they have no known competing interests that could have influenced the work reported in this paper. All authors have seen and approved the final version of the manuscript., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Published
2024
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5. Whole genome sequencing reveals two genetically distinct MRSA outbreaks among people who inject drugs and homeless people in Copenhagen.

Author

Bartels MD, Holm MKA, Worning P, Stavad B, Schneider UV, Meiniche H, Thiesen H, and Westh H

Subjects
Humans, Multilocus Sequence Typing, Disease Outbreaks, Whole Genome Sequencing, Methicillin-Resistant Staphylococcus aureus genetics, Staphylococcal Infections, Substance Abuse, Intravenous, Drug Users, Bacteremia epidemiology, Ill-Housed Persons
Abstract

Whole genome sequencing (WGS) has greatly improved the detection of methicillin-resistant Staphylococcus aureus (MRSA) transmission between people. We describe the transmission of two unique MRSA clones among homeless people in Copenhagen using WGS and core genome MLST (cgMLST). In 2014, an accumulation of MRSA bacteremia cases among homeless people admitted to our hospital was recognized, all having the rare MRSA spa t5147/ST88. The European Typology of Homelessness and Housing Exclusion (ETHOS) categories revealed that people who inject drugs (PWID) frequently visiting the milieu but living in private accommodation accounted for most cases. Hoping to terminate the transmission, 161 homeless people were MRSA screened in 2015, but no additional cases were found. From 2009 to 2018, 60 patients with genomically related t5147/ST88 isolates were found, of these 70% were confirmed to come from the homeless setting and 17% had bacteremia. From 2017 to 2020, cgMLST revealed a smaller MRSA outbreak including 13 PWID with a completely different clone, t1476/ST8, of which 15% had bacteremia. Our study confirms that WGS and cgMLST is excellent to reveal MRSA outbreaks. The ETHOS categorization can be useful to find the primary source of spread in the homeless community., (© 2023 The Authors. APMIS published by John Wiley & Sons Ltd on behalf of Scandinavian Societies for Pathology, Medical Microbiology and Immunology.)

Published
2023
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