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Dimitriou V, Biehl LM, Hamprecht A, Vogel W, Dörfel D, Peter S, Schafhausen P, Rohde H, von Lilienfeld-Toal M, Klassert TE, Slickers P, Ehricht R, Slevogt H, Christ H, Hellmich M, Farowski F, Tsakmaklis A, Higgins PG, Seifert H, Vehreschild MJGT. Controlling intestinal colonization of high-risk haematology patients with ESBL-producing Enterobacteriaceae: a randomized, placebo-controlled, multicentre, Phase II trial (CLEAR). J Antimicrob Chemother 2020; 74:2065-2074. [PMID: 31220256 DOI: 10.1093/jac/dkz124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/01/2019] [Accepted: 03/02/2019] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVES We assessed the efficacy and safety of an oral antimicrobial regimen for short- and long-term intestinal eradication of ESBL-producing Escherichia coli and Klebsiella pneumoniae (ESBL-EC/KP) in immunocompromised patients. METHODS We performed a randomized (2:1), double-blind multicentre Phase II study in four haematology-oncology departments. Patients colonized with ESBL-EC/KP received a 7 day antimicrobial regimen of oral colistin (2 × 106 IU 4×/day), gentamicin (80 mg 4×/day) and fosfomycin (three administrations of 3 g every 72 h), or placebo. Faecal, throat and urine specimens were collected on day 0, 6 ± 2, 11 ± 2, 28 ± 4 and 42 ± 4 after treatment initiation, and the quantitative burden of ESBL-EC/KP, resistance genes and changes in intestinal microbiota were analysed. Clinicaltrials.gov: NCT01931592. RESULTS As the manufacture of colistin powder was suspended worldwide, the study was terminated prematurely. Overall, 29 (18 verum/11 placebo) out of 47 patients were enrolled. The short-term intestinal eradication was marginal at day 6 (verum group 15/18, 83.3% versus placebo 2/11, 18.2%; relative risk 4.58, 95% CI 1.29-16.33; Fisher's exact test P = 0.001) and not evident at later timepoints. Quantitative analysis showed a significant decrease of intestinal ESBL-EC/KP burden on day 6. Sustained intestinal eradication (day 28 + 42) was not achieved (verum, 38.9% versus placebo, 27.3%; P = 0.299). In the verum group, mcr-1 genes were detected in two faecal samples collected after treatment. Microbiome analysis showed a significant decrease in alpha diversity and a shift in beta diversity. CONCLUSIONS In this prematurely terminated study of a 7 day oral antimicrobial eradication regimen, short-term ESBL-EC/KP suppression was marginal, while an altered intestinal microbiota composition was clearly apparent.
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Affiliation(s)
- Vassiliki Dimitriou
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Lena M Biehl
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Axel Hamprecht
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Wichard Vogel
- Department of Oncology, Haematology, Immunology, Rheumatology and Pulmonology, Internal Medicine II, University Hospital Tübingen, Tübingen, Germany
| | - Daniela Dörfel
- Department of Oncology, Haematology, Immunology, Rheumatology and Pulmonology, Internal Medicine II, University Hospital Tübingen, Tübingen, Germany
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Philippe Schafhausen
- Department of Oncology and Haematology, Hubertus Wald Tumorzentrum/University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Holger Rohde
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Tilman E Klassert
- Host Septomics Research Group, Jena University Hospital, Jena, Germany
| | | | - Ralf Ehricht
- Center for Applied Research, InfectoGnostics Research Campus, Jena, Germany.,Department for Optical Molecular Diagnostics and Systems Technology, Leibniz-Institute of Photonic Technology (IPHT), Jena, Germany
| | - Hortense Slevogt
- Host Septomics Research Group, Jena University Hospital, Jena, Germany
| | - Hildegard Christ
- Institute of Medical Statistics, Informatics and Epidemiology, University of Cologne, Cologne, Germany
| | - Martin Hellmich
- Institute of Medical Statistics, Informatics and Epidemiology, University of Cologne, Cologne, Germany
| | - Fedja Farowski
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Anastasia Tsakmaklis
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Paul G Higgins
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Harald Seifert
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Maria J G T Vehreschild
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany.,Department of Internal Medicine, Infectious Diseases, Goethe University Frankfurt, Frankfurt am Main, Germany
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2
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Steinig EJ, Duchene S, Robinson DA, Monecke S, Yokoyama M, Laabei M, Slickers P, Andersson P, Williamson D, Kearns A, Goering RV, Dickson E, Ehricht R, Ip M, O'Sullivan MVN, Coombs GW, Petersen A, Brennan G, Shore AC, Coleman DC, Pantosti A, de Lencastre H, Westh H, Kobayashi N, Heffernan H, Strommenger B, Layer F, Weber S, Aamot HV, Skakni L, Peacock SJ, Sarovich D, Harris S, Parkhill J, Massey RC, Holden MTG, Bentley SD, Tong SYC. Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent. mBio 2019; 10:e01105-19. [PMID: 31772058 PMCID: PMC6879714 DOI: 10.1128/mbio.01105-19] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 10/15/2019] [Indexed: 01/21/2023] Open
Abstract
The evolution and global transmission of antimicrobial resistance have been well documented for Gram-negative bacteria and health care-associated epidemic pathogens, often emerging from regions with heavy antimicrobial use. However, the degree to which similar processes occur with Gram-positive bacteria in the community setting is less well understood. In this study, we traced the recent origins and global spread of a multidrug-resistant, community-associated Staphylococcus aureus lineage from the Indian subcontinent, the Bengal Bay clone (ST772). We generated whole-genome sequence data of 340 isolates from 14 countries, including the first isolates from Bangladesh and India, to reconstruct the evolutionary history and genomic epidemiology of the lineage. Our data show that the clone emerged on the Indian subcontinent in the early 1960s and disseminated rapidly in the 1990s. Short-term outbreaks in community and health care settings occurred following intercontinental transmission, typically associated with travel and family contacts on the subcontinent, but ongoing endemic transmission was uncommon. Acquisition of a multidrug resistance integrated plasmid was instrumental in the emergence of a single dominant and globally disseminated clade in the early 1990s. Phenotypic data on biofilm, growth, and toxicity point to antimicrobial resistance as the driving force in the evolution of ST772. The Bengal Bay clone therefore combines the multidrug resistance of traditional health care-associated clones with the epidemiological transmission of community-associated methicillin-resistant S. aureus (MRSA). Our study demonstrates the importance of whole-genome sequencing for tracking the evolution of emerging and resistant pathogens. It provides a critical framework for ongoing surveillance of the clone on the Indian subcontinent and elsewhere.IMPORTANCE The Bengal Bay clone (ST772) is a community-associated and multidrug-resistant Staphylococcus aureus lineage first isolated from Bangladesh and India in 2004. In this study, we showed that the Bengal Bay clone emerged from a virulent progenitor circulating on the Indian subcontinent. Its subsequent global transmission was associated with travel or family contact in the region. ST772 progressively acquired specific resistance elements at limited cost to its fitness and continues to be exported globally, resulting in small-scale community and health care outbreaks. The Bengal Bay clone therefore combines the virulence potential and epidemiology of community-associated clones with the multidrug resistance of health care-associated S. aureus lineages. This study demonstrates the importance of whole-genome sequencing for the surveillance of highly antibiotic-resistant pathogens, which may emerge in the community setting of regions with poor antibiotic stewardship and rapidly spread into hospitals and communities across the world.
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Affiliation(s)
- Eike J Steinig
- Menzies School of Health Research, Darwin, Australia
- Australian Institute of Tropical Health and Medicine, Townsville, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | | | - Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
- Technical University of Dresden, Dresden, Germany
| | - Maho Yokoyama
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Maisem Laabei
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Peter Slickers
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
| | | | - Deborah Williamson
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Angela Kearns
- Public Health England, National Infection Service, London, United Kingdom
| | | | - Elizabeth Dickson
- Scottish Microbiology Reference Laboratories, Glasgow, United Kingdom
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- Technical University of Dresden, Dresden, Germany
| | - Margaret Ip
- The Chinese University of Hong Kong, Hong Kong
| | - Matthew V N O'Sullivan
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia, and New Wales Health Pathology, Westmead Hospital, Sydney, Australia
| | - Geoffrey W Coombs
- School of Veterinary and Laboratory Sciences, Murdoch University, Murdoch, Australia
| | | | - Grainne Brennan
- National MRSA Reference Laboratory, St. James's Hospital, Dublin, Ireland
| | - Anna C Shore
- Microbiology Research Unit, School of Dental Science, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - David C Coleman
- Microbiology Research Unit, School of Dental Science, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | | | - Herminia de Lencastre
- Instituto de Tecnologia Química e Biológica, Oeiras, Portugal
- The Rockefeller University, New York, New York, USA
| | - Henrik Westh
- University of Copenhagen, Copenhagen, Denmark
- Hvidovre University Hospital, Hvidovre, Denmark
| | | | - Helen Heffernan
- Institute of Environmental Science and Research, Wellington, New Zealand
| | | | | | - Stefan Weber
- Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | | | - Leila Skakni
- King Fahd Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Sharon J Peacock
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Derek Sarovich
- Menzies School of Health Research, Darwin, Australia
- Sunshine Coast University, Sippy Downs, Australia
| | - Simon Harris
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Mathew T G Holden
- Wellcome Sanger Institute, Cambridge, United Kingdom
- University of St. Andrews, St. Andrews, United Kingdom
| | | | - Steven Y C Tong
- Menzies School of Health Research, Darwin, Australia
- Victorian Infectious Disease Service, The Royal Melbourne Hospital, and Doherty Department, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Victoria, Australia
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3
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Senok A, Slickers P, Hotzel H, Boswihi S, Braun SD, Gawlik D, Müller E, Nabi A, Nassar R, Nitschke H, Reissig A, Ruppelt-Lorz A, Mafofo J, Somily AM, Udo E, Ehricht R, Monecke S. Characterisation of a novel SCCmec VI element harbouring fusC in an emerging Staphylococcus aureus strain from the Arabian Gulf region. PLoS One 2019; 14:e0223985. [PMID: 31689288 PMCID: PMC6830749 DOI: 10.1371/journal.pone.0223985] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 10/02/2019] [Indexed: 12/01/2022] Open
Abstract
Fusidic acid is a steroid antibiotic known since the 1960s. It is frequently used in topical preparations, i.e., ointments, for the treatment of skin and soft tissue infections caused by Staphylococcus aureus. There is an increasing number of methicillin-resistant S. aureus (MRSA) strains that harbour plasmid-borne fusB/far1 or fusC that is localised on SCC elements. In this study we examined a series of related CC30-MRSA isolates from the Arabian Gulf countries that presented with SCCmec elements and fusC, including a variant that-to the best of our knowledge-has not yet formally been described. It consisted of a class B mec complex and ccrA/B-4 genes. The fusidic acid resistance gene fusC was present, but contrary to the previously sequenced element of HDE288, it was not accompanied by tirS. This element was identified in CC30 MRSA from Kuwait, Saudi Arabia and the United Arab Emirates that usually also harbour the Panton-Valentin leukocidin (PVL) genes. It was also identified in CC8 and ST834 isolates. In addition, further CC30 MRSA strains with other SCCmec VI elements harbouring fusC were found to circulate in the Arabian Gulf region. It can be assumed that MRSA strains with SCCmec elements that include fusC have a selective advantage in both hospital and community settings warranting a review of the use of topical antibiotics and indicating the necessity of reducing over-the-counter sale of antibiotics, including fusidic acid, without prescription.
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Affiliation(s)
- Abiola Senok
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Peter Slickers
- InfectoGnostics Research Campus Jena, Jena, Germany
- Abbott (Alere Technologies GmbH), Jena, Germany
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Samar Boswihi
- Department of Microbiology, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
| | - Sascha D. Braun
- InfectoGnostics Research Campus Jena, Jena, Germany
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
| | | | - Elke Müller
- InfectoGnostics Research Campus Jena, Jena, Germany
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
| | - Anju Nabi
- Microbiology & Infection Control Unit, Pathology Department, Rashid Hospital, Dubai Health Authority, Dubai, United Arab Emirates
| | - Rania Nassar
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Hedda Nitschke
- Department of Laboratory Medicine, Hospital Dresden-Neustadt, Dresden, Germany
| | - Annett Reissig
- InfectoGnostics Research Campus Jena, Jena, Germany
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
| | - Antje Ruppelt-Lorz
- Institute for Medical Microbiology and Hygiene, Medical Faculty "Carl Gustav Carus", Technische Universität Dresden, Dresden, Germany
| | - Joseph Mafofo
- Agiomix FZ-LLC, Dubai Science Park Warehouse Complex, Dubai, United Arab Emirates
| | - Ali M. Somily
- Department of Pathology and Laboratory Medicine, College of Medicine, King Khalid University Hospital and King Saud University, Riyadh, Saudi Arabia
| | - Edet Udo
- Department of Microbiology, Faculty of Medicine, Kuwait University, Jabriya, Kuwait
| | - Ralf Ehricht
- InfectoGnostics Research Campus Jena, Jena, Germany
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
| | - Stefan Monecke
- InfectoGnostics Research Campus Jena, Jena, Germany
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- Institute for Medical Microbiology and Hygiene, Medical Faculty "Carl Gustav Carus", Technische Universität Dresden, Dresden, Germany
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4
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Loncaric I, Kübber-Heiss A, Posautz A, Ruppitsch W, Lepuschitz S, Schauer B, Feßler AT, Krametter-Frötscher R, Harrison EM, Holmes MA, Künzel F, Szostak MP, Hauschild T, Desvars-Larrive A, Misic D, Rosengarten R, Walzer C, Slickers P, Monecke S, Ehricht R, Schwarz S, Spergser J. Characterization of mecC gene-carrying coagulase-negative Staphylococcus spp. isolated from various animals. Vet Microbiol 2019; 230:138-144. [PMID: 30827379 DOI: 10.1016/j.vetmic.2019.02.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/02/2019] [Accepted: 02/05/2019] [Indexed: 11/30/2022]
Abstract
The presence of the methicillin resistance gene mecC in coagulase-negative Staphylococcus spp. (CoNS) is scarce. The aim of this study was to characterize mecC-positive CoNS isolated from various wild and domestic animals. The presence of the mecC gene was screened in 4299 samples from wild animals and domestic animals. Fifteen coagulase-negative staphylococci, that displayed a cefoxitin-resistant phenotype, were tested mecC-positive by PCR. Antimicrobial susceptibility testing was performed for all isolates. The 15 isolates were genotyped by sequencing of the entire class E mec gene complex (blaZ-mecC-mecR1-mecI), the ccrA and ccrB recombinase genes and other determinants within the type XI SCCmec element. DNA microarray analysis was performed and five selected isolates were additionally whole genome sequenced and analyzed. S. stepanovicii (n = 3), S. caprae (n = 1), S. warneri (n = 1), S. xylosus (n = 1) and S. sciuri (n = 9) were detected. All but the S. sciuri isolates were found to be susceptible to all non-beta lactams. The entire class E mec gene complex was detected in all isolates but ccrA and ccrB genes were not identified in S. stepanovicii and S. xylosus. The genes erm(B) and fexA (n = 4, each) were the most predominant non-beta lactam resistance genes detected in the S. sciuri isolates. Even though the presence of the mecC gene among CoNS is a rare observation, this study further expands our knowledge by showing that the mecC gene, including its allotypes, are present in more staphylococcal species from different animal species than has been previously described.
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Affiliation(s)
- Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria.
| | - Anna Kübber-Heiss
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Annika Posautz
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Sarah Lepuschitz
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Bernhard Schauer
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Andrea T Feßler
- Institute of Microbiology and Epizootics, Centre of Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | | | - Ewan M Harrison
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Mark A Holmes
- Departement of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Frank Künzel
- Clinical Unit of Internal Medicine Small Animals, University of Veterinary Medicine, Vienna, Austria
| | - Michael P Szostak
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Tomasz Hauschild
- Department of Microbiology, Institute of Biology, University of Bialystok, Bialystok, Poland
| | - Amélie Desvars-Larrive
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Dusan Misic
- Department for Microbiology, Faculty of Veterinary Medicine, University of Belgrade, Belgrade, Serbia
| | - Renate Rosengarten
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Chris Walzer
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria; Wildlife Health Program, Wildlife Conservation Society, Bronx, NY, USA
| | | | - Stefan Monecke
- InfectoGnostics research campus, Jena, Germany; Leibniz Institute of Photonic Technology (IPHT), Jena, Germany; Institute for Medical Microbiology and Hygiene, Technical University of Dresden, Dresden, Germany
| | - Ralf Ehricht
- InfectoGnostics research campus, Jena, Germany; Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre of Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Joachim Spergser
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
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5
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Earls MR, Shore AC, Brennan GI, Simbeck A, Schneider-Brachert W, Vremerǎ T, Dorneanu OS, Slickers P, Ehricht R, Monecke S, Coleman DC. A novel multidrug-resistant PVL-negative CC1-MRSA-IV clone emerging in Ireland and Germany likely originated in South-Eastern Europe. Infect Genet Evol 2019; 69:117-126. [PMID: 30677533 DOI: 10.1016/j.meegid.2019.01.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/20/2018] [Accepted: 01/15/2019] [Indexed: 12/19/2022]
Abstract
This study investigated the recent emergence of multidrug-resistant Panton-Valentine leukocidin (PVL)-negative CC1-MRSA-IV in Ireland and Germany. Ten CC1-MSSA and 139 CC1-MRSA isolates recovered in Ireland between 2004 and 2017 were investigated. These were compared to 21 German CC1-MRSA, 10 Romanian CC1-MSSA, five Romanian CC1-MRSA and two UAE CC1-MRSA, which were selected from an extensive global database, based on similar DNA microarray profiles to the Irish isolates. All isolates subsequently underwent whole-genome sequencing, core-genome single nucleotide polymorphism (cgSNP) analysis and enhanced SCCmec subtyping. Two PVL-negative clades (A and B1) were identified among four main clades. Clade A included 20 German isolates, 119 Irish isolates, and all Romanian MRSA and MSSA isolates, the latter of which differed from clade A MRSA by 47-130 cgSNPs. Eighty-six Irish clade A isolates formed a tight subclade (A1) exhibiting 0-49 pairwise cgSNPs, 80 of which harboured a 46 kb conjugative plasmid carrying both ileS2, encoding high-level mupirocin resistance, and qacA, encoding chlorhexidine resistance. The resistance genes aadE, aphA3 and sat were detected in all clade A MRSA and the majority (8/10) of clade A MSSA isolates. None of the clade A isolates harboured any enterotoxin genes other than seh, which is universally present in CC1. Clade B1 included the remaining German isolate, 17 Irish isolates and the two UAE isolates, all of which corresponded to the Western Australia MRSA-1 (WA MRSA-1) clone based on genotypic characteristics. MRSA within clades A and B1 differed by 188 cgSNPs and clade-specific SCCmec characteristics were identified, indicating independent acquisition of the SCCmec element. This study demonstrated the existence of a European PVL-negative CC1-MRSA-IV clone that is distinctly different from the well-defined PVL-negative CC1-MRSA-IV clone, WA MRSA-1. Furthermore, cgSNP analysis revealed that this newly defined clone may have originated in South-Eastern Europe, before spreading to both Ireland and Germany.
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Affiliation(s)
- Megan R Earls
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, Trinity College, University of Dublin, Dublin, Ireland.
| | - Anna C Shore
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, Trinity College, University of Dublin, Dublin, Ireland.
| | - Gráinne I Brennan
- National MRSA Reference Laboratory, St. James's Hospital, James's Street, Dublin, Ireland.
| | - Alexandra Simbeck
- Institute for Clinical Microbiology and Hygiene, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany.
| | - Wulf Schneider-Brachert
- Institute for Clinical Microbiology and Hygiene, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany.
| | - Teodora Vremerǎ
- Microbiology Unit, Department of Preventive and Interdisciplinary Medicine, University of Medicine & Pharmacy "Grigore T Popa", Iaşi, Romania.
| | - Olivia S Dorneanu
- Microbiology Unit, Department of Preventive and Interdisciplinary Medicine, University of Medicine & Pharmacy "Grigore T Popa", Iaşi, Romania.
| | - Peter Slickers
- Abbott (Alere Technologies GmbH), Jena, Germany; InfectoGnostics Research Campus, Jena, Germany.
| | - Ralf Ehricht
- InfectoGnostics Research Campus, Jena, Germany; Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany.
| | - Stefan Monecke
- InfectoGnostics Research Campus, Jena, Germany; Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany; Institute for Medical Microbiology and Hygiene, Medical Faculty "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany.
| | - David C Coleman
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, Trinity College, University of Dublin, Dublin, Ireland.
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6
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Havlicek J, Dachsel B, Slickers P, Andres S, Beckert P, Feuerriegel S, Niemann S, Merker M, Labugger I. Rapid microarray-based assay for detection of pyrazinamide resistant Mycobacterium tuberculosis. Diagn Microbiol Infect Dis 2018; 94:147-154. [PMID: 30733004 PMCID: PMC6531379 DOI: 10.1016/j.diagmicrobio.2018.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/17/2018] [Accepted: 12/24/2018] [Indexed: 01/25/2023]
Abstract
Pyrazinamide (PZA) is a key antibiotic for the treatment of drug susceptible tuberculosis. PZA-resistance is mainly mediated by mutations in the pncA gene; however the current gold standard is a phenotypic drug susceptibility test requiring a well-adjusted pH-value for reliable results. Our melting curve assay detects a non-wild type genotype in selected pncA regions in at least 3750 gene copies/mL within 2.5 hours. The prototype assay was further evaluated by analyzing 271 Mycobacterium tuberculosis complex isolates from Swaziland originating from a previously published drug resistance survey and including 118 isolates with pncA mutations. Sensitivity was 83% (95% CI 75-89%) and specificity was 100% (95% CI 98-100%). Under consideration of further improvements with regard to the target range our melting curve assay has the potential as a rapid rule-in test for PZA susceptibility (wild type pncA), however false resistant results (mutant pncA, but PZA susceptible) cannot be ruled out completely.
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Affiliation(s)
| | | | | | - Sönke Andres
- National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Patrick Beckert
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-, Borstel, -Riems, Germany
| | - Silke Feuerriegel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-, Borstel, -Riems, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-, Borstel, -Riems, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-, Borstel, -Riems, Germany.
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Weiss D, Gawlik D, Hotzel H, Engelmann I, Mueller E, Slickers P, Braun SD, Monecke S, Ehricht R. Fast, economic and simultaneous identification of clinically relevant Gram-negative species with multiplex real-time PCR. Future Microbiol 2018; 14:23-32. [PMID: 30539662 DOI: 10.2217/fmb-2018-0197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
AIM A newly designed multiplex real-time PCR (rt-PCR) was validated to detect four clinically relevant Gram-negative bacteria (Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae and Pseudomonas aeruginosa). MATERIALS & METHODS Serial dilutions of genomic DNA were used to determine the limit of detection. Colony PCR was performed with isolates of the four selected species and other species as negative controls. Isolates were characterized genotypically and phenotypically to evaluate the assay. RESULTS Specific signals of all target genes were detected with diluted templates comprising ten genomic equivalents. Using colony rt-PCR, all isolates of the target species were identified correctly. All negative control isolates were negative. CONCLUSION The genes gad, basC, khe and ecfX can reliably identify these four species via multiplex colony rt-PCR.
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Affiliation(s)
- Daniel Weiss
- Research & Development, Abbott (Alere Technologies GmbH), Jena, Germany.,Center for Applied Research, InfectoGnostics Research Campus, Jena, Germany.,Institute for Infectious Diseases and Infection Control, University Medical Center of Jena, Jena, Germany
| | - Darius Gawlik
- Research & Development, Abbott (Alere Technologies GmbH), Jena, Germany.,Center for Applied Research, InfectoGnostics Research Campus, Jena, Germany
| | - Helmut Hotzel
- Institute of Bacterial Infections & Zoonoses, Friedrich-Loeffler-Institute, Jena, Germany
| | - Ines Engelmann
- Research & Development, Abbott (Alere Technologies GmbH), Jena, Germany.,Center for Applied Research, InfectoGnostics Research Campus, Jena, Germany
| | - Elke Mueller
- Research & Development, Abbott (Alere Technologies GmbH), Jena, Germany.,Center for Applied Research, InfectoGnostics Research Campus, Jena, Germany
| | - Peter Slickers
- Research & Development, Abbott (Alere Technologies GmbH), Jena, Germany
| | - Sascha D Braun
- Research & Development, Abbott (Alere Technologies GmbH), Jena, Germany.,Center for Applied Research, InfectoGnostics Research Campus, Jena, Germany
| | - Stefan Monecke
- Research & Development, Abbott (Alere Technologies GmbH), Jena, Germany.,Center for Applied Research, InfectoGnostics Research Campus, Jena, Germany.,Institute for Medical Microbiology & Hygiene, Technical University of Dresden, Dresden, Germany
| | - Ralf Ehricht
- Research & Development, Abbott (Alere Technologies GmbH), Jena, Germany.,Center for Applied Research, InfectoGnostics Research Campus, Jena, Germany.,Department for Optical Molecular Diagnostics and Systems Technology, Leibniz-Institute of Photonic Technology, Jena, Germany
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8
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Monecke S, Slickers P, Gawlik D, Müller E, Reissig A, Ruppelt-Lorz A, Akpaka PE, Bandt D, Bes M, Boswihi SS, Coleman DC, Coombs GW, Dorneanu OS, Gostev VV, Ip M, Jamil B, Jatzwauk L, Narvaez M, Roberts R, Senok A, Shore AC, Sidorenko SV, Skakni L, Somily AM, Syed MA, Thürmer A, Udo EE, Vremerǎ T, Zurita J, Ehricht R. Molecular Typing of ST239-MRSA-III From Diverse Geographic Locations and the Evolution of the SCC mec III Element During Its Intercontinental Spread. Front Microbiol 2018; 9:1436. [PMID: 30087657 PMCID: PMC6066798 DOI: 10.3389/fmicb.2018.01436] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/11/2018] [Indexed: 11/13/2022] Open
Abstract
ST239-MRSA-III is probably the oldest truly pandemic MRSA strain, circulating in many countries since the 1970s. It is still frequently isolated in some parts of the world although it has been replaced by other MRSA strains in, e.g., most of Europe. Previous genotyping work (Harris et al., 2010; Castillo-Ramírez et al., 2012) suggested a split in geographically defined clades. In the present study, a collection of 184 ST239-MRSA-III isolates, mainly from countries not covered by the previous studies were characterized using two DNA microarrays (i) targeting an extensive range of typing markers, virulence and resistance genes and (ii) a SCCmec subtyping array. Thirty additional isolates underwent whole-genome sequencing (WGS) and, together with published WGS data for 215 ST239-MRSA-III isolates, were analyzed using in-silico analysis for comparison with the microarray data and with special regard to variation within SCCmec elements. This permitted the assignment of isolates and sequences to 39 different SCCmec III subtypes, and to three major and several minor clades. One clade, characterized by the integration of a transposon into nsaB and by the loss of fnbB and splE was detected among isolates from Turkey, Romania and other Eastern European countries, Russia, Pakistan, and (mainly Northern) China. Another clade, harboring sasX/sesI is widespread in South-East Asia including China/Hong Kong, and surprisingly also in Trinidad & Tobago. A third, related, but sasX/sesI-negative clade occurs not only in Latin America but also in Russia and in the Middle East from where it apparently originated and from where it also was transferred to Ireland. Minor clades exist or existed in Western Europe and Greece, in Portugal, in Australia and New Zealand as well as in the Middle East. Isolates from countries where this strain is not epidemic (such as Germany) frequently are associated with foreign travel and/or hospitalization abroad. The wide dissemination of this strain and the fact that it was able to cause a hospital-borne pandemic that lasted nearly 50 years emphasizes the need for stringent infection prevention and control and admission screening.
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Affiliation(s)
- Stefan Monecke
- Abbott (Alere Technologies GmbH), Jena, Germany.,InfectoGnostics Research Campus Jena, Jena, Germany.,Medical Faculty "Carl Gustav Carus", Institute for Medical Microbiology and Hygiene, Technische Universität Dresden, Dresden, Germany
| | - Peter Slickers
- Abbott (Alere Technologies GmbH), Jena, Germany.,InfectoGnostics Research Campus Jena, Jena, Germany
| | - Darius Gawlik
- Abbott (Alere Technologies GmbH), Jena, Germany.,InfectoGnostics Research Campus Jena, Jena, Germany
| | - Elke Müller
- Abbott (Alere Technologies GmbH), Jena, Germany.,InfectoGnostics Research Campus Jena, Jena, Germany
| | - Annett Reissig
- Abbott (Alere Technologies GmbH), Jena, Germany.,InfectoGnostics Research Campus Jena, Jena, Germany
| | - Antje Ruppelt-Lorz
- Medical Faculty "Carl Gustav Carus", Institute for Medical Microbiology and Hygiene, Technische Universität Dresden, Dresden, Germany
| | - Patrick E Akpaka
- Department of Paraclinical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Dirk Bandt
- Instituts für Labordiagnostik, Mikrobiologie und Krankenhaushygiene, Oberlausitz-Kliniken, Bautzen, Germany
| | - Michele Bes
- Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Samar S Boswihi
- Microbiology Department, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - David C Coleman
- Microbiology Research Unit, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - Geoffrey W Coombs
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Olivia S Dorneanu
- Microbiology Unit, Department of Preventive and Interdisciplinary Medicine, University of Medicine & Pharmacy "Grigore T Popa", Iaşi, Romania
| | - Vladimir V Gostev
- Pediatric Research and Clinical Center for Infectious Diseases, Saint Petersburg, Russia
| | - Margaret Ip
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Bushra Jamil
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan.,Department of Biogenetics, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Lutz Jatzwauk
- Department of Hospital Infection Control, Dresden University Hospital, Dresden, Germany
| | - Marco Narvaez
- Department of Hospital Infection Control, Dresden University Hospital, Dresden, Germany
| | - Rashida Roberts
- Department of Paraclinical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Abiola Senok
- Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Anna C Shore
- Microbiology Research Unit, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - Sergey V Sidorenko
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Leila Skakni
- Molecular Pathology Laboratory, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ali M Somily
- Department of Pathology and Laboratory Medicine, College of Medicine, King Saud University and King Saud University Medical City, Riyadh, Saudi Arabia
| | - Muhammad Ali Syed
- Department of Microbiology, University of Haripur, Haripur, Pakistan
| | - Alexander Thürmer
- Medical Faculty "Carl Gustav Carus", Institute for Medical Microbiology and Hygiene, Technische Universität Dresden, Dresden, Germany
| | - Edet E Udo
- Microbiology Research Unit, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland
| | - Teodora Vremerǎ
- Microbiology Unit, Department of Preventive and Interdisciplinary Medicine, University of Medicine & Pharmacy "Grigore T Popa", Iaşi, Romania
| | - Jeannete Zurita
- Facultad de Medicina, Pontificia Universidad Catolica del Ecuador, Quito, Ecuador.,Zurita & Zurita Laboratorios, Unidad de Investigaciones en Biomedicina, Quito, Ecuador
| | - Ralf Ehricht
- Abbott (Alere Technologies GmbH), Jena, Germany.,InfectoGnostics Research Campus Jena, Jena, Germany
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9
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Earls MR, Coleman DC, Brennan GI, Fleming T, Monecke S, Slickers P, Ehricht R, Shore AC. Intra-Hospital, Inter-Hospital and Intercontinental Spread of ST78 MRSA From Two Neonatal Intensive Care Unit Outbreaks Established Using Whole-Genome Sequencing. Front Microbiol 2018; 9:1485. [PMID: 30022976 PMCID: PMC6039561 DOI: 10.3389/fmicb.2018.01485] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/14/2018] [Indexed: 01/22/2023] Open
Abstract
From 2009 to 2011 [transmission period (TP) 1] and 2014 to 2017 (TP2), two outbreaks involving community-associated clonal complex (CC) 88-MRSA spa types t186 and t786, respectively, occurred in the Neonatal Intensive Care Unit (NICU) of an Irish hospital (H1). This study investigated the relatedness of these isolates, their relationship to other CC88 MRSA from Ireland and their likely geographic origin, using whole-genome sequencing (WGS). All 28 CC88-MRSA isolates identified at the Irish National MRSA Reference Laboratory between 2009 and 2017 were investigated including 20 H1 patient isolates, two H1 isolates recovered from a single healthcare worker (HCW) 2 years apart, three patient isolates from a second hospital (H2) and one patient isolate from each of three different hospitals (H3, H4, and H5). All isolates underwent DNA microarray profiling. Thirteen international isolates with similar microarray profiles to at least one Irish isolate were selected from an extensive global database. All isolates underwent Illumina MiSeq WGS. The majority of Irish isolates (25/28; all H1 isolates, two H2 isolates and the H3 isolate) were identified as ST78-MRSA-IVa and formed a large cluster, exhibiting 1–71 pairwise allelic differences, in a whole-genome MLST-based minimum spanning tree (MST) involving all Irish isolates. A H1/H2, H1/H3, and H1 HCW/patient isolate pair each exhibited one allelic difference. The TP2 isolates were characterised by a different spa type and the loss of hsdS. The three remaining Irish isolates (from H2, H4, and H5) were identified as ST88-MRSA-IVa and dispersed at the opposite end of the MST, exhibiting 81–211 pairwise allelic differences. Core-genome MLST and sequence-based plasmid analysis revealed the recent shared ancestry of Irish and Australian ST78-MRSA-IVa, and of Irish and French/Egyptian ST88-MRSA-IVa. This study revealed the homogeneity of isolates recovered during two NICU outbreaks (despite spa type and hsdS carriage variances), HCW involvement in the outbreak transmission chain and the strain's spread to two other Irish hospitals. The outbreak strain, CC88/ST78-MRSA-IVa, was likely imported from Australia, where it is prevalent. CC88/ST88-MRSA-IVa was also identified in Irish hospitals and was likely imported from Africa, where it is predominant, and/or a country with a large population of African descent.
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Affiliation(s)
- Megan R Earls
- Microbiology Research Unit, Dublin Dental University Hospital, Trinity College, University of Dublin, Dublin, Ireland
| | - David C Coleman
- Microbiology Research Unit, Dublin Dental University Hospital, Trinity College, University of Dublin, Dublin, Ireland
| | - Gráinne I Brennan
- National MRSA Reference Laboratory, St. James's Hospital, Dublin, Ireland
| | - Tanya Fleming
- National MRSA Reference Laboratory, St. James's Hospital, Dublin, Ireland
| | - Stefan Monecke
- Abbott (Alere Technologies GmbH), Jena, Germany.,InfectGnostics Research Campus, Jena, Germany
| | - Peter Slickers
- Abbott (Alere Technologies GmbH), Jena, Germany.,InfectGnostics Research Campus, Jena, Germany
| | - Ralf Ehricht
- Abbott (Alere Technologies GmbH), Jena, Germany.,InfectGnostics Research Campus, Jena, Germany
| | - Anna C Shore
- Microbiology Research Unit, Dublin Dental University Hospital, Trinity College, University of Dublin, Dublin, Ireland
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10
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Braun SD, Jamil B, Syed MA, Abbasi SA, Weiß D, Slickers P, Monecke S, Engelmann I, Ehricht R. Prevalence of carbapenemase-producing organisms at the Kidney Center of Rawalpindi (Pakistan) and evaluation of an advanced molecular microarray-based carbapenemase assay. Future Microbiol 2018; 13:1225-1246. [PMID: 29938540 DOI: 10.2217/fmb-2018-0082] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM A DNA microarray-based assay for the detection of antimicrobial resistance (AMR) genes was used to study carbapenemase-producing organisms at the Kidney Center of Rawalpindi, Pakistan. METHODS The evaluation of this assay was performed using 97 reference strains with confirmed AMR genes. Testing of 7857 clinical samples identified 425 Gram-negative bacteria out of which 82 appeared carbapenem resistant. These isolates were analyzed using VITEK-2 for phenotyping and the described AMR assay for genotyping. RESULTS The most prevalent carbapenemase gene was blaNDM and in 12 isolates we detected two carbapenemase genes (e.g., blaNDM/blaOXA-48). CONCLUSION Our prevalence data from Pakistan show that - as in other parts of the world - carbapenemase-producing organisms with different underlying resistance mechanisms are emerging, and this warrants intensified and constant surveillance.
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Affiliation(s)
- Sascha D Braun
- Research & Development, Abbott (Alere Technologies GmbH), Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
| | - Bushra Jamil
- Department of Biogenetics, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Muhammad A Syed
- Department of Microbiology, University of Haripur, Haripur, Pakistan
| | - Shahid A Abbasi
- Department of Pathology, Al-Sayed Hospital (Pvt) Ltd, 1-Hill Park, Opp. Ayub Park, Jhelum Road, Rawalpindi, Pakistan
| | - Daniel Weiß
- Research & Development, Abbott (Alere Technologies GmbH), Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
| | - Peter Slickers
- Research & Development, Abbott (Alere Technologies GmbH), Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
| | - Stefan Monecke
- Research & Development, Abbott (Alere Technologies GmbH), Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany.,Technische Universität Dresden, Medizinische Fakultät "Carl Gustav Carus", Dresden, Germany
| | - Ines Engelmann
- Research & Development, Abbott (Alere Technologies GmbH), Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
| | - Ralf Ehricht
- Research & Development, Abbott (Alere Technologies GmbH), Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
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11
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Monecke S, Slickers P, Gawlik D, Müller E, Reissig A, Ruppelt-Lorz A, de Jäckel SC, Feßler AT, Frank M, Hotzel H, Kadlec K, Jatzwauk L, Loncaric I, Schwarz S, Schlotter K, Thürmer A, Wendlandt S, Ehricht R. Variability of SCCmec elements in livestock-associated CC398 MRSA. Vet Microbiol 2018; 217:36-46. [PMID: 29615254 DOI: 10.1016/j.vetmic.2018.02.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/16/2018] [Accepted: 02/02/2018] [Indexed: 10/17/2022]
Abstract
The most common livestock-associated lineage of methicillin-resistant Staphylococcus aureus (MRSA) in Western Europe is currently clonal complex (CC) 398. CC398-MRSA spread extensively across livestock populations in several Western European countries, and livestock-derived CC398-MRSA strains can also be detected in humans. Based on their SCCmec elements, different CC398 strains can be distinguished. SCCmec elements of 100 veterinary and human CC398-MRSA isolates from Germany and Austria were examined using DNA microarray-based assays. In addition, 589 published SCC and/or genome sequences of CC398-MRSA (including both, fully finished and partially assembled sequences) were analysed by mapping them to the probe sequences of the microarrays. Several isolates and sequences showed an insertion of a large fragment of CC9 genomic DNA into the CC398 chromosome. Fifteen subtypes of SCCmec elements were detected among the 100 CC398 isolates and 41 subtypes could be discerned among the published CC398 sequences. Eleven of these were also experimentally detected within our strain collection, while four subtypes identified in the isolates where not found among the sequences. A high prevalence of heavy metal resistance genes, especially of czrC, was observed among CC398-MRSA. A possible co-selection of resistances to antibiotics and zinc/copper supplements in animal feed as well as a spill-over of SCCmec elements that have evolved in CC398-MRSA to other, possibly more virulent and/or medically relevant S. aureus lineages might pose public health problems in future.
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Affiliation(s)
- Stefan Monecke
- Abbott (Alere Technologies GmbH), Jena, Germany; Institute for Medical Microbiology and Hygiene, Medical Faculty "Carl Gustav Carus", Technische Universität Dresden, Dresden, Germany; InfectoGnostics Research Campus Jena, Jena, Germany.
| | - Peter Slickers
- Abbott (Alere Technologies GmbH), Jena, Germany; InfectoGnostics Research Campus Jena, Jena, Germany
| | - Darius Gawlik
- Abbott (Alere Technologies GmbH), Jena, Germany; InfectoGnostics Research Campus Jena, Jena, Germany
| | - Elke Müller
- Abbott (Alere Technologies GmbH), Jena, Germany; InfectoGnostics Research Campus Jena, Jena, Germany
| | - Annett Reissig
- Abbott (Alere Technologies GmbH), Jena, Germany; InfectoGnostics Research Campus Jena, Jena, Germany
| | - Antje Ruppelt-Lorz
- Institute for Medical Microbiology and Hygiene, Medical Faculty "Carl Gustav Carus", Technische Universität Dresden, Dresden, Germany
| | | | - Andrea T Feßler
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | | | - Helmut Hotzel
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut (FLI), Jena, Germany
| | - Kristina Kadlec
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt, Mariensee, Germany
| | - Lutz Jatzwauk
- Department of Hospital Infection Control, Dresden University Hospital, Dresden, Germany
| | - Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | | | - Alexander Thürmer
- Institute for Medical Microbiology and Hygiene, Medical Faculty "Carl Gustav Carus", Technische Universität Dresden, Dresden, Germany
| | - Sarah Wendlandt
- Department of Clinical Microbiology, Medical Care Centre SYNLAB Leverkusen GmbH, Leverkusen, Germany
| | - Ralf Ehricht
- Abbott (Alere Technologies GmbH), Jena, Germany; InfectoGnostics Research Campus Jena, Jena, Germany
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12
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Stieber B, Sabat A, Monecke S, Slickers P, Akkerboom V, Müller E, Friedrich AW, Ehricht R. PVL overexpression due to genomic rearrangements and mutations in the S. aureus reference strain ATCC25923. BMC Res Notes 2017; 10:576. [PMID: 29115975 PMCID: PMC5678758 DOI: 10.1186/s13104-017-2891-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/31/2017] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE ATCC25923 is a Staphylococcus aureus strain that is positive for the Panton Valentin leukocidin. It has been used for decades as reference strain. We observed that two separately maintained clones of ATCC25923 ("G477 and G478") differed grossly in the expression of this toxin. For that reason, both clones were sequenced using an Illumina MiSeq instrument. After assembling, the final sequences were analyzed and mapped to a previously published ATCC25923 sequence (GenBank CP009361) using bl2seq from the NCBI Blast2 package. RESULTS The genomes of G477 and G478 size 2778,859 and 2792,213 nucleotides, respectively. Both genomes include a circular plasmid of 27,490 nucleotides. The sequence of the G477 chromosome maps nearly exactly to CP009361. G478 has a slightly larger size because of the presence of an additional transposable element tnp13k. The second copy of that tnp13k element is located in an intergenic region between the genes mazF and rsbU. The sequences of the ATCC25923 clones G477 and G478 differ mainly in the insertion of a second tnp13k element between the genes mazF and rsbU. That insertion may lead to a different transcription of that genome region resulting in upregulation of the expression of the Panton-Valentine leukocidin in the ATCC25923 clone G478.
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Affiliation(s)
- Bettina Stieber
- Alere Technologies GmbH (Abbott Rapid Diagnostics), Jena, Germany. .,InfectoGnostics Research Campus, Jena, Germany.
| | - Artur Sabat
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stefan Monecke
- Alere Technologies GmbH (Abbott Rapid Diagnostics), Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany.,Institute for Medical Microbiology and Hygiene, Technische Universität Dresden, Dresden, Germany
| | - Peter Slickers
- Alere Technologies GmbH (Abbott Rapid Diagnostics), Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
| | - Viktoria Akkerboom
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Elke Müller
- Alere Technologies GmbH (Abbott Rapid Diagnostics), Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
| | - Alexander W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ralf Ehricht
- Alere Technologies GmbH (Abbott Rapid Diagnostics), Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
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13
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Senok AC, Somily AM, Slickers P, Raji MA, Garaween G, Shibl A, Monecke S, Ehricht R. Investigating a rare methicillin-resistant Staphylococcus aureus strain: first description of genome sequencing and molecular characterization of CC15-MRSA. Infect Drug Resist 2017; 10:307-315. [PMID: 29042801 PMCID: PMC5633289 DOI: 10.2147/idr.s145394] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Purpose Methicillin resistant Staphylococcus aureus CC15 strains (CC15-MRSA) have only been sporadically described in literature. This study was carried out to describe the genetic make-up for this rare MRSA strain. Methods Four CC15-MRSA isolates collected in Riyadh, Saudi Arabia, between 2013 and 2014 were studied. Two isolates were from clinical infection and 2 from retail meat products. Whole genome sequencing was carried out using Illumina HiSeq2500 genome analyzer. Results All the CC15-MRSA isolates had the multilocus sequence typing profile ST1535, 13–13-1–1-81-11-13, which is a single locus variant of ST15. Of the 6 contigs related to the SCC element, one comprised a recombinase gene ccrAA, ccrC-PM1, fusC and a helicase, another one included mvaS, dru, mecA and 1 had yobV and Q4LAG7. The SCC element had 5 transposase genes, namely 3 identical paralogs of tnpIS431 and 2 identical paralogs of tnpIS256. Two identical copies of a tnpIS256-based insertion element flank the aacA-aphD gene. Two copies of this insertion element were present with 1 located in the SCC element and another inserted into the sasC gene. A short 3 kb region, which lacks any bacteriophage structural genes and site-specific DNA integrase, was inserted into the hlb gene. The hsdM and the 5’-part of the hsdS gene are replaced by a copy of the hsdM/hsdS paralogs from νSaβ giving rise to a new chimeric paralog of hsdS in νSaα. Conclusion CC15-MRSA shows a novel SCCmecV/SCCfus composite element. Its variant of hsdM/hsdS probably facilitated uptake of foreign mobile genetic elements that promoted emergence of CC15-MRSA. Close surveillance is needed to monitor spread and emergence of further CC15 MRSA strains.
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Affiliation(s)
- Abiola C Senok
- Department of Basic Science, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Ali M Somily
- Department of Pathology and Laboratory Medicine, College of Medicine, King Khalid University Hospital and King Saud University, Riyadh, Saudi Arabia
| | - Peter Slickers
- Alere Technologies GmbH, Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
| | - Muhabat A Raji
- Department of Microbiology and Immunology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Ghada Garaween
- Department of Microbiology and Immunology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Atef Shibl
- Department of Microbiology and Immunology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Stefan Monecke
- Alere Technologies GmbH, Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany.,Institute for Medical Microbiology and Hygiene (IMMH), Technische Universität Dresden, Dresden, Germany
| | - Ralf Ehricht
- Alere Technologies GmbH, Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
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14
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Brandt C, Braun SD, Stein C, Slickers P, Ehricht R, Pletz MW, Makarewicz O. In silico serine β-lactamases analysis reveals a huge potential resistome in environmental and pathogenic species. Sci Rep 2017; 7:43232. [PMID: 28233789 PMCID: PMC5324141 DOI: 10.1038/srep43232] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/20/2017] [Indexed: 12/30/2022] Open
Abstract
The secretion of antimicrobial compounds is an ancient mechanism with clear survival benefits for microbes competing with other microorganisms. Consequently, mechanisms that confer resistance are also ancient and may represent an underestimated reservoir in environmental bacteria. In this context, β-lactamases (BLs) are of great interest due to their long-term presence and diversification in the hospital environment, leading to the emergence of Gram-negative pathogens that are resistant to cephalosporins (extended spectrum BLs = ESBLs) and carbapenems (carbapenemases). In the current study, protein sequence databases were used to analyze BLs, and the results revealed a substantial number of unknown and functionally uncharacterized BLs in a multitude of environmental and pathogenic species. Together, these BLs represent an uncharacterized reservoir of potentially transferable resistance genes. Considering all available data, in silico approaches appear to more adequately reflect a given resistome than analyses of limited datasets. This approach leads to a more precise definition of BL clades and conserved motifs. Moreover, it may support the prediction of new resistance determinants and improve the tailored development of robust molecular diagnostics.
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Affiliation(s)
- Christian Brandt
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
| | - Sascha D Braun
- InfectoGnostics Research Campus, Jena, Germany.,Alere Technologies GmbH, Jena, Germany
| | - Claudia Stein
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
| | - Peter Slickers
- InfectoGnostics Research Campus, Jena, Germany.,Alere Technologies GmbH, Jena, Germany
| | - Ralf Ehricht
- InfectoGnostics Research Campus, Jena, Germany.,Alere Technologies GmbH, Jena, Germany
| | - Mathias W Pletz
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
| | - Oliwia Makarewicz
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany.,InfectoGnostics Research Campus, Jena, Germany
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Monecke S, Jatzwauk L, Müller E, Nitschke H, Pfohl K, Slickers P, Reissig A, Ruppelt-Lorz A, Ehricht R. Diversity of SCCmec Elements in Staphylococcus aureus as Observed in South-Eastern Germany. PLoS One 2016; 11:e0162654. [PMID: 27648947 PMCID: PMC5029946 DOI: 10.1371/journal.pone.0162654] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/28/2016] [Indexed: 12/21/2022] Open
Abstract
SCCmec elements are very important mobile genetic elements in Staphylococci that carry beta-lactam resistance genes mecA/mecC, recombinase genes and a variety of accessory genes. Twelve main types and a couple of variants have yet been described. In addition, there are also other SCC elements harbouring other markers. In order to subtype strains of methicillin-resistant S. aureus (MRSA) based on variations within their SCCmec elements, 86 markers were selected from published SCC sequences for an assay based on multiplexed primer extension reactions followed by hybridisation to the specific probes. These included mecA/mecC, fusC, regulatory genes, recombinase genes, genes from ACME and heavy metal resistance loci as well as several genes of unknown function. Hybridisation patterns for published genome or SCC sequences were theoretically predicted. For validation of the microarray based assay and for stringent hybridisation protocol optimization, real hybridization experiments with fully sequenced reference strains were performed modifying protocols until yielded the results were in concordance to the theoretical predictions. Subsequently, 226 clinical isolates from two hospitals in the city of Dresden, Germany, were characterised in detail. Beside previously described types and subtypes, a wide variety of additional SCC types or subtypes and pseudoSCC elements were observed as well as numerous composite elements. Within the study collection, 61 different such elements have been identified. Since hybridisation cannot recognise the localisation of target genes, gene duplications or inversions, this is a rather conservative estimate. Interestingly, some widespread epidemic strains engulf distinct variants with different SCCmec subtypes. Notable examples are ST239-MRSA-III, CC5-, CC22-, CC30-, and CC45-MRSA-IV or CC398-MRSA-V. Conversely, identical SCC elements were observed in different strains with SCCmec IVa being spread among the highest number of Clonal Complexes. The proposed microarray can help to distinguish isolates that appear similar or identical by other typing methods and it can be used as high-throughput screening tool for the detection of putative new SCC types or variants that warrant further investigation and sequencing. The high degree of diversity of SCC elements even within so-called strains could be helpful for epidemiological typing. It also raises the question on scale and speed of the evolution of SCC elements.
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Affiliation(s)
- Stefan Monecke
- Institute for Medical Microbiology and Hygiene (IMMH), Technische Universität Dresden, Dresden, Germany
- Alere Technologies GmbH, Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
- * E-mail:
| | - Lutz Jatzwauk
- Department of Hospital Infection Control, Dresden University Hospital, Dresden, Germany
| | - Elke Müller
- Alere Technologies GmbH, Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
| | - Hedda Nitschke
- Department of Laboratory Medicine, Hospital Dresden Neustadt, Dresden, Germany
| | - Katharina Pfohl
- Institute for Medical Microbiology and Hygiene (IMMH), Technische Universität Dresden, Dresden, Germany
| | - Peter Slickers
- Alere Technologies GmbH, Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
| | - Annett Reissig
- Alere Technologies GmbH, Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
| | - Antje Ruppelt-Lorz
- Institute for Medical Microbiology and Hygiene (IMMH), Technische Universität Dresden, Dresden, Germany
| | - Ralf Ehricht
- Alere Technologies GmbH, Jena, Germany
- InfectoGnostics Research Campus, Jena, Germany
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16
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Petzold M, Ehricht R, Slickers P, Pleischl S, Brockmann A, Exner M, Monecke S, Lück C. Rapid genotyping of Legionella pneumophila serogroup 1 strains by a novel DNA microarray-based assay during the outbreak investigation in Warstein, Germany 2013. Int J Hyg Environ Health 2016; 220:673-678. [PMID: 28501485 DOI: 10.1016/j.ijheh.2016.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 02/12/2016] [Accepted: 02/12/2016] [Indexed: 10/22/2022]
Abstract
Between 1 August and 6 September 2013, an outbreak of Legionnaires' disease (LD) with 78 cases confirmed by positive urinary antigen tests occurred in Warstein, North Rhine-Westphalia, Germany. Legionella (L.) pneumophila, serogroup (Sg) 1, monoclonal antibody (mAb) subgroup Knoxville, sequence type (ST) 345, was identified as the epidemic strain. This strain was isolated from seven patients. To detect the source of the infection, epidemiological typing of clinical and environmental strains was performed in two consecutive steps. First, strains were typed by monoclonal antibodies. Indistinguishable strains were further subtyped by sequence-based typing (SBT) which is the internationally recognized standard method for epidemiological genotyping of L. pneumophila. In an early stage of the outbreak investigation, many environmental isolates were found to belong to the mAb subgroup Knoxville, but to two different STs, namely to ST 345, the epidemic strain, and to ST 600. A majority of environmental isolates belonged to ST 600 whereas the epidemic ST 345 strain was less common in environmental samples. To rapidly distinguish both Knoxville strains, we applied a novel typing method based on DNA-hybridization on glass chips. The new assay can easily and rapidly discriminate L. pneumophila Sg 1 strains. Thus, we were able to quickly identify the sources harboring the epidemic strain, i.e., two cooling towers of different companies, the waste water treatment plants (WWTP) of the city and one company as well as water samples of the river Wester and its branches.
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Affiliation(s)
- Markus Petzold
- Institute of Medical Microbiology and Hygiene, German Reference Laboratory for Legionella, Dresden University of Technology, Fetscherstraße 74, 01307 Dresden, Germany.
| | - Ralf Ehricht
- Alere Technologies GmbH, Löbstedter Straße 103-105, 07749 Jena, Germany.
| | - Peter Slickers
- Alere Technologies GmbH, Löbstedter Straße 103-105, 07749 Jena, Germany.
| | - Stefan Pleischl
- Institute for Hygiene and Public Health, University of Bonn, Sigmund-Freud-Straße 25, 53105 Bonn, Germany.
| | - Ansgar Brockmann
- Regional Public Health Department Soest, Mastholter Straße 230, 59558 Lippstadt, Germany.
| | - Martin Exner
- Institute for Hygiene and Public Health, University of Bonn, Sigmund-Freud-Straße 25, 53105 Bonn, Germany.
| | - Stefan Monecke
- Institute of Medical Microbiology and Hygiene, German Reference Laboratory for Legionella, Dresden University of Technology, Fetscherstraße 74, 01307 Dresden, Germany; Alere Technologies GmbH, Löbstedter Straße 103-105, 07749 Jena, Germany.
| | - Christian Lück
- Institute of Medical Microbiology and Hygiene, German Reference Laboratory for Legionella, Dresden University of Technology, Fetscherstraße 74, 01307 Dresden, Germany.
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Gawlik D, Slickers P, Engelmann I, Müller E, Lück C, Friedrichs A, Ehricht R, Monecke S. DNA-Microarray-based Genotyping of Clostridium difficile. BMC Microbiol 2015; 15:158. [PMID: 26242247 PMCID: PMC4526300 DOI: 10.1186/s12866-015-0489-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 07/20/2015] [Indexed: 01/05/2023] Open
Abstract
Background Clostridium difficile can cause antibiotic-associated diarrhea and a possibility of outbreaks in hospital settings warrants molecular typing. A microarray was designed that included toxin genes (tcdA/B, cdtA/B), genes related to antimicrobial resistance, the slpA gene and additional variable genes. Results DNA of six reference strains and 234 clinical isolates from South-Western and Eastern Germany was subjected to linear amplification and labeling with dUTP-linked biotin. Amplicons were hybridized to microarrays providing information on the presence of target genes and on their alleles. Tested isolates were assigned to 37 distinct profiles that clustered mainly according to MLST-defined clades. Three additional profiles were predicted from published genome sequences, although they were not found experimentally. Conclusions The microarray based assay allows rapid and high-throughput genotyping of clinical C. difficile isolates including toxin gene detection and strain assignment. Overall hybridization profiles correlated with MLST-derived clades. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0489-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Darius Gawlik
- Institute for Medical Microbiology and Hygiene, Technische Universität Dresden, Dresden, Germany. .,Hamm-Lippstedt University, Hamm, Germany.
| | - Peter Slickers
- Alere Technologies GmbH, Jena, Germany. .,Infectognostics Research Campus, Jena, Germany.
| | - Ines Engelmann
- Alere Technologies GmbH, Jena, Germany. .,Infectognostics Research Campus, Jena, Germany.
| | - Elke Müller
- Alere Technologies GmbH, Jena, Germany. .,Infectognostics Research Campus, Jena, Germany.
| | - Christian Lück
- Institute for Medical Microbiology and Hygiene, Technische Universität Dresden, Dresden, Germany.
| | - Anette Friedrichs
- Department of Internal Medicine I, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
| | - Ralf Ehricht
- Alere Technologies GmbH, Jena, Germany. .,Infectognostics Research Campus, Jena, Germany.
| | - Stefan Monecke
- Institute for Medical Microbiology and Hygiene, Technische Universität Dresden, Dresden, Germany. .,Alere Technologies GmbH, Jena, Germany. .,Infectognostics Research Campus, Jena, Germany.
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18
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Nimmo GR, Steen JA, Monecke S, Ehricht R, Slickers P, Thomas JC, Appleton S, Goering RV, Robinson DA, Coombs GW. ST2249-MRSA-III: a second major recombinant methicillin-resistant Staphylococcus aureus clone causing healthcare infection in the 1970s. Clin Microbiol Infect 2015; 21:444-50. [PMID: 25708549 DOI: 10.1016/j.cmi.2014.12.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 12/04/2014] [Accepted: 12/19/2014] [Indexed: 11/24/2022]
Abstract
Typing of healthcare-associated methicillin-resistant Staphylococcus aureus (MRSA) from Australia in the 1970s revealed a novel clone, ST2249-MRSA-III (CC45), present from 1973 to 1979. This clone was present before the Australian epidemic caused by the recombinant clone, ST239-MRSA-III. This study aimed to characterize the genome of ST2249-MRSA-III to establish its relationship to other MRSA clones. DNA microarray analysis was conducted and a draft genome sequence of ST2249 was obtained. The recombinant structure of the ST2249 genome was revealed by comparisons to publicly available ST239 and ST45 genomes. Microarray analysis of genomic DNA of 13 ST2249 isolates showed gross similarities with the ST239 chromosome in a segment around the origin of replication and with ST45 for the remainder of the chromosome. Recombination breakpoints were precisely determined by the changing pattern of nucleotide polymorphisms in the genome sequence of ST2249 isolate SK1585 compared with ST239 and ST45. One breakpoint was identified to the right of oriC, between sites 1014 and 1065 of the gene D484_00045. Another was identified to the left of oriC, between sites 1185 and 1248 of D484_01632. These results indicate that ST2249 inherited approximately 35.3% of its chromosome from an ST239-like parent and 64.7% from an ST45-like parent. ST2249-MRSA-III resulted from a major recombination between parents that resemble ST239 and ST45. Although only limited Australian archival material is available, the oldest extant isolate of ST2249 predates the oldest Australian isolate of ST239 by 3 years. It is therefore plausible that these two recombinant clones were introduced into Australia separately.
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Affiliation(s)
- G R Nimmo
- Pathology Queensland Central Laboratory, Brisbane, Qld, Australia; Griffith University School of Medicine, Gold Coast, Qld, Australia.
| | - J A Steen
- Queensland Centre for Medical Genomics, University of Queensland, Qld, Australia
| | - S Monecke
- Alere Technologies GmbH, Jena, Germany; Institute for Medical Microbiology and Hygiene, Technische Universitat Dresden, Dresden, Germany
| | - R Ehricht
- Alere Technologies GmbH, Jena, Germany
| | | | - J C Thomas
- Department of Microbiology, University of Mississippi Medical Center, Jackson, MS, USA; Department of Biology, University of Bolton, Bolton, United Kingdom
| | - S Appleton
- Queensland Medical Laboratory, Murrarie, Qld, Australia
| | | | - D A Robinson
- Department of Microbiology, University of Mississippi Medical Center, Jackson, MS, USA
| | - G W Coombs
- Australian Collaborating Centre for Enterococcus and Staphylococcus Species (ACCESS) Typing and Research, Curtin University, Perth, WA, Australia; Pathwest Laboratory Medicine-WA, Royal Perth Hospital, Perth, WA, Australia
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Nitschke H, Slickers P, Müller E, Ehricht R, Monecke S. DNA microarray-based typing of Streptococcus agalactiae isolates. J Clin Microbiol 2014; 52:3933-43. [PMID: 25165085 PMCID: PMC4313228 DOI: 10.1128/jcm.02411-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 08/23/2014] [Indexed: 11/20/2022] Open
Abstract
Streptococcus agalactiae frequently colonizes the urogenital tract, and it is a major cause of bacterial septicemia, meningitis, and pneumonia in newborns. For typing purposes, a microarray targeting group B streptococcus (GBS) virulence-associated markers and resistance genes was designed and validated with reference strains, as well as clinical and veterinary isolates. Selected isolates were also subjected to multilocus sequence typing. It was observed that putative typing markers, such as alleles of the alpha-like protein or capsule types, vary independently of each other, and they also vary independently from the affiliation to their multilocus sequence typing (MLST)-defined sequence types. Thus, it is not possible to assign isolates to sequence types based on the identification of a single distinct marker, such as a capsule type or alp allele. This suggests the occurrence of frequent genomic recombination. For array-based typing, a set of 11 markers (bac, alp, pil1 locus, pepS8, fbsB, capsule locus, hylB, abiG-I/-II plus Q8DZ34, pil2 locus, nss plus srr plus rogB2, and rgfC/A/D/B) was defined that provides a framework for splitting the tested 448 S. agalactiae isolates into 76 strains that clustered mainly according to MLST-defined clonal complexes. There was evidence for region- and host-specific differences in the population structure of S. agalactiae, as well as an overrepresentation of strains related to sequence type 17 among the invasive isolates. The arrays and typing scheme described here proved to be a convenient tool for genotyping large numbers of clinical/veterinary isolates and thus might help obtain insight into the epidemiology of S. agalactiae.
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Affiliation(s)
- Heike Nitschke
- Institute for Medical Microbiology and Hygiene, Technische Universität Dresden, Dresden, Germany Department of Obstetrics and Gynecology, Elblandklinikum Meißen, Meissen, Germany
| | | | | | | | - Stefan Monecke
- Institute for Medical Microbiology and Hygiene, Technische Universität Dresden, Dresden, Germany Alere Technologies GmbH, Jena, Germany
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Geue L, Monecke S, Engelmann I, Braun S, Slickers P, Ehricht R. Rapid microarray-based DNA genoserotyping of Escherichia coli. Microbiol Immunol 2014; 58:77-86. [PMID: 24298918 DOI: 10.1111/1348-0421.12120] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 11/22/2013] [Accepted: 11/26/2013] [Indexed: 12/01/2022]
Abstract
In this study, an improvement in the oligonucleotide-based DNA microarray for the genoserotyping of Escherichia coli is presented. Primer and probes for additional 70 O antigen groups were developed. The microarray was transferred to a new platform, the ArrayStrip format, which allows high through-put tests in 96-well formats and fully automated microarray analysis. Thus, starting from a single colony, it is possible to determine within a few hours and a single experiment, 94 of the over 180 known O antigen groups as well as 47 of the 53 different H antigens. The microarray was initially validated with a set of defined reference strains that had previously been serotyped by conventional agglutination in various reference centers. For further validation of the microarray, 180 clinical E. coli isolates of human origin (from urine samples, blood cultures, bronchial secretions, and wound swabs) and 53 E. coli isolates from cattle, pigs, and poultry were used. A high degree of concordance between the results of classical antibody-based serotyping and DNA-based genoserotyping was demonstrated during validation of the new 70 O antigen groups as well as for the field strains of human and animal origin. Therefore, this oligonucleotide array is a diagnostic tool that is user-friendly and more efficient than classical serotyping by agglutination. Furthermore, the tests can be performed in almost every routine lab and are easily expanded and standardized.
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Affiliation(s)
- Lutz Geue
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Wusterhausen
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21
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Monecke S, Stieber B, Roberts R, Akpaka PE, Slickers P, Ehricht R. Population structure of Staphylococcus aureus from Trinidad & Tobago. PLoS One 2014; 9:e89120. [PMID: 24586536 PMCID: PMC3929661 DOI: 10.1371/journal.pone.0089120] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 01/20/2014] [Indexed: 11/18/2022] Open
Abstract
It has been shown previously that high rates of methicillin- and mupirocin-resistant Staphylococcus aureus exist in the Caribbean islands of Trinidad and Tobago, as well as a high prevalence of Panton-Valentine leukocidin-positive S. aureus. Beyond these studies, limited typing data have been published. In order to obtain insight into the population structure not only of MRSA but also of methicillin-susceptible S. aureus, 294 clinical isolates collected in 2012/2013 were typed by microarray hybridisation. A total of 15.31% of the tested isolates were MRSA and 50.00% were PVL-positive. The most common MSSA strains were PVL-positive CC8-MSSA (20.41% of all isolates tested), PVL-positive CC152-MSSA (9.52%) and PVL-positive CC30-MSSA (8.84%) while the most common MRSA were ST239-MRSA-III&SCCmer (9.18%) and ST8-MRSA-IV, “USA300” (5.78%). 2.38% of characterised isolates belonged to distinct strains likely to be related to “Staphylococcus argenteus” lineages. The population structure of S. aureus isolates suggests an importation of strains from Africa, endemicity of PVL-positive MSSA (mainly CC8) and of ST239-MRSA-III, and a recent emergence of the PVL-positive CC8-MRSA-IV strain “USA300”.
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Affiliation(s)
- Stefan Monecke
- Institute for Medical Microbiology and Hygiene, Technical University of Dresden, Dresden, Germany
- Alere Technologies GmbH, Jena, Germany
- * E-mail:
| | - Bettina Stieber
- Institute for Medical Microbiology and Hygiene, Technical University of Dresden, Dresden, Germany
- Alere Technologies GmbH, Jena, Germany
| | - Rashida Roberts
- Department of Para-Clinical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Patrick Eberechi Akpaka
- Department of Para-Clinical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
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Monecke S, Baier V, Coombs GW, Slickers P, Ziegler A, Ehricht R. Genome sequencing and molecular characterisation of Staphylococcus aureus ST772-MRSA-V, "Bengal Bay Clone". BMC Res Notes 2013; 6:548. [PMID: 24359724 PMCID: PMC3878137 DOI: 10.1186/1756-0500-6-548] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 12/17/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The PVL-positive ST772-MRSA-V is an emerging community-associated (CA-) MRSA clone that has been named Bengal Bay Clone since most patients have epidemiological connections to the Indian subcontinent. It is found increasingly common in other areas of the world. METHODS One isolate of ST772-MRSA-V was sequenced using the Illumina Genome Analyzer System. After initial assembling the multiple sequence contigs were analysed using different in-house annotation scripts. Results were compared to microarray hybridisation results of clinical isolates of ST772-MRSA-V, of related strains and to another ST772-MRSA-V genome sequence. RESULTS According to MLST e-burst analysis, ST772-MRSA-V belongs to Clonal Complex (CC)1, differing from ST1 only in one MLST allele (pta-22). However, there are several additional differences including agr alleles (group II rather than III), capsule type (5 rather than 8), the presence of the egc enterotoxin gene cluster and of the enterotoxin homologue ORF CM14 as well as the absence of the enterotoxin H gene seh. Enterotoxin genes sec and sel are present. ST772-MRSA-V harbours the genes encoding enterotoxin A (sea) and PVL (lukS/F-PV). Both are located on the same prophage. CONCLUSIONS ST772-MRSA-V may have emerged from the same lineage as globally spread CC1 and CC5 strains. It has acquired a variety of virulence factors, and for a CA-MRSA strain it has an unusually high number of genes associated with antibiotic resistance.
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Affiliation(s)
- Stefan Monecke
- Institute for Medical Microbiology and Hygiene, Technical University of Dresden, Dresden, Germany.
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Monecke S, Ruppelt A, Wendlandt S, Schwarz S, Slickers P, Ehricht R, Jäckel SCD. Genotyping of Staphylococcus aureus isolates from diseased poultry. Vet Microbiol 2013; 162:806-812. [DOI: 10.1016/j.vetmic.2012.10.018] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 08/06/2012] [Accepted: 10/15/2012] [Indexed: 11/17/2022]
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Braun SD, Ziegler A, Methner U, Slickers P, Keiling S, Monecke S, Ehricht R. Fast DNA serotyping and antimicrobial resistance gene determination of salmonella enterica with an oligonucleotide microarray-based assay. PLoS One 2012; 7:e46489. [PMID: 23056321 PMCID: PMC3464306 DOI: 10.1371/journal.pone.0046489] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 09/04/2012] [Indexed: 01/21/2023] Open
Abstract
Salmonellosis caused by Salmonella (S.) belongs to the most prevalent food-borne zoonotic diseases throughout the world. Therefore, serotype identification for all culture-confirmed cases of Salmonella infection is important for epidemiological purposes. As a standard, the traditional culture method (ISO 6579:2002) is used to identify Salmonella. Classical serotyping takes 4–5 days to be completed, it is labor-intensive, expensive and more than 250 non-standardized sera are necessary to characterize more than 2,500 Salmonella serovars currently known. These technical difficulties could be overcome with modern molecular methods. We developed a microarray based serogenotyping assay for the most prevalent Salmonella serovars in Europe and North America. The current assay version could theoretically discriminate 28 O-antigens and 86 H-antigens. Additionally, we included 77 targets analyzing antimicrobial resistance genes. The Salmonella assay was evaluated with a set of 168 reference strains representing 132 serovars previously serotyped by conventional agglutination through various reference centers. 117 of 132 (81%) tested serovars showed an unique microarray pattern. 15 of 132 serovars generated a pattern which was shared by multiple serovars (e.g., S. ser. Enteritidis and S. ser. Nitra). These shared patterns mainly resulted from the high similarity of the genotypes of serogroup A and D1. Using patterns of the known reference strains, a database was build which represents the basis of a new PatternMatch software that can serotype unknown Salmonella isolates automatically. After assay verification, the Salmonella serogenotyping assay was used to identify a field panel of 105 Salmonella isolates. All were identified as Salmonella and 93 of 105 isolates (88.6%) were typed in full concordance with conventional serotyping. This microarray based assay is a powerful tool for serogenotyping.
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Monecke S, Skakni L, Hasan R, Ruppelt A, Ghazal SS, Hakawi A, Slickers P, Ehricht R. Characterisation of MRSA strains isolated from patients in a hospital in Riyadh, Kingdom of Saudi Arabia. BMC Microbiol 2012; 12:146. [PMID: 22823982 PMCID: PMC3464608 DOI: 10.1186/1471-2180-12-146] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 07/02/2012] [Indexed: 11/26/2022] Open
Abstract
Background Methicillin-resistant Staphylococcus aureus (MRSA) is spreading worldwide and poses a serious public health problem, being present in hospital settings and communities. However, from the Middle East and the Arabian Peninsula few molecular typing data on MRSA strains are currently available. In order to obtain data on the population structure of MRSA in Riyadh, Saudi Arabia, 107 clinical and environmental MRSA isolates were genotyped using a microarray-based assay. Results Five major MRSA strains from four clonal complexes were identified CC8/ST239-III (20.75%), PVL-positive as well as -negative CC22-IV (18.87% and 9.43%, respectively), PVL-positive CC30-IV (12.26%) and PVL-positive CC80-IV (17.92%). Minor strains, which accounted for less than 3% each, included CC1-IV/SCCfus, PVL-positive CC1/ST772-V, PVL-positive as well as- negative CC5-IV, CC5-IV/SCCfus, CC5-V, CC6-IV, CC45-IV, PVL-negative CC80-IV, PVL-positive CC88-IV, CC97-V and a CC9/ST834-MRSA strain. Conclusions Typing of MRSA strains from Riyadh revealed a high diversity of clonal complexes. The prevalence of the genes encoding the Panton-Valentine leukocidin was surprisingly high (54.21%), and a significant rate of resistance markers was detected also in strains considered as community-associated.
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Affiliation(s)
- Stefan Monecke
- Institute for Medical Microbiology and Hygiene, Technical University of Dresden, Dresden, Germany.
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Monecke S, Engelmann I, Archambault M, Coleman DC, Coombs GW, Cortez de Jäckel S, Pelletier-Jacques G, Schwarz S, Shore AC, Slickers P, Ehricht R. Distribution of SCCmec-associated phenol-soluble modulin in staphylococci. Mol Cell Probes 2012; 26:99-103. [DOI: 10.1016/j.mcp.2012.01.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 12/16/2011] [Accepted: 01/03/2012] [Indexed: 10/14/2022]
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Monecke S, Coombs G, Shore AC, Coleman DC, Akpaka P, Borg M, Chow H, Ip M, Jatzwauk L, Jonas D, Kadlec K, Kearns A, Laurent F, O'Brien FG, Pearson J, Ruppelt A, Schwarz S, Scicluna E, Slickers P, Tan HL, Weber S, Ehricht R. A field guide to pandemic, epidemic and sporadic clones of methicillin-resistant Staphylococcus aureus. PLoS One 2011; 6:e17936. [PMID: 21494333 PMCID: PMC3071808 DOI: 10.1371/journal.pone.0017936] [Citation(s) in RCA: 625] [Impact Index Per Article: 48.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 02/16/2011] [Indexed: 01/28/2023] Open
Abstract
In recent years, methicillin-resistant Staphylococcus aureus
(MRSA) have become a truly global challenge. In addition to the long-known
healthcare-associated clones, novel strains have also emerged outside of the
hospital settings, in the community as well as in livestock. The emergence and
spread of virulent clones expressing Panton-Valentine leukocidin (PVL) is an
additional cause for concern. In order to provide an overview of pandemic,
epidemic and sporadic strains, more than 3,000 clinical and veterinary isolates
of MRSA mainly from Germany, the United Kingdom, Ireland, France, Malta, Abu
Dhabi, Hong Kong, Australia, Trinidad & Tobago as well as some reference
strains from the United States have been genotyped by DNA microarray analysis.
This technique allowed the assignment of the MRSA isolates to 34 distinct
lineages which can be clearly defined based on non-mobile genes. The results
were in accordance with data from multilocus sequence typing. More than 100
different strains were distinguished based on affiliation to these lineages,
SCCmec type and the presence or absence of PVL. These
strains are described here mainly with regard to clinically relevant
antimicrobial resistance- and virulence-associated markers, but also in relation
to epidemiology and geographic distribution. The findings of the study show a
high level of biodiversity among MRSA, especially among strains harbouring
SCCmec IV and V elements. The data also indicate a high
rate of genetic recombination in MRSA involving SCC elements, bacteriophages or
other mobile genetic elements and large-scale chromosomal replacements.
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Affiliation(s)
- Stefan Monecke
- Institute for Medical Microbiology and Hygiene, Technical University of Dresden, Dresden, Germany.
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Anjum MF, Choudhary S, Morrison V, Snow LC, Mafura M, Slickers P, Ehricht R, Woodward MJ. Identifying antimicrobial resistance genes of human clinical relevance within Salmonella isolated from food animals in Great Britain. J Antimicrob Chemother 2011; 66:550-9. [PMID: 21393227 DOI: 10.1093/jac/dkq498] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES To investigate the occurrence of antimicrobial resistance genes of human clinical relevance in Salmonella isolated from livestock in Great Britain. METHODS Two hundred and twenty-five Salmonella enterica isolates were characterized using an antimicrobial resistance gene chip and disc diffusion assays. Plasmid profiling, conjugation experiments and identification of Salmonella genomic island 1 (SGI1) were performed for selected isolates. RESULTS Approximately 43% of Salmonella harboured single or multiple antimicrobial resistance genes with pig isolates showing the highest numbers where 96% of Salmonella Typhimurium harboured one or more resistance genes. Isolates harbouring multiple resistances divided into three groups. Group 1 isolates harboured ampicillin/streptomycin/sulphonamide/tetracycline resistance and similar phenotypes. This group contained isolates from pigs, cattle and poultry that were from several serovars including Typhimurium, 4,[5],12:i:-, Derby, Ohio and Indiana. All Group 2 isolates were from pigs and were Salmonella Typhimurium. They contained a non-sul-type class 1 integron and up to 13 transferrable resistances. All Group 3 isolates harboured a class 1 integron and were isolated from all animal species included in the study. Most isolates were Salmonella Typhimurium and harboured SGI1. CONCLUSIONS Salmonella isolated from livestock was shown to harbour antimicrobial resistance genes although no or little resistance to third-generation cephalosporins or ciprofloxacin, respectively, was detected. The preponderance in pigs of multidrug-resistant Salmonella Typhimurium makes it important to introduce control measures such as improved biosecurity to ensure that they do not pass through the food chain and limit human therapeutic options.
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Affiliation(s)
- Muna F Anjum
- Department of Bacteriology, Veterinary Laboratories Agency-Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK.
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Monecke S, Kanig H, Rudolph W, Müller E, Coombs G, Hotzel H, Slickers P, Ehricht R. Characterisation of Australian MRSA strains ST75- and ST883-MRSA-IV and analysis of their accessory gene regulator locus. PLoS One 2010; 5:e14025. [PMID: 21103340 PMCID: PMC2984443 DOI: 10.1371/journal.pone.0014025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 10/27/2010] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Community-acquired methicillin-resistant Staphylococcus aureus have become a major problem in Australia. These strains have now been isolated throughout Australia including remote Indigenous communities that have had minimal exposure to healthcare facilities. Some of these strains, belonging to sequence types ST75 and ST883, have previously been reported to harbour highly divergent alleles of the housekeeping genes used in multilocus sequence typing. METHODOLOGY/PRINCIPAL FINDINGS ST75-MRSA-IV and ST883-MRSA-IV isolates were characterised in detail. Morphological features as well as 16S sequences were identical to other S. aureus strains. Although a partial rnpB gene sequence was not identical to previously known S. aureus sequences, it was found to be more closely related to S. aureus than to other staphylococci. Isolates also were screened using diagnostic DNA microarrays. These isolates yielded hybridisation results atypical for S. aureus. Primer directed amplification assays failed to detect species markers (femA, katA, sbi, spa). However, arbitrarily primed amplification indicated the presence of unknown alleles of these genes. Isolates could not be assigned to capsule types 1, 5 or 8. The allelic group of the accessory gene regulator (agr) locus was not determinable. Sequencing of a region of agrB, agrC and agrD (approximately 2,100 bp) revealed a divergent sequence. However, this sequence is more related to S. aureus agr alleles I and IV than to agr sequences from other Staphylococcus species. The predicted auto-inducing peptide (AIP) sequence of ST75 was identical to that of agr group I, while the predicted AIP sequence of ST883 was identical to agr group IV. CONCLUSIONS/SIGNIFICANCE The genetic properties of ST75/ST883-MRSA may be due to a series of evolutionary events in ancient insulated S. aureus strains including a convergent evolution leading to agr group I- or IV-like AIP sequences and a recent acquisition of SCCmec IV elements.
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Affiliation(s)
- Stefan Monecke
- Faculty of Medicine Carl Gustav Carus, Institute for Medical Microbiology and Hygiene, Technical University of Dresden, Dresden, Germany.
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Ruettger A, Feige J, Slickers P, Schubert E, Morré SA, Pannekoek Y, Herrmann B, de Vries HJC, Ehricht R, Sachse K. Genotyping of Chlamydia trachomatis strains from culture and clinical samples using an ompA-based DNA microarray assay. Mol Cell Probes 2010; 25:19-27. [PMID: 20934507 DOI: 10.1016/j.mcp.2010.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 09/26/2010] [Accepted: 09/29/2010] [Indexed: 10/19/2022]
Abstract
Current typing methods of Chlamydia (C.) trachomatis are mainly based on the diversity of the ompA gene, which is coding for the major outer membrane protein A. The present study aimed at facilitating genotyping of strains of this obligate intracellular human pathogen by developing a DNA microarray assay using the ArrayTube™ format for individual samples and the ArrayStrip™ format for higher throughput. The new test is exploiting multiple discriminatory sites by involving a total of 61 oligonucleotide probes representing genotype-specific polymorphisms in variable domains 1, 2 and 4 of the ompA gene. After multiplex amplification of these domains using biotinylated primers, the sample is hybridized in the microarray vessel under highly stringent conditions. The resulting binding pattern is genotype specific, thus allowing direct identification. We were able to show that DNA from each of the currently accepted genotypes (serovars) yielded a unique, theoretically expected and distinct hybridization pattern. The assay was also shown to be highly sensitive as a dilution containing the equivalent of 1 inclusion-forming unit was still correctly genotyped. In addition, when 62 clinical samples were examined and compared to PCR-RFLP typing results, the genotype was correctly identified by the DNA microarray in all cases. The present test is easy to handle and economically affordable, and it allows genotyping of C. trachomatis to be accomplished within a working day, thus lending itself for epidemiological studies and routine diagnosis.
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Affiliation(s)
- Anke Ruettger
- Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany.
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Coombs GW, Monecke S, Ehricht R, Slickers P, Pearson JC, Tan HL, Christiansen KJ, O'Brien FG. Differentiation of clonal complex 59 community-associated methicillin-resistant Staphylococcus aureus in Western Australia. Antimicrob Agents Chemother 2010; 54:1914-21. [PMID: 20211891 PMCID: PMC2863625 DOI: 10.1128/aac.01287-09] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 12/11/2009] [Accepted: 03/01/2010] [Indexed: 11/20/2022] Open
Abstract
Clonal complex 59 (CC59) community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strains were characterized using pulsed-field gel electrophoresis, spa typing, multilocus sequence typing, diagnostic DNA microarrays, and PCRs targeting staphylococcal cassette chromosome mec (SCCmec) elements and Panton-Valentine leukocidin (PVL). Six distinct groups within CC59 were characterized. At least seven different variants of SCCmec elements were identified (IVa [2B], IVb [2B], IVd [2B], IV variant [2B], IVa [2B&5], V variant [5C2], and V [5C2&5]). (The structural type is indicated by a Roman numeral, with a lowercase letter indicating the subtype, and the ccr complex and the mec complex are indicated by an Arabic numeral and an uppercase letter, respectively. Where there is an extra ccr element, this is indicated by "&" and an Arabic numeral designating the ccr type.) The first group is similar to the American sequence type 59 (ST59) MRSA-IV CA-MRSA strain USA1000. The second group includes a PVL-negative ST87 strain with an SCCmec element of subtype IVb (2B). The third group comprises PVL-variable ST59 MRSA-IV strains harboring multiple SCCmec IV subtypes. PVL-negative ST59 MRSA strains with multiple or composite SCCmec elements (IVa [2B&5]) form the fourth group. Group 5 corresponds to the internationally known "Taiwan clone," a PVL-positive strain with a variant SCCmec element (V [5C2&5]). This strain proved to be the most common CC59 MRSA strain isolated in Western Australia. Finally, group 6 encompasses the ST59 MRSA-V variant (5C2). The differentiation of CC59 into groups and strains indicates a rapid evolution and spread of SCCmec elements. Observed differences between groups of strains as well as intrastrain variability within a group facilitate the tracing of their spread.
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Affiliation(s)
- Geoffrey W Coombs
- Department of Microbiology and Infectious Diseases, PathWest Laboratory Medicine WA, Royal Perth Hospital, Perth, Western Australia, Australia.
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Luedicke C, Slickers P, Ehricht R, Monecke S. Molecular fingerprinting of Staphylococcus aureus from bone and joint infections. Eur J Clin Microbiol Infect Dis 2010; 29:457-63. [PMID: 20186451 DOI: 10.1007/s10096-010-0884-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2009] [Accepted: 01/31/2010] [Indexed: 11/25/2022]
Abstract
The objective of the study was to determine if a clonal complex (CC) of Staphylococcus aureus or certain virulence and adhesion factors were associated with infections of bones and prosthetic implants. One hundred and nineteen isolates were characterised using microarrays. There was no evidence for a single virulence factor or CC being causative for bone and implant infections. Isolates belonged to 20 different CCs, with CC8 (19.33%), CC45 (17.65%) and CC30 (12.61%) being dominant. Population structure and the relative abundances of virulence genes was similar to previously described isolates from healthy carriers. Differences to carrier isolates included a higher proportion of CC45, a lower proportion of CC15, as well as a higher abundance of sak (staphylokinase) among patient isolates. For 23 patients with infections of total knee or hip prosthetics, it was possible to simultaneously obtain nasal swabs. Fifteen (65.2%) carried S. aureus in their anterior nares. In nine of them (39.1%), isolates from the infection site were identical to carriage isolates. This suggests an elevated risk of infection for S. aureus carriers and the possibility of endogenous infection in a high proportion of them. Therefore, the pre-operative screening and eradication of S. aureus in patients receiving total joint prosthetics should be considered.
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Affiliation(s)
- C Luedicke
- Medical Clinic and Policlinic I, University Hospital Dresden, Dresden, Germany
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Scicluna EA, Shore AC, Thürmer A, Ehricht R, Slickers P, Borg MA, Coleman DC, Monecke S. Characterisation of MRSA from Malta and the description of a Maltese epidemic MRSA strain. Eur J Clin Microbiol Infect Dis 2009; 29:163-70. [PMID: 19911206 DOI: 10.1007/s10096-009-0834-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Accepted: 10/17/2009] [Indexed: 01/09/2023]
Abstract
Malta has one of the highest prevalence rates of methicillin-resistant Staphylococcus aureus (MRSA) in Europe. However, only limited typing data are currently available. In order to address this situation, 45 MRSA isolates from the Mater Dei Hospital in Msida, Malta, were characterised using DNA microarrays. The most common strain was ST22-MRSA-IV (UK-EMRSA-15, 30 isolates). Sporadic strains included ST36-MRSA-II (UK-EMRSA-16, two isolates), PVL-positive ST80-MRSA-IV (European Clone, one isolate), ST228-MRSA-I (Italian Clone/South German Epidemic Strain, one isolate) and ST239-MRSA-III (Vienna/Hungarian/Brazilian Epidemic Strain, one isolate). Ten MRSA isolates belonged to a clonal complex (CC) 5/ST149, spa type t002 strain. This strain harboured an SCCmec IV element (mecA, delta mecR, ugpQ, dcs, ccrA2 and ccrB2), as well as novel alleles of ccrA/B and the fusidic acid resistance element Q6GD50 (previously described in the sequenced strain MSSA476, BX571857.1:SAS0043). It also carried the gene for enterotoxin A (sea) and the egc enterotoxin locus, as well as (in nine out of ten isolates) genes encoding the toxic shock syndrome toxin (tst1) and enterotoxins C and L (sec, sel). While the presence of the other MRSA strains suggests foreign importation due to travel between Malta and other European countries, the CC5/t002 strain appears, so far, to be restricted to Malta.
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Affiliation(s)
- E A Scicluna
- Infection Control Unit, Mater Dei Hospital, Msida, Malta
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Monecke S, Ehricht R, Slickers P, Wiese N, Jonas D. Intra-strain variability of methicillin-resistant Staphylococcus aureus strains ST228-MRSA-I and ST5-MRSA-II. Eur J Clin Microbiol Infect Dis 2009; 28:1383-90. [DOI: 10.1007/s10096-009-0796-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Accepted: 07/24/2009] [Indexed: 11/28/2022]
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Monecke S, Ehricht R, Slickers P, Tan HL, Coombs G. The molecular epidemiology and evolution of the Panton–Valentine leukocidin-positive, methicillin-resistant Staphylococcus aureus strain USA300 in Western Australia. Clin Microbiol Infect 2009; 15:770-6. [DOI: 10.1111/j.1469-0691.2009.02792.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Monecke S, Luedicke C, Slickers P, Ehricht R. Molecular epidemiology of Staphylococcus aureus in asymptomatic carriers. Eur J Clin Microbiol Infect Dis 2009; 28:1159-65. [DOI: 10.1007/s10096-009-0752-2] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Accepted: 04/22/2009] [Indexed: 11/25/2022]
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Sachse K, Laroucau K, Vorimore F, Magnino S, Feige J, Müller W, Kube S, Hotzel H, Schubert E, Slickers P, Ehricht R. DNA microarray-based genotyping of Chlamydophila psittaci strains from culture and clinical samples. Vet Microbiol 2008; 135:22-30. [PMID: 18950965 DOI: 10.1016/j.vetmic.2008.09.041] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The avian and human pathogen Chlamydophila (C.) psittaci represents a genetically heterogeneous species. To facilitate epidemiological surveys, more rapid yet highly specific molecular tests are needed. Currently used typing methods, i.e. serotyping and PCR-RFLP, have only limited sensitivity and are incapable of covering the wide spectrum of naturally occurring types of C. psittaci strains. In the present study, a new DNA microarray assay based on the ArrayTube (AT) technology was used to genotype C. psittaci in 98 isolates and 23 clinical tissue samples. The present array carries 35 oligonucleotide probes derived from variable domains 2 and 4 of the ompA gene. The assay proved highly sensitive, allowing correct genotyping of DNA from 2 inclusion-forming units. The results of DNA microarray genotyping of cultured strains proved highly concordant with the data from PCR-RFLP typing and serotyping. Sequencing of the ompA gene served as the reference test to verify the accuracy of AT genotyping results. In 15 instances (15.3%), strains were successfully typed by the AT assay, while serotyping and/or PCR-RFLP genotyping failed to produce unambiguous results. Eleven of these samples were ompA sequenced to confirm the AT findings. In addition to the currently accepted nine ompA genotypes, the microarray test was shown to recognise new provisional genotypes, such as Mat116 and YP84. In conclusion, the new AT assay proved to be suitable for rapid, sensitive and reproducible genotyping of C. psittaci strains and can be recommended for routine diagnosis.
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Affiliation(s)
- Konrad Sachse
- Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Institute of Molecular Pathogenesis, Jena, Germany.
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Monecke S, Slickers P, Ehricht R. Assignment of Staphylococcus aureus isolates to clonal complexes based on microarray analysis and pattern recognition. ACTA ACUST UNITED AC 2008; 53:237-51. [PMID: 18507678 DOI: 10.1111/j.1574-695x.2008.00426.x] [Citation(s) in RCA: 237] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A DNA microarray was designed for the rapid genotyping of Staphylococcus aureus. It covers 185 distinct genes and about 300 alleles thereof, including species-specific controls, accessory gene regulator (agr) alleles, genes encoding virulence factors, and microbial surface components recognizing adhesive matrix molecules, capsule type-specific genes, as well as resistance determinants. It was used to examine 100 clinical isolates and reference strains. Relationships of leukocidin and ssl/set (staphylococcal superantigen-like or exotoxin-like) genes were reviewed considering these experimental results as well as published sequences. A good correlation of overall hybridization pattern and multilocus sequence typing was found. Analysis of hybridization profiles thus allowed not only to assess virulence and drug resistance, but also to assign isolates to strains and to clonal complexes. Hybridization data were used to construct a split network tree and to analyse relationships between strains. Allelic variations of a number of genes indicate a division of S. aureus into three major branches that are not in accordance to agr group or capsule-type affiliations. Additionally, there are some isolated lineages, such as ST75, ST93, or ST152. These strains produce aberrant hybridization profiles, indicating that only a part of the gene pool of S. aureus has been investigated yet.
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Affiliation(s)
- Stefan Monecke
- Institute for Medical Microbiology and Hygiene, Faculty of Medicine Carl Gustav Carus, Technical University of Dresden, Dresden, Germany.
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Monecke S, Jatzwauk L, Weber S, Slickers P, Ehricht R. DNA microarray-based genotyping of methicillin-resistant Staphylococcus aureus strains from Eastern Saxony. Clin Microbiol Infect 2008; 14:534-45. [PMID: 18373691 DOI: 10.1111/j.1469-0691.2008.01986.x] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A diagnostic microarray was used to characterise a collection of methicillin-resistant Staphylococcus aureus (MRSA) isolates from hospitals in the German region of Eastern Saxony. The most abundant epidemic MRSA (EMRSA) strains were ST5-MRSA II (Rhine-Hesse EMRSA, EMRSA-3), CC5/ST228-MRSA I (South German EMRSA), ST22-MRSA IV (Barnim EMRSA, EMRSA-15) and ST45-MRSA IV (Berlin EMRSA). Other strains were found only as sporadic isolates or in minor outbreaks. These strains included ST1-MRSA IV, ST8-MRSA IV (Hannover EMRSA and others), clonal group 5 strains carrying SCCmec type IV elements (Paediatric clone), ST45-MRSA V, CC8/ST239-MRSA III and ST398-MRSA V. Panton-Valentine leukocidin-positive MRSA isolates were still very rare. The predominant strain was ST80-MRSA IV, although increasing numbers of different strains have recently been detected (ST8-MRSA IV, ST30-MRSA IV and ST59-MRSA V). For more common MRSA strains, it was possible to detect variants that differed mainly in the carriage of additional resistance determinants and certain virulence-associated genes. Detection of such variants can sometimes allow epidemic strains to be resolved beyond spa types to a hospital-specific level, which is of significant value for epidemiological purposes.
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Affiliation(s)
- S Monecke
- Institute for Medical Microbiology and Hygiene, Faculty of Medicine Carl Gustav Carus, Technical University of Dresden, Dresden, Germany.
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Monecke S, Slickers P, Ellington MJ, Kearns AM, Ehricht R. High diversity of Panton-Valentine leukocidin-positive, methicillin-susceptible isolates of Staphylococcus aureus and implications for the evolution of community-associated methicillin-resistant S. aureus. Clin Microbiol Infect 2007; 13:1157-64. [PMID: 17949441 DOI: 10.1111/j.1469-0691.2007.01833.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In total, 100 Staphylococcus aureus isolates from diverse cases of skin and soft-tissue infection at a university hospital in Saxony, Germany, were characterised using diagnostic microarrays. Virulence factors, including Panton-Valentine leukocidin (PVL), were detected and the isolates were assigned to clonal groups. Thirty isolates were positive for the genes encoding PVL. Only three PVL-positive methicillin-resistant S. aureus (MRSA) isolates were found, two of which belonged to European clone ST80-MRSA IV and one to USA300 strain ST8-MRSA IV. The remaining methicillin-susceptible PVL-positive isolates belonged to a variety of different multilocus sequence types. The predominant strains were agrI/ST22, agrII/CC5, agrIII/CC30 and agrIV/ST121. In order to check for possible bias caused by regional or local outbreak strains, an additional 18 methicillin-susceptible, PVL-positive isolates from the UK were tested. Approximately two-thirds of the UK isolates belonged to types that also comprised approximately two-thirds of the isolates from Saxony. Some methicillin-susceptible PVL-positive isolates (agrI/ST152, agrIII/ST80 and agrIII/ST96) closely resembled known epidemic community-acquired MRSA (CaMRSA) strains. These findings indicate that the current rise in PVL-positive CaMRSA could be caused by the dissemination of novel SCCmec elements among pre-existing PVL-positive strains, rather than by the spread of PVL phages among MRSA strains.
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Affiliation(s)
- S Monecke
- Institute for Medical Microbiology and Hygiene, Faculty of Medicine Carl Gustav Carus, Technical University of Dresden, Dresden, Germany.
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Anjum MF, Mafura M, Slickers P, Ballmer K, Kuhnert P, Woodward MJ, Ehricht R. Pathotyping Escherichia coli by using miniaturized DNA microarrays. Appl Environ Microbiol 2007; 73:5692-7. [PMID: 17630299 PMCID: PMC2042074 DOI: 10.1128/aem.00419-07] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The detection of virulence determinants harbored by pathogenic Escherichia coli is important for establishing the pathotype responsible for infection. A sensitive and specific miniaturized virulence microarray containing 60 oligonucleotide probes was developed. It detected six E. coli pathotypes and will be suitable in the future for high-throughput use.
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Affiliation(s)
- Muna F Anjum
- Department of Food and Environmental Safety, Veterinary Laboratories Agency-Weybridge, New Haw, Addlestone, Surrey KT15 3NB, United Kingdom.
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Borel N, Kempf E, Hotzel H, Schubert E, Torgerson P, Slickers P, Ehricht R, Tasara T, Pospischil A, Sachse K. Direct identification of chlamydiae from clinical samples using a DNA microarray assay: a validation study. Mol Cell Probes 2007; 22:55-64. [PMID: 17714911 DOI: 10.1016/j.mcp.2007.06.003] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Revised: 06/19/2007] [Accepted: 06/21/2007] [Indexed: 11/24/2022]
Abstract
While DNA microarrays have become a widely accepted tool for mRNA expression monitoring, their use in rapid diagnosis of bacterial and viral pathogens is only emerging. So far, insufficient sensitivity and high costs have been the major limiting factors preventing more widespread use of microarray platforms in direct testing of clinical samples. In the present study, a total of 339 samples, among them 293 clinical specimens from animals and humans, were examined by the ArrayTube (AT) DNA microarray assay to detect chlamydial DNA and identify the species of Chlamydia and Chlamydophila involved. Samples included nasal and conjunctival swabs, formalin-fixed, paraffin-embedded and fresh organ tissue, milk, feces and cell culture. Notably, the AT test was shown to detect mixed infections in clinical samples. The calculated median sensitivity of 0.81 over the entire panel of clinical samples was comparable to conventional 16S PCR, but slightly lower than real-time PCR and other PCR assays. However, when a panel of long-time stored swab samples was excluded from the calculation, the sensitivity was clearly higher (0.87) and equivalent to that of real-time PCR. Altogether, the data demonstrate the suitability of this DNA microarray assay for routine diagnosis.
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Affiliation(s)
- Nicole Borel
- Institute of Veterinary Pathology, University of Zurich, Switzerland
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Monecke S, Kuhnert P, Hotzel H, Slickers P, Ehricht R. Microarray based study on virulence-associated genes and resistance determinants of Staphylococcus aureus isolates from cattle. Vet Microbiol 2007; 125:128-40. [PMID: 17614219 DOI: 10.1016/j.vetmic.2007.05.016] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Revised: 04/12/2007] [Accepted: 05/10/2007] [Indexed: 11/26/2022]
Abstract
Staphylococcus aureus is a common pathogen which can colonise and infect not only man, but also domestic animals. Especially, infection of cattle is of high economic relevance as S. aureus is an important causal agent of bovine mastitis. In the present contribution, a DNA microarray was applied for the study of 144 different gene targets, including resistance genes and genes encoding exotoxins, in S. aureus isolated from cows. One hundred and twenty-eight isolates from Germany and Switzerland were tested. These isolates were assigned to 20 different strains and nine clonal complexes. The majority of isolates belonged either to apparently closely related clonal complexes 8, 25, and 97 (together 34.4%) or were related to the sequenced bovine strain RF122 (48.4%). Notable characteristics of S. aureus of bovine origin are the carriage of intact haemolysin beta (in 82% of isolates tested), the absence of staphylokinase (in 89.1%), the presence of allelic variants of several exotoxins such as toxic shock syndrome toxin and enterotoxin N, and the occurrence of the leukocidin lukF-P83/lukM (in 53.1%). Two isolates were methicillin-resistant S. aureus (MRSA). One of them was a clonal complex 8 MRSA related to the epidemic MRSA strain Irish 01. The other one belonged to ST398/spa-type 34 resembling a newly emerging MRSA strain which has been described to occur in humans as well as in domestic animals. The presence of these two strains highlights the possibility of transfers of S. aureus strains between different host species.
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Affiliation(s)
- Stefan Monecke
- Institute for Medical Microbiology and Hygiene, Faculty of Medicine, Carl Gustav Carus at the Technical University of Dresden, Fetscherstrasse 74, D-01307, Dresden, Germany.
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Wiehlmann L, Wagner G, Cramer N, Siebert B, Gudowius P, Morales G, Köhler T, van Delden C, Weinel C, Slickers P, Tümmler B. Population structure of Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2007; 104:8101-6. [PMID: 17468398 PMCID: PMC1876578 DOI: 10.1073/pnas.0609213104] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The metabolically versatile Gram-negative bacterium Pseudomonas aeruginosa inhabits terrestrial, aquatic, animal-, human-, and plant-host-associated environments and is an important causative agent of nosocomial infections, particularly in intensive-care units. The population genetics of P. aeruginosa was investigated by an approach that is generally applicable to the rapid, robust, and informative genotyping of bacteria. DNA, amplified from the bacterial colony by circles of multiplex primer extension, is hybridized onto a microarray to yield an electronically portable binary multimarker genotype that represents the core genome by single nucleotide polymorphisms and the accessory genome by markers of genomic islets and islands. The 240 typed P. aeruginosa strains of diverse habitats and geographic origin segregated into two large nonoverlapping clusters and 45 isolated clonal complexes with few or no partners. The majority of strains belonged to few dominant clones widespread in disease and environmental habitats. The most frequent genotype was represented by the sequenced strain PA14. Core and accessory genome were found to be nonrandomly assembled in P. aeruginosa. Individual clones preferred a specific repertoire of accessory segments. Even the most promiscuous genomic island, pKLC102, had integrated preferentially into a subset of clones. Moreover, some physically distant loci of the core genome, including oriC, showed nonrandom associations of genotypes, whereas other segments in between were freely recombining. Thus, the P. aeruginosa genome is made up of clone-typical segments in core and accessory genome and of blocks in the core with unrestricted gene flow in the population.
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Affiliation(s)
- Lutz Wiehlmann
- *Klinische Forschergruppe, OE 6710, Medizinische Hochschule Hannover, Carl-Neuberg Strasse 1, D-30625 Hannover, Germany
- To whom correspondence may be addressed. E-mail: or
| | - Gerd Wagner
- CLONDIAG Chip Technologies GmbH, Löbstedter Strasse 103–105, D-07749 Jena, Germany
| | - Nina Cramer
- *Klinische Forschergruppe, OE 6710, Medizinische Hochschule Hannover, Carl-Neuberg Strasse 1, D-30625 Hannover, Germany
| | - Benny Siebert
- *Klinische Forschergruppe, OE 6710, Medizinische Hochschule Hannover, Carl-Neuberg Strasse 1, D-30625 Hannover, Germany
| | - Peter Gudowius
- *Klinische Forschergruppe, OE 6710, Medizinische Hochschule Hannover, Carl-Neuberg Strasse 1, D-30625 Hannover, Germany
| | - Gracia Morales
- Departamento de Biotecnologia Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, Campus Universidad Autónoma de Madrid, Cantoblanco, E-28049 Madrid, Spain
| | - Thilo Köhler
- Département de Microbiologie et de Médecine Moléculaire, Centre Medical Universitaire, Université de Genève, 9 Avenue Champel, CH-1211 Geneva, Switzerland; and
| | - Christian van Delden
- Département de Microbiologie et de Médecine Moléculaire, Centre Medical Universitaire, Université de Genève, 9 Avenue Champel, CH-1211 Geneva, Switzerland; and
- Service des Maladies Infectieuses, Hôpital Universitaire de Genève, Rue Micheli-du-Crest 24, CH-1211 Geneva 14, Switzerland
| | - Christian Weinel
- *Klinische Forschergruppe, OE 6710, Medizinische Hochschule Hannover, Carl-Neuberg Strasse 1, D-30625 Hannover, Germany
| | - Peter Slickers
- CLONDIAG Chip Technologies GmbH, Löbstedter Strasse 103–105, D-07749 Jena, Germany
| | - Burkhard Tümmler
- *Klinische Forschergruppe, OE 6710, Medizinische Hochschule Hannover, Carl-Neuberg Strasse 1, D-30625 Hannover, Germany
- To whom correspondence may be addressed. E-mail: or
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Monecke S, Berger-Bächi B, Coombs G, Holmes A, Kay I, Kearns A, Linde HJ, O'Brien F, Slickers P, Ehricht R. Comparative genomics and DNA array-based genotyping of pandemic Staphylococcus aureus strains encoding Panton-Valentine leukocidin. Clin Microbiol Infect 2007; 13:236-49. [PMID: 17391377 DOI: 10.1111/j.1469-0691.2006.01635.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Within the last few years, methicillin-resistant Staphylococcus aureus (MRSA) strains encoding Panton-Valentine leukocidin (PVL) have emerged and spread worldwide. This epidemic can be attributed to a small number of distinct clones. The present study used a novel assay, based on multiplex linear DNA amplification and subsequent microarray hybridisation, to simultaneously detect all relevant exotoxins, antimicrobial resistance determinants and the allelic variants of agr. The genes of the staphylococcal exotoxin-like (set) locus were also included for typing purposes. This assay, together with multilocus sequence typing (MLST) and spa typing, was applied to 56 clinical isolates and reference strains representing all major pandemic PVL-MRSA lineages, as well as to phylogenetically-related strains and putative ancestors. Array hybridisation results allowed the assignment of isolates to clonal groups, which were in accordance with MLST and spa typing data. Ten distinct clonal groups of PVL-MRSA (ST1, ST5, ST8, ST22, ST30, ST59/359, ST80/583, ST88, ST93 and ST152), including 12 MLST types, were identified and analysed with regard to resistance determinants and genes coding for exotoxins. The array hybridisation data confirmed that pandemic PVL-positive strains originate from very diverse genetic backgrounds, and provided insights into the evolution of some lineages. The DNA microarray technique provides a valuable epidemiological tool for the detailed characterisation of clinical isolates and comparison of strains at a global level.
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Affiliation(s)
- S Monecke
- Institute for Medical Microbiology and Hygiene, Faculty of Medicine Carl Gustav Carus, Technical University of Dresden, Dresden, Germany.
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Ballmer K, Korczak BM, Kuhnert P, Slickers P, Ehricht R, Hächler H. Fast DNA serotyping of Escherichia coli by use of an oligonucleotide microarray. J Clin Microbiol 2006; 45:370-9. [PMID: 17108073 PMCID: PMC1829071 DOI: 10.1128/jcm.01361-06] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Classical antibody-based serotyping of Escherichia coli is an important method in diagnostic microbiology for epidemiological purposes, as well as for a rough virulence assessment. However, serotyping is so tedious that its use is restricted to a few reference laboratories. To improve this situation we developed and validated a genetic approach for serotyping based on the microarray technology. The genes encoding the O-antigen flippase (wzx) and the O-antigen polymerase (wzy) were selected as target sequences for the O antigen, whereas fliC and related genes, which code for the flagellar monomer, were chosen as representatives for the H phenotype. Starting with a detailed bioinformatic analysis and oligonucleotide design, an ArrayTube-based assay was established: a fast and robust DNA extraction method was coupled with a site-specific, linear multiplex labeling procedure and hybridization analysis of the biotinylated amplicons. The microarray contained oligonucleotide DNA probes, each in duplicate, representing 24 of the epidemiologically most relevant of the over 180 known O antigens (O antigens 4, 6 to 9, 15, 26, 52, 53, 55, 79, 86, 91, 101, 103, 104, 111, 113, 114, 121, 128, 145, 157, and 172) as well as 47 of the 53 different H antigens (H antigens 1 to 12, 14 to 16, 18 to 21, 23 to 34, 37 to 43, 45, 46, 48, 49, 51 to 54, and 56). Evaluation of the microarray with a set of defined strains representing all O and H serotypes covered revealed that it has a high sensitivity and a high specificity. All of the conventionally typed 24 O groups and all of the 47 H serotypes were correctly identified. Moreover, strains which were nonmotile or nontypeable by previous serotyping assays yielded unequivocal results with the novel ArrayTube assay, which proved to be a valuable alternative to classical serotyping, allowing processing of single colonies within a single working day.
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Affiliation(s)
- Karin Ballmer
- Institute of Veterinary Bacteriology, NENT, Vetsuisse-Faculty, University of Berne, Berne, Switzerland
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47
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Monecke S, Slickers P, Hotzel H, Richter-Huhn G, Pohle M, Weber S, Witte W, Ehricht R. Microarray-based characterisation of a Panton-Valentine leukocidin-positive community-acquired strain of methicillin-resistant Staphylococcus aureus. Clin Microbiol Infect 2006; 12:718-28. [PMID: 16842566 DOI: 10.1111/j.1469-0691.2006.01420.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent years have witnessed the emergence of novel methicillin-resistant Staphylococcus aureus (MRSA) strains that produce the potent toxin Panton-Valentine leukocidin (PVL). PVL-positive strains can cause complicated skin infections or necrotising pneumonia with high mortality, and these strains have the potential for epidemic spread in the community. In 2004-2005, two case clusters and two isolated cases were observed in eastern Saxony and southern Brandenburg. These were the first known infections with PVL-positive community-acquired MRSA (caMRSA) in this part of Germany. The isolates belonged to agr type III, spa type 44 or spa type 131, and showed a SmaI macrorestriction pattern that corresponded to caMRSA of clonal group ST80. The isolates were susceptible to levofloxacin, macrolides, clindamycin, gentamicin and vancomycin. Most isolates showed resistance to tetracycline and fusidic acid because of the presence of the tetK and far1 genes. A novel plasmid (designated pUB102) harbouring far1, tetK and blaZ was characterised and partially sequenced. Microarray analysis revealed that the caMRSA isolates harboured genes encoding several bi-component toxins (lukF/S-PVL, lukD/E, lukS/F plus hlgA, and another putative leukocidin homologue). Neither tst1 nor genes for enterotoxins A-Y were detected, but the isolates harboured several staphylococcal enterotoxin-like toxin genes (set genes), as well as genes encoding an epidermal cell differentiation inhibitor (edinB) and exfoliative toxin D (etD). Comparative analysis of other isolates from Australia, Germany, Switzerland and the UK showed that these isolates were representative of a widespread clone of caMRSA.
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Affiliation(s)
- S Monecke
- Institute for Medical Microbiology and Hygiene, Faculty of Medicine, Carl Gustav Carus at the Technical University of Dresden, Dresden, Germany.
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Ehricht R, Hotzel H, Sachse K, Slickers P. Residual DNA in thermostable DNA polymerases - a cause of irritation in diagnostic PCR and microarray assays. Biologicals 2006; 35:145-7. [PMID: 16905333 DOI: 10.1016/j.biologicals.2006.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2006] [Revised: 04/13/2006] [Accepted: 04/25/2006] [Indexed: 10/24/2022] Open
Abstract
In a validation trial of a DNA microarray test for chlamydiae we repeatedly observed false-positive PCR amplicons from truly negative samples and non-template controls. Various PCR tests, microarray hybridization and DNA sequencing, revealed that residual Escherichia coli DNA from thermostable DNA polymerases was the cause of this cross-reaction. A subsequent survey showed that only five out of 23 commercial polymerases were free of E. coli DNA. When designing generic oligonucleotide sequences for PCR and PCR microarray-based assays one should be aware of such possible internal contamination, particularly when the target organism is E. coli.
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Affiliation(s)
- Ralf Ehricht
- CLONDIAG chip technologies GmbH, Loebstedter Strasse 103-105, 07749 Jena, Germany.
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49
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Schüler S, Wenz I, Wiederanders B, Slickers P, Ehricht R. An alternative method to amplify RNA without loss of signal conservation for expression analysis with a proteinase DNA microarray in the ArrayTube format. BMC Genomics 2006; 7:144. [PMID: 16768788 PMCID: PMC1526438 DOI: 10.1186/1471-2164-7-144] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2006] [Accepted: 06/12/2006] [Indexed: 11/30/2022] Open
Abstract
Background Recent developments in DNA microarray technology led to a variety of open and closed devices and systems including high and low density microarrays for high-throughput screening applications as well as microarrays of lower density for specific diagnostic purposes. Beside predefined microarrays for specific applications manufacturers offer the production of custom-designed microarrays adapted to customers' wishes. Array based assays demand complex procedures including several steps for sample preparation (RNA extraction, amplification and sample labelling), hybridization and detection, thus leading to a high variability between several approaches and resulting in the necessity of extensive standardization and normalization procedures. Results In the present work a custom designed human proteinase DNA microarray of lower density in ArrayTube® format was established. This highly economic open platform only requires standard laboratory equipment and allows the study of the molecular regulation of cell behaviour by proteinases. We established a procedure for sample preparation and hybridization and verified the array based gene expression profile by quantitative real-time PCR (QRT-PCR). Moreover, we compared the results with the well established Affymetrix microarray. By application of standard labelling procedures with e.g. Klenow fragment exo-, single primer amplification (SPA) or In Vitro Transcription (IVT) we noticed a loss of signal conservation for some genes. To overcome this problem we developed a protocol in accordance with the SPA protocol, in which we included target specific primers designed individually for each spotted oligomer. Here we present a complete array based assay in which only the specific transcripts of interest are amplified in parallel and in a linear manner. The array represents a proof of principle which can be adapted to other species as well. Conclusion As the designed protocol for amplifying mRNA starts from as little as 100 ng total RNA, it presents an alternative method for detecting even low expressed genes by microarray experiments in a highly reproducible and sensitive manner. Preservation of signal integrity is demonstrated out by QRT-PCR measurements. The little amounts of total RNA necessary for the analyses make this method applicable for investigations with limited material as in clinical samples from, for example, organ or tumour biopsies. Those are arguments in favour of the high potential of our assay compared to established procedures for amplification within the field of diagnostic expression profiling. Nevertheless, the screening character of microarray data must be mentioned, and independent methods should verify the results.
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Affiliation(s)
- Susann Schüler
- Institute of Biochemistry, Klinikum, Friedrich-Schiller-Universität Jena, Germany
| | - Ingrid Wenz
- Institute of Biochemistry, Klinikum, Friedrich-Schiller-Universität Jena, Germany
| | - B Wiederanders
- Institute of Biochemistry, Klinikum, Friedrich-Schiller-Universität Jena, Germany
| | - P Slickers
- Clondiag chip technologies GmbH Jena, Germany
| | - R Ehricht
- Clondiag chip technologies GmbH Jena, Germany
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Sachse K, Hotzel H, Slickers P, Ehricht R. The use of DNA microarray technology for detection and genetic characterisation of chlamydiae. Dev Biol (Basel) 2006; 126:203-10; discussion 326-7. [PMID: 17058496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Due to its highly parallel approach, DNA microarray technology opens up new possibilities that may be particularly beneficial for laboratory diagnosis of infectious diseases. We developed a microarray assay for detection and differentiation of all currently defined chlamydial species belonging to the genera Chlamydia and Chlamydophila using the ArrayTube system, which we found to be particularly user-friendly and economical. The test includes PCR amplification of a 23S rDNA target region with concurrent biotinylation and subsequent hybridisation in the ArrayTube, a micro-reaction tube carrying the microarray chip on the bottom. In addition to high specificity, the assay was shown to allow detection and genetic characterisation of single PCR-amplifiable target DNA copies.
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Affiliation(s)
- K Sachse
- Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Institute of Bacterial Infections and Zoonoses, Jena, Germany.
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