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Croucher NJ, Hanage WP, Harris SR, McGee L, van der Linden M, de Lencastre H, Sá-Leão R, Song JH, Ko KS, Beall B, Klugman KP, Parkhill J, Tomasz A, Kristinsson KG, Bentley SD. Variable recombination dynamics during the emergence, transmission and 'disarming' of a multidrug-resistant pneumococcal clone. BMC Biol 2014; 12:49. [PMID: 24957517 PMCID: PMC4094930 DOI: 10.1186/1741-7007-12-49] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 06/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pneumococcal β-lactam resistance was first detected in Iceland in the late 1980s, and subsequently peaked at almost 25% of clinical isolates in the mid-1990s largely due to the spread of the internationally-disseminated multidrug-resistant PMEN2 (or Spain6B-2) clone of Streptococcus pneumoniae. RESULTS Whole genome sequencing of an international collection of 189 isolates estimated that PMEN2 emerged around the late 1960s, developing resistance through multiple homologous recombinations and the acquisition of a Tn5253-type integrative and conjugative element (ICE). Two distinct clades entered Iceland in the 1980s, one of which had acquired a macrolide resistance cassette and was estimated to have risen sharply in its prevalence by coalescent analysis. Transmission within the island appeared to mainly emanate from Reykjavík and the Southern Peninsular, with evolution of the bacteria effectively clonal, mainly due to a prophage disrupting a gene necessary for genetic transformation in many isolates. A subsequent decline in PMEN2's prevalence in Iceland coincided with a nationwide campaign that reduced dispensing of antibiotics to children in an attempt to limit its spread. Specific mutations causing inactivation or loss of ICE-borne resistance genes were identified from the genome sequences of isolates that reverted to drug susceptible phenotypes around this time. Phylogenetic analysis revealed some of these occurred on multiple occasions in parallel, suggesting they may have been at least temporarily advantageous. However, alteration of 'core' sequences associated with resistance was precluded by the absence of any substantial homologous recombination events. CONCLUSIONS PMEN2's clonal evolution was successful over the short-term in a limited geographical region, but its inability to alter major antigens or 'core' gene sequences associated with resistance may have prevented persistence over longer timespans.
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Affiliation(s)
- Nicholas J Croucher
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, 677 Huntington Avenue, Boston MA 02115, USA
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Infectious Disease Epidemiology, Imperial College, Norfolk Place, London W2 1NY, UK
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, 677 Huntington Avenue, Boston MA 02115, USA
| | - Simon R Harris
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mark van der Linden
- Institute for Medical Microbiology, National Reference Center for Streptococci, University Hospital, RWTH Aachen, Pauwelsstrasse 30, Aachen, Germany
| | - Herminia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Microbiology, The Rockefeller University, New York, New York, USA
| | - Raquel Sá-Leão
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Jae-Hoon Song
- Samsung Medical Centre, Sungkyunkwan University School of Medicine and Asia Pacific Foundation for Infectious Disease, Seoul, South Korea
| | - Kwan Soo Ko
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Bernard Beall
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health and Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, Georgia, USA
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Gauteng, South Africa
| | - Julian Parkhill
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Alexander Tomasz
- Laboratory of Microbiology, The Rockefeller University, New York, New York, USA
| | - Karl G Kristinsson
- Clinical Microbiology Department, Landspitali University Hospital and University of Iceland, Reykjavík, Iceland
| | - Stephen D Bentley
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0SP, UK
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Marchese A, Mannelli S, Tonoli E, Gorlero F, Toni M, Schito GC. Prevalence of antimicrobial resistance in Streptococcus pneumoniae circulating in Italy: results of the Italian Epidemiological Observatory Survey (1997-1999). Microb Drug Resist 2002; 7:277-87. [PMID: 11759090 DOI: 10.1089/10766290152652837] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Italian Epidemiological Observatory (IEO), a surveillance program supported by the SmithKline Foundation, analyzed the susceptibility of 2,664 community-acquired respiratory Streptococcus pneumoniae derived from over 50 clinical microbiology laboratories during 1997-1999, against 21 antibiotics adopting a quantitative methodology. Throughout these years, total penicillin resistance varied from 14.3% to 10.2%. High-level resistance has remained stable, ranging from 3.8% to 4.1%, while a decrease in low-level resistance (from 10.3% to 6.1%) has been recorded. Lack of susceptibility to macrolides ranged from 29.1% in 1997 to 25.5% in 1999. Similar figures have also been observed with tetracycline and co-trimoxazole (rates of resistance around 30%). As expected, large geographical variations in resistance rates were found for all drugs. Amoxicillin and amoxicillin-clavulanate were 100% active on penicillin-intermediate isolates. Injectable third-generation cephalosporins and carbapenems were also capable of inhibiting a large proportion of these microorganisms. Rifampin was the most potent non-beta-lactam compound tested. In contrast to the situation prevailing elsewhere, in Italian children (aged 0-5 years) presenting with respiratory conditions, the total rate of penicillin resistance (3%) was lower than that shown by the adult population (10.9%). However, lack of susceptibility to macrolides, tetracycline, and cotrimoxazole (35%, 41%, 44%) was more incident in pediatric than in adult patients (25%, 26%, 28% respectively). Strains recovered from blood in 1999 (67) were much more susceptible to penicillin (98.5%) than respiratory pneumococci (89.8%), whereas macrolides, tetracycline, and cotrimoxazole were consistently less active (75%, 67%, 64%).
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Affiliation(s)
- A Marchese
- Institute of Microbiology, University of Genoa, Italy
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