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Gómez P, Aspiroz C, Hadjirin NF, Benito D, Zarazaga M, Torres C, Holmes MA. Simultaneous Nasal Carriage by Methicillin-Resistant and Methicillin Susceptible Staphylococcus aureus of Lineage ST398 in a Live Pig Transporter. Pathogens 2020; 9:E401. [PMID: 32455801 PMCID: PMC7281718 DOI: 10.3390/pathogens9050401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/18/2020] [Accepted: 05/18/2020] [Indexed: 11/16/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) sequence type (ST)398 is a livestock associated (LA) lineage with zoonotic potential, especially in humans with live pig contact. The objective of this study was to characterize two S. aureus strains of lineage ST398 (one methicillin-resistant (MRSA), one methicillin-susceptible (MSSA)) isolated from the same nasal sample of a patient admitted in the Intensive-Care Unit of a Spanish Hospital, and with previous occupational exposure to live pigs, by whole-genome-sequencing (WGS). The sample was obtained during routine surveillance for MRSA colonization. Purified genomic DNA was sequenced using Illumina HiSeq 2000 and processed using conventional bioinformatics software. The two isolates recovered were both S. aureus t011/ST398 and showed similar resistance-phenotypes, other than methicillin susceptibility. The possession of antibiotic resistance genes was the same, except for the mecA-gene located in SCCmecV in the MRSA isolate. The MSSA isolate harbored remnants of a SCCmec following the deletion of 17342bp from a recombination between two putative primases. Both isolates belonged to the livestock-associated clade as defined by three canonical single-nucleotide-polymorphisms, and neither possessed the human immune evasion cluster genes, chp, scn, or sak. The core genome alignment showed a similarity of 99.6%, and both isolates harbored the same mobile genetic elements. The two nasal ST398 isolates recovered from the patient with previous occupational exposure to pigs appeared to have a livestock origin and could represent different evolutionary steps of animal-human interface lineage. The MSSA strain was formed as a result of the loss of the mecA gene from the livestock-associated-MRSA lineage.
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Affiliation(s)
- Paula Gómez
- Area of Biochemistry and Molecular Biology, University of La Rioja, 26006 Logroño, Spain; (P.G.); (D.B.); (M.Z.)
| | - Carmen Aspiroz
- Department of Microbiology, Hospital Royo Villanova, 50015 Zaragoza, Spain;
| | - Nazreen F. Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK; (N.F.H.); (M.A.H.)
| | - Daniel Benito
- Area of Biochemistry and Molecular Biology, University of La Rioja, 26006 Logroño, Spain; (P.G.); (D.B.); (M.Z.)
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, University of La Rioja, 26006 Logroño, Spain; (P.G.); (D.B.); (M.Z.)
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, University of La Rioja, 26006 Logroño, Spain; (P.G.); (D.B.); (M.Z.)
| | - Mark A. Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK; (N.F.H.); (M.A.H.)
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Dahyot S, Lebeurre J, Laumay F, Argemi X, Dubos C, Lemée L, Prévost G, François P, Pestel-Caron M. fbl-Typing of Staphylococcus lugdunensis: A Frontline Tool for Epidemiological Studies, but Not Predictive of Fibrinogen Binding Ability. Front Microbiol 2019; 10:1109. [PMID: 31156610 PMCID: PMC6533592 DOI: 10.3389/fmicb.2019.01109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/01/2019] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus lugdunensis is increasingly recognized as a potent pathogen, responsible for severe infections with an outcome resembling that of Staphylococcus aureus. Here, we developed and evaluated a tool for S. lugdunensis typing, using DNA sequence analysis of the repeat-encoding region (R-domain) in the gene encoding the fibrinogen (Fg)-binding protein Fbl (fbl-typing). We typed 240 S. lugdunensis isolates from various clinical and geographical origins. The length of the R-domain ranged from 9 to 52 repeats. fbl-typing identified 54 unique 18-bp repeat sequences and 92 distinct fbl-types. The discriminatory power of fbl-typing was higher than that of multilocus sequence typing (MLST) and equivalent to that of tandem repeat sequence typing. fbl-types could assign isolates to MLST clonal complexes with excellent predictive power. The ability to promote adherence to immobilized human Fg was evaluated for 55 isolates chosen to reflect the genetic diversity of the fbl gene. We observed no direct correlation between Fg binding ability and fbl-types. However, the lowest percentage of Fg binding was observed for isolates carrying a 5'-end frameshift mutation of the fbl gene and for those harboring fewer than 43 repeats in the R-domain. qRT-PCR assays for some isolates revealed no correlation between fbl gene expression and Fg binding capacity. In conclusion, this study shows that fbl-typing is a useful tool in S. lugdunensis epidemiology, especially because it is an easy, cost-effective, rapid and portable method (http://fbl-typing.univ-rouen.fr/). The impact of fbl polymorphism on the structure of the protein, its expression on the cell surface and in virulence remains to be determined.
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Affiliation(s)
- Sandrine Dahyot
- UNIROUEN, GRAM EA2656, Rouen University Hospital, Normandie Université, Rouen, France
| | | | - Floriane Laumay
- Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, Geneva, Switzerland
| | - Xavier Argemi
- VBP EA7290, Fédération de Médecine Translationnelle de Strasbourg, Institut de Bactériologie, Centre Hospitalier Régional Universitaire, Université de Strasbourg, Strasbourg, France.,Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Charline Dubos
- UNIROUEN, GRAM EA2656, Rouen University Hospital, Normandie Université, Rouen, France
| | - Ludovic Lemée
- UNIROUEN, GRAM EA2656, Rouen University Hospital, Normandie Université, Rouen, France
| | - Gilles Prévost
- VBP EA7290, Fédération de Médecine Translationnelle de Strasbourg, Institut de Bactériologie, Centre Hospitalier Régional Universitaire, Université de Strasbourg, Strasbourg, France
| | - Patrice François
- Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, Geneva, Switzerland
| | - Martine Pestel-Caron
- UNIROUEN, GRAM EA2656, Rouen University Hospital, Normandie Université, Rouen, France
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Sato T, Usui M, Maetani S, Tamura Y. Prevalence of methicillin-resistant Staphylococcus aureus among veterinary staff in small animal hospitals in Sapporo, Japan, between 2008 and 2016: A follow up study. J Infect Chemother 2018; 24:588-591. [DOI: 10.1016/j.jiac.2018.01.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/30/2017] [Accepted: 01/28/2018] [Indexed: 11/16/2022]
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Huang CC, Ho CM, Chen HC, Li CY, Tien N, Fan HM, Ge MC, Lu JJ. Evaluation of double locus (clfB and spa) sequence typing for studying molecular epidemiology of methicillin-resistant Staphylococcus aureus in Taiwan. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2015; 50:604-612. [PMID: 26705140 DOI: 10.1016/j.jmii.2015.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 08/25/2015] [Accepted: 10/14/2015] [Indexed: 11/16/2022]
Abstract
BACKGROUND Pulsed-field gel electrophoresis (PFGE) is the "gold standard" for epidemiological investigation of methicillin-resistant Staphylococcus aureus (MRSA), but several DNA sequence-based methods have been developed in MRSA typing because of the unambiguous results. METHODS Ninety-one MRSA isolates were collected from the blood cultures of different patients from July 2008 to December 2008 in central Taiwan. The molecular characteristics of each isolate, including double locus sequence typing (DLST; spa and clfB typing), Staphylococcus cassette chromosome mec (SCCmec), and PFGE were determined for comparison. RESULTS Five major clfB types (types A-E), 18 spa types, 33 DLST genotypes, five SCCmec types, 17 pulsotypes have been observed. Three major DLST genotypes (A1-t002, C0-t037, and B1-t437) and two major pulsotypes (6 and 8) were identified. Most clfB type A isolates (97.1%) were SCCmec type II and all clfB type C isolates (100%) were SCCmec type III. Most clfB type B isolates (88.9%) were SCCmec type IV (59.3%) and VT (29.6%). All (100%) clfB subtypes A1, A2, and C isolates and 70.4% of clfB type B isolates belonged to healthcare-associated-MRSA. The average congruence was 57.7% between DLST and PFGE, and 96.6% between clfB and SCCmec type. The index of discrimination of SCCmec, clfB, spa, PFGE, and DLST was 0.72, 0.79, 0.80, 0.81, and 0.87, respectively. CONCLUSION ClfB type has high congruence with SCCmec type. The DLST method in this study yielded a higher discriminatory power than PFGE in local investigation of molecular epidemiology of MRSA and a promising alternative to PFGE.
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Affiliation(s)
- Chen-Cheng Huang
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Taichung Hospital, Ministry of Health and Welfare, Taichung, Taiwan; Graduate Institute of Clinical Medical Science, China Medical University, Taichung, Taiwan
| | - Cheng-Mao Ho
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Hui-Chen Chen
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chi-Yuan Li
- Graduate Institute of Clinical Medical Science, China Medical University, Taichung, Taiwan
| | - Ni Tien
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Hsiu-Mei Fan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Mao-Cheng Ge
- Department of Laboratory Medicine, Linkou Chang-Gung Memorial Hospital, Taoyuan, Taiwan
| | - Jang-Jih Lu
- Department of Laboratory Medicine, Linkou Chang-Gung Memorial Hospital, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Kweishan, Taoyuan, Taiwan.
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Muthukrishnan G, Lamers RP, Ellis A, Paramanandam V, Persaud AB, Tafur S, Parkinson CL, Cole AM. Longitudinal genetic analyses of Staphylococcus aureus nasal carriage dynamics in a diverse population. BMC Infect Dis 2013; 13:221. [PMID: 23679038 PMCID: PMC3673815 DOI: 10.1186/1471-2334-13-221] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 05/08/2013] [Indexed: 02/03/2023] Open
Abstract
Background Staphylococcus aureus (SA) nasal colonization plays a critical role in the pathogenesis of staphylococcal infections and SA eradication from the nares has proven to be effective in reducing endogenous infections. To understand SA nasal colonization and its relation with consequent disease, assessment of nasal carriage dynamics and genotypic diversity among a diverse population is a necessity. Results We have performed extensive longitudinal monitoring of SA nasal carriage isolates in 109 healthy individuals over a period of up to three years. Longitudinal sampling revealed that 24% of the individuals were persistent SA nasal carriers while 32% were intermittent. To assess the genetic relatedness between different SA isolates within our cohort, multi locus sequence typing (MLST) was performed. MLST revealed that not only were strains colonizing intermittent and persistent nasal carriers genetically similar, belonging to the same clonal complexes, but strain changes within the same host were also observed over time for both types of carriers. More highly discriminating genetic analyses using the hypervariable regions of staphylococcal protein A and clumping factor B virulence genes revealed no preferential colonization of specific SA strains in persistent or intermittent carriers. Moreover, we observed that a subset of persistent and intermittent carriers retained clinically relevant community-acquired methicillin-resistant SA (CA-MRSA) strains in their nares over time. Conclusions The findings of this study provides added perspective on the nasal carriage dynamics between strains colonizing persistent and intermittent carriers; an area currently in need of assessment given that persistent carriers are at greater risk of autoinfection than intermittent carriers.
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Affiliation(s)
- Gowrishankar Muthukrishnan
- Department of Molecular Biology and Microbiology, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, 4000 Central Florida Boulevard, Orlando, FL 32816, USA
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Verghese B, Schwalm ND, Dudley EG, Knabel SJ. A combined multi-virulence-locus sequence typing and Staphylococcal Cassette Chromosome mec typing scheme possesses enhanced discriminatory power for genotyping MRSA. INFECTION GENETICS AND EVOLUTION 2012; 12:1816-21. [PMID: 22948087 DOI: 10.1016/j.meegid.2012.07.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 07/30/2012] [Accepted: 07/31/2012] [Indexed: 11/15/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) remains a major threat to human populations worldwide. Knowing the extent of MRSA genetic diversity within a healthcare facility may provide important insights into the epidemiology of this important pathogen. MRSA isolates recovered from nasal swabs of patients entering the Intensive Care Unit of the Penn State Milton S. Hershey Medical Center, USA, from 2008 to 2009 were genotyped using Staphylococcal Cassette Chromosome mec (SCCmec), multilocus sequence typing (MLST) and a newly developed multi-virulence-locus sequence typing (MVLST) scheme. Sequence data for seven housekeeping genes (arcC, aroE, glpF, gmk, pta, tpi and yqiL) and six virulence genes (alt, essC, geh, hlgA, htrA and sdrC) were used for MLST and MVLST analyses, respectively. MLST identified 12 sequence types (STs) within the hospital isolates. One ST designated ST5 was the most common subtype (38.8%) followed by ST105 (22.4%) and ST8 (16.4%). In contrast, MVLST identified 29 STs (Virulence Types, VTs) from the same set of isolates, with VT6 (32.8%) being the predominant subtype followed by VT9 (8.9%) and VT2 (8.9%). Subsequent analysis of 25 MRSA isolates associated with an outbreak at a Pennsylvania state prison revealed all isolates were VT2 and SCCmec type IVa. These results suggest that a combination of MVLST and SCCmec typing may clarify the epidemiology of MRSA. Additional research with a more diverse set of strains and correlation with conventional epidemiologic data are needed to validate this new subtyping strategy.
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Affiliation(s)
- Bindhu Verghese
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA
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TANG JUNNI, CHEN JUAN, LIU JI, ZHANG RONG, YANG RONGSHENG, CHEN LIANGHONG. EFFECTS OF DIFFERENT CULTIVATION CONDITIONS ON STAPHYLOCOCCUS AUREUS BIOFILM FORMATION AND DIVERSITY OF ADHESIN GENES. J Food Saf 2012. [DOI: 10.1111/j.1745-4565.2012.00370.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ugolotti E, Bandettini R, Marchese A, Gualco L, Vanni I, Borzi L, Di Marco E, Castagnola E, Melioli G, Biassoni R. Molecular characterization of hospital-acquired methicillin-resistant Staphylococcus aureus strains in pediatric outbreaks using variable tandem repeat analysis with spa and ClfB typing. Diagn Microbiol Infect Dis 2011; 69:213-7. [PMID: 21251569 DOI: 10.1016/j.diagmicrobio.2010.08.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 07/29/2010] [Accepted: 08/23/2010] [Indexed: 11/30/2022]
Abstract
To analyze 67 clinical methicillin-resistant Staphylococcus aureus (MRSA) isolated from pediatric hospital infections, we used multilocus variable-number tandem-repeat DNA sequence-based techniques, targeting the protein A polymorphic X region and the clumping factor B complete R domain. We define a "clfB similarity score" and then compare the double loci analysis of closely related MRSA isolates with pulsed-field gel electrophoresis (PFGE). We found an endemic clone (MLST-ST8, spa-t008, SCCmecIV, ClfB lineage 1) able to originate 3 possible outbreaks and a second clone (MLST-ST152, spa-t355, SCCmecV, ClfB lineage 4) responsible for limited cases of MRSA infections, indicating that the combination of spa and clfB-lineage typing is useful to trace MRSA pediatric outbreaks.
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Affiliation(s)
- Elisabetta Ugolotti
- Molecular Medicine, Deparment of Experimental Medicine Istituto Giannina Gaslini, Largo G. Gaslini 5, 16147 Genoa, Italy
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Lamers RP, Stinnett JW, Muthukrishnan G, Parkinson CL, Cole AM. Evolutionary analyses of Staphylococcus aureus identify genetic relationships between nasal carriage and clinical isolates. PLoS One 2011; 6:e16426. [PMID: 21283661 PMCID: PMC3025037 DOI: 10.1371/journal.pone.0016426] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Accepted: 12/16/2010] [Indexed: 11/18/2022] Open
Abstract
Nasal carriage of Staphylococcus aureus has long been hypothesized to be a major vector for the transmission of virulent strains throughout the community. To address this hypothesis, we have analyzed the relatedness between a cohort of nasal carriage strains and clinical isolates to understand better the genetic conformity therein. To assess the relatedness between nasal carriage and clinical isolates of S. aureus, a genetic association study was conducted using multilocus sequence typing (MLST) and typing of the hypervariable regions of clumping factor and fibronectin binding protein genes. At all loci analyzed, genetic associations between both nasal carriage and clinical isolates were observed. Computational analyses of MLST data indicate that nasal carriage and clinical isolates belong to the same genetic clusters (clades), despite differences in sequence type assignments. Genetic analyses of the hypervariable regions from the clumping factor and fibronectin binding protein genes revealed that not only do clinically relevant strains belong to identical genetic lineages as the nasal carriage isolates within our cohort, but they also exhibit 100% sequence similarity within these regions. The findings of this report indicate that strains of S. aureus being carried asymptomatically throughout the community via nasal colonization are genetically related to those responsible for high levels of morbidity and mortality.
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Affiliation(s)
- Ryan P. Lamers
- Department of Molecular Biology and Microbiology, University of Central Florida College of Medicine, Orlando, Florida, United States of America
| | - Jason W. Stinnett
- School of Electrical Engineering and Computer Science, University of Central Florida, Orlando, Florida, United States of America
| | - Gowrishankar Muthukrishnan
- Department of Molecular Biology and Microbiology, University of Central Florida College of Medicine, Orlando, Florida, United States of America
| | - Christopher L. Parkinson
- Department of Biology, University of Central Florida, Orlando, Florida, United States of America
| | - Alexander M. Cole
- Department of Molecular Biology and Microbiology, University of Central Florida College of Medicine, Orlando, Florida, United States of America
- * E-mail:
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Said KB, Zhu G, Zhao X. Organ- and Host-Specific Clonal Groups ofStaphylococcus aureusfrom Human Infections and Bovine Mastitis Revealed by the Clumping Factor A Gene. Foodborne Pathog Dis 2010; 7:111-9. [DOI: 10.1089/fpd.2009.0334] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - Guoqiang Zhu
- Department of Microbiology, College of Veterinary Science, Yanzhou University, Yanzhou, China
| | - Xin Zhao
- Department of Animal Science, McGill University, Quebec, Canada
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Sivaraman K, Venkataraman N, Cole AM. Staphylococcus aureus nasal carriage and its contributing factors. Future Microbiol 2010; 4:999-1008. [PMID: 19824791 DOI: 10.2217/fmb.09.79] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Staphylococcus aureus is a medically important pathogen that is often acquired from hospital settings (nosocomial) as well as from the community (community acquired). Bacteria that reside in anterior nares of hosts serve as reservoirs for both the spread of the pathogen and predispose the host to subsequent infections. Here, we will review the extent and variability of nasal carriage, and the possible causative factors--both from the host and the bacterium. We also discuss the existing molecular typing techniques used for studying variations among strains of S. aureus. Finally, we discuss the possible areas of studies that are open in this field. Given the pathogen's importance in healthcare setting, such areas of study vary vastly, from fundamental research to applied medical care and use of alternative medical regimes for control of S. aureus nasal carriage. Unsurprisingly, our conclusions also underscore the importance of making policy decisions based on local ethnic and socioeconomic population structure.
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Affiliation(s)
- Karthikeyan Sivaraman
- SBG, Center for Microbial & Plant Genetics, Katholieke Universiteit Leuven, Leuven, Belgium.
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Regional profiling for determination of genotype diversity of mastitis-specific Staphylococcus aureus lineage in Canada by use of clumping factor A, pulsed-field gel electrophoresis, and spa typing. J Clin Microbiol 2009; 48:375-86. [PMID: 19955267 DOI: 10.1128/jcm.01768-09] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
One of the major concerns in global public health and the dairy industry is the emergence of host-specific virulent Staphylococcus aureus strains. The high degree of stability of the species genome renders detection of genetic microvariations difficult. Thus, approaches for the rapid tracking of specialized lineages are urgently needed. We used clumping factor A (clfA) to profile 87 bovine mastitis isolates from four regions in Canada and compared the results to those obtained by pulsed-field gel electrophoresis (PFGE) and spa typing. Twenty-five pulsotypes were obtained by PFGE with an index of discrimination of 0.91. These were assigned to six PFGE lineage groups A to F and seven spa types, including two novel ones. Group A had 48.3% of the isolates and group D had 43.7% of the isolates, while only 8% of the isolates were variable. The results of antimicrobial susceptibility testing indicated that all isolates were sensitive to methicillin and the non-beta-lactam antibiotics, while three isolates were resistant to penicillin and one isolate was resistant to tetracycline. All isolates had the clfA gene and belonged to 20 clfA repeat types with an index of discrimination of 0.90. The dominant clfA types, types X, Q, C, and Z, formed 82% and 43% of PFGE groups A and D, respectively, and had copy numbers that varied only within a narrow range of between 46 and 52 copies, implying clonal selection. The rest were variable and region specific. Furthermore, the dominant groups contained subpopulations in different regions across Canada. Sequence information confirmed the relatedness obtained by the use of clfA repeat copy numbers and other methods and further revealed the occurrence of full-repeat deletions and conserved host-specific codon-triplet position biases at 18-bp units. Thus, concordant with the results of PFGE and spa typing, clfA typing proved useful for revealing the clonal nature of the mastitis isolate lineage and for the rapid profiling of subpopulations with comparable discriminatory powers.
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Rapid molecular genotyping and clonal complex assignment of Staphylococcus aureus isolates by PCR coupled to electrospray ionization-mass spectrometry. J Clin Microbiol 2009; 47:1733-41. [PMID: 19297593 DOI: 10.1128/jcm.02175-08] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We describe a high-throughput assay using PCR coupled to electrospray ionization-mass spectrometry (PCR/ESI-MS) to determine the genotypes of Staphylococcus aureus isolates. The primer sets used in the PCR/ESI-MS assay were designed to amplify the same genes analyzed in multilocus sequence typing (MLST). The method was used to identify the clonal complex and USA type of each isolate and is suitable for use in a clinical or public-health setting. The method was validated using a panel of diverse isolates from the Centers for Disease Control and Prevention that were previously characterized by MLST and pulsed-field gel electrophoresis (PFGE). Clinical isolates from two geographically distinct hospitals were characterized, and the clustering results were in agreement with those for repetitive-element PCR and PFGE. The PCR/ESI-MS method enables genotyping of over 180 samples of S. aureus per day in an automated fashion.
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Multiplexed genotyping of methicillin-resistant Staphylococcus aureus isolates by use of padlock probes and tag microarrays. J Clin Microbiol 2009; 47:577-85. [PMID: 19158261 DOI: 10.1128/jcm.01347-08] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We developed and tested a ligase-based assay for simultaneous probing of core genome diversity and typing of methicillin resistance determinants in Staphylococcus aureus isolates. This assay uses oligonucleotide padlock probes whose two ends are joined through ligation when they hybridize to matching target DNA. Circularized probes are subsequently amplified by PCR with common primers and analyzed by using a microarray equipped with universal tag probes. Our set of padlock probes includes oligonucleotides targeting diagnostic regions in the mecA, ccrB, and ccrC genes of the SCCmec cassette in methicillin-resistant S. aureus (MRSA). These probes determine the presence and type of SCCmec cassettes (i.e., SCCmec types I to VI). Additional oligonucleotides interrogate a number of highly informative single nucleotide polymorphisms retrieved from a multilocus sequence typing (MLST) database. These latter probes enable the exploration of isolates' phylogenetic affiliation with clonal lineages of MRSA as revealed by MLST. The described assay enables multiplexed genotyping of MRSA based on a single-tube reaction. With a set of clinical isolates of MRSA and methicillin-susceptible S. aureus (n=66), 100% typeability and 100% accuracy were achieved. The assay described here provides valuable genotypic information that may usefully complement existing genotyping procedures. Moreover, the assay is easily extendable by incorporating additional padlock probes and will be valuable for the quick and cost-effective probing of large numbers of polymorphisms at different genomic locations, such as those ascertained through currently ongoing mutation discovery and genome resequencing projects.
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Said KB, Ramotar K, Zhu G, Zhao X. Repeat-based subtyping and grouping of Staphylococcus aureus from human infections and bovine mastitis using the R-domain of the clumping factor A gene. Diagn Microbiol Infect Dis 2008; 63:24-37. [PMID: 18990534 DOI: 10.1016/j.diagmicrobio.2008.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2008] [Revised: 09/04/2008] [Accepted: 09/11/2008] [Indexed: 10/21/2022]
Abstract
Staphylococcus aureus has become an emerging public health concern. Markers capable of differentiating separate host-specific lineages are needed for tracing strain sources. Thus, a coding variable number tandem repeat-based typing was explored in this study, based on R-domain of clumping factor A (clfA) gene. DNA from isolates and strains of human infections and bovine mastitis were amplified and sequenced. Sequences of clfA from published strains were also analyzed. Results indicate that except one with 36 copies, 44 of the 55 R-domains had repeat copies between 44 and 57, whereas the remaining 10 had 59.5 to 73 copies. Furthermore, human isolates were polymorphic, while mastitis isolates were clonal. Phylogenetic grouping assigned host-specific strains into respective clusters. The repeats were stable during passages in milk, nutrient broth, and invasion of mammary cells showing suitability for typing. Our data show that the R-domain can be useful for typing and grouping host-specific lineages. Moreover, existence of variant repeats in human strains and the dominance of a clonal motif in mastitis may imply that a specific selection has occurred in the mammary gland.
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Affiliation(s)
- Kamaleldin B Said
- Department of Animal Science, McGill University, Ste Anne de Bellevue, Quebec H9X 3V9, Canada
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Krziwanek K, Luger C, Sammer B, Stumvoll S, Stammler M, Sagel U, Witte W, Mittermayer H. MRSA in Austria—an overview. Clin Microbiol Infect 2008; 14:250-9. [DOI: 10.1111/j.1469-0691.2007.01896.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Application of variable number of tandem repeat analysis to determine the origin of S. aureus contamination from milk to cheese in goat cheese farms. Food Control 2008. [DOI: 10.1016/j.foodcont.2007.02.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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18
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Tormo MÁ, Úbeda C, Martí M, Maiques E, Cucarella C, Valle J, Foster TJ, Lasa Í, Penadés JR. Phase-variable expression of the biofilm-associated protein (Bap) in Staphylococcus aureus. MICROBIOLOGY-SGM 2007; 153:1702-1710. [PMID: 17526828 DOI: 10.1099/mic.0.2006/005744-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A process of phase variation is described that affects the expression of Bap (biofilm-associated protein) in Staphylococcus aureus. Upon subculture of the Bap-positive S. aureus strain V329 on Congo red agar, spontaneous smooth biofilm-negative colonies appeared at a low frequency (5 x 10(-4)). Northern blot analysis of these variants with a bap-specific gene probe showed that transcription of the bap gene did not occur. However, DNA typing, Southern blot hybridization and DNA sequencing did not show any differences between the parent V329 strain and the biofilm-negative variants. The biofilm-negative phenotype reverted to wild-type at a similar frequency upon subculture of Bap-negative variants in liquid media. Experimental infection of ovine mammary glands with Bap-negative variants showed that phase variation occurred in vivo, because Bap-expressing, biofilm-positive revertants were isolated from infected mammary glands. The absence of Bap correlated with increased adherence to fibrinogen and fibronectin. It is possible that S. aureus can detach from a biofilm by switching to a Bap-negative state.
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MESH Headings
- Animals
- Bacterial Adhesion
- Bacterial Proteins/genetics
- Biofilms/growth & development
- Blotting, Northern
- Blotting, Southern
- DNA, Bacterial/genetics
- Disease Models, Animal
- Fibrinogen/metabolism
- Fibronectins/metabolism
- Gene Expression Regulation, Bacterial
- Mammary Glands, Animal/microbiology
- Polymorphism, Restriction Fragment Length
- RNA, Bacterial/genetics
- RNA, Messenger/genetics
- Sequence Analysis, DNA
- Sheep
- Staphylococcal Infections/microbiology
- Staphylococcus aureus/genetics
- Staphylococcus aureus/growth & development
- Staphylococcus aureus/metabolism
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Affiliation(s)
- M Ángeles Tormo
- Departamento de Química, Bioquímica y Biología Molecular, Universidad Cardenal Herrera-CEU, 46113 Moncada, Valencia, Spain
- Centro de Investigación y Tecnología Animal, Instituto Valenciano de Investigaciones Agrarias (CITA-IVIA), Apdo. 187, 12.400 Segorbe, Castellón, Spain
| | - Carles Úbeda
- Departamento de Química, Bioquímica y Biología Molecular, Universidad Cardenal Herrera-CEU, 46113 Moncada, Valencia, Spain
- Centro de Investigación y Tecnología Animal, Instituto Valenciano de Investigaciones Agrarias (CITA-IVIA), Apdo. 187, 12.400 Segorbe, Castellón, Spain
| | - Miguel Martí
- Departamento de Química, Bioquímica y Biología Molecular, Universidad Cardenal Herrera-CEU, 46113 Moncada, Valencia, Spain
- Centro de Investigación y Tecnología Animal, Instituto Valenciano de Investigaciones Agrarias (CITA-IVIA), Apdo. 187, 12.400 Segorbe, Castellón, Spain
| | - Elisa Maiques
- Departamento de Química, Bioquímica y Biología Molecular, Universidad Cardenal Herrera-CEU, 46113 Moncada, Valencia, Spain
- Centro de Investigación y Tecnología Animal, Instituto Valenciano de Investigaciones Agrarias (CITA-IVIA), Apdo. 187, 12.400 Segorbe, Castellón, Spain
| | - Carme Cucarella
- Departamento de Química, Bioquímica y Biología Molecular, Universidad Cardenal Herrera-CEU, 46113 Moncada, Valencia, Spain
| | - Jaione Valle
- Instituto de Agrobiotecnología, CSIC-Universidad Pública de Navarra, 31006 Pamplona, Navarra, Spain
| | - Timothy J Foster
- Microbiology Department, Moyne Institute of Preventive Medicine, Trinity College, Dublin 2, Ireland
| | - Íñigo Lasa
- Instituto de Agrobiotecnología, CSIC-Universidad Pública de Navarra, 31006 Pamplona, Navarra, Spain
| | - José R Penadés
- Departamento de Química, Bioquímica y Biología Molecular, Universidad Cardenal Herrera-CEU, 46113 Moncada, Valencia, Spain
- Centro de Investigación y Tecnología Animal, Instituto Valenciano de Investigaciones Agrarias (CITA-IVIA), Apdo. 187, 12.400 Segorbe, Castellón, Spain
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Balajee SA, Tay ST, Lasker BA, Hurst SF, Rooney AP. Characterization of a novel gene for strain typing reveals substructuring of Aspergillus fumigatus across North America. EUKARYOTIC CELL 2007; 6:1392-9. [PMID: 17557880 PMCID: PMC1951133 DOI: 10.1128/ec.00164-07] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Fifty-five epidemiologically linked Aspergillus fumigatus isolates obtained from six nosocomial outbreaks of invasive aspergillosis were subtyped by sequencing the polymorphic region of the gene encoding a putative cell surface protein, Afu3g08990 (denoted as CSP). Comparative sequence analysis showed that genetic diversity was generated in the coding region of this gene by both tandem repeats and point mutations. Each unique sequence in an outbreak cluster was assigned an arbitrary number or CSP sequence type. The CSP typing method was able to identify "clonal" and genotypically distinct A. fumigatus isolates, and the results of this method were concordant with those of another discriminatory genotyping technique, the Afut1 restriction fragment length polymorphism typing method. The novel single-locus sequence typing (CSP typing) strategy appears to be a simple, rapid, discriminatory tool that can be readily shared across laboratories. In addition, we found that A. fumigatus isolates substructured into multiple clades; interestingly, one clade consisted of isolates predominantly representing invasive clinical isolates recovered from cardiac transplant patients from two different outbreak situations. We also found that the A. fumigatus isolate Af293, whose genome has been sequenced, possesses a CSP gene structure that is substantially different from those of the other A. fumigatus strains studied here, highlighting the need for further taxonomic study.
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Affiliation(s)
- S Arunmozhi Balajee
- Mycotic Diseases Branch, Centers for Disease Control and Prevention, Mail stop G 11, 1600 Clifton Road, Atlanta, GA 30333, USA.
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20
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Monk AB, Archer GL. Use of outer surface protein repeat regions for improved genotyping of Staphylococcus epidermidis. J Clin Microbiol 2007; 45:730-5. [PMID: 17202277 PMCID: PMC1829099 DOI: 10.1128/jcm.02317-06] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus epidermidis is an important nosocomial pathogen, but little is known of its epidemiology. Accurate, reproducible typing systems would greatly improve epidemiologic investigations of S. epidermidis. The sequence-based typing technique most recently evaluated, multilocus sequence typing (MLST), often lacks discrimination and can be expensive. PCR and sequence-based analyses of the serine-aspartate repeat region of sdrG (Fbe) and the repeat region of the accumulation-associated protein gene (aap) were evaluated for the ability to discriminate among previously well-characterized S. epidermidis clinical isolates. Forty-eight strains were investigated, with sdrG found in 100% and aap found in 79% of all strains tested. Both genes demonstrated PCR product size and nucleotide sequence variation. Each system by itself gave an index of discrimination similar in value to that of MLST (0.924 and 0.953 compared to 0.96), but discrimination was further improved when combinations of the three systems were used. We conclude that typing systems using amino acid and nucleotide repeat regions of the S. epidermidis surface proteins SdrG and Aap show promise as typing tools and should be investigated using a larger panel of clinically relevant isolates.
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Affiliation(s)
- Alastair B Monk
- Division of Infectious Diseases, Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298, USA
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21
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Viana D, Selva L, Segura P, Penadés JR, Corpa JM. Genotypic characterization of Staphylococcus aureus strains isolated from rabbit lesions. Vet Microbiol 2006; 121:288-98. [PMID: 17208392 DOI: 10.1016/j.vetmic.2006.12.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Revised: 12/09/2006] [Accepted: 12/13/2006] [Indexed: 01/30/2023]
Abstract
Since staphylococcal infections are the main pathological problem in rabbit does, the objective of this study was to characterize epidemiologically Staphylococcus aureus isolates from different lesion types in rabbits. Using 3 genetic markers (coagulase, staphylococcal protein A and clumping factor B genes), 22 different genotypes were identified among 301 isolates recovered from 259 rabbit does with 10 different kinds of chronic purulent lesions. These infected rabbits were obtained from 30 herds located in the Valencia province on the Spanish Mediterranean coast. The most frequent genotype was designated A1/II1/delta (coa/spa/clfB combination genotype) and represented 70.76% of the isolates. Although most genotypes were previously identified in other countries, novel types were also documented. No specificity between genotypes and nature of the pathologic process could be identified. After genetic comparison between strains from different origins, the results may suggest that rabbit, bovine and human S. aureus isolates are not clonally related, suggesting that specific host-dependent pathogenic factors may have evolved independently in these species. These differences indicate that a rational and effective strategy to control infections caused by rabbit-specific isolates may be advantageous.
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Affiliation(s)
- D Viana
- Department of Atención Sanitaria, Salud Pública y Sanidad Animal (Histología y Anatomía Patológica), Facultad de Ciencias Experimentales y de la Salud, CEU-Cardenal Herrera University, Edificio Seminario, s/n, 46113 Moncada (Valencia), Spain
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22
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Kuhn G, Francioli P, Blanc DS. Double-locus sequence typing using clfB and spa, a fast and simple method for epidemiological typing of methicillin-resistant Staphylococcus aureus. J Clin Microbiol 2006; 45:54-62. [PMID: 17093014 PMCID: PMC1828982 DOI: 10.1128/jcm.01457-06] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sequence-based epidemiological typing of methicillin-resistant Staphylococcus aureus (MRSA) has recently been promoted because it results in unambiguous data sets that can be organized in local and global databases. The replacement of previous typing methods, such as the highly discriminatory pulsed-field gel electrophoresis (PFGE), has been attempted with various markers and typing schemes, including spa typing and multilocus sequence typing. However, despite a number of advantages, none of these methods showed convincing evidence for performance in epidemiological typing comparable to that of PFGE. By using three sets of 48 MRSA strains comprising isolates that were (i) genetically highly diverse, (ii) genetically related, and (iii) obtained from long-term carriers, we analyzed the performance of the four highly polymorphic S. aureus markers: clfA, clfB, fnbA, and spa. Typeability, discriminatory power, in vivo stability, and evolution of these markers were compared to those of PFGE. Clearly, none of the markers alone could match the discriminatory power of PFGE (63 genotypes; index of discrimination of 0.96). Instead, this could be achieved by combining markers in pairs. We showed that by using only 3' partial sequences of approximately 500 bp, the majority of each marker's discriminatory power was displayed, and using the partial sequences, the best performance was obtained with the combination of clfB and spa (57 genotypes; index of discrimination of 0.94). Genetic changes were not observed for any of the sequence markers over a period of 3 years and in the case of partial sequences for a period of more than 4 years. This is in contrast to PFGE where changes occurred after several months. The genetic differences found between isolate pairs of long-term carriers and among highly related isolates indicated clonal evolution. A typing scheme based on 500-bp 3' partial sequences of clfB and spa is proposed.
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Affiliation(s)
- G Kuhn
- Hospital Preventive Medicine, University Hospital of Lausanne (CHUV), 1011 Lausanne, Switzerland.
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23
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Strommenger B, Kettlitz C, Weniger T, Harmsen D, Friedrich AW, Witte W. Assignment of Staphylococcus isolates to groups by spa typing, SmaI macrorestriction analysis, and multilocus sequence typing. J Clin Microbiol 2006; 44:2533-40. [PMID: 16825376 PMCID: PMC1489514 DOI: 10.1128/jcm.00420-06] [Citation(s) in RCA: 228] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The implementation of the new clustering algorithm Based Upon Repeat Pattern (BURP) into the Ridom StaphType software tool enables clustering based on spa typing data for Staphylococcus aureus. We compared clustering results obtained by spa typing/BURP to those obtained by currently well-established methods, i.e., SmaI macrorestriction analysis and multilocus sequence typing/eBURST. A total of 99 clinical S. aureus strains, including MRSA and representing major clonal lineages associated with important kinds of infections which have been prevalent in Germany and Central Europe during the last 10 years, were used for comparison. SmaI macrorestriction analysis revealed the highest discriminatory power, and clustering results for all three methods resulted in concordance values ranging from 96.8% between the two sequence-based methods to 93.4% between spa typing/BURP and SmaI macrorestriction/cluster analysis. The results of this study indicate that spa typing, together with BURP clustering, is a useful tool in S. aureus epidemiology, especially because of ease of use and the advantages of unambiguous sequence analysis as well as reproducibility and exchange of typing data.
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Affiliation(s)
- B Strommenger
- Wernigerode Branch, Robert Koch Institute, Burgstr. 37, D-38855 Wernigerode, and Department of Periodontology, University Hospital Münster, Germany.
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