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Rocha J, Silva V, Poeta P, Botelho J, Manaia CM. Searching for links between environmental and clinical mecA +Staphylococcus aureus: A comparative genomics study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:165078. [PMID: 37356759 DOI: 10.1016/j.scitotenv.2023.165078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/18/2023] [Accepted: 06/20/2023] [Indexed: 06/27/2023]
Abstract
Staphylococcus aureus integrate the list of highly virulent and antibiotic resistant pathogens, mainly due to the mecA gene, associated with methicillin resistance. Given the ubiquity of this species, the aim of this study was to investigate whether closely related mecA+S. aureus found in the environment can be also thrive as clinical isolates and if the respective accessory genome may suggest bacterial adaptation. The genomes of environmental (water, animal facilities, food products, n = 111) isolates were compared with closely related genomes of clinical origin (human patients, n = 103). These genomes, available in the public database NCBI, were analysed for phylogeny, accessory genome, and presence of selected clinically relevant genes (n = 104). The genomes of environmental isolates belonged to 18 multi-locus sequence types (MLSTs), 11 of which also included clinical genomes, a result confirmed based on core-genome analysis. Genes significantly (p ≤ 0.05) more frequent among environmental genomes were related with resistance to β-lactams (blaI, blaPCI), aminoglycosides (ant(6)-Ia), macrolides (mph(C), erm(B)), enterotoxins (seg, sei, sem, sen, seo, seu) and serine protease functions (splB), among others. Genes significantly more frequent among clinical genomes were associated with resistance to macrolides (erm(C)), phenicols (fexA), fosfomycin (murA), the leucocidin virulence gene (lukS-PV), and serine protease functions (splA, splE). It is suggested that mecA+S. aureus can be exchanged between clinical and environmental settings, with accessory traits (particularly antibiotic resistance, virulence and stress response) possibly being associated with the habitat. The interplay between phylogeny and accessory genome is an interesting contribution to better understanding the ecology and evolution of mecA+S. aureus.
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Affiliation(s)
- Jaqueline Rocha
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Vanessa Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; CECAV - Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, Portugal
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, Portugal
| | - João Botelho
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal.
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Diversity of community acquired MRSA carrying the PVL gene in Queensland and New South Wales, Australia. Eur J Clin Microbiol Infect Dis 2011; 30:1163-7. [PMID: 21424382 DOI: 10.1007/s10096-011-1203-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 02/10/2011] [Indexed: 10/18/2022]
Abstract
Emergence and dissemination of community acquired methicillin resistant Staphylococcus aureus (CA-MRSA) strains are being reported with increasing frequency in Australia and worldwide. These strains of CA-MRSA are genetically diverse and distinct in Australia. Genotyping of CA-MRSA using eight highly-discriminatory single nucleotide polymorphisms (SNPs) is a rapid and robust method for monitoring the dissemination of these strains in the community. In this study, a SNP genotyping method was used to investigate the molecular epidemiology of 249 community acquired non-multiresistant MRSA (nm-MRSA) isolates over a 12-month period from routine diagnostic specimens. A real-time PCR for the presence of Panton-Valentine leukocidin (PVL) was also performed on these isolates. The CA-MRSA isolates were sourced from a large private laboratory in Brisbane, Australia that serves a wide geographic region encompassing Queensland and Northern New South Wales. This study identified 16 different STs and 98% of the CA-MRSA isolates were positive for the PVL gene. The most common ST was ST93 with 41% of isolates testing positive for this clone.
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Cai L, Kong F, Wang Q, Wang H, Xiao M, Sintchenko V, Gilbert GL. A new multiplex PCR-based reverse line-blot hybridization (mPCR/RLB) assay for rapid staphylococcal cassette chromosome mec (SCCmec) typing. J Med Microbiol 2009; 58:1045-1057. [PMID: 19528184 DOI: 10.1099/jmm.0.007955-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The aim of this study was to develop a new discriminatory method for MRSA SCCmec typing based on multiplex PCR-based reverse line-blot hybridization (mPCR/RLB) assay to enable rapid identification and classification of MRSA SCCmec types in a clinical laboratory. Forty-five primer sets and 49 probes were designed and tested in uniplex PCR (uPCR) and mPCR/RLB. Probes were compared in silico to 14 whole-genome sequences and 18 partial SCCmec gene sequences of Staphylococcus aureus and complete genome and partial SCCmec genes of seven non-MRSA strains, including meticillin-susceptible S. aureus and meticillin-resistant coagulase-negative staphylococci. The method was tested on a set of 42 well-characterized reference MRSA strains. It identified all five epidemiologically relevant SCCmec types and 26 subtypes, including established and new subtypes of SCCmec III, IV (eight subtypes each) and V (three subtypes). The discriminatory power of mPCR/RLB SCCmec typing was similar to that of MLST and spa typing (Simpson indices of diversity of 0.916, 0.926 and 0.882, respectively; differences not statistically significant). The application of mPCR/RLB hybridization assay to MRSA SCCmec typing can improve the specificity, discriminatory power and throughput of the typing procedure. The detection of up to 43 mPCR products in a single hybridization assay transforms MRSA SCCmec typing from passive epidemiological library typing into a potential tool for near-real-time infection control surveillance and tracking of MRSA transmission in hospitals.
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Affiliation(s)
- Lin Cai
- Department of Dermatology, Peking University People's Hospital, Beijing 100044, PR China
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology and Medical Research (ICPMR), Westmead, New South Wales, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology and Medical Research (ICPMR), Westmead, New South Wales, Australia
| | - Huiping Wang
- Department of Dermatology, Tianjin Medical University General Hospital, Tianjin, PR China
| | - Meng Xiao
- Life Science College, Peking University, Beijing, PR China
| | - Vitali Sintchenko
- Western Clinical School, University of Sydney, Sydney, Australia.,Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology and Medical Research (ICPMR), Westmead, New South Wales, Australia
| | - Gwendolyn L Gilbert
- Western Clinical School, University of Sydney, Sydney, Australia.,Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology and Medical Research (ICPMR), Westmead, New South Wales, Australia
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Matouskova I, Janout V. Current knowledge of methicillin-resistant Staphylococcus aureus and community-associated methicillin-resistant Staphylococcus aureus. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2009; 152:191-202. [PMID: 19219207 DOI: 10.5507/bp.2008.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Bacterial strains that are oxacillin and methicillin-resistant, historically termed methicillin-resistant Staphylococcus aureus (MRSA) are resistant to all beta-lactam agents, including cephalosporins and carbapenems. MRSA are pathogenic and have a number of virulence factors that enable them to result in disease. They are transmissible and important causes of nosocomial infections worldwide. An MRSA outbreak can occur when one strain is transmitted to other patients or through close contacts of infected persons in the community. Hospital-associated MRSA (HA-MRSA) isolates are also frequent causes of healthcare-associated bloodstream and catheter-related infections. Community-associated MRSA (CA-MRSA) isolates are often only resistant to beta-lactam agents and erythromycin but they are an emerging cause of community-associated infections, especially skin and soft tissue infections (SSTI) and necrotizing pneumonia. METHODS Current possibilities for detecting MRSA strains in the laboratory are reviewed and discussed in the context of the recent literature. RESULTS AND CONCLUSION The active surveillance and prevention of MRSA occurrence and spreading in hospitals are discussed in the context of recent literature.
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Affiliation(s)
- Ivanka Matouskova
- Department of Preventive Medicine, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, Olomouc, Czech Republic.
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Epstein C, Yam W, Peiris J, Epstein R. Methicillin-resistant commensal staphylococci in healthy dogs as a potential zoonotic reservoir for community-acquired antibiotic resistance. INFECTION GENETICS AND EVOLUTION 2009; 9:283-5. [DOI: 10.1016/j.meegid.2008.11.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Revised: 11/19/2008] [Accepted: 11/19/2008] [Indexed: 11/26/2022]
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Stephens AJ, Inman-Bamber J, Giffard PM, Huygens F. High-Resolution Melting Analysis of the spa Repeat Region of Staphylococcus aureus. Clin Chem 2008; 54:432-6. [DOI: 10.1373/clinchem.2007.093658] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
AbstractBackground: The staphylococcal protein A (spa) locus of Staphylococcus aureus contains a complex repeat structure and is commonly used for single-locus sequence-based genotyping. The real-time PCR platform supports genotyping methods that are single step and closed tube and potentially can be carried out simultaneously with diagnosis. We describe here a method for genotyping S. aureus using high-resolution melting (HRM) analysis of the spa polymorphic region X.Methods: The conventional PCR spa assay was modified and optimized for the Rotor-Gene 6000 instrument (Corbett Life Science). HRM analysis on the Corbett Rotor-Gene 6000 instrument was used to test 22 known spa sequences obtained from 44 diverse methicillin-resistant S. aureus (MRSA) isolates. Criteria for calling pairs of melting curves “same” or “different” were developed empirically by converting the data to difference graph format with one curve defined as the control. HRM curve comparison between runs was done to determine the portability of the method. The assay performance was assessed by genotyping uncharacterized isolates, carrying out blind trials, and comparing HRM profiles from different runs.Results: HRM analysis of 44 diverse MRSA isolates generated 20 profiles from 22 spa sequence types. The 2 unresolved HRM spa types differed by only 1 bp. Two blind trials demonstrated complete reproducibility with respect to calling the different spa types. Interrun comparisons of HRM curves were successfully developed, indicating the robustness of the method.Conclusion: Analysis of the spa locus by HRM resolves spa sequence variants. This single- and closed-tube single-step method for S. aureus genotyping can be easily combined with the interrogation of other genetic markers.
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Affiliation(s)
- Alex J Stephens
- Cooperative Research Centre for Diagnostics, Institute of Health and Biomedical Innovation, Queensland University of Technology, Queensland, Australia
| | - John Inman-Bamber
- Cooperative Research Centre for Diagnostics, Institute of Health and Biomedical Innovation, Queensland University of Technology, Queensland, Australia
| | - Philip M Giffard
- Cooperative Research Centre for Diagnostics, Institute of Health and Biomedical Innovation, Queensland University of Technology, Queensland, Australia
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Cai Y, Kong F, Wang Q, Tong Z, Sintchenko V, Zeng X, Gilbert GL. Comparison of single- and multilocus sequence typing and toxin gene profiling for characterization of methicillin-resistant Staphylococcus aureus. J Clin Microbiol 2007; 45:3302-8. [PMID: 17715374 PMCID: PMC2045362 DOI: 10.1128/jcm.01082-07] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We compared three novel methicillin-resistant Staphylococcus aureus (MRSA) genotyping methods with multilocus sequence typing (MLST) and spa typing to assess their utility for routine strain typing. The new methods were femA and nuc sequence typing and toxin gene profiling (TGP), using a multiplex-PCR-based reverse line blot assay to detect 13 pyrogenic superantigen and exfoliative toxin genes. Forty-two well-characterized MRSA strains, representing 15 MLSTs or 9 clonal clusters (CCs), were genotyped by all methods. Twenty-two spa, nine femA, and seven nuc sequence types were identified. The femA sequence types correlated exactly with CCs; nuc sequences types were less discriminatory but generally correlated well with femA types and CCs. Ten isolates contained none of 13 toxin genes; TGPs of the remainder comprised 1 to 5 toxin genes. The combination of spa typing and TGPs identified 26 genotypes among the 42 strains studied. A combination of two or three rapid, inexpensive genotyping methods could potentially provide rapid MRSA strain typing as well as useful information about clonal origin and virulence.
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Affiliation(s)
- Yongwei Cai
- Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Darcy Road, Westmead, New South Wales 2145, Australia
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Price EP, Smith H, Huygens F, Giffard PM. High-resolution DNA melt curve analysis of the clustered, regularly interspaced short-palindromic-repeat locus of Campylobacter jejuni. Appl Environ Microbiol 2007; 73:3431-6. [PMID: 17400785 PMCID: PMC1907115 DOI: 10.1128/aem.02702-06] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel method for genotyping the clustered, regularly interspaced short-palindromic-repeat (CRISPR) locus of Campylobacter jejuni is described. Following real-time PCR, CRISPR products were subjected to high-resolution melt (HRM) analysis, a new technology that allows precise melt profile determination of amplicons. This investigation shows that the CRISPR HRM assay provides a powerful addition to existing C. jejuni genotyping methods and emphasizes the potential of HRM for genotyping short sequence repeats in other species.
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Affiliation(s)
- Erin P Price
- Cooperative Research Centre for Diagnostics, Institute of Health and Biomedical Innovation, Queensland University of Technology, Cnr Blamey St. and Musk Ave., Kelvin Grove, Queensland 4059, Australia
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Price EP, Huygens F, Giffard PM. Fingerprinting of Campylobacter jejuni by using resolution-optimized binary gene targets derived from comparative genome hybridization studies. Appl Environ Microbiol 2006; 72:7793-803. [PMID: 16997982 PMCID: PMC1694235 DOI: 10.1128/aem.01338-06] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2006] [Accepted: 09/17/2006] [Indexed: 11/20/2022] Open
Abstract
The aim of this investigation was to exploit the vast comparative data generated by comparative genome hybridization (CGH) studies of Campylobacter jejuni in developing a genotyping method. We examined genes in C. jejuni that exhibit binary status (present or absent between strains) within known plasticity regions, in order to identify a minimal subset of gene targets that provide high-resolution genetic fingerprints. Using CGH data from three studies as input, binary gene sets were identified with "Minimum SNPs" software. "Minimum SNPs" selects for the minimum number of targets required to obtain a predefined resolution, based on Simpson's index of diversity (D). After implementation of stringent criteria for gene presence/absence, eight binary genes were found that provided 100% resolution (D=1) of 20 C. jejuni strains. A real-time PCR assay was developed and tested on 181 C. jejuni and Campylobacter coli isolates, a subset of which have previously been characterized by multilocus sequence typing, flaA short variable region sequencing, and pulsed-field gel electrophoresis. In addition to the binary gene real-time PCR assay, we refined the seven-member single nucleotide polymorphism (SNP) real-time PCR assay previously described for C. jejuni and C. coli. By normalizing the SNP assay with the respective C. jejuni and C. coli ubiquitous genes, mapA and ceuE, the polymorphisms at each SNP could be determined without separate reactions for every polymorphism. We have developed and refined a rapid, highly discriminatory genotyping method for C. jejuni and C. coli that uses generic technology and is amenable to high-throughput analyses.
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Affiliation(s)
- Erin P Price
- Cooperative Research Centre for Diagnostics, Institute of Health and Biomedical Innovation, Queensland University of Technology, Cnr Blamey St. and Musk Ave., Kelvin Grove, Queensland 4059, Australia
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McDonald M, Dougall A, Holt D, Huygens F, Oppedisano F, Giffard PM, Inman-Bamber J, Stephens AJ, Towers R, Carapetis JR, Currie BJ. Use of a single-nucleotide polymorphism genotyping system to demonstrate the unique epidemiology of methicillin-resistant Staphylococcus aureus in remote aboriginal communities. J Clin Microbiol 2006; 44:3720-7. [PMID: 17021102 PMCID: PMC1594797 DOI: 10.1128/jcm.00836-06] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) has emerged as a major public health problem in Australia, as in many other parts of the world. High rates of CA-MRSA skin and soft tissue infection have been reported from Aboriginal communities. We used a single-nucleotide polymorphism (SNP) genotyping typing system based on the multilocus sequence type (MLST) database to investigate the epidemiology of CA-MRSA and methicillin-sensitive S. aureus (MSSA) over a 12-month period in three remote Aboriginal communities of Northern Australia. This was supplemented by real-time PCR for Panton-Valentine leukocidin (PVL) genes, staphylococcal cassette chromosome mec (SCCmec) typing, and antimicrobial susceptibility testing. S. aureus was recovered from pyoderma lesions on 221 occasions and throat swabs on 44 occasions. The median monthly recovery rate of S. aureus from skin sores was 58% (interquartile range, 62 to 78%), and there was no seasonal variation. Twenty-three percent of isolates were CA-MRSA; the proportion was similar across the communities and did not vary over the study period. Erythromycin resistance was found in 47% of CA-MRSA and 21% of MSSA. SNP-based typing identified 14 different clonal complexes (cc); however, cc75 was predominant, accounting for 71% of CA-MRSA isolates. These were confirmed as ST75-like by using an additional SNP and MLST of selected isolates. All but one of the cc75 isolates had SSCmec type IV (one had type V), and all were PVL negative. Monthly tracking of SNP-based cc types showed a highly dynamic process. ST75-MRSA-IV appears to be unique to the region and probably evolved de novo in remote Aboriginal communities.
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Affiliation(s)
- Malcolm McDonald
- Menzies School of Health Research, P.O. Box 41096, Casuarina, 0811 Northern Territory, Australia.
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Suzuki M, Tawada Y, Kato M, Hori H, Mamiya N, Hayashi Y, Nakano M, Fukushima R, Katai A, Tanaka T, Hata M, Matsumoto M, Takahashi M, Sakae K. Development of a rapid strain differentiation method for methicillin-resistant Staphylococcus aureus isolated in Japan by detecting phage-derived open-reading frames. J Appl Microbiol 2006; 101:938-47. [PMID: 16968305 DOI: 10.1111/j.1365-2672.2006.02932.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To develop a rapid genotyping method for investigating outbreaks of methicillin-resistant strains of Staphylococcus aureus (MRSA) isolated in Japan. METHODS AND RESULTS Isolates were genotyped by detecting the keeping pattern of 16 open-reading frames (ORFs), a process we call phage ORF typing (POT). Thirteen of the ORFs were selected from phage genomes and one from a genomic island SaGIm in the genome of strain Mu50. The other two ORFs, one from Tn554 and one from staphylococcal cassette chromosome mec (SCCmec) type II, were used as strain markers. Three hundred and sixty-eight isolates from five hospitals were classified into 133 types by POT, whereas they were classified into 139 types by pulsed-field gel electrophoresis (PFGE) subtyping. The discriminatory power of POT (D=0.989) was equal to that of PFGE subtyping (D=0.986). CONCLUSIONS MRSA isolates collected in Japan can be genotyped by detecting the keeping pattern of phage-derived ORFs with a discriminatory power equal to that of PFGE subtyping. SIGNIFICANCE AND IMPACT OF THE STUDY MRSA isolates can be genotyped rapidly by detecting phage-derived ORFs. As particular pandemic clones can be found in a specific region, a typing method localized to a pandemic clone may be effective for the rapid genotyping of MRSA during outbreaks.
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Affiliation(s)
- M Suzuki
- Department of Microbiology, Aichi Prefectural Institute of Public Health, Tsuji-machi, Kita-ku, Nagoya, Japan.
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Price EP, Thiruvenkataswamy V, Mickan L, Unicomb L, Rios RE, Huygens F, Giffard PM. Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA short variable region sequencing. J Med Microbiol 2006; 55:1061-1070. [PMID: 16849726 DOI: 10.1099/jmm.0.46460-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This investigation describes the development of a generally applicable, bioinformatics-driven, single-nucleotide polymorphism (SNP) genotyping assay for the common bacterial gastrointestinal pathogen Campylobacter jejuni. SNPs were identified in silico using the program 'Minimum SNPs', which selects for polymorphisms providing the greatest resolution of bacterial populations based on Simpson's index of diversity (D). The high-D SNPs identified in this study were derived from the combined C. jejuni/Campylobacter coli multilocus sequence typing (MLST) database. Seven SNPs were found that provided a D of 0.98 compared with full MLST characterization, based on 959 sequence types (STs). The seven high-D SNPs were interrogated using allele-specific real-time PCR (AS kinetic PCR), which negates the need for expensive labelled primers or probes and requires minimal assay optimization. The total turnaround time of the SNP typing assay was approximately 2 h. Concurrently, 69 C. jejuni isolates were subjected to MLST and flagellin A short variable region (flaA SVR) sequencing and combined with a population of 84 C. jejuni and C. coli isolates previously characterized by these methods. Within this collection of 153 isolates, 19 flaA SVR types (D=0.857) were identified, compared with 40 different STs (D=0.939). When MLST and flaA SVR sequencing were used in combination, the discriminatory power was increased to 0.959. In comparison, SNP typing of the 153 isolates alone provided a D of 0.920 and was unable to resolve a small number of unrelated isolates. However, addition of the flaA SVR locus to the SNP typing procedure increased the resolving power to 0.952 and clustered isolates similarly to MLST/flaA SVR. This investigation has shown that a seven-member C. jejuni SNP typing assay, used in combination with sequencing of the flaA SVR, efficiently discriminates C. jejuni isolates.
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Affiliation(s)
- Erin P Price
- Cooperative Research Centre for Diagnostics, Queensland University of Technology (Gardens Point Campus), GPO Box 2434, Brisbane, Queensland 4001, Australia
| | - Venugopal Thiruvenkataswamy
- Cooperative Research Centre for Diagnostics, Queensland University of Technology (Gardens Point Campus), GPO Box 2434, Brisbane, Queensland 4001, Australia
| | - Lance Mickan
- Institute of Medical and Veterinary Science, Adelaide, Australia
| | - Leanne Unicomb
- OzFoodNet, Hunter New England Population Health, Wallsend, Australia and the National Centre for Epidemiology and Population Health, Australian National University, Canberra, Australia
| | - Rosa E Rios
- Microbiological Diagnostic Unit, University of Melbourne, Melbourne, Australia
| | - Flavia Huygens
- Cooperative Research Centre for Diagnostics, Queensland University of Technology (Gardens Point Campus), GPO Box 2434, Brisbane, Queensland 4001, Australia
| | - Philip M Giffard
- Cooperative Research Centre for Diagnostics, Queensland University of Technology (Gardens Point Campus), GPO Box 2434, Brisbane, Queensland 4001, Australia
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Stephens AJ, Huygens F, Inman-Bamber J, Price EP, Nimmo GR, Schooneveldt J, Munckhof W, Giffard PM. Methicillin-resistant Staphylococcus aureus genotyping using a small set of polymorphisms. J Med Microbiol 2006; 55:43-51. [PMID: 16388029 DOI: 10.1099/jmm.0.46157-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The aim of this study was to identify a set of genetic polymorphisms that efficiently divides methicillin-resistant Staphylococcus aureus (MRSA) strains into groups consistent with the population structure. The rationale was that such polymorphisms could underpin rapid real-time PCR or low-density array-based methods for monitoring MRSA dissemination in a cost-effective manner. Previously, the authors devised a computerized method for identifying sets of single nucleotide polymorphisms (SNPs) with high resolving power that are defined by multilocus sequence typing (MLST) databases, and also developed a real-time PCR method for interrogating a seven-member SNP set for genotyping S. aureus. Here, it is shown that these seven SNPs efficiently resolve the major MRSA lineages and define 27 genotypes. The SNP-based genotypes are consistent with the MRSA population structure as defined by eBURST analysis. The capacity of binary markers to improve resolution was tested using 107 diverse MRSA isolates of Australian origin that encompass nine SNP-based genotypes. The addition of the virulence-associated genes cna, pvl and bbp/sdrE, and the integrated plasmids pT181, pI258 and pUB110, resolved the nine SNP-based genotypes into 21 combinatorial genotypes. Subtyping of the SCCmec locus revealed new SCCmec types and increased the number of combinatorial genotypes to 24. It was concluded that these polymorphisms provide a facile means of assigning MRSA isolates into well-recognized lineages.
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Affiliation(s)
- Alex J Stephens
- Cooperative Research Centre for Diagnostics, Queensland University of Technology, GPO Box 2434, Brisbane, Queensland 4001, Australia
| | - Flavia Huygens
- Cooperative Research Centre for Diagnostics, Queensland University of Technology, GPO Box 2434, Brisbane, Queensland 4001, Australia
| | - John Inman-Bamber
- Cooperative Research Centre for Diagnostics, Queensland University of Technology, GPO Box 2434, Brisbane, Queensland 4001, Australia
| | - Erin P Price
- Cooperative Research Centre for Diagnostics, Queensland University of Technology, GPO Box 2434, Brisbane, Queensland 4001, Australia
| | - Graeme R Nimmo
- Queensland Health Pathology Services, Princess Alexandra Hospital, Brisbane, Australia
| | | | - Wendy Munckhof
- Infection Management Services, Princess Alexandra Hospital and District Health Service, Brisbane, Australia
| | - Philip M Giffard
- Cooperative Research Centre for Diagnostics, Queensland University of Technology, GPO Box 2434, Brisbane, Queensland 4001, Australia
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Soo Ko K, Peck KR, Sup Oh W, Lee NY, Hiramatsu K, Song JH. Genetic differentiation of methicillin-resistant Staphylococcus aureus strains from Korea and Japan. Microb Drug Resist 2005; 11:279-86. [PMID: 16201932 DOI: 10.1089/mdr.2005.11.279] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this study, we evaluated genetic differentiation between methicillin-resistant Staphylococcus aureus (MRSA) strains from Korea and Japan. Seventy-five MRSA strains, including 25 h VISA strains, were analyzed by molecular typing methods, including multilocus sequence typing (MLST), SCC mec typing, and spa typing. The most prevalent genotype of MRSA strains, in both Korea and Japan, was ST 5-MRSA-II with the DMGMK spa motif, characteristic of the New York/Japan MRSA clone. In spite of these common features in MRSA strains from Korea and Japan, we also observed some genotypic divergence in MRSA from the two countries. Several spa types might be differentiated from a prevalent prototype (TJMBMDMGMK) that is shared by the two countries, revealing a unique geographic distribution. SCC mec type II lacking pUB110, designated type IIA, was found more frequently in Korea than in Japan. The rate of gentamicin resistance was also dramatically different between the two countries: 87.2% (Korea) vs. 28.6% (Japan). These preliminary findings suggested that MRSA strains from Korea and Japan might have originated from a common ancestor, but then clearly differentiated according to locality. A further comprehensive study should be performed to document the hypotheses from this study.
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Affiliation(s)
- Kwan Soo Ko
- Asian-Pacific Research Foundation for Infectious Diseases (ARFID), Seoul, Korea
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Peleg AY, Munckhof WJ, Kleinschmidt SL, Stephens AJ, Huygens F. Life-threatening community-acquired methicillin-resistant Staphylococcus aureus infection in Australia. Eur J Clin Microbiol Infect Dis 2005; 24:384-7. [PMID: 15926063 DOI: 10.1007/s10096-005-1329-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Eight patients with invasive bacteremic community-acquired methicillin-resistant Staphylococcus aureus infection in southeast Queensland, Australia, are reported. One patient died of septic shock. Haematogenous seeding to lungs, bone, and other sites was common. All isolates carried the virulence factor Panton-Valentine leukocidin and were either the southwest Pacific clone or the newly described Queensland clone. Clinicians should consider community-acquired methicillin-resistant Staphylococcus aureus infection in any patient presenting to hospital with severe staphylococcal sepsis or pneumonia.
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Affiliation(s)
- A Y Peleg
- Infectious Diseases Unit, The Alfred Hospital, Commercial Road, Prahran, Melbourne, Victoria 3181, Australia.
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Coombs GW, Nimmo GR, Bell JM, Huygens F, O'Brien FG, Malkowski MJ, Pearson JC, Stephens AJ, Giffard PM. Genetic diversity among community methicillin-resistant Staphylococcus aureus strains causing outpatient infections in Australia. J Clin Microbiol 2004; 42:4735-43. [PMID: 15472334 PMCID: PMC522360 DOI: 10.1128/jcm.42.10.4735-4743.2004] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Increasing reports of the appearance of novel nonmultiresistant methicillin-resistant Staphylococcus aureus MRSA (MRSA) strains in the community and of the spread of hospital MRSA strains into the community are cause for public health concern. We conducted two national surveys of unique isolates of S. aureus from clinical specimens collected from nonhospitalized patients commencing in 2000 and 2002, respectively. A total of 11.7% of 2,498 isolates from 2000 and 15.4% of 2,486 isolates from 2002 were MRSA. Approximately 54% of the MRSA isolates were nonmultiresistant (resistant to less than three of nine antibiotics) in both surveys. The majority of multiresistant MRSA isolates in both surveys belonged to two strains (strains AUS-2 and AUS-3), as determined by pulsed-field gel electrophoresis (PFGE) and resistogram typing. The 3 AUS-2 isolates and 10 of the 11 AUS-3 isolates selected for multilocus sequence typing (MLST) and staphylococcal chromosomal cassette mec (SCCmec) analysis were ST239-MRSA-III (where ST is the sequence type) and thus belonged to the same clone as the eastern Australian MRSA strain of the 1980s, which spread internationally. Four predominant clones of novel nonmultiresistant MRSA were identified by PFGE, MLST, and SCCmec analysis: ST22-MRSA-IV (strain EMRSA-15), ST1-MRSA-IV (strain WA-1), ST30-MRSA-IV (strain SWP), and ST93-MRSA-IV (strain Queensland). The last three clones are associated with community acquisition. A total of 14 STs were identified in the surveys, including six unique clones of novel nonmultiresistant MRSA, namely, STs 73, 93, 129, 75, and 80slv and a new ST. SCCmec types IV and V were present in diverse genetic backgrounds. These findings provide support for the acquisition of SCCmec by multiple lineages of S. aureus. They also confirm that both hospital and community strains of MRSA are now common in nonhospitalized patients throughout Australia.
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Affiliation(s)
- Geoffrey W Coombs
- Gram-Positive Bacteria Typing and Research Unit, Royal Perth Hospital, Australia
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