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Hoon KS, Holt DC, Auburn S, Shaw P, Giffard PM. minSNPs: an R package for the derivation of resolution-optimised SNP sets from microbial genomic data. PeerJ 2023; 11:e15339. [PMID: 37250706 PMCID: PMC10224671 DOI: 10.7717/peerj.15339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 04/12/2023] [Indexed: 05/31/2023] Open
Abstract
Here, we present the R package, minSNPs. This is a re-development of a previously described Java application named Minimum SNPs. MinSNPs assembles resolution-optimised sets of single nucleotide polymorphisms (SNPs) from sequence alignments such as genome-wide orthologous SNP matrices. MinSNPs can derive sets of SNPs optimised for discriminating any user-defined combination of sequences from all others. Alternatively, SNP sets may be optimised to determine all sequences from all other sequences, i.e., to maximise diversity. MinSNPs encompasses functions that facilitate rapid and flexible SNP mining, and clear and comprehensive presentation of the results. The minSNPs' running time scales in a linear fashion with input data volume and the numbers of SNPs and SNPs sets specified in the output. MinSNPs was tested using a previously reported orthologous SNP matrix of Staphylococcus aureus and an orthologous SNP matrix of 3,279 genomes with 164,335 SNPs assembled from four S. aureus short read genomic data sets. MinSNPs was shown to be effective for deriving discriminatory SNP sets for potential surveillance targets and in identifying SNP sets optimised to discriminate isolates from different clonal complexes. MinSNPs was also tested with a large Plasmodium vivax orthologous SNP matrix. A set of five SNPs was derived that reliably indicated the country of origin within three south-east Asian countries. In summary, we report the capacity to assemble comprehensive SNP matrices that effectively capture microbial genomic diversity, and to rapidly and flexibly mine these entities for optimised marker sets.
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Affiliation(s)
- Kian Soon Hoon
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Deborah C. Holt
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- CDU Menzies School of Medicine, Faculty of Health, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Sarah Auburn
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Peter Shaw
- Oujian Laboratory, Wenzhou, Zhejiang, China
| | - Philip M. Giffard
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- CDU Menzies School of Medicine, Faculty of Health, Charles Darwin University, Darwin, Northern Territory, Australia
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Liu W, Zhao H, Qiu Z, Jin M, Yang D, Xu Q, Feng H, Li J, Shen Z. Identifying geographic origins of the Escherichia coli isolates from food by a method based on single-nucleotide polymorphisms. J Microbiol Methods 2019; 168:105807. [PMID: 31837351 DOI: 10.1016/j.mimet.2019.105807] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND E.coli is an important foodborne pathogen. Rapid and robust tracking of the source of E. coli is the key step to control foodborne infections. RESULTS In this study, a genotyping and tracing method based on highly discriminatory single nucleotide polymorphisms (SNPs) was developed to investigate the geographical origin of E. coli in food. A highly informative set of 12 SNPs was derived from 4 housekeeping genes in E. coli multilocus sequence typing (MLST) database. A collection of 253 E. coli isolates from food in 12 countries and regions were screened, resulting in a total of 61 profiles, 35 geographically specific SNP profiles were revealed and further verified by blind sample test. Also, the evolutionary relationship of 61 SNP profiles with different geographical origins was established by the enhanced analysis Based Upon Related Sequence Types (eBURST) analysis, which provided evidence that strains of different geographical origins owned the same ancestor strain. CONCLUSIONS Our study established a powerful method based on a set of 12 SNPs for identifying geographical origins. The blind sample analysis proved that this SNPs panel had a high traceability of E. coli in food. Furthermore, this method based on SNPs combined with eBURST analysis revealed the potential evolutionary relationship between E.coli strains of different geographical origins.
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Affiliation(s)
- Weili Liu
- Tianjin Institute of Environmental and Operational Medicine. Tianjin 300050, China
| | - Hong Zhao
- Animals, plants and food testing center of Tianjin Exit-Entry Inspection & Quarantine Bureau, Tianjin 300461, China
| | - Zhigang Qiu
- Tianjin Institute of Environmental and Operational Medicine. Tianjin 300050, China
| | - Min Jin
- Tianjin Institute of Environmental and Operational Medicine. Tianjin 300050, China
| | - Dong Yang
- Tianjin Institute of Environmental and Operational Medicine. Tianjin 300050, China
| | - Qunying Xu
- School of Public Health, Nanchang University, Jiangxi 330006, China
| | - Hua Feng
- School of Public Health, Nanchang University, Jiangxi 330006, China
| | - Junwen Li
- Tianjin Institute of Environmental and Operational Medicine. Tianjin 300050, China.
| | - Zhiqiang Shen
- Tianjin Institute of Environmental and Operational Medicine. Tianjin 300050, China.
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Nyasinga J, Kyany'a C, Okoth R, Oundo V, Matano D, Wacira S, Sang W, Musembi S, Musila L. A six-member SNP assay on the iPlex MassARRAY platform provides a rapid and affordable alternative for typing major African Staphylococcus aureus types. Access Microbiol 2019; 1:e000018. [PMID: 32974514 PMCID: PMC7471782 DOI: 10.1099/acmi.0.000018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 03/03/2019] [Indexed: 11/18/2022] Open
Abstract
Purpose Data on the clonal distribution of Staphylococcus aureus in Africa are scanty, partly due to the high costs and long turnaround times imposed by conventional genotyping methods such as spa and multilocus sequence typing (MLST), which means there is a need for alternative typing approaches. This study evaluated the discriminatory power, cost of and time required for genotyping Kenyan staphylococcal isolates using iPlex MassARRAY compared to conventional methods. Methodology Fifty-four clinical S. aureus isolates from three counties were characterized using iPlex MassARRAY, spa and MLST typing methods. Ten single-nucleotide polymorphisms (SNPs) from the S. aureus MLST loci were assessed by MassARRAY. >Results The MassARRAY assay identified 14 unique SNP genotypes, while spa typing and MLST revealed 22 spa types and 21 sequence types (STs) that displayed unique regional distribution. spa type t355 (ST152) was the dominant type overall while t037/t2029 (ST 241) dominated among the methicillin-resistant S. aureus (MRSA) isolates. MassARRAY showed 83 % and 82 % accuracy against spa typing and MLST, respectively, in isolate classification. Moreover, MassARRAY identified all MRSA strains and a novel spa type. MassARRAY had a reduced turnaround time (<12 h) compared to spa typing (4 days) and MLST (20 days). The MassARRAY reagent and consumable costs per isolate were approximately $18 USD compared to spa typing ($30 USD) and MLST ($126 USD). Conclusion This study demonstrated that iPlex MassARRAY can be adapted as a useful surveillance tool to provide a faster, more affordable and fairly accurate method for genotyping African S. aureus isolates to identify clinically significant genotypes, MRSA strains and emerging strain types.
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Affiliation(s)
- Justin Nyasinga
- Kenyatta University, Nairobi, Kenya.,Technical University of Kenya, Nairobi, Kenya
| | - Cecilia Kyany'a
- United States Army Medical Research Directorate - Africa, Nairobi, Kenya
| | - Raphael Okoth
- United States Army Medical Research Directorate - Africa, Nairobi, Kenya
| | - Valerie Oundo
- United States Army Medical Research Directorate - Africa, Nairobi, Kenya
| | - Daniel Matano
- United States Army Medical Research Directorate - Africa, Nairobi, Kenya
| | - Simon Wacira
- United States Army Medical Research Directorate - Africa, Nairobi, Kenya
| | - Willie Sang
- Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Lillian Musila
- United States Army Medical Research Directorate - Africa, Nairobi, Kenya
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Identification and Discrimination of Chlamydia trachomatis Ocular and Urogenital Strains and Major Phylogenetic Lineages by CtGEM Typing, A Double-Locus Genotyping Method. Methods Mol Biol 2019; 2042:87-122. [PMID: 31385272 DOI: 10.1007/978-1-4939-9694-0_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
CtGEM typing was developed to subdivide the bacterial species Chlamydia trachomatis on the basis of genome phylogeny and anatomical tropism. The rationale was facilitation of surveillance for ocular strains, although the method is applicable to essentially any C. trachomatis surveillance application that does not require high resolution. CtGEM is a double-locus genotyping method. The loci included in the assay were identified by computerized analysis of 65 complete genomes for resolution optimized sets of single nucleotide polymorphisms (SNPs). From this, two PCR amplifiable fragments were defined. One, rg1, is within a hypothetical gene annotated as Jali-1891 within the C. trachomatis B_Jali20 genome. The other, ofr, is within the ompA gene which encodes the major outer membrane protein. Variation in rg1 is conferred by two SNPs defining four haplotypes that exhibit concordance with genome phylogeny. Variation within ofr is more complex and allows for inference of ompA genotype, either to the level of single genotype, or group of closely related genotypes. Two CtGEM formats were developed. One is based on interrogation of the two loci by high resolution melting analysis (HRMA), and the other based on analysis of the loci by Sanger sequencing. The genotypes defined identify known ocular genotypes, discriminate known ocular genotypes from each other, discriminate the major phylogenetic lineages of the species, and discriminate all ompA genotypes with the exception of closely related variants within the genotypes H, I, J cluster. The Sanger sequencing format provides slightly more resolution that the HRMA format with respect to ompA genotype. An unusual aspect of this method is that all possible combinations of rg1 haplotype, and inferred ompA genotype(s) have been given CtGEM typing numbers. This includes types that at this time have not been shown to exist.
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Epidemiology, Biology, and Impact of Clonal Pseudomonas aeruginosa Infections in Cystic Fibrosis. Clin Microbiol Rev 2018; 31:31/4/e00019-18. [PMID: 30158299 DOI: 10.1128/cmr.00019-18] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Chronic lower airway infection with Pseudomonas aeruginosa is a major contributor to morbidity and mortality in individuals suffering from the genetic disease cystic fibrosis (CF). Whereas it was long presumed that each patient independently acquired unique strains of P. aeruginosa present in their living environment, multiple studies have since demonstrated that shared strains of P. aeruginosa exist among individuals with CF. Many of these shared strains, often referred to as clonal or epidemic strains, can be transmitted from one CF individual to another, potentially reaching epidemic status. Numerous epidemic P. aeruginosa strains have been described from different parts of the world and are often associated with an antibiotic-resistant phenotype. Importantly, infection with these strains often portends a worse prognosis than for infection with nonclonal strains, including an increased pulmonary exacerbation rate, exaggerated lung function decline, and progression to end-stage lung disease. This review describes the global epidemiology of clonal P. aeruginosa strains in CF and summarizes the current literature regarding the underlying biology and clinical impact of globally important CF clones. Mechanisms associated with patient-to-patient transmission are discussed, and best-evidence practices to prevent infections are highlighted. Preventing new infections with epidemic P. aeruginosa strains is of paramount importance in mitigating CF disease progression.
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Giffard PM, Andersson P, Wilson J, Buckley C, Lilliebridge R, Harris TM, Kleinecke M, O’Grady KAF, Huston WM, Lambert SB, Whiley DM, Holt DC. CtGEM typing: Discrimination of Chlamydia trachomatis ocular and urogenital strains and major evolutionary lineages by high resolution melting analysis of two amplified DNA fragments. PLoS One 2018; 13:e0195454. [PMID: 29634761 PMCID: PMC5892870 DOI: 10.1371/journal.pone.0195454] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/22/2018] [Indexed: 12/03/2022] Open
Abstract
Chlamydia trachomatis infects the urogenital tract (UGT) and eyes. Anatomical tropism is correlated with variation in the major outer membrane protein encoded by ompA. Strains possessing the ocular ompA variants A, B, Ba and C are typically found within the phylogenetically coherent “classical ocular lineage”. However, variants B, Ba and C have also been found within three distinct strains in Australia, all associated with ocular disease in children and outside the classical ocular lineage. CtGEM genotyping is a method for detecting and discriminating ocular strains and also the major phylogenetic lineages. The rationale was facilitation of surveillance to inform responses to C. trachomatis detection in UGT specimens from young children. CtGEM typing is based on high resolution melting analysis (HRMA) of two PCR amplified fragments with high combinatorial resolving power, as defined by computerised comparison of 65 whole genomes. One fragment is from the hypothetical gene defined by Jali-1891 in the C. trachomatis B_Jali20 genome, while the other is from ompA. Twenty combinatorial CtGEM types have been shown to exist, and these encompass unique genotypes for all known ocular strains, and also delineate the TI and T2 major phylogenetic lineages, identify LGV strains and provide additional resolution beyond this. CtGEM typing and Sanger sequencing were compared with 42 C. trachomatis positive clinical specimens, and there were no disjunctions. CtGEM typing is a highly efficient method designed and tested using large scale comparative genomics. It divides C. trachomatis into clinically and biologically meaningful groups, and may have broad application in surveillance.
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Affiliation(s)
- Philip M. Giffard
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- School of Psychological and Clinical Sciences, Charles Darwin University, Darwin, Northern Territory, Australia
- * E-mail:
| | - Patiyan Andersson
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Judith Wilson
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Cameron Buckley
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Herston, Queensland, Australia
| | - Rachael Lilliebridge
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Herston, Queensland, Australia
| | - Tegan M. Harris
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Mariana Kleinecke
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Kerry-Ann F. O’Grady
- Centre for Children’s Health Research, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Wilhelmina M. Huston
- School of Life Sciences, University of Technology, Sydney, New South Wales, Australia
| | - Stephen B. Lambert
- UQ Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - David M. Whiley
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Herston, Queensland, Australia
- UQ Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- Pathology Queensland Central Laboratory, Brisbane, Queensland, Australia
| | - Deborah C. Holt
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- School of Psychological and Clinical Sciences, Charles Darwin University, Darwin, Northern Territory, Australia
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Roychowdhury T, Singh VK, Bhattacharya A. Classification of pathogenic microbes using a minimal set of single nucleotide polymorphisms derived from whole genome sequences. Genomics 2018; 111:205-211. [PMID: 29432978 DOI: 10.1016/j.ygeno.2018.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 02/04/2018] [Accepted: 02/08/2018] [Indexed: 11/16/2022]
Abstract
In a context specific manner, Intra-species genomic variation plays an important role in phenotypic diversity observed among pathogenic microbes. Efficient classification of these pathogens is important for diagnosis and treatment of several infectious diseases. NGS technologies have provided access to wealth of data that can be utilized to discover important markers for pathogen classification. In this paper, we described three different approaches (Jensen-Shannon divergence, random forest and Shewhart control chart) for identification of a minimal set of SNPs that can be used for classification of organisms. These methods are generic and can be implemented for analysis of any organism. We have shown usefulness of these approaches for analysis of Mycobacterium tuberculosis and Escherichia coli isolates. We were able to identify a minimal set of 18 SNPs that can be used as molecular markers for phylogroup based classification and 8 SNPs for pathogroup based classification of E. coli.
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Affiliation(s)
- Tanmoy Roychowdhury
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Vinod Kumar Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Alok Bhattacharya
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India; School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
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8
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Larssen KW, Nor A, Bergh K. Rapid discrimination of Staphylococcus epidermidis genotypes in a routine clinical microbiological laboratory using single nucleotide polymorphisms in housekeeping genes. J Med Microbiol 2018; 67:169-182. [PMID: 29293080 DOI: 10.1099/jmm.0.000663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Staphylococcus epidermidis colonies often display several morphologies and antimicrobial susceptibility patterns when cultured from device-related infections, and may represent one or multiple genotypes. Genotyping may be helpful in the clinical interpretation, but is time consuming and expensive. We wanted to establish a method for rapid discrimination of S. epidermidis genotypes for use in a routine microbiology laboratory. METHODOLOGY A real-time PCR targeting eight discriminatory class I or II single-nucleotide polymorphisms (SNPs) in six of the seven housekeeping genes was constructed. Post PCR, high-resolution melt (HRM) analysis using EvaGreen as fluorophore discriminated amplicons based on their percentage GC content. RESULTS In silico, 42 representative sequence types (STs), including all major MLST group and subgroup founders, were separated into 23 different cluster profiles with a Simpson's index of diversity of 0.97. By HRM-PCR, 11 commonly encountered hospital and outbreak STs were separated into eight HRM patterns. CONCLUSION This method can rapidly establish whether S. epidermidis strains belong to different genotypes. It can be used in patients with S. epidermidis infections, as an aid in outbreak investigations and to select strains for investigation with more discriminatory methods, saving workload and costs. Results may be obtained the same day as culture results. Its strength lies mainly in indicating differences, as some STs may have the same melt profile. Changes in S. epidermidis epidemiology may warrant alterations in the inclusion of SNPs. We believe this method can reduce the threshold for performing genotyping analysis on an increasingly important nosocomial pathogen.
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Affiliation(s)
- Kjersti Wik Larssen
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Anne Nor
- Department of Laboratory medicine, Children's and Women's health, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kåre Bergh
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Laboratory medicine, Children's and Women's health, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
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Hewagama S, Spelman T, Woolley M, McLeod J, Gordon D, Einsiedel L. The Epidemiology of Staphylococcus aureus and Panton-Valentine Leucocidin (pvl) in Central Australia, 2006-2010. BMC Infect Dis 2016; 16:382. [PMID: 27502499 PMCID: PMC4977826 DOI: 10.1186/s12879-016-1698-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 07/08/2016] [Indexed: 11/21/2022] Open
Abstract
Background The Central Australian Indigenous population has a high incidence of Staphylococcus aureus bacteremia (SAB) but little is known about the local molecular epidemiology. Methods Prospective observational study of bacteremic and nasal colonizing S.aureus isolates between June 2006 to June 2010. All isolates underwent single nucleotide polymorphism (SNP) genotyping and testing for the presence of the Panton-Valentine Leucocidin (pvl) gene. Results Invasive isolates (n = 97) were predominantly ST93 (26.6 %) and pvl positive (54.3 %), which was associated with skin and soft tissue infections (OR 4.35, 95 % CI 1.16, 16.31). Non-multiresistant MRSA accounted for 31.9 % of bacteremic samples and showed a trend to being healthcare associated (OR 2.16, 95 % CI 0.86, 5.40). Non-invasive isolates (n = 54) were rarely ST93 (1.9 %) or pvl positive (7.4 %). Conclusions In Central Australia, ST93 was the dominant S.aureus clone, and was frequently pvl positive and associated with an aggressive clinical phenotype. Whether non-nasal carriage is more important with invasive clones or whether colonization occurs only transiently remains to be elucidated.
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Affiliation(s)
- S Hewagama
- Alice Springs Hospital, Alice Springs, NT, Australia.
| | - T Spelman
- Flinders University/Northern Territory Rural Clinical School, Alice Springs, NT, Australia
| | | | - J McLeod
- Alice Springs Hospital, Alice Springs, NT, Australia.,NT Pathology, Alice Springs, NT, Australia
| | - D Gordon
- SA Pathology, Adelaide, Australia
| | - L Einsiedel
- Alice Springs Hospital, Alice Springs, NT, Australia.,Flinders University/Northern Territory Rural Clinical School, Alice Springs, NT, Australia.,Baker IDI Heart and Diabetes Institute, Alice Springs, NT, Australia
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10
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Tolo I, Thomas JC, Fischer RSB, Brown EL, Gray BM, Robinson DA. Do Staphylococcus epidermidis Genetic Clusters Predict Isolation Sources? J Clin Microbiol 2016; 54:1711-1719. [PMID: 27076664 PMCID: PMC4922092 DOI: 10.1128/jcm.03345-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/07/2016] [Indexed: 12/24/2022] Open
Abstract
Staphylococcus epidermidis is a ubiquitous colonizer of human skin and a common cause of medical device-associated infections. The extent to which the population genetic structure of S. epidermidis distinguishes commensal from pathogenic isolates is unclear. Previously, Bayesian clustering of 437 multilocus sequence types (STs) in the international database revealed a population structure of six genetic clusters (GCs) that may reflect the species' ecology. Here, we first verified the presence of six GCs, including two (GC3 and GC5) with significant admixture, in an updated database of 578 STs. Next, a single nucleotide polymorphism (SNP) assay was developed that accurately assigned 545 (94%) of 578 STs to GCs. Finally, the hypothesis that GCs could distinguish isolation sources was tested by SNP typing and GC assignment of 154 isolates from hospital patients with bacteremia and those with blood culture contaminants and from nonhospital carriage. GC5 was isolated almost exclusively from hospital sources. GC1 and GC6 were isolated from all sources but were overrepresented in isolates from nonhospital and infection sources, respectively. GC2, GC3, and GC4 were relatively rare in this collection. No association was detected between fdh-positive isolates (GC2 and GC4) and nonhospital sources. Using a machine learning algorithm, GCs predicted hospital and nonhospital sources with 80% accuracy and predicted infection and contaminant sources with 45% accuracy, which was comparable to the results seen with a combination of five genetic markers (icaA, IS256, sesD [bhp], mecA, and arginine catabolic mobile element [ACME]). Thus, analysis of population structure with subgenomic data shows the distinction of hospital and nonhospital sources and the near-inseparability of sources within a hospital.
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Affiliation(s)
- Isaiah Tolo
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | | | - Rebecca S B Fischer
- Center for Infectious Disease, University of Texas Health Science Center, Houston, Texas, USA
| | - Eric L Brown
- Center for Infectious Disease, University of Texas Health Science Center, Houston, Texas, USA
| | - Barry M Gray
- Department of Pediatrics, University of Illinois College of Medicine at Peoria, Peoria, Illinois, USA
| | - D Ashley Robinson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, USA
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Liu R, Liu Z, Xu Y, Liao Y, Hu Q, Huang J, Shi X, Li Y, Niu J, Li Q. Multicolor Melting Curve Analysis-Based Multilocus Melt Typing of Vibrio parahaemolyticus. PLoS One 2015; 10:e0136998. [PMID: 26368129 PMCID: PMC4569271 DOI: 10.1371/journal.pone.0136998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 08/11/2015] [Indexed: 12/02/2022] Open
Abstract
Vibrio parahaemolyticus is the leading cause of seafood-borne gastroenteritis outbreaks. To track the source of these diseases in a timely manner, a high throughput typing method is critical. We hereby describe a novel genotyping method for V. parahaemolyticus, termed multilocus melt typing (MLMT), based on multilocus sequence typing (MLST). MLMT utilizes melting curve analysis to interrogate the allelic types of a set of informative single nucleotide polymorphisms (SNPs) derived from the housekeeping genes used in MLST. For each SNP, one allelic type generates distinct Tm values, which are converted into a binary code. Multiple SNPs thus generate a series of binary codes, forming a melt type (MT) corresponding with a sequence type (ST) of MLST. Using a set of 12 SNPs, the MLMT scheme could resolve 218 V.parahaemolyticus isolates into 50 MTs corresponding with 56 STs. The discriminatory power of MLMT and MLST was similar with Simpson’s index of diversity of 0.638 and 0.646, respectively. The global (adjusted Rand index = 0.982) and directional congruence (adjusted Wallace coefficient, MT→ST = 0.965; ST→MT = 1.000) between the two typing approaches was high. The entire procedure of MLMT could be finished within 3 h with negligible hands on time in a real-time PCR machine. We conclude that MLMT provides a reliable and efficient approach for V. parahaemolyticus genotyping and might also find use in other pathogens.
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Affiliation(s)
- Ran Liu
- Engineering Research Centre of Molecular Diagnostics, Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Zanzan Liu
- Engineering Research Centre of Molecular Diagnostics, Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Ye Xu
- Engineering Research Centre of Molecular Diagnostics, Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yiqun Liao
- Engineering Research Centre of Molecular Diagnostics, Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostic, School of Public Health, Xiamen University, Xiamen, Fujian, China
| | - Qinghua Hu
- Shenzhen Major Infectious Disease Control Key Laboratory, Shenzhen Centre for Disease Control and Prevention, Shenzhen, Guangdong, China
- School of Life Sciences, Shenzhen University, Shenzhen, Guangdong, China
| | - Jianwei Huang
- Xiamen Center for Disease Control and Prevention, Xiamen, Fujian, China
| | - Xiaolu Shi
- Shenzhen Major Infectious Disease Control Key Laboratory, Shenzhen Centre for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Yinghui Li
- Shenzhen Major Infectious Disease Control Key Laboratory, Shenzhen Centre for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Jianjun Niu
- Zhongshan Hospital of Xiamen, Xiamen University, Xiamen, Fujian, China
- * E-mail: (JN); (QL)
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics, Ministry of Education, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostic, School of Public Health, Xiamen University, Xiamen, Fujian, China
- Shenzhen Research Institute of Xiamen University, Shenzhen, Guangdong, China
- * E-mail: (JN); (QL)
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12
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Rayner RE, Savill J, Hafner LM, Huygens F. Genotyping Streptococcus pneumoniae. Future Microbiol 2015; 10:653-64. [DOI: 10.2217/fmb.14.153] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
ABSTRACT Streptococcus pneumoniae is a potentially deadly human pathogen associated with high morbidity, mortality and global economic burden. The universally used bacterial genotyping methods are multilocus sequence typing and pulsed field gel electrophoresis. However, another highly discriminatory, rapid and less expensive genotyping technique, multilocus variable number of tandem repeat analysis (MLVA), has been developed. Unfortunately, no universal MLVA protocol exists, and some MLVA protocols do not amplify certain loci for all pneumococcal serotypes, leaving genotyping profiles incomplete. A number of other genotyping or characterization methods have been developed and will be discussed. This review examines the various protocols for genotyping S. pneumoniae and highlights the current direction technology and research is heading to understand this bacterium.
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Affiliation(s)
- Rachael E Rayner
- Institute of Health & Biomedical Innovation (IHBI), 60 Musk Ave, Kelvin Grove, 4059, Queensland, Australia
| | - John Savill
- Public Health Microbiology Laboratory, Queensland Health Forensic & Scientific Services, Coopers Plains, Queensland, Australia
| | - Louise M Hafner
- Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Flavia Huygens
- Institute of Health & Biomedical Innovation (IHBI), 60 Musk Ave, Kelvin Grove, 4059, Queensland, Australia
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13
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Xu D, Sun L, Liu S, Zhang L, Yang H. Polymorphisms of heat shock protein 90 (Hsp90) in the sea cucumber Apostichopus japonicus and their association with heat-resistance. FISH & SHELLFISH IMMUNOLOGY 2014; 41:428-436. [PMID: 25270529 DOI: 10.1016/j.fsi.2014.09.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/09/2014] [Accepted: 09/20/2014] [Indexed: 06/03/2023]
Abstract
Heat shock protein 90 (Hsp90) functions as a molecular chaperone and plays an important role in the resistance of organisms to stress, particularly heat-stress. In our study, 12 exons and 11 introns of hsp90 were identified in the sea cucumber Apostichopus japonicus. Twenty-two single nucleotide polymorphisms (SNPs), including three non-synonymous mutations, were detected in the exons. Susceptible and resistant individuals were distinguished using a high-temperature (32 °C) challenge experiment. Three blocks with high linkage disequilibrium were detected among these SNPs. Five of the twenty-two SNPs were shown to be significantly associated with susceptibility/resistance to high temperature by correlation analysis (chi-square test, P < 0.05). To confirm the importance of these five SNPs, a heat-resistance strain (HRS) was selected through three generations. Using the common population as the control group, it was shown that the distributions of genotypes and alleles of SNP e10-1 and e11-6 were significantly different between the two groups (P < 0.05). SNP e10-1 was trimorphic, with three alleles (A, C and T) and five genotypes (AA, CC, AT, CT and AC). The allele frequency of SNP e2-3 was also significantly associated with this trait (P < 0.05). This is the first demonstration of SNPs related to heat-resistance in A. japonicus and supports the use of SNP markers in the selective breeding of sea cucumbers.
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Affiliation(s)
- Dongxue Xu
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Lina Sun
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China
| | - Shilin Liu
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China
| | - Libin Zhang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China
| | - Hongsheng Yang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China.
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14
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Syrmis MW, Kidd TJ, Moser RJ, Ramsay KA, Gibson KM, Anuj S, Bell SC, Wainwright CE, Grimwood K, Nissen M, Sloots TP, Whiley DM. A comparison of two informative SNP-based strategies for typing Pseudomonas aeruginosa isolates from patients with cystic fibrosis. BMC Infect Dis 2014; 14:307. [PMID: 24902856 PMCID: PMC4053291 DOI: 10.1186/1471-2334-14-307] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 05/28/2014] [Indexed: 12/26/2022] Open
Abstract
Background Molecular typing is integral for identifying Pseudomonas aeruginosa strains that may be shared between patients with cystic fibrosis (CF). We conducted a side-by-side comparison of two P. aeruginosa genotyping methods utilising informative-single nucleotide polymorphism (SNP) methods; one targeting 10 P. aeruginosa SNPs and using real-time polymerase chain reaction technology (HRM10SNP) and the other targeting 20 SNPs and based on the Sequenom MassARRAY platform (iPLEX20SNP). Methods An in-silico analysis of the 20 SNPs used for the iPLEX20SNP method was initially conducted using sequence type (ST) data on the P. aeruginosa PubMLST website. A total of 506 clinical isolates collected from patients attending 11 CF centres throughout Australia were then tested by both the HRM10SNP and iPLEX20SNP assays. Type-ability and discriminatory power of the methods, as well as their ability to identify commonly shared P. aeruginosa strains, were compared. Results The in-silico analyses showed that the 1401 STs available on the PubMLST website could be divided into 927 different 20-SNP profiles (D-value = 0.999), and that most STs of national or international importance in CF could be distinguished either individually or as belonging to closely related single- or double-locus variant groups. When applied to the 506 clinical isolates, the iPLEX20SNP provided better discrimination over the HRM10SNP method with 147 different 20-SNP and 92 different 10-SNP profiles observed, respectively. For detecting the three most commonly shared Australian P. aeruginosa strains AUST-01, AUST-02 and AUST-06, the two methods were in agreement for 80/81 (98.8%), 48/49 (97.8%) and 11/12 (91.7%) isolates, respectively. Conclusions The iPLEX20SNP is a superior new method for broader SNP-based MLST-style investigations of P. aeruginosa. However, because of convenience and availability, the HRM10SNP method remains better suited for clinical microbiology laboratories that only utilise real-time PCR technology and where the main interest is detection of the most highly-prevalent P. aeruginosa CF strains within Australian clinics.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - David M Whiley
- Queensland Children's Medical Research Institute, The University of Queensland, Brisbane, Queensland 4029, Australia.
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15
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O'Sullivan MVN, Sintchenko V, Gilbert GL. Software for selecting the most informative sets of genomic loci for multi-target microbial typing. BMC Bioinformatics 2013; 14:148. [PMID: 23635100 PMCID: PMC3660239 DOI: 10.1186/1471-2105-14-148] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 04/30/2013] [Indexed: 11/17/2022] Open
Abstract
Background High-throughput sequencing can identify numerous potential genomic targets for microbial strain typing, but identification of the most informative combinations requires the use of computational screening tools. This paper describes novel software – Automated Selection of Typing Target Subsets (AuSeTTS) - that allows intelligent selection of optimal targets for pathogen strain typing. The objective of this software is to maximise both discriminatory power, using Simpson’s index of diversity (D), and concordance with existing typing methods, using the adjusted Wallace coefficient (AW). The program interrogates molecular typing results for panels of isolates, based on large target sets, and iteratively examines each target, one-by-one, to determine the most informative subset. Results AuSeTTS was evaluated using three target sets: 51 binary targets (13 toxin genes, 16 phage-related loci and 22 SCCmec elements), used for multilocus typing of 153 methicillin-resistant Staphylococcus aureus (MRSA) isolates; 17 MLVA loci in 502 Streptococcus pneumoniae isolates from the MLVA database (http://www.mlva.eu) and 12 MLST loci for 98 Cryptococcus spp. isolates. The maximum D for MRSA, 0.984, was achieved with a subset of 20 targets and a D value of 0.954 with 7 targets. Twelve targets predicted MLST with a maximum AW of 0.9994. All 17 S. pneumoniae MLVA targets were required to achieve maximum D of 0.997, but 4 targets reached D of 0.990. Twelve targets predicted pneumococcal serotype with a maximum AW of 0.899 and 9 predicted MLST with maximum AW of 0.963. Eight of the 12 MLST loci were sufficient to achieve the maximum D of 0.963 for Cryptococcus spp. Conclusions Computerised analysis with AuSeTTS allows rapid selection of the most discriminatory targets for incorporation into typing schemes. Output of the program is presented in both tabular and graphical formats and the software is available for free download from http://www.cidmpublichealth.org/pages/ausetts.html.
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Affiliation(s)
- Matthew V N O'Sullivan
- Centre for Infectious Diseases and Microbiology and Sydney Institute for Emerging Infections and Biosecurity, University of Sydney, Westmead Hospital, Hawkesbury Road, Westmead, NSW 2145, Australia.
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16
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Fujii H, Ogata T, Shimada T, Endo T, Iketani H, Shimizu T, Yamamoto T, Omura M. Minimal marker: an algorithm and computer program for the identification of minimal sets of discriminating DNA markers for efficient variety identification. J Bioinform Comput Biol 2012; 11:1250022. [PMID: 23600813 DOI: 10.1142/s0219720012500229] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
DNA markers are frequently used to analyze crop varieties, with the coded marker data summarized in a computer-generated table. Such summary tables often provide extraneous data about individual crop genotypes, needlessly complicating and prolonging DNA-based differentiation between crop varieties. At present, it is difficult to identify minimal marker sets--the smallest sets that can distinguish between all crop varieties listed in a marker-summary table--due to the absence of algorithms capable of such characterization. Here, we describe the development of just such an algorithm and MinimalMarker, its accompanying Perl-based computer program. MinimalMarker has been validated in variety identification of fruit trees using published datasets and is available for use with both dominant and co-dominant markers, regardless of the number of alleles, including SSR markers with numeric notation. We expect that this program will prove useful not only to genomics researchers but also to government agencies that use DNA markers to support a variety of food-inspection and -labeling regulations.
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Affiliation(s)
- Hiroshi Fujii
- Citrus Research Division, NARO Institute of Fruit Tree Science, National Agriculture and Food Research Organization, 485-6 Okitsunaka-cho, Shimizu-ku, Shizuoka 424-0292, Japan.
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17
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Ahmed MU, Dunn L, Ivanova EP. Evaluation of Current Molecular Approaches for Genotyping ofCampylobacter jejuniStrains. Foodborne Pathog Dis 2012; 9:375-85. [DOI: 10.1089/fpd.2011.0988] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Monir U. Ahmed
- Faculty of Life & Social Sciences, Swinburne University of Technology, Hawthorn, Australia
| | - Louise Dunn
- Faculty of Life & Social Sciences, Swinburne University of Technology, Hawthorn, Australia
| | - Elena P. Ivanova
- Faculty of Life & Social Sciences, Swinburne University of Technology, Hawthorn, Australia
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18
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Minim typing--a rapid and low cost MLST based typing tool for Klebsiella pneumoniae. PLoS One 2012; 7:e33530. [PMID: 22428067 PMCID: PMC3299796 DOI: 10.1371/journal.pone.0033530] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Accepted: 02/15/2012] [Indexed: 11/25/2022] Open
Abstract
Here we report a single nucleotide polymorphism (SNP) based genotyping method for Klebsiella pneumoniae utilising high-resolution melting (HRM) analysis of fragments within the multilocus sequence typing (MLST) loci. The approach is termed mini-MLST or Minim typing and it has previously been applied to Streptococcus pyogenes, Staphylococcus aureus and Enterococcus faecium. Six SNPs were derived from concatenated MLST sequences on the basis of maximisation of the Simpsons Index of Diversity (D). DNA fragments incorporating these SNPs and predicted to be suitable for HRM analysis were designed. Using the assumption that HRM alleles are defined by G+C content, Minim typing using six fragments was predicted to provide a D = 0.979 against known STs. The method was tested against 202 K. pneumoniae using a blinded approach in which the MLST analyses were performed after the HRM analyses. The HRM-based alleles were indeed in accordance with G+C content, and the Minim typing identified known STs and flagged new STs. The tonB MLST locus was determined to be very diverse, and the two Minim fragments located herein contribute greatly to the resolving power. However these fragments are refractory to amplification in a minority of isolates. Therefore, we assessed the performance of two additional formats: one using only the four fragments located outside the tonB gene (D = 0.929), and the other using HRM data from these four fragments in conjunction with sequencing of the tonB MLST fragment (D = 0.995). The HRM assays were developed on the Rotorgene 6000, and the method was shown to also be robust on the LightCycler 480, allowing a 384-well high through-put format. The assay provides rapid, robust and low-cost typing with fully portable results that can directly be related to current MLST data. Minim typing in combination with molecular screening for antibiotic resistance markers can be a powerful surveillance tool kit.
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19
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Tong SYC, Xie S, Richardson LJ, Ballard SA, Dakh F, Grabsch EA, Grayson ML, Howden BP, Johnson PDR, Giffard PM. High-resolution melting genotyping of Enterococcus faecium based on multilocus sequence typing derived single nucleotide polymorphisms. PLoS One 2011; 6:e29189. [PMID: 22195020 PMCID: PMC3241712 DOI: 10.1371/journal.pone.0029189] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 11/22/2011] [Indexed: 11/18/2022] Open
Abstract
We have developed a single nucleotide polymorphism (SNP) nucleated high-resolution melting (HRM) technique to genotype Enterococcus faecium. Eight SNPs were derived from the E. faecium multilocus sequence typing (MLST) database and amplified fragments containing these SNPs were interrogated by HRM. We tested the HRM genotyping scheme on 85 E. faecium bloodstream isolates and compared the results with MLST, pulsed-field gel electrophoresis (PFGE) and an allele specific real-time PCR (AS kinetic PCR) SNP typing method. In silico analysis based on predicted HRM curves according to the G+C content of each fragment for all 567 sequence types (STs) in the MLST database together with empiric data from the 85 isolates demonstrated that HRM analysis resolves E. faecium into 231 "melting types" (MelTs) and provides a Simpson's Index of Diversity (D) of 0.991 with respect to MLST. This is a significant improvement on the AS kinetic PCR SNP typing scheme that resolves 61 SNP types with D of 0.95. The MelTs were concordant with the known ST of the isolates. For the 85 isolates, there were 13 PFGE patterns, 17 STs, 14 MelTs and eight SNP types. There was excellent concordance between PFGE, MLST and MelTs with Adjusted Rand Indices of PFGE to MelT 0.936 and ST to MelT 0.973. In conclusion, this HRM based method appears rapid and reproducible. The results are concordant with MLST and the MLST based population structure.
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Affiliation(s)
- Steven Y C Tong
- Menzies School of Health Research, Darwin, Northern Territory, Australia.
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20
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Sheludchenko MS, Huygens F, Hargreaves MH. Human-specific E.coli single nucleotide polymorphism (SNP) genotypes detected in a South East Queensland waterway, Australia. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:10331-10336. [PMID: 22029388 DOI: 10.1021/es201599u] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The World Health Organization recommends that the majority of water monitoring laboratories in the world test for E. coli daily since thermotolerant coliforms and E. coli are key indicators for risk assessment of recreational waters. Recently, we developed a new SNP method for typing E. coli strains, by which human-specific genotypes were identified. Here, we report the presence of these previously described specific SNP profiles in environmental water, sourced from the Coomera River, located in South East Queensland, Australia, over a period of two years. This study tested for the presence of human-specific E. coli to ascertain whether hydrologic and anthropogenic activity plays a key role in the pollution of the investigated watershed or whether the pollution is from other sources. We found six human-specific SNP profiles and one animal-specific SNP profile consistently across sampling sites and times. We have demonstrated that our SNP genotyping method is able to rapidly identify and characterize human- and animal-specific E. coli isolates in water sources.
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Affiliation(s)
- Maxim S Sheludchenko
- Cell and Molecular Biosciences, Faculty of Science and Technology, Queensland University of Technology, Brisbane, Queensland, Australia
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21
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Dale J, Price EP, Hornstra H, Busch JD, Mayo M, Godoy D, Wuthiekanun V, Baker A, Foster JT, Wagner DM, Tuanyok A, Warner J, Spratt BG, Peacock SJ, Currie BJ, Keim P, Pearson T. Epidemiological tracking and population assignment of the non-clonal bacterium, Burkholderia pseudomallei. PLoS Negl Trop Dis 2011; 5:e1381. [PMID: 22180792 PMCID: PMC3236730 DOI: 10.1371/journal.pntd.0001381] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 09/16/2011] [Indexed: 11/24/2022] Open
Abstract
Rapid assignment of bacterial pathogens into predefined populations is an important first step for epidemiological tracking. For clonal species, a single allele can theoretically define a population. For non-clonal species such as Burkholderia pseudomallei, however, shared allelic states between distantly related isolates make it more difficult to identify population defining characteristics. Two distinct B. pseudomallei populations have been previously identified using multilocus sequence typing (MLST). These populations correlate with the major foci of endemicity (Australia and Southeast Asia). Here, we use multiple Bayesian approaches to evaluate the compositional robustness of these populations, and provide assignment results for MLST sequence types (STs). Our goal was to provide a reference for assigning STs to an established population without the need for further computational analyses. We also provide allele frequency results for each population to enable estimation of population assignment even when novel STs are discovered. The ability for humans and potentially contaminated goods to move rapidly across the globe complicates the task of identifying the source of an infection or outbreak. Population genetic dynamics of B. pseudomallei are particularly complicated relative to other bacterial pathogens, but the work here provides the ability for broad scale population assignment. As there is currently no independent empirical measure of successful population assignment, we provide comprehensive analytical details of our comparisons to enable the reader to evaluate the robustness of population designations and assignments as they pertain to individual research questions. Finer scale subdivision and verification of current population compositions will likely be possible with genotyping data that more comprehensively samples the genome. The approach used here may be valuable for other non-clonal pathogens that lack simple group-defining genetic characteristics and provides a rapid reference for epidemiologists wishing to track the origin of infection without the need to compile population data and learn population assignment algorithms. Burkholderia pseudomallei is a soil-dwelling bacterium that can infect a large range of hosts. In humans, B. pseudomallei causes melioidosis, and typical routes of entry include open wounds, inhalation, or ingestion. Clinical features are diverse, although pneumonia and abscess formation are common. High rates of recombination within the genome of this bacterium have confounded attempts to match clinical samples to geographically defined populations. Here we provide a reference that simplifies source attribution issues. We applied population assignment software to previously generated sequence data from seven B. pseudomallei genes to define the major geographic populations within this species. We evaluated the robustness of our results by comparison with two additional population assignment programs. We present the likelihood that each variant is assigned to a particular geographic population. This information can be used to assign novel B. pseudomallei isolates to a geographic population without needing to learn and run cumbersome population assignment applications. This method can also be used for other bacteria that are difficult to source-attribute due to high levels of genomic variation and recombination.
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Affiliation(s)
- Julia Dale
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Erin P. Price
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Heidie Hornstra
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Joseph D. Busch
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Mark Mayo
- Menzies School of Health Research and Northern Territory Clinical School, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Daniel Godoy
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Anthony Baker
- Microbiology and Immunology, School of Veterinary and Biomedical Sciences, James Cook University, Townsville, Queensland, Australia
| | - Jeffrey T. Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - David M. Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Apichai Tuanyok
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jeffrey Warner
- Microbiology and Immunology, School of Veterinary and Biomedical Sciences, James Cook University, Townsville, Queensland, Australia
| | - Brian G. Spratt
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Sharon J. Peacock
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Bart J. Currie
- Menzies School of Health Research and Northern Territory Clinical School, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Talima Pearson
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail:
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Fernández-Romero N, Romero-Gómez MP, Gómez-Gil MR, Mingorance J. Epidemic population structure of extraintestinal pathogenic Escherichia coli determined by single nucleotide polymorphism pyrosequencing. INFECTION GENETICS AND EVOLUTION 2011; 11:1655-63. [PMID: 21723423 DOI: 10.1016/j.meegid.2011.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 06/10/2011] [Accepted: 06/16/2011] [Indexed: 12/01/2022]
Abstract
We have developed an MLST-based scheme for typing Escherichia coli isolates using pyrosequencing of single nucleotide polymorphic positions (SNP). The SNP sequences are converted into allelic patterns and analyzed using the same approach used for MLST analyses. We have tested the method in two unselected collections of clinical isolates of E. coli obtained from blood and urine cultures. The two collections had a similar structure, 25% of the profiles (representing 68% of the isolates) were common to both, and 62% of the profiles (nearly 20% of the isolates) were unique. The four major profiles accounted for 44% of the isolates, and among these the most frequent one was related to the pandemic ST131 clone. The method is easy to implement and might be useful for typing large microbial collections.
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Affiliation(s)
- Natalia Fernández-Romero
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana, Madrid, Spain
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23
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Lilliebridge RA, Tong SY, Giffard PM, Holt DC. The utility of high-resolution melting analysis of SNP nucleated PCR amplicons--an MLST based Staphylococcus aureus typing scheme. PLoS One 2011; 6:e19749. [PMID: 21731606 PMCID: PMC3120814 DOI: 10.1371/journal.pone.0019749] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 04/15/2011] [Indexed: 11/19/2022] Open
Abstract
High resolution melting (HRM) analysis is gaining prominence as a method for discriminating DNA sequence variants. Its advantage is that it is performed in a real-time PCR device, and the PCR amplification and HRM analysis are closed tube, and effectively single step. We have developed an HRM-based method for Staphylococcus aureus genotyping. Eight single nucleotide polymorphisms (SNPs) were derived from the S. aureus multi-locus sequence typing (MLST) database on the basis of maximized Simpson's Index of Diversity. Only G↔A, G↔T, C↔A, C↔T SNPs were considered for inclusion, to facilitate allele discrimination by HRM. In silico experiments revealed that DNA fragments incorporating the SNPs give much higher resolving power than randomly selected fragments. It was shown that the predicted optimum fragment size for HRM analysis was 200 bp, and that other SNPs within the fragments contribute to the resolving power. Six DNA fragments ranging from 83 bp to 219 bp, incorporating the resolution optimized SNPs were designed. HRM analysis of these fragments using 94 diverse S. aureus isolates of known sequence type or clonal complex (CC) revealed that sequence variants are resolved largely in accordance with G+C content. A combination of experimental results and in silico prediction indicates that HRM analysis resolves S. aureus into 268 “melt types” (MelTs), and provides a Simpson's Index of Diversity of 0.978 with respect to MLST. There is a high concordance between HRM analysis and the MLST defined CCs. We have generated a Microsoft Excel key which facilitates data interpretation and translation between MelT and MLST data. The potential of this approach for genotyping other bacterial pathogens was investigated using a computerized approach to estimate the densities of SNPs with unlinked allelic states. The MLST databases for all species tested contained abundant unlinked SNPs, thus suggesting that high resolving power is not dependent upon large numbers of SNPs.
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Affiliation(s)
- Rachael A. Lilliebridge
- Tropical and Emerging Infectious Diseases Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Steven Y.C. Tong
- Tropical and Emerging Infectious Diseases Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Philip M. Giffard
- Tropical and Emerging Infectious Diseases Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Deborah C. Holt
- Tropical and Emerging Infectious Diseases Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- * E-mail:
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24
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Fevre C, Passet V, Deletoile A, Barbe V, Frangeul L, Almeida AS, Sansonetti P, Tournebize R, Brisse S. PCR-based identification of Klebsiella pneumoniae subsp. rhinoscleromatis, the agent of rhinoscleroma. PLoS Negl Trop Dis 2011; 5:e1052. [PMID: 21629720 PMCID: PMC3101168 DOI: 10.1371/journal.pntd.0001052] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 04/26/2011] [Indexed: 11/21/2022] Open
Abstract
Rhinoscleroma is a chronic granulomatous infection of the upper airways caused by the bacterium Klebsiella pneumoniae subsp. rhinoscleromatis. The disease is endemic in tropical and subtropical areas, but its diagnosis remains difficult. As a consequence, and despite available antibiotherapy, some patients evolve advanced stages that can lead to disfiguration, severe respiratory impairment and death by anoxia. Because identification of the etiologic agent is crucial for the definitive diagnosis of the disease, the aim of this study was to develop two simple PCR assays. We took advantage of the fact that all Klebsiella pneumoniae subsp. rhinoscleromatis isolates are (i) of capsular serotype K3; and (ii) belong to a single clone with diagnostic single nucleotide polymorphisms (SNP). The complete sequence of the genomic region comprising the capsular polysaccharide synthesis (cps) gene cluster was determined. Putative functions of the 21 genes identified were consistent with the structure of the K3 antigen. The K3-specific sequence of gene Kr11509 (wzy) was exploited to set up a PCR test, which was positive for 40 K3 strains but negative when assayed on the 76 other Klebsiella capsular types. Further, to discriminate Klebsiella pneumoniae subsp. rhinoscleromatis from other K3 Klebsiella strains, a specific PCR assay was developed based on diagnostic SNPs in the phosphate porin gene phoE. This work provides rapid and simple molecular tools to confirm the diagnostic of rhinoscleroma, which should improve patient care as well as knowledge on the prevalence and epidemiology of rhinoscleroma.
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Affiliation(s)
- Cindy Fevre
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
| | - Virginie Passet
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
| | - Alexis Deletoile
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
| | | | - Lionel Frangeul
- Institut Pasteur, Intégration et Analyse Génomique, Paris, France
| | - Ana S. Almeida
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, Paris, France
- Unité INSERM U786, Institut Pasteur, Paris, France
| | - Philippe Sansonetti
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, Paris, France
- Unité INSERM U786, Institut Pasteur, Paris, France
| | - Régis Tournebize
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, Paris, France
- Unité INSERM U786, Institut Pasteur, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
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25
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Richardson LJ, Tong SYC, Towers RJ, Huygens F, McGregor K, Fagan PK, Currie BJ, Carapetis JR, Giffard PM. Preliminary validation of a novel high-resolution melt-based typing method based on the multilocus sequence typing scheme of Streptococcus pyogenes. Clin Microbiol Infect 2011; 17:1426-34. [PMID: 21091832 DOI: 10.1111/j.1469-0691.2010.03433.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The major limitation of current typing methods for Streptococcus pyogenes, such as emm sequence typing and T typing, is that these are based on regions subject to considerable selective pressure. Multilocus sequence typing (MLST) is a better indicator of the genetic backbone of a strain but is not widely used due to high costs. The objective of this study was to develop a robust and cost-effective alternative to S. pyogenes MLST. A 10-member single nucleotide polymorphism (SNP) set that provides a Simpson's Index of Diversity (D) of 0.99 with respect to the S. pyogenes MLST database was derived. A typing format involving high-resolution melting (HRM) analysis of small fragments nucleated by each of the resolution-optimized SNPs was developed. The fragments were 59-119 bp in size and, based on differences in G+C content, were predicted to generate three to six resolvable HRM curves. The combination of curves across each of the 10 fragments can be used to generate a melt type (MelT) for each sequence type (ST). The 525 STs currently in the S. pyogenes MLST database are predicted to resolve into 298 distinct MelTs and the method is calculated to provide a D of 0.996 against the MLST database. The MelTs are concordant with the S. pyogenes population structure. To validate the method we examined clinical isolates of S. pyogenes of 70 STs. Curves were generated as predicted by G+C content discriminating the 70 STs into 65 distinct MelTs.
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Affiliation(s)
- L J Richardson
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
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26
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Genotyping of Enterococcus faecalis and Enterococcus faecium isolates by use of a set of eight single nucleotide polymorphisms. J Clin Microbiol 2010; 49:367-72. [PMID: 20980566 DOI: 10.1128/jcm.01120-10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A single nucleotide polymorphism (SNP) genotyping method for Enterococcus faecalis and Enterococcus faecium was developed using the "Minimum SNPs" program. SNP sets were interrogated using allele-specific real-time PCR. SNP typing subdivided clonal complexes 2 and 9 of E. faecalis and 17 of E. faecium, members of which cause the majority of nosocomial infections globally.
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Travers KJ, Chin CS, Rank DR, Eid JS, Turner SW. A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res 2010; 38:e159. [PMID: 20571086 PMCID: PMC2926623 DOI: 10.1093/nar/gkq543] [Citation(s) in RCA: 273] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A novel template design for single-molecule sequencing is introduced, a structure we refer to as a SMRTbell™ template. This structure consists of a double-stranded portion, containing the insert of interest, and a single-stranded hairpin loop on either end, which provides a site for primer binding. Structurally, this format resembles a linear double-stranded molecule, and yet it is topologically circular. When placed into a single-molecule sequencing reaction, the SMRTbell template format enables a consensus sequence to be obtained from multiple passes on a single molecule. Furthermore, this consensus sequence is obtained from both the sense and antisense strands of the insert region. In this article, we present a universal method for constructing these templates, as well as an application of their use. We demonstrate the generation of high-quality consensus accuracy from single molecules, as well as the use of SMRTbell templates in the identification of rare sequence variants.
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Highly discriminatory single-nucleotide polymorphism interrogation of Escherichia coli by use of allele-specific real-time PCR and eBURST analysis. Appl Environ Microbiol 2010; 76:4337-45. [PMID: 20453128 DOI: 10.1128/aem.00128-10] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In total, 782 Escherichia coli strains originating from various host sources have been analyzed in this study by using a highly discriminatory single-nucleotide polymorphism (SNP) approach. A set of eight SNPs, with a discrimination value (Simpson's index of diversity [D]) of 0.96, was determined using the Minimum SNPs software, based on sequences of housekeeping genes from the E. coli multilocus sequence typing (MLST) database. Allele-specific real-time PCR was used to screen 114 E. coli isolates from various fecal sources in Southeast Queensland (SEQ). The combined analysis of both the MLST database and SEQ E. coli isolates using eight high-D SNPs resolved the isolates into 74 SNP profiles. The data obtained suggest that SNP typing is a promising approach for the discrimination of host-specific groups and allows for the identification of human-specific E. coli in environmental samples. However, a more diverse E. coli collection is required to determine animal- and environment-specific E. coli SNP profiles due to the abundance of human E. coli strains (56%) in the MLST database.
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Petersen A, Bisgaard M, Christensen H. Real-time PCR detection of Enterococcus faecalis associated with amyloid arthropathy. Lett Appl Microbiol 2010; 51:61-4. [PMID: 20497496 DOI: 10.1111/j.1472-765x.2010.02861.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AIMS To develop a RT-PCR method for detection of the multilocus sequence type 82 of Enterococcus faecalis associated with amyloid arthropathy (AA) in layers. METHODS AND RESULTS Bacteria were selected from lesions including AA in layers. The primers were designed based on the phosphate ATP binding cassette transporter (pstS) and xanthine phosphoribosyltransferase (xpt) genes and first tested against three isolates with known base pairs at the specific sites. Subsequently, 12 isolates were selected from our collection by one researcher, and RT-PCR was performed blinded. The sequence type (ST) was then confirmed by multilocus sequence analysis. Two single-nucleotide polymorphisms in the pstS and xpt genes allowed an unambiguous identification of ST82. As an alternative to DNA extraction, a boiling method for release of DNA from cells was used. CONCLUSIONS The real-time PCR targeting ST82 enables rapid screening of Ent. faecalis cultured from suspect cases with results available after a few hours, much faster than multilocus sequence typing and pulse field gel electrophoresis. SIGNIFICANCE AND IMPACT OF THE STUDY The new method allows a rapid screening of isolates with results available after only few hours. This RT-PCR method could be a useful tool for molecular epidemiological studies on the spread of arthropathic and amyloidogenic Ent. faecalis within and between birds more efficiently.
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Affiliation(s)
- A Petersen
- Department of Veterinary Disease Biology, Faculty of Life Sciences, University of Copenhagen, Copenhagen, Denmark
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30
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Development of a multiplex primer extension assay for rapid detection of Salmonella isolates of diverse serotypes. J Clin Microbiol 2010; 48:1055-60. [PMID: 20164272 DOI: 10.1128/jcm.01566-09] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Food-borne salmonellosis is a major manifestation of gastrointestinal disease in humans across the globe. Accurate and rapid identification methods could positively impact the identification of isolates, enhance outbreak investigation, and aid infection control. The SNaPshot multiplex system is a primer extension-based method that enables multiplexing of single nucleotide polymorphisms (SNPs). Here the method has been developed for the identification of five Salmonella serotypes, commonly detected in the United Kingdom, based on serotype-specific SNPs identified in the multilocus sequence typing (MLST) database of Salmonella enterica. The SNPs, in genes hemD, thrA, purE, and sucA, acted as surrogate markers for S. enterica serovars Typhimurium, Enteritidis, Virchow, Infantis, and Braenderup. The multiplex primer extension assay (MPEA) was conducted in two separate panels and evaluated using 152 Salmonella enterica isolates that were characterized by MLST. The MPEA was shown to be 100% specific and sensitive, within this collection of isolates. The MPEA is a sensitive and specific method for the identification and detection of Salmonella serotypes based upon SNPs seen in MLST data. The method can be applied in less than 6 h and has the potential to improve patient care and source tracing. The utility of the assay for identification of Salmonella serotypes directly from clinical specimens and food samples warrants further investigation.
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Pearson T, Giffard P, Beckstrom-Sternberg S, Auerbach R, Hornstra H, Tuanyok A, Price EP, Glass MB, Leadem B, Beckstrom-Sternberg JS, Allan GJ, Foster JT, Wagner DM, Okinaka RT, Sim SH, Pearson O, Wu Z, Chang J, Kaul R, Hoffmaster AR, Brettin TS, Robison RA, Mayo M, Gee JE, Tan P, Currie BJ, Keim P. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer. BMC Biol 2009; 7:78. [PMID: 19922616 PMCID: PMC2784454 DOI: 10.1186/1741-7007-7-78] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Accepted: 11/18/2009] [Indexed: 12/02/2022] Open
Abstract
Background Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia. Conclusion We describe an Australian origin for B. pseudomallei, characterized by a single introduction event into Southeast Asia during a recent glacial period, and variable levels of lateral gene transfer within populations. These patterns provide insights into mechanisms of genetic diversification in B. pseudomallei and its closest relatives, and provide a framework for integrating the traditionally separate fields of population genetics and phylogenetics for other bacterial species with high levels of lateral gene transfer.
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Affiliation(s)
- Talima Pearson
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, USA.
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32
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Stone M, Bamford K, Wain J. Detection of single nucleotide polymorphisms based on the multilocus sequence typing database of Staphylococcus aureus using locked nucleic acid oligonucleotides. J Med Microbiol 2009; 58:693-695. [PMID: 19369537 DOI: 10.1099/jmm.0.007534-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- M Stone
- Department of Infection & Immunity, Imperial College, London, UK.,Division of Medical Microbiology and Virology, Imperial College Healthcare NHS Trust, London, UK
| | - K Bamford
- Department of Infection & Immunity, Imperial College, London, UK.,Division of Medical Microbiology and Virology, Imperial College Healthcare NHS Trust, London, UK
| | - J Wain
- Molecular Microbiology, Wellcome Trust Sanger Institute, Cambridgeshire, UK
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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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Munckhof WJ, Nimmo GR, Schooneveldt JM, Schlebusch S, Stephens AJ, Williams G, Huygens F, Giffard P. Nasal carriage of Staphylococcus aureus, including community-associated methicillin-resistant strains, in Queensland adults. Clin Microbiol Infect 2009; 15:149-55. [PMID: 19154489 DOI: 10.1111/j.1469-0691.2008.02652.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infections are emerging in southeast Queensland, Australia, but the incidence of carriage of CA-MRSA strains is unknown. The aim of this study was to assess the nasal carriage rate of S. aureus, including CA-MRSA strains, in the general adult population of southeast Queensland. 396 patients presenting to general practices in two Brisbane suburbs and 303 volunteers randomly selected from the electoral rolls in the same suburbs completed a medical questionnaire and had nasal swabs performed for S. aureus. All isolates of S. aureus underwent antibiotic susceptibility testing and single-nucleotide polymorphism (SNP) and binary typing, including determination of Panton-Valentine leukocidin (PVL). The nasal carriage rate of methicillin-susceptible S. aureus (MSSA) was 202/699 (28%), a rate similar to that found in other community-based nasal carriage studies. According to multivariate analysis, nasal carriage of S. aureus was associated with male sex, young adult age group and Caucasian ethnicity. Only two study isolates (one MSSA and one CA-MRSA) carried PVL. The nasal carriage rate of MRSA was low, at 5/699 (0.7%), and only two study participants (0.3%) had CA-MRSA strains. CA-MRSA is an emerging cause of infection in southeast Queensland, but as yet the incidence of carriage of CA-MRSA in the general community is low.
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Affiliation(s)
- W J Munckhof
- Infection Management Service, Princess Alexandra Hospital, Brisbane, Queensland, Australia.
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35
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Lomonaco S, Chen Y, Knabel SJ. Analysis of additional virulence genes and virulence gene regions in Listeria monocytogenes confirms the epidemiologic relevance of multi-virulence-locus sequence typing. J Food Prot 2008; 71:2559-66. [PMID: 19244915 DOI: 10.4315/0362-028x-71.12.2559] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Previous molecular subtyping studies have defined four epidemic clones (ECs) of Listeria monocytogenes (ECI, ECII, ECIII, and ECIV). Partial sequences of eight virulence genes were previously shown to be identical within individual ECs of L. monocytogenes. The present study was conducted to determine if the sequences of other virulence genes and virulence gene regions are also conserved within these ECs. Six additional virulence genes--bsh, hly, inlJ, IplA1, pgdA, and srtA--and three additional virulence gene regions of actA, inlA, and inlB were selected based on their role in L. monocytogenes virulence, and intragenic regions of each gene were sequenced. Sequencing was performed on a diverse set of 44 to 48 L. monocytogenes strains. Results demonstrated that the sequenced regions of the nine virulence genes were identical within each of the ECs, and 257 new single nucleotide polymorphism (SNPs) were identified. ECIII (lineage II) was easily distinguishable from the other ECs, as 238 SNPs were observed in ECIII due to its significant evolutionary divergence from lineage I. With regard to the other ECs, there were 5 SNPs that represented an informative set, since these SNPs were able to differentiate specific ECs from all other unrelated strains used in this study. This study confirms our previous finding that virulence gene sequences are highly conserved within individual ECs and contain stable SNPs that can be used to very accurately differentiate ECs of L. monocytogenes from each other and from other diverse strains.
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Affiliation(s)
- Sara Lomonaco
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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36
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Meraz IM, Jiang ZD, Ericsson CD, Bourgeois AL, Steffen R, Taylor DN, Hernandez N, DuPont HL. Enterotoxigenic Escherichia coli and diffusely adherent E. coli as likely causes of a proportion of pathogen-negative travelers' diarrhea--a PCR-based study. J Travel Med 2008; 15:412-8. [PMID: 19090795 DOI: 10.1111/j.1708-8305.2008.00249.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Enteropathogens cannot be identified in 40% to 50% of subjects with travelers' diarrhea (TD). METHODS We used polymerase chain reaction (PCR) methods to look for the presence of two bacterial causes of diarrhea in a large group of international travelers after failing to detect a pathogen by conventional tests. DNA was isolated from the diarrheal stool and subjected to PCR from 162 subjects from whom we earlier failed to identify a pathogen in a previous study and included 54 from Antigua, Guatemala, 39 from Guadalajara, Mexico, 29 from Kolkata, India, and 40 from Goa, India. Gene products for enterotoxigenic Escherichia coli (ETEC)--LT (heat-labile enterotoxin) and ST (heat-stable enterotoxin)--and diffusely adherent E. coli (DAEC), afa/dr (Afa fimbrial and Dr nonfimbrial family of adhesins), were used. RESULTS At least one gene product was identified in diarrhea stool samples of 47 of 162 (29%) subjects. ETEC virulence genes (LT, ST) were found in 34 (21%) samples studied, with rates of occurrence ranging from 8% in Goa to 39% for the samples from Guatemala (p = 0.0006). A large number of ST-only strains explained the high ETEC rate in Guatemala. DAEC afa/dr family of adhesions was identified in between 8 and 14% of the samples. CONCLUSIONS ETEC and DAEC were implicated in nearly one-third of the subjects initially diagnosed as pathogen negative. Direct PCR results from stools are consistent with the previous assumption that most undiagnosed TD is bacterial in nature and also highlights the potential value that PCR can add to studies designed to evaluate treatment and preventive interventions for TD, including vaccines.
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Affiliation(s)
- Ismail M Meraz
- School of Public Health, University of Texas, Houston, TX 77030, USA
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Merchant-Patel S, Blackall PJ, Templeton J, Price EP, Miflin JK, Huygens F, Giffard PM. Characterisation of chicken Campylobacter jejuni isolates using resolution optimised single nucleotide polymorphisms and binary gene markers. Int J Food Microbiol 2008; 128:304-8. [PMID: 18835503 DOI: 10.1016/j.ijfoodmicro.2008.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Revised: 09/01/2008] [Accepted: 09/02/2008] [Indexed: 11/25/2022]
Abstract
The principal objective of this study was to determine if Campylobacter jejuni genotyping methods based upon resolution optimised sets of single nucleotide polymorphisms (SNPs) and binary genetic markers were capable of identifying epidemiologically linked clusters of chicken-derived isolates. Eighty-eight C. jejuni isolates of known flaA RFLP type were included in the study. They encompassed three groups of ten isolates that were obtained at the same time and place and possessed the same flaA type. These were regarded as being epidemiologically linked. Twenty-six unlinked C. jejuni flaA type I isolates were included to test the ability of SNP and binary typing to resolve isolates that were not resolved by flaA RFLP. The remaining isolates were of different flaA types. All isolates were typed by real-time PCR interrogation of the resolution optimised sets of SNPs and binary markers. According to each typing method, the three epidemiologically linked clusters were three different clones that were well resolved from the other isolates. The 26 unlinked C. jejuni flaA type I isolates were resolved into 14 SNP-binary types, indicating that flaA typing can be unreliable for revealing epidemiological linkage. Comparison of the data with data from a fully typed set of isolates associated with human infection revealed that abundant lineages in the chicken isolates that were also found in the human isolates belonged to clonal complex (CC) -21 and CC-353, with the usually rare C-353 member ST-524 being especially abundant in the chicken collection. The chicken isolates selected to be diverse according to flaA were also diverse according to SNP and binary typing. It was observed that CC-48 was absent in the chicken isolates, despite being very common in Australian human infection isolates, indicating that this may be a major cause of human disease that is not chicken associated.
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Affiliation(s)
- Shreema Merchant-Patel
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
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Honsa E, Fricke T, Stephens AJ, Ko D, Kong F, Gilbert GL, Huygens F, Giffard PM. Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms. BMC Microbiol 2008; 8:140. [PMID: 18710585 PMCID: PMC2533671 DOI: 10.1186/1471-2180-8-140] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Accepted: 08/19/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Streptococcus agalactiae (Group B Streptococcus (GBS)) is an important human pathogen, particularly of newborns. Emerging evidence for a relationship between genotype and virulence has accentuated the need for efficient and well-defined typing methods. The objective of this study was to develop a single nucleotide polymorphism (SNP) based method for assigning GBS isolates to multilocus sequence typing (MLST)-defined clonal complexes. RESULTS It was found that a SNP set derived from the MLST database on the basis of maximization of Simpsons Index of Diversity provided poor resolution and did not define groups concordant with the population structure as defined by eBURST analysis of the MLST database. This was interpreted as being a consequence of low diversity and high frequency horizontal gene transfer. Accordingly, a different approach to SNP identification was developed. This entailed use of the "Not-N" bioinformatic algorithm that identifies SNPs diagnostic for groups of known sequence variants, together with an empirical process of SNP testing. This yielded a four member SNP set that divides GBS into 10 groups that are concordant with the population structure. A fifth SNP was identified that increased the sensitivity for the clinically significant clonal complex 17 to 100%. Kinetic PCR methods for the interrogation of these SNPs were developed, and used to genotype 116 well characterized isolates. CONCLUSION A five SNP method for dividing GBS into biologically valid groups has been developed. These SNPs are ideal for high throughput surveillance activities, and combining with more rapidly evolving loci when additional resolution is required.
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Affiliation(s)
- Erin Honsa
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Queensland, Australia.
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Medini D, Serruto D, Parkhill J, Relman DA, Donati C, Moxon R, Falkow S, Rappuoli R. Microbiology in the post-genomic era. Nat Rev Microbiol 2008; 6:419-30. [PMID: 18475305 DOI: 10.1038/nrmicro1901] [Citation(s) in RCA: 265] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Genomics has revolutionized every aspect of microbiology. Now, 13 years after the first bacterial genome was sequenced, it is important to pause and consider what has changed in microbiology research as a consequence of genomics. In this article, we review the evolving field of bacterial typing and the genomic technologies that enable comparative analysis of multiple genomes and the metagenomes of complex microbial environments, and address the implications of the genomic era for the future of microbiology.
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Affiliation(s)
- Duccio Medini
- Novartis Vaccines and Diagnostics, 53100 Siena, Italy
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Methicillin-susceptible, non-multiresistant methicillin-resistant and multiresistant methicillin-resistant Staphylococcus aureus infections: a clinical, epidemiological and microbiological comparative study. Eur J Clin Microbiol Infect Dis 2008; 27:355-64. [DOI: 10.1007/s10096-007-0449-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Accepted: 12/10/2007] [Indexed: 11/25/2022]
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Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants. BMC Bioinformatics 2007; 8:278. [PMID: 17672919 PMCID: PMC1973086 DOI: 10.1186/1471-2105-8-278] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2007] [Accepted: 08/01/2007] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) and genes that exhibit presence/absence variation have provided informative marker sets for bacterial and viral genotyping. Identification of marker sets optimised for these purposes has been based on maximal generalized discriminatory power as measured by Simpson's Index of Diversity, or on the ability to identify specific variants. Here we describe the Not-N algorithm, which is designed to identify small sets of genetic markers diagnostic for user-specified subsets of known genetic variants. The algorithm does not treat the user-specified subset and the remaining genetic variants equally. Rather Not-N analysis is designed to underpin assays that provide 0% false negatives, which is very important for e.g. diagnostic procedures for clinically significant subgroups within microbial species. RESULTS The Not-N algorithm has been incorporated into the "Minimum SNPs" computer program and used to derive genetic markers diagnostic for multilocus sequence typing-defined clonal complexes, hepatitis C virus (HCV) subtypes, and phylogenetic clades defined by comparative genome hybridization (CGH) data for Campylobacter jejuni, Yersinia enterocolitica and Clostridium difficile. CONCLUSION Not-N analysis is effective for identifying small sets of genetic markers diagnostic for microbial sub-groups. The best results to date have been obtained with CGH data from several bacterial species, and HCV sequence data.
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Stephens AJ, Huygens F, Giffard PM. Systematic derivation of marker sets for staphylococcal cassette chromosome mec typing. Antimicrob Agents Chemother 2007; 51:2954-64. [PMID: 17517844 PMCID: PMC1932536 DOI: 10.1128/aac.01323-06] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to identify optimized sets of genotyping targets for the staphylococcal cassette chromosome mec (SCCmec). We analyzed the gene contents of 46 SCCmec variants in order to identify minimal subsets of targets that provide useful resolution. This was achieved by firstly identifying and characterizing each available SCCmec element based on the presence or absence of 34 binary targets. This information was used as input for the software "Minimum SNPs," which identifies the minimum number of targets required to differentiate a set of genotypes up to a predefined Simpson's index of diversity (D) value. It was determined that 22 of the 34 targets were required to genotype the 46 SCCmec variants to a D of 1. The first 6, 9, 12, and 15 targets were found to define 21, 29, 35, and 39 SCCmec variants, respectively. The genotypes defined by these marker subsets were largely consistent with the relationships between SCCmec variants and the accepted nomenclature. Consistency was made virtually complete by forcing the computer program to include ccr1 and ccr5 in the target set. An alternative target set biased towards discriminating abundant SCCmec variants was derived by analyzing an input file in which common SCCmec variants were repeated, thus ensuring that markers that discriminate abundant variants had a large effect on D. Finally, it was determined that mecA single nucleotide polymorphisms (SNPs) can increase the overall genotyping resolution, as different mecA alleles were found in otherwise identical SCCmec variants.
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Affiliation(s)
- Alex J Stephens
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, 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: 83] [Impact Index Per Article: 4.9] [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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46
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Huygens F, Inman-Bamber J, Nimmo GR, Munckhof W, Schooneveldt J, Harrison B, McMahon JA, Giffard PM. Staphylococcus aureus genotyping using novel real-time PCR formats. J Clin Microbiol 2006; 44:3712-9. [PMID: 17021101 PMCID: PMC1594813 DOI: 10.1128/jcm.00843-06] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One approach to microbial genotyping is to make use of sets of single-nucleotide polymorphisms (SNPs) in combination with binary markers. Here we report the modification and automation of a SNP-plus-binary-marker-based approach to the genotyping of Staphylococcus aureus and its application to 391 S. aureus isolates from southeast Queensland, Australia. The SNPs used were arcC210, tpi243, arcC162, gmk318, pta294, tpi36, tpi241, and pta383. These provide a Simpson's index of diversity (D) of 0.95 with respect to the S. aureus multilocus sequence typing database and define 61 genotypes and the major clonal complexes. The binary markers used were pvl, cna, sdrE, pT181, and pUB110. Two novel real-time PCR formats for interrogating these markers were compared. One of these makes use of "light upon extension" (LUX) primers and biplexed reactions, while the other is a streamlined modification of kinetic PCR using SYBR green. The latter format proved to be more robust. In addition, automated methods for DNA template preparation, reaction setup, and data analysis were developed. A single SNP-based method for ST-93 (Queensland clone) identification was also devised. The genotyping revealed the numerical importance of the "South West Pacific" and "Queensland" community-acquired methicillin-resistant S. aureus (MRSA) clones and the clonal complex 239 "Aus-1/Aus-2" hospital-associated MRSA. There was a strong association between the community-acquired clones and pvl.
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Affiliation(s)
- Flavia Huygens
- Cooperative Research Centre for Diagnostics, Institute of Health and Biomedical Innovation, QUT, GPO Box 2434, Brisbane Q 4001, Australia
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Best EL, Fox AJ, Owen RJ, Cheesbrough J, Bolton FJ. Specific detection of Campylobacter jejuni from faeces using single nucleotide polymorphisms. Epidemiol Infect 2006; 135:839-46. [PMID: 17109769 PMCID: PMC2870630 DOI: 10.1017/s0950268806007461] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Specimens of human faeces were tested by a rapid strategy for detection of Campylobacter jejuni lineages by the presence of specific single nucleotide polymorphisms (SNPs) based on the C. jejuni multi locus sequence typing (MLST) scheme. This strategy was derived from analysis of the MLST databases to identify clonal complex specific SNPs followed by the design of real-time PCR assays to enable identification of six major C. jejuni clonal complexes associated with cases of human infection. The objective was to use the MLST SNP-based assays for the direct detection of C. jejuni by clonal complex from specimens of human faeces, and then confirm the accuracy of the clonal complex designation from the SNP-based assays by performing MLST on the cultured faecal material, this targeted at determining the validity of direct molecular specimen identification. Results showed it was possible to identify 38% of the isolates to one of the six major MLST clonal complexes using a rapid DNA extraction method directly from faeces in under 3 h. This method provides a novel strategy for the use of real-time PCR for detection and characterization beyond species level, supplying real-time epidemiological data, which is comparable with MLST results.
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Affiliation(s)
- E L Best
- Laboratory of Enteric Pathogens, Centre for Infections, Health Protection Agency, London, UK.
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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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Vlack S, Cox L, Peleg AY, Canuto C, Stewart C, Conlon A, Stephens A, Giffard P, Huygens F, Mollinger A, Vohra R, McCarthy JS. Carriage of methicillin-resistant Staphylococcus aureus in a Queensland Indigenous community. Med J Aust 2006; 184:556-9. [PMID: 16768661 DOI: 10.5694/j.1326-5377.2006.tb00379.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2005] [Accepted: 04/10/2006] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To determine the prevalence of community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) carriage and infection among children living in an Indigenous community in Queensland. DESIGN, SETTING AND PARTICIPANTS Swabs for culture of S. aureus were collected from the nose, throat and skin wounds of primary school children. MAIN OUTCOME MEASURES MRSA carriage, antibiotic sensitivity, genotype, and presence of the virulence factor Panton-Valentine leukocidin (PVL); and epidemiological risk factors for MRSA carriage. RESULTS 92 (59%) of 157 eligible children were included in the study. Twenty-seven (29%) carried S. aureus; 14 of these (15% of total) carried MRSA. MRSA was isolated from 29% of wound swabs, 8% of nose swabs, and 1% of throat swabs. Fourteen of 15 MRSA isolates were sensitive to all non-beta-lactam antibiotics tested. Eight children (9%) carried CA-MRSA clonal types: six carried the Queensland clone (ST93), and two carried the South West Pacific clone (ST30). All these isolates carried the virulence factor PVL. The remaining six children carried a hospital-associated MRSA strain (ST5), negative for PVL. CONCLUSIONS We have identified a high prevalence of CA-MRSA carriage in school children from a Queensland Indigenous community. In this setting, antibiotics with activity against CA-MRSA should be considered for empiric therapy of suspected staphylococcal infection. Larger community-based studies are needed to improve our understanding of the epidemiology of CA-MRSA, and to assist in the development of therapeutic guidelines for this important infection.
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Affiliation(s)
- Susan Vlack
- School of Population Health, University of Queensland, Brisbane, QLD
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50
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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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