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Żaczek A, Struś K, Sokołowska A, Parniewski P, Wojtasik A, Dziadek J. Differentiation of Clavibacter michiganensis subsp. sepedonicus using PCR melting profile and variable number of tandem repeat methods. Lett Appl Microbiol 2018; 68:24-30. [PMID: 30269341 DOI: 10.1111/lam.13081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/03/2018] [Accepted: 09/21/2018] [Indexed: 11/26/2022]
Abstract
The potato phytopathogen Clavibacter michiganensis subsp. sepedonicus (Cms) is a causative agent of bacterial ring rot, which is a serious threat to crops. In EU member countries, Cms is subject to quarantine and has to be combated. The knowledge about the transmission of C. michiganensis strains is limited due to a lack of methods which could be used for epidemiological analysis. In this study, PCR melting profile (PCR MP) and variable number tandem repeat methods were used in Cms epidemiological analysis for the first time. PCR MP was based on the melting temperature analysis of BamHI restriction fragments of chromosomal DNA. Respectively, for the variable number tandem repeat (VNTR) method, six loci were identified and used in the differentiation of Cms isolates. PCR MP was used for 93 Cms isolated in Poland. Both PCR MP and VNTR methods were used for the differentiation of 47 Cms strains in this collection. Both these methods were found to be useful for the epidemiological analysis of Cms. SIGNIFICANCE AND IMPACT OF THE STUDY: The potato phytopathogen, Clavibacter michiganensis subsp. sepedonicus (Cms), is a serious threat to crops and lead to significant economic losses. The only way to control and eliminate the disease caused by this pathogen is the use of certified seed potato and strict quarantine of infected fields. Here, for the first time, two molecular typing methods (PCR melting profile (PCR MP) and variable number tandem repeat (VNTR)) were evaluated in respect of their potential in differentiation of Cms isolates. As a result, we obtained characteristic profiles of DNA fragments (PCR MP) and numeric patterns (VNTR), which enable the intraspecies genotyping of Cms strains confirming the effectiveness of PCR MP and VNTR methods in differentiation of Cms strains.
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Affiliation(s)
- A Żaczek
- Department of Biochemistry and Cell Biology, Rzeszow University, Rzeszow, Poland
| | - K Struś
- Podkarpackie Center for Environmental Research and Development in Rzeszow, Rzeszow, Poland
| | - A Sokołowska
- Department of Biochemistry and Cell Biology, Rzeszow University, Rzeszow, Poland
| | - P Parniewski
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - A Wojtasik
- Proteon Pharmaceuticals S.A., Lodz, Poland
| | - J Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
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Abstract
The availability of complete fungal genomes is expanding rapidly and is offering an extensive and accurate view of this "kingdom." The scientific milestone of free access to more than 1000 fungal genomes of different species was reached, and new and stimulating projects have meanwhile been released. The "1000 Fungal Genomes Project" represents one of the largest sequencing initiative regarding fungal organisms trying to fill some gaps on fungal genomics. Presently, there are 329 fungal families with at least one representative genome sequenced, but there is still a large number of fungal families without a single sequenced genome. In addition, additional sequencing projects helped to understand the genetic diversity within some fungal species. The availability of multiple genomes per species allows to support taxonomic organization, brings new insights for fungal evolution in short-time scales, clarifies geographical and dispersion patterns, elucidates outbreaks and transmission routes, among other objectives. Genotyping methodologies analyze only a small fraction of an individual's genome but facilitate the comparison of hundreds or thousands of isolates in a small fraction of the time and at low cost. The integration of whole genome strategies and improved genotyping panels targeting specific and relevant SNPs and/or repeated regions can represent fast and practical strategies for studying local, regional, and global epidemiology of fungi.
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Affiliation(s)
- Ricardo Araujo
- University of Porto, Porto, Portugal; School of Medicine and Health Sciences, Flinders University, Adelaide, SA, Australia.
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Xiao J, Moon Y, Li L, Rustchenko E, Wakabayashi H, Zhao X, Feng C, Gill SR, McLaren S, Malmstrom H, Ren Y, Quivey R, Koo H, Kopycka-Kedzierawski DT. Candida albicans Carriage in Children with Severe Early Childhood Caries (S-ECC) and Maternal Relatedness. PLoS One 2016; 11:e0164242. [PMID: 27741258 PMCID: PMC5065202 DOI: 10.1371/journal.pone.0164242] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 08/26/2016] [Indexed: 11/23/2022] Open
Abstract
Introduction Candida albicans has been detected together with Streptococcus mutans in high numbers in plaque-biofilm from children with early childhood caries (ECC). The goal of this study was to examine the C. albicans carriage in children with severe early childhood caries (S-ECC) and the maternal relatedness. Methods Subjects in this pilot cross-sectional study were recruited based on a convenient sample. DMFT(S)/dmft(s) caries and plaque scores were assessed during a comprehensive oral exam. Social-demographic and related background information was collected through a questionnaire. Saliva and plaque sample from all children and mother subjects were collected. C. albicans were isolated by BBL™ CHROMagar™ and also identified using germ tube test. S. mutans was isolated using Mitis Salivarius with Bacitracin selective medium and identified by colony morphology. Genetic relatedness was examined using restriction endonuclease analysis of the C. albicans genome using BssHII (REAG-B). Multilocus sequence typing was used to examine the clustering information of isolated C. albicans. Spot assay was performed to examine the C. albicans Caspofungin susceptibility between S-ECC children and their mothers. All statistical analyses (power analysis for sample size, Spearman’s correlation coefficient and multiple regression analyses) were implemented with SAS 9.4 Results A total of 18 S-ECC child-mother pairs and 17 caries free child-mother pairs were enrolled in the study. Results indicated high C. albicans carriage rate in the oral cavity (saliva and plaque) of both S-ECC children and their mothers (>80%). Spearman’s correlation coefficient also indicated a significant correlation between salivary and plaque C. albicans and S. mutans carriage (p<0.01) and caries severity (p<0.05). The levels of C. albicans in the prepared saliva and plaque sample (1ml resuspension) of S-ECC children were 1.3 ± 4.5 x104 cfu/ml and 1.2 ± 3.5 x104 cfu/ml (~3-log higher vs. caries-free children). Among 18 child-mother pairs, >60% of them demonstrated identical C. albicans REAG-B pattern. C. albicans isolated from >65% of child-mother pairs demonstrated similar susceptibility to caspofungin in spot assay, while no caspofungin resistant strains were seen when compared with C. albicans wild-type strain SC5314. Interestingly, the regression analysis showed that factors such as antibiotic usage, birth weight, inhaler use, brushing frequency, and daycare attendance had no significant effect on the oral carriage of C. albicans in the S-ECC children. Conclusions Our results reveal that both the child with S-ECC and the mother were highly infected with C. albicans, while most of the strains were genetically related, suggesting that the mother might be a source for C. albicans acquisition in the oral cavity of children affected by the disease.
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Affiliation(s)
- Jin Xiao
- Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, United States of America
- * E-mail:
| | - Yonghwi Moon
- Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Lihua Li
- Department of Dentistry, North Sichuan Medical University, Sichuan, China
| | - Elena Rustchenko
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Hironao Wakabayashi
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Xiaoyi Zhao
- School of Dentistry, Peking University, Beijing, China
| | - Changyong Feng
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Steven R. Gill
- Genomics Research Center, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Sean McLaren
- Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Hans Malmstrom
- Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Yanfang Ren
- Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Robert Quivey
- Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, United States of America
| | - Hyun Koo
- Department of Orthodontics and Pediatric Dentistry & Community Oral Health Divisions, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
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Paluchowska P, Tokarczyk M, Bogusz B, Skiba I, Budak A. Molecular epidemiology of Candida albicans and Candida glabrata strains isolated from intensive care unit patients in Poland. Mem Inst Oswaldo Cruz 2015; 109:436-41. [PMID: 25075783 PMCID: PMC4155844 DOI: 10.1590/0074-0276140099] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 05/24/2014] [Indexed: 11/22/2022] Open
Abstract
Over the last decades, Candida spp have been responsible for an increasing number of infections, especially in patients requiring intensive care. Knowledge of local epidemiology and analysis of the spread of these pathogens is important in understanding and controlling their transmission. The aim of this study was to evaluate the genetic diversity of 31 Candida albicans and 17 Candida glabrata isolates recovered from intensive care unit patients from the tertiary hospital in Krakow between 2011-2012. The strains were typed by random amplified polymorphic DNA (RAPD) polymerase chain reaction using five primers (CD16AS, HP1247, ERIC-2, OPE-3 and OPE-18). The results of the present investigation revealed a high degree of genetic diversity among the isolates. No clonal relationship was found among the C. albicans strains, whereas two C. glabrata isolates were identical. The source of Candida infection appeared to be mostly endogenous; however, the presence of two clonal C. glabrata strains suggested the possibility of cross-transmission of these pathogens. Our study confirmed the high discriminatory power of the RAPD technique in the molecular typing of Candida clinical isolates. This method may be applied to the evaluation of transmission routes of pathogenic fungi on a local level.
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Affiliation(s)
- Paulina Paluchowska
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Jagiellonian University Medical College, Krakow, Poland
| | - Marianna Tokarczyk
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Jagiellonian University Medical College, Krakow, Poland
| | - Bozena Bogusz
- Microbiological Laboratory, Department of Laboratory Diagnostics, Rydygier?s Specialized Hospital, Krakow, Poland
| | - Iwona Skiba
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Jagiellonian University Medical College, Krakow, Poland
| | - Alicja Budak
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Jagiellonian University Medical College, Krakow, Poland
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Zaczek A, Wojtasik A, Izdebski R, Gorecka E, Wojcik EA, Nowak T, Kwiecinski P, Dziadek J. PCR melting profile as a tool for outbreak studies of Salmonella enterica in chickens. BMC Vet Res 2015; 11:137. [PMID: 26100129 PMCID: PMC4476179 DOI: 10.1186/s12917-015-0451-4] [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: 03/15/2015] [Accepted: 06/08/2015] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Salmonellosis is of great economic concern in all phases of the poultry industry, from production to marketing, leading to severe economic losses. Monitoring the source of the bacterial contamination has fundamental importance in the spreading of salmonellosis. RESULTS We applied a ligation-mediated PCR method, PCR MP (PCR melting profile), to type S. enterica ssp. enterica ser. Enteritidis (56 strains) and 43 control strains classified to other serovars isolated from poultry. We demonstrated the PCR MP potential for salmonellosis spreading monitoring. Our rapid test presents higher discriminatory power (0.939 vs. 0.608) compared to current molecular subtyping tool such as pulsed-field gel electrophoresis (PFGE), which ineffectiveness underlies the high degree of clonality of S. Enteritidis. CONCLUSIONS PCR MP was found to be a highly discriminating, sensitive and specific method that could be a valuable molecular tool, particularly for analyzing epidemiological links of limited number of S. enterica ser. Enteritidis strains.
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Affiliation(s)
- Anna Zaczek
- Department of Biochemistry and Cell Biology, University of Rzeszów, Rejtana 16c, 35-959, Rzeszów, Poland.
| | | | - Radosław Izdebski
- Molecular Microbiology Department, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland.
| | | | | | - Tomasz Nowak
- Vet- Lab Brudzew, Turkowska 58C, 62-720, Brudzew, Poland.
| | | | - Jaroslaw Dziadek
- Institute of Medical Biology, Polish Academy of Science, Lodowa 106, 93-232, Łódź, Poland.
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Mohammed SAS, Rana MJ, Nihad HAA, Moatasem HAB, Salam YAZ, Omar YM, Rania MJ. Genotyping and antifungal susceptibility of Candida albicans strains from patients with vulvovaginal and cutaneous candidiasis in Palestine. ACTA ACUST UNITED AC 2015. [DOI: 10.5897/ajmr2014.7350] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Golas M, Netsvyetayeva I, Piskorska K, Sikora M, Jaworska-Zaremba M, Mierzwinska-Nastalska E, Paczek L, Swoboda-Kopec E. Polymerase chain reaction melting profiles of Candida glabrata clinical isolates in solid organ transplant recipients in comparison to the other group of surgical patients. Transplant Proc 2014; 46:1366-70. [PMID: 24836833 DOI: 10.1016/j.transproceed.2014.02.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 02/27/2014] [Indexed: 10/25/2022]
Abstract
The aim of the retrospective study were to estimate the prevalence of Candida glabrata in liver and kidney transplant recipients compared to patients with short bowel syndrome receiving chronic total parenteral nutrition and relevance of the polymerase chain reaction melting profile (PCR MP) method for Candida glabrata strains differentiation. C. glabrata clinical strains isolated from patients were identified by using standard mycological procedures. The analysis of genetic relatedness of the isolated strains was conducted using the PCR MP method. The prevalence of C. glabrata comprised 29% of all episodes of fungal colonization and infection in solid organ transplant recipients, and 54% of those in hospitalized patients receiving long-term total parenteral nutrition. Among 78 isolates obtained from 55 solid organ transplant recipients and 2 organ donors, 44 different C. glabrata PCR MP fingerprints were observed. Forty-seven organ recipients and one organ donor carried unique C. glabrata strains. Among 37 isolates obtained from 31 patients receiving long-term TPN, 8 different PCR MP profiles of C. glabrata strains were observed. Two patients carried unique C. glabrata strains. Most of the C. glabrata colonization and infections in solid-organ transplant recipients were caused by endogenic strains. Most of the C. glabrata colonization and infections in hospitalized patients receiving long-term total parenteral nutrition could result by patient-to-patient transmission. The results showed that the PCR MP technique is a good discriminatory method for genotyping for C. glabrata strains.
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Affiliation(s)
- M Golas
- Department of Medical Microbiology, Warsaw Medical University, Warsaw, Poland.
| | - I Netsvyetayeva
- Department of Medical Microbiology, Warsaw Medical University, Warsaw, Poland
| | - K Piskorska
- Department of Medical Microbiology, Warsaw Medical University, Warsaw, Poland
| | - M Sikora
- Department of Dentistry Microbiology, Warsaw Medical University, Warsaw, Poland
| | - M Jaworska-Zaremba
- Department of Prosthetic Dentistry, Warsaw Medical University, Warsaw, Poland
| | | | - L Paczek
- Transplantation Institute, Medical University of Warsaw, Warsaw, Poland
| | - E Swoboda-Kopec
- Department of Dentistry Microbiology, Warsaw Medical University, Warsaw, Poland
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Zasada AA, Formińska K, Wołkowicz T, Badell E, Guiso N. The utility of the PCR melting profile technique for typing Corynebacterium diphtheriae isolates. Lett Appl Microbiol 2014; 59:292-8. [PMID: 24749659 DOI: 10.1111/lam.12274] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/09/2014] [Accepted: 04/09/2014] [Indexed: 11/30/2022]
Abstract
UNLABELLED Selection of appropriate typing method depends on a number of factors, including the scale of the investigation, the rapidity required of the results and the financial and technical resources available. Several typing methods have been applied to Corynebacterium diphtheriae genotyping, but most are laborious and time-consuming or require expensive equipment. We report an evaluation of the utility of the PCR melting profile technique for simple and easy-to-perform genotyping of C. diphtheriae. We compared the method with ribotyping-the 'gold standard' for C. diphtheriae typing-and PFGE, MLST, AFLP, RAPD and spoligotyping. SIGNIFICANCE AND IMPACT OF THE STUDY Occurrence of Corynebacterium diphtheriae infections-in the form of diphtheria in endemic countries and in the form of invasive infections in countries with high antidiphtheria vaccination coverage-indicates the need for maintenance of ability to genotype this pathogen by laboratories. Application of an appropriate typing method is essential not only in outbreak investigations for understanding and predicting epidemics but also in monitoring of the evolution and spread of epidemic clones of C. diphtheriae. The PCR melting profile method presented in the study is a good alternative for C. diphtheriae typing.
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Affiliation(s)
- A A Zasada
- Department of Bacteriology, National Institute of Public Health - National Institute of Hygiene, Warsaw, Poland
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Saghrouni F, Ben Abdeljelil J, Boukadida J, Ben Said M. Molecular methods for strain typing of Candida albicans
: a review. J Appl Microbiol 2013; 114:1559-74. [DOI: 10.1111/jam.12132] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 01/03/2013] [Accepted: 01/06/2013] [Indexed: 11/28/2022]
Affiliation(s)
- F. Saghrouni
- UR02SP13 Research Unit; Ministry of Public Health; Tunisia Tunisia
| | | | - J. Boukadida
- UR02SP13 Research Unit; Ministry of Public Health; Tunisia Tunisia
| | - M. Ben Said
- UR02SP13 Research Unit; Ministry of Public Health; Tunisia Tunisia
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Emmanuel NN, Romeo O, Mebi AG, Mark OO, Scordino F, Bessy EI, Criseo G. Genotyping and fluconazole susceptibility of Candida albicans strains from patients with vulvovaginal candidiasis in Jos, Nigeria. ASIAN PACIFIC JOURNAL OF TROPICAL DISEASE 2012. [DOI: 10.1016/s2222-1808(12)60011-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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High-resolution melting-curve analysis of ligation-mediated real-time PCR for rapid evaluation of an epidemiological outbreak of extended-spectrum-beta-lactamase-producing Escherichia coli. J Clin Microbiol 2011; 49:4032-9. [PMID: 21956981 DOI: 10.1128/jcm.01042-11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methods for the confirmation of nosocomial outbreaks of bacterial pathogens are complex, expensive, and time-consuming. Recently, a method based on ligation-mediated PCR (LM/PCR) using a low denaturation temperature which produces specific melting-profile patterns of DNA products has been described. Our objective was to further develop this method for real-time PCR and high-resolution melting analysis (HRM) in a single-tube system optimized in order to achieve results within 1 day. Following the optimization of LM/PCR for real-time PCR and HRM (LM/HRM), the method was applied for a nosocomial outbreak of extended-spectrum-beta-lactamase (ESBL)-producing and ST131-associated Escherichia coli isolates (n = 15) and control isolates (n = 29), including four previous clusters. The results from LM/HRM were compared to results from pulsed-field gel electrophoresis (PFGE), which served as the gold standard. All isolates from the nosocomial outbreak clustered by LM/HRM, which was confirmed by gel electrophoresis of the LM/PCR products and PFGE. Control isolates that clustered by LM/PCR (n = 4) but not by PFGE were resolved by confirmatory gel electrophoresis. We conclude that LM/HRM is a rapid method for the detection of nosocomial outbreaks of bacterial infections caused by ESBL-producing E. coli strains. It allows the analysis of isolates in a single-tube system within a day, and the discriminatory power is comparable to that of PFGE.
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Kothavade RJ, Kura MM, Valand AG, Panthaki MH. Candida tropicalis: its prevalence, pathogenicity and increasing resistance to fluconazole. J Med Microbiol 2010; 59:873-880. [PMID: 20413622 DOI: 10.1099/jmm.0.013227-0] [Citation(s) in RCA: 189] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Candida tropicalis has been identified as the most prevalent pathogenic yeast species of the Candida-non-albicans group. Historically, Candida albicans has been the major species responsible for causing candidiasis in immunocompromised and immunocompetent patients. However, infections (candidiasis) due to C. tropicalis have increased dramatically on a global scale thus proclaiming this organism to be an emerging pathogenic yeast. The reasons for this organism's dominance and its resistance to fluconazole have been difficult to elucidate. In addition, the mechanism of this organism's pathogenicity and the consequent immune response remain to be clarified. This paper describes certain predisposing factors potentially responsible for these characteristics and presents a 'root cause analysis' to explain the increasing prevalence of C. tropicalis in developed and undeveloped countries, as well as the organism's acquired drug resistance. Control measures against fluconazole resistance in clinical management have also been discussed.
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Affiliation(s)
- Rajendra J Kothavade
- Microbiology Section, WQA Laboratory, EPCOR, 9469 Rossdale Rd NW, Edmonton, AB T5K 0S5, Canada
| | - M M Kura
- Department of Dermatology, Grant Medical College and Sir J. J. Group of Hospitals, Mumbai 400 008, India
| | - Arvind G Valand
- Department of Pathology, Grant Medical College and Sir J. J. Group of Hospitals, Mumbai 400 008, India
| | - M H Panthaki
- Department of Immunocytobiology and Pathology, Sir H. N. Hospital and Medical Research Centre, Mumbai 400 004, India
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