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Zhang H, Tang M, Li D, Xu M, Ao Y, Lin L. Applications and advances in molecular diagnostics: revolutionizing non-tuberculous mycobacteria species and subspecies identification. Front Public Health 2024; 12:1410672. [PMID: 38962772 PMCID: PMC11220129 DOI: 10.3389/fpubh.2024.1410672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/10/2024] [Indexed: 07/05/2024] Open
Abstract
Non-tuberculous mycobacteria (NTM) infections pose a significant public health challenge worldwide, affecting individuals across a wide spectrum of immune statuses. Recent epidemiological studies indicate rising incidence rates in both immunocompromised and immunocompetent populations, underscoring the need for enhanced diagnostic and therapeutic approaches. NTM infections often present with symptoms similar to those of tuberculosis, yet with less specificity, increasing the risk of misdiagnosis and potentially adverse outcomes for patients. Consequently, rapid and accurate identification of the pathogen is crucial for precise diagnosis and treatment. Traditional detection methods, notably microbiological culture, are hampered by lengthy incubation periods and a limited capacity to differentiate closely related NTM subtypes, thereby delaying diagnosis and the initiation of targeted therapies. Emerging diagnostic technologies offer new possibilities for the swift detection and accurate identification of NTM infections, playing a critical role in early diagnosis and providing more accurate and comprehensive information. This review delineates the current molecular methodologies for NTM species and subspecies identification. We critically assess the limitations and challenges inherent in these technologies for diagnosing NTM and explore potential future directions for their advancement. It aims to provide valuable insights into advancing the application of molecular diagnostic techniques in NTM infection identification.
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Affiliation(s)
- Haiyang Zhang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Maoting Tang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Deyuan Li
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Min Xu
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Yusen Ao
- Department of Pediatrics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Liangkang Lin
- Department of Pediatrics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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Ilham HM, Wijaya M, Suwanto A, Rusmana I. Dominant Enterobacteriaceae in tempeh were primarily originated from soybean. Food Sci Biotechnol 2021; 30:861-868. [PMID: 34249392 DOI: 10.1007/s10068-021-00915-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 11/29/2022] Open
Abstract
During tempeh production, boiling was considered as heat treatment that could significantly reduce or eliminate bacterial population in soybean before fungal inoculation. The objective of this study was to enumerate and trace Enterobacteriaceae communities in pre-boiling soybean, post-boiling soybean, and fresh tempeh designated as RTI and EMP. Standard plate count and qRT-PCR were employed to determine the culturable and non-culturable bacteria, while Enterobacterial Repetitive Intragenic Consensus PCR was conducted to determine the intraspecies genomic variations. Fresh tempeh from both RTI and EMP contained approximately 107 and 108 CFU/g of Enterobacteriaceae respectively. The number of bacteria in pre-boiling soybean were 10,000 times lower than in fresh tempeh. Our study showed that most Enterobacteriaceae were severely injured or quiescent during boiling process and quickly recovered up to 109 CFU/g in fresh tempeh. Some Klebsiella isolates found in tempeh were genetically identical to isolates in soybean, but different from those of medical isolates. This study suggested that soybean could be the main origin of Klebsiella in fresh tempeh.
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Affiliation(s)
- Horizon M Ilham
- Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor, 16680 Indonesia
| | - Michael Wijaya
- Biotechnology Research and Development Department, PT Wilmar Benih Indonesia, Bekasi, 17539 Indonesia
| | - Antonius Suwanto
- Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor, 16680 Indonesia.,Department of Biology, Faculty of Biotechnology, Universitas Katolik Atma Jaya, Jalan Jenderal Sudirman 51, Jakarta, 12930 Indonesia
| | - Iman Rusmana
- Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor, 16680 Indonesia
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Eladawy M, El-Mowafy M, El-Sokkary MMA, Barwa R. Antimicrobial resistance and virulence characteristics in ERIC-PCR typed biofilm forming isolates of P. aeruginosa. Microb Pathog 2021; 158:105042. [PMID: 34119625 DOI: 10.1016/j.micpath.2021.105042] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/22/2021] [Accepted: 06/04/2021] [Indexed: 10/21/2022]
Abstract
Pseudomonas aeruginosa is a serious pathogen particularly in immunocompromised patients. In this work, 103 clinical isolates of P. aeruginosa were collected and classified into weak, moderate, and strong biofilm producers according to their biofilm forming abilities via tissue culture plate method. The antimicrobial resistance and the presence of different virulence genes were investigated via disc diffusion method and polymerase chain reaction respectively. Moreover, ERIC-PCR typing was performed to investigate the genetic diversity among the clinical isolates. No significant correlation was observed between biofilm formation and resistance to each antimicrobial agent. Similar observation was detected concerning the multidrug resistance and biofilm formation. Regarding virulence genes, algD gene was harbored by all isolates (100%). Only pelA and phzM were significantly prevalent in strong biofilm producers. Additionally, the mean virulence score was higher in strong biofilm producers (9.33) than moderate (8.62) and weak (7) biofilm producers. Moreover, there was a significant correlation between the overall virulence score of the isolates and its ability to form biofilm. ERIC-PCR genotyping revealed the presence of 99 different ERIC patterns based on 70% similarity, and the different ERIC patterns were categorized into 8 clusters. 100% similarity indicates the possibility of cross-colonization in P. aeruginosa infections.
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Affiliation(s)
- Mohamed Eladawy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Egypt
| | - Mohammed El-Mowafy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Egypt
| | - Mohamed M A El-Sokkary
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Egypt.
| | - Rasha Barwa
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Egypt
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RANJBAR R, AFSHAR D. Evaluation of (GTG) 5-PCR for Genotyping of Klebsiella pneumonia Strains Isolated from Patients with Urinary Tract Infections. IRANIAN JOURNAL OF PUBLIC HEALTH 2019; 48:1879-1884. [PMID: 31850266 PMCID: PMC6908898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Klebsiella pneumonia is one of the common causes of pneumonia and bacteremia in intensive care patients. The present study was aimed to determine the capability of (GTG) 5-PCR assay for molecular typing of K. pneumonia strains isolated from patients with urinary tract infections. METHODS In this descriptive-sectional study, K. pneumoniae strains were collected from hospitalized patients with urinary tract infection in Baqiyatallah Hospital, Tehran, Iran during 2017-2018. Isolates were identified by conventional microbiological tests. Bacterial DNA was extracted using boiling method and (GTG) 5-PCR assay was used for subtyping of the isolates. For clustering of isolates, dendrogram was generated according to the un-weighted pair group method with arithmetic (UPGMA). RESULTS Overall, 88 K. pneumoniae isolates were isolated and subjected to the molecular typing study. The (GTG) 5-PCR assay was able to differentiate the K. pneumoniae strains into 9 clusters including G1-G9. Genotype clusters G4 and G9 consist of highest (26) and lowest (1) number isolate, respectively. CONCLUSION The K. pneumonia strains isolated under the study belonged to various clones and the (GTG) 5-PCR assay as simple and rapid method can be a powerful tool for molecular typing of K. pneumoniae strains.
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Affiliation(s)
- Reza RANJBAR
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran,Corresponding Author:
| | - Davoud AFSHAR
- Department of Microbiology and Virology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
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Caleffi-Ferracioli KR, Baldin VP, Noguti ÉN, Siqueira VLD, Scodro RBL, Pavan FR, Hirata MH, Cardoso RF. Molecular characterization of Mycobacterium tuberculosis and Mycobacterium bovis isolates by Enterobacterial Repetitive Intergenic Consensus-PCR. BRAZ J PHARM SCI 2018. [DOI: 10.1590/s2175-97902018000317554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria. Clin Microbiol Rev 2016; 29:239-90. [PMID: 26912567 DOI: 10.1128/cmr.00055-15] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.
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Cannas A, Mazzarelli A, Di Caro A, Delogu G, Girardi E. Molecular Typing of Mycobacterium Tuberculosis Strains: A Fundamental Tool for Tuberculosis Control and Elimination. Infect Dis Rep 2016; 8:6567. [PMID: 27403266 PMCID: PMC4927935 DOI: 10.4081/idr.2016.6567] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 04/29/2016] [Indexed: 11/23/2022] Open
Abstract
Tuberculosis (TB) is still an important cause of morbidity and mortality worldwide. An improvement of the strategies for disease control is necessary in both low- and high-incidence TB countries. Clinicians, epidemiologists, laboratory specialists, and public health players should work together in order to achieve a significant reduction in TB transmission and spread of drug-resistant strains. Effective TB surveillance relies on early diagnosis of new cases, appropriate therapy, and accurate detection of outbreaks in the community, in order to implement proper TB control strategies. To achieve this goal, information from classical and molecular epidemiology, together with patient clinical data need to be combined. In this review, we summarize the methodologies currently used in molecular epidemiology, namely molecular typing. We will discuss their efficiency to phylogenetically characterize Mycobacterium tuberculosis isolates, and their ability to provide information that can be useful for disease control. We will also introduce next generation sequencing as the methodology that potentially could provide in a short time both, detection of new outbreaks and identification of resistance patterns. This could envision a potential of next generation sequencing as an important tool for accurate patient management and disease control.
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Affiliation(s)
- Angela Cannas
- National Institute for Infectious Diseases L. Spallanzani , Rome, Italy
| | | | - Antonino Di Caro
- National Institute for Infectious Diseases L. Spallanzani , Rome, Italy
| | - Giovanni Delogu
- National Institute for Infectious Diseases L. Spallanzani, Rome, Italy; Institute of Microbiology, Sacro Cuore Catholic University, Rome, Italy
| | - Enrico Girardi
- National Institute for Infectious Diseases L. Spallanzani , Rome, Italy
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Khosravi AD, Mehrabzadeh RS, Farahani A, Jamali H. Molecular Identification of Clinical Isolates of Mycobacterium fortuitum by Random Amplified Polymorphic DNA (RAPD) Polymerase Chain Reaction and ERIC PCR. J Clin Diagn Res 2015; 9:DC01-5. [PMID: 26816886 DOI: 10.7860/jcdr/2015/15504.6909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/11/2015] [Indexed: 11/24/2022]
Abstract
BACKGROUNDS Non tuberculous mycobacteria (NTM) are of importance now-a-days due to their increasing virulence outbreaks and emerging antibiotic resistance. Since the most common NTM in Iran is reportedly Mycobacterium fortuitum, the present study was designed with the aim of molecular identification of clinical isolates of M. foruitum to analyse their heterogeneity. MATERIALS AND METHODS A total of 81 isolates of NTM isolated from various samples were collected. The clinical isolates were assigned to species M. fortuitum by using conventional and molecular methods. The DNA banding patterns of ERIC- PCR and RAPD- PCR were analysed by using Bionumeric 7.5 software. RESULTS Out of 81 tested NTM, 36 strains of M. fortuitum were identified. 33 isolates were selected for molecular typing in this study. Based on RAPD and ERIC analysis, M. fortuitum isolates were divided into 3 and 6 clusters, respectively. Most of the isolates were distributed into types of II RAPD (20 members/ 60.6 %) and V (14 members/ 42.4% with sub cluster I & II) of ERIC. In RAPD analysis, the major fragments were 300 bp, followed by fragment 1000. In ERIC analysis, the major fragments were 280 bp followed by fragment 1200 bp. CONCLUSION In conclusion, though the results from this study represented higher discriminatory power of ERIC, however the combination of RAPD and ERIC analysis were able to sufficiently discriminate the genotypic diversity, infection control, and gain useful epidemiological information regarding M. fortuitum isolates.
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Affiliation(s)
- Azar Dokht Khosravi
- Professor, Department of Microbiology, School of Medicine, Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences , Ahvaz, Iran
| | - Rasa Sheini Mehrabzadeh
- Research Assistant, Department of Microbiology, Islamic Azad University , Jahrom Branch, Iran
| | - Abbas Farahani
- PhD Candidate, Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences , Ahvaz, Iran
| | - Hooshang Jamali
- Assistant Professor, Department of Immunology, Islamic Azad University , Jahrom Branch, Iran
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Current methods in the molecular typing of Mycobacterium tuberculosis and other mycobacteria. BIOMED RESEARCH INTERNATIONAL 2014; 2014:645802. [PMID: 24527454 PMCID: PMC3914561 DOI: 10.1155/2014/645802] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/18/2013] [Indexed: 11/18/2022]
Abstract
In the epidemiology of tuberculosis (TB) and nontuberculous mycobacterial (NTM) diseases, as in all infectious diseases, the key issue is to define the source of infection and to disclose its routes of transmission and dissemination in the environment. For this to be accomplished, the ability of discerning and tracking individual Mycobacterium strains is of critical importance. Molecular typing methods have greatly improved our understanding of the biology of mycobacteria and provide powerful tools to combat the diseases caused by these pathogens. The utility of various typing methods depends on the Mycobacterium species under investigation as well as on the research question. For tuberculosis, different methods have different roles in phylogenetic analyses and person-to-person transmission studies. In NTM diseases, most investigations involve the search for environmental sources or phylogenetic relationships. Here, too, the type of setting determines which methodology is most suitable. Within this review, we summarize currently available molecular methods for strain typing of M. tuberculosis and some NTM species, most commonly associated with human disease. For the various methods, technical practicalities as well as discriminatory power and accomplishments are reviewed.
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BARUS TATI, HANJAYA IVAN, SADELI JOANITA, LAY BIBIANAWIDIYATI, SUWANTO ANTONIUS, YULANDI ADI. Genetic Diversity of Klebsiella spp. Isolated from Tempe based on Enterobacterial Repetitive Intergenic Consensus-Polymerase Chain Reaction (ERIC-PCR). HAYATI JOURNAL OF BIOSCIENCES 2013. [DOI: 10.4308/hjb.20.4.171] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Okada T, Fujita K, Suzuki H, Tsuzukibashi O, Umezawa K, Nagahama F, Ikemi T, Takada K. Distribution and sequencing of enterobacterial repetitive intergenic consensus sequence elements in Streptococcus mutans serotype c. J Oral Biosci 2013. [DOI: 10.1016/j.job.2013.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kreutzfeldt KM, McAdam PR, Claxton P, Holmes A, Seagar AL, Laurenson IF, Fitzgerald JR. Molecular longitudinal tracking of Mycobacterium abscessus spp. during chronic infection of the human lung. PLoS One 2013; 8:e63237. [PMID: 23696800 PMCID: PMC3655965 DOI: 10.1371/journal.pone.0063237] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 04/02/2013] [Indexed: 11/21/2022] Open
Abstract
The Mycobacterium abscessus complex is an emerging cause of chronic pulmonary infection in patients with underlying lung disease. The M. abscessus complex is regarded as an environmental pathogen but its molecular adaptation to the human lung during long-term infection is poorly understood. Here we carried out a longitudinal molecular epidemiological analysis of 178 M. abscessus spp. isolates obtained from 10 cystic fibrosis (CF) and 2 non CF patients over a 13 year period. Multi-locus sequence and molecular typing analysis revealed that 11 of 12 patients were persistently colonized with the same genotype during the course of the infection while replacement of a M. abscessus sensu stricto strain with a Mycobacterium massiliense strain was observed for a single patient. Of note, several patients including a pair of siblings were colonized with closely-related strains consistent with intra-familial transmission or a common infection reservoir. In general, a switch from smooth to rough colony morphology was observed during the course of long-term infection, which in some cases correlated with an increasing severity of clinical symptoms. To examine evolution during long-term infection of the CF lung we compared the genome sequences of 6 sequential isolates of Mycobacterium bolletii obtained from a single patient over an 11 year period, revealing a heterogeneous clonal infecting population with mutations in regulators controlling the expression of virulence factors and complex lipids. Taken together, these data provide new insights into the epidemiology of M. abscessus spp. during long-term infection of the CF lung, and the molecular transition from saprophytic organism to human pathogen.
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Affiliation(s)
- Kaj M. Kreutzfeldt
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush Campus, Edinburgh, United Kingdom
| | - Paul R. McAdam
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush Campus, Edinburgh, United Kingdom
| | - Pauline Claxton
- Scottish Mycobacteria Reference Laboratory (SMRL), Clinical Microbiology, Royal Infirmary of Edinburgh, Little France, Edinburgh, United Kingdom
| | - Anne Holmes
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush Campus, Edinburgh, United Kingdom
| | - A. Louise Seagar
- Scottish Mycobacteria Reference Laboratory (SMRL), Clinical Microbiology, Royal Infirmary of Edinburgh, Little France, Edinburgh, United Kingdom
| | - Ian F. Laurenson
- Scottish Mycobacteria Reference Laboratory (SMRL), Clinical Microbiology, Royal Infirmary of Edinburgh, Little France, Edinburgh, United Kingdom
| | - J. Ross Fitzgerald
- The Roslin Institute and Edinburgh Infectious Diseases, University of Edinburgh, Easter Bush Campus, Edinburgh, United Kingdom
- * E-mail:
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Terta M, Azelmat S, M’hand RA, Achbani EH, Barakate M, Bouteau F, Ennaji MM. Molecular typing of Pectobacterium carotovorum isolated from potato tuber soft rot in Morocco. ANN MICROBIOL 2011. [DOI: 10.1007/s13213-011-0391-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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14
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Trinucleotide repeat sequence-based PCR as a potential approach for genotyping Mycobacterium gordonae strains. J Microbiol Methods 2011; 85:28-32. [PMID: 21276824 DOI: 10.1016/j.mimet.2011.01.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Revised: 12/14/2010] [Accepted: 01/03/2011] [Indexed: 11/20/2022]
Abstract
Diseases that are caused by non-tuberculous mycobacteria (NTM) continue to pose difficult clinical problems, and the epidemiological aspect of NTM-caused diseases is of great importance. In the case of Mycobacterium gordonae there is no adequate genotyping scheme. Here we present a potential rapid and reproducible genetic assay that uses trinucleotide repeat sequence-based PCR (TRS-PCR) for genotyping M. gordonae. The proposed method constitutes a useful single-primer PCR screen for genotyping this species. Among 10 TRS-containing primers, after applying (CAC)₄-based PCR to 36 strains of M. gordonae, we found a discriminatory index of 0.975. The accuracy of this analysis was supported by a reasonable reproducibility of 92%. These results were compared with the Enterobacterial Repetitive Intergenic Consensus Sequences (ERIC)-PCR typing scheme which had lower discriminatory index of 0.93 and its reproducibility was only 86.3%.
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Bishi DK, Verghese S, Verma RS. Molecular typing of colonizing Streptococcus agalactiae strains by enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) in a Chennai based hospital. Indian J Microbiol 2008; 48:291-6. [PMID: 23100723 DOI: 10.1007/s12088-008-0017-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 01/15/2008] [Accepted: 01/18/2008] [Indexed: 10/22/2022] Open
Abstract
Streptococcus agalactiae is reported to be an asymptomatic vaginal colonizer in Indian women, although it is considered one of the major causes of neonatal infections in many European countries. DNA based molecular typing methods are more reliable than the conventional serotyping method for identification and typing of this pathogen. In the present study, we have evaluated genetic diversity among colonizing S. agalactiae strains (n=86) by using a PCR-based genotyping method i.e. Enterobacterial Repetitive Intergenic Consensus PCR (ERIC-PCR). With ERIC-PCR fingerprinting at 60% similarity level in a dendrogram generated by UPGMA cluster analysis, 10 different ERIC groups were identified, which were subdivided into 62 distinct genotypes at ≥ 95% similarity level. Based on these findings, we demonstrate that ERIC-PCR is a simple, rapid, and inexpensive tool with sufficient discriminatory power and is applicable for characterization and genotyping of a large number of clinical isolates of S. agalactiae at molecular level.
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Affiliation(s)
- D K Bishi
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, 600 036 India ; Department of Microbiology, Frontier Lifeline Pvt. Ltd., Chennai, 600101 India
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Ahmed N, Saini V, Raghuvanshi S, Khurana JP, Tyagi AK, Tyagi AK, Hasnain SE. Molecular analysis of a leprosy immunotherapeutic bacillus provides insights into Mycobacterium evolution. PLoS One 2007; 2:e968. [PMID: 17912347 PMCID: PMC1989137 DOI: 10.1371/journal.pone.0000968] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2007] [Accepted: 09/10/2007] [Indexed: 11/18/2022] Open
Abstract
Background Evolutionary dynamics plays a central role in facilitating the mechanisms of species divergence among pathogenic and saprophytic mycobacteria. The ability of mycobacteria to colonize hosts, to proliferate and to cause diseases has evolved due to its predisposition to various evolutionary forces acting over a period of time. Mycobacterium indicus pranii (MIP), a taxonomically unknown ‘generalist’ mycobacterium, acts as an immunotherapeutic against leprosy and is approved for use as a vaccine against it. The large-scale field trials of this MIP based leprosy vaccine coupled with its demonstrated immunomodulatory and adjuvant property has led to human clinical evaluations of MIP in interventions against HIV-AIDS, psoriasis and bladder cancer. MIP, commercially available as ‘Immuvac’, is currently the focus of advanced phase III clinical trials for its antituberculosis efficacy. Thus a comprehensive analysis of MIP vis-à-vis evolutionary path, underpinning its immanent immunomodulating properties is of the highest desiderata. Principal Findings Genome wide comparisons together with molecular phylogenetic analyses by fluorescent amplified fragment length polymorphism (FAFLP), enterobacterial repetitive intergenic consensus (ERIC) based genotyping and candidate orthologues sequencing revealed that MIP has been the predecessor of highly pathogenic Mycobacterium avium intracellulare complex (MAIC) that did not resort to parasitic adaptation by reductional gene evolution and therefore, preferred a free living life-style. Further analysis suggested a shared aquatic phase of MAIC bacilli with the early pathogenic forms of Mycobacterium, well before the latter diverged as ‘specialists’. Conclusions/Significance This evolutionary paradigm possibly affirms to marshal our understanding about the acquisition and optimization of virulence in mycobacteria and determinants of boundaries therein.
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Affiliation(s)
- Niyaz Ahmed
- Pathogen Evolution Laboratory, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Vikram Saini
- Interdisciplinary Centre for Plant Genomics, Department of Plant Molecular Biology, University of Delhi, New Delhi, India
- Department of Biochemistry, University of Delhi, New Delhi, India
| | - Saurabh Raghuvanshi
- Interdisciplinary Centre for Plant Genomics, Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Jitendra P. Khurana
- Interdisciplinary Centre for Plant Genomics, Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Akhilesh K. Tyagi
- Interdisciplinary Centre for Plant Genomics, Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Anil K. Tyagi
- Department of Biochemistry, University of Delhi, New Delhi, India
| | - Seyed E. Hasnain
- University of Hyderabad, Hyderabad, India
- Institute of Life Sciences, University of Hyderabad, Hyderabad, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
- * To whom correspondence should be addressed. E-mail:
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Sampaio JLM, Chimara E, Ferrazoli L, da Silva Telles MA, Del Guercio VMF, Jericó ZVN, Miyashiro K, Fortaleza CMCB, Padoveze MC, Leão SC. Application of four molecular typing methods for analysis of Mycobacterium fortuitum group strains causing post-mammaplasty infections. Clin Microbiol Infect 2006; 12:142-9. [PMID: 16441452 DOI: 10.1111/j.1469-0691.2005.01312.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A cluster of cases of post-augmentation mammaplasty surgical site infections occurred between 2002 and 2004 in Campinas, in the southern region of Brazil. Rapidly growing mycobacteria were isolated from samples from 12 patients. Eleven isolates were identified as Mycobacterium fortuitum and one as Mycobacterium porcinum by PCR-restriction digestion of the hsp65 gene. These 12 isolates, plus six additional M. fortuitum isolates from non-related patients, were typed by pulsed-field gel electrophoresis (PFGE) and three PCR-based techniques: 16S-23S rRNA internal transcribed spacer (ITS) genotyping; randomly amplified polymorphic DNA (RAPD) PCR; and enterobacterial repetitive intergenic consensus (ERIC) PCR. Four novel M. fortuitum allelic variants were identified by restriction analysis of the ITS fragment. One major cluster, comprising six M. fortuitum isolates, and a second cluster of two isolates, were identified by the four methods. RAPD-PCR and ITS genotyping were less discriminative than ERIC-PCR. ERIC-PCR was comparable to PFGE as a valuable complementary tool for investigation of this type of outbreak.
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Affiliation(s)
- J L M Sampaio
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, Escola Paulista de Medicina, São Paulo, Brazil
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18
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Sampaio JLM, Viana-Niero C, de Freitas D, Höfling-Lima AL, Leão SC. Enterobacterial repetitive intergenic consensus PCR is a useful tool for typing Mycobacterium chelonae and Mycobacterium abscessus isolates. Diagn Microbiol Infect Dis 2006; 55:107-18. [PMID: 16529900 DOI: 10.1016/j.diagmicrobio.2006.01.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2005] [Revised: 12/22/2005] [Accepted: 01/03/2006] [Indexed: 10/24/2022]
Abstract
Outbreaks of rapidly growing mycobacterium (RGM) infections are increasingly being reported worldwide. Information about genetic relatedness of isolates obtained during outbreaks can provide opportunities for prompt intervention. Pulsed-field gel electrophoresis (PFGE) is expensive, time consuming, and labor intensive. Other than that, Mycobacterium abscessus isolates can suffer DNA degradation during electrophoresis. Polymerase chain reaction (PCR)-based methods are cheaper, faster, and easier to perform, but discriminatory power varies depending on the primer used. In this study, we tested the competence of enterobacterial repetitive intergenic consensus (ERIC) PCR in comparison with PFGE to distinguish unrelated isolates (24 Mycobacterium chelonae and 24 M. abscessus) obtained from human and/or environmental samples and to group 56 isolates from 6 outbreaks confirmed epidemiologically, caused by M. chelonae and M. abscessus after ophthalmologic refractive surgery and mesotherapy. Enterobacterial repetitive intergenic consensus PCR presented discriminatory power, calculated using Simpson's index of diversity, of 0.989 for M. abscessus and 0.975 for M. chelonae and grouped outbreak isolates in distinct groups showing epidemiologic concordance. Pulsed-field gel electrophoresis also grouped outbreak isolates and presented discriminatory power of 0.972 and 0.993 for M. abscessus and M. chelonae, respectively. DNA from 8 (22%) of 36 M. abscessus isolates analyzed showed degradation during electrophoresis. Compared with PFGE and epidemiologic information as the gold standard, ERIC PCR is a simple, high throughput, affordable, reproducible, and discriminatory molecular typing method for inference of genetic relatedness of RGMs of the M. chelonae-abscessus group.
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MESH Headings
- Bacteriological Techniques
- DNA, Bacterial/genetics
- DNA, Intergenic/genetics
- Disease Outbreaks
- Electrophoresis, Gel, Pulsed-Field
- Eye Infections, Bacterial/diagnosis
- Eye Infections, Bacterial/epidemiology
- Eye Infections, Bacterial/microbiology
- Gene Expression Regulation, Bacterial
- Humans
- Interspersed Repetitive Sequences/genetics
- Mycobacterium/classification
- Mycobacterium/genetics
- Mycobacterium Infections/diagnosis
- Mycobacterium Infections/epidemiology
- Mycobacterium Infections/microbiology
- Phylogeny
- Polymerase Chain Reaction/methods
- Skin Diseases, Bacterial/diagnosis
- Skin Diseases, Bacterial/epidemiology
- Skin Diseases, Bacterial/microbiology
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Affiliation(s)
- Jorge Luiz Mello Sampaio
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo-Escola Paulista de Medicina, Rua Botucatu, 862-3 andar-04023-062, São Paulo, Brazil
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19
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Kremer K, Arnold C, Cataldi A, Gutiérrez MC, Haas WH, Panaiotov S, Skuce RA, Supply P, van der Zanden AGM, van Soolingen D. Discriminatory power and reproducibility of novel DNA typing methods for Mycobacterium tuberculosis complex strains. J Clin Microbiol 2005; 43:5628-38. [PMID: 16272496 PMCID: PMC1287774 DOI: 10.1128/jcm.43.11.5628-5638.2005] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2005] [Revised: 04/18/2005] [Accepted: 06/23/2005] [Indexed: 11/20/2022] Open
Abstract
In recent years various novel DNA typing methods have been developed which are faster and easier to perform than the current internationally standardized IS6110 restriction fragment length polymorphism typing method. However, there has been no overview of the utility of these novel typing methods, and it is largely unknown how they compare to previously published methods. In this study, the discriminative power and reproducibility of nine recently described PCR-based typing methods for Mycobacterium tuberculosis were investigated using the strain collection of the interlaboratory study of Kremer et al. This strain collection contains 90 M. tuberculosis complex and 10 non-M. tuberculosis complex mycobacterial strains, as well as 31 duplicated DNA samples to assess reproducibility. The highest reproducibility was found with variable numbers of tandem repeat typing using mycobacterial interspersed repetitive units (MIRU VNTR) and fast ligation-mediated PCR (FLiP), followed by second-generation spoligotyping, ligation-mediated PCR (LM-PCR), VNTR typing using five repeat loci identified at the Queens University of Belfast (QUB VNTR), and the Amadio speciation PCR. Poor reproducibility was associated with fluorescent amplified fragment length polymorphism typing, which was performed in three different laboratories. The methods were ordered from highest discrimination to lowest by the Hunter-Gaston discriminative index as follows: QUB VNTR typing, MIRU VNTR typing, FLiP, LM-PCR, and spoligotyping. We conclude that both VNTR typing methods and FLiP typing are rapid, highly reliable, and discriminative epidemiological typing methods for M. tuberculosis and that VNTR typing is the epidemiological typing method of choice for the near future.
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Affiliation(s)
- Kristin Kremer
- Mycobacteria Reference Unit, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, P.O. Box 1, 3720 BA Bilthoven, The Netherlands.
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20
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Hussain MA, Kauser F, Khan AA, Tiwari S, Habibullah CM, Ahmed N. Implications of molecular genotyping of Helicobacter pylori isolates from different human populations by genomic fingerprinting of enterobacterial repetitive intergenic consensus regions for strain identification and geographic evolution. J Clin Microbiol 2004; 42:2372-8. [PMID: 15184407 PMCID: PMC427806 DOI: 10.1128/jcm.42.6.2372-2378.2004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2004] [Revised: 02/06/2004] [Accepted: 02/26/2004] [Indexed: 11/20/2022] Open
Abstract
Biogeographic partitioning of the genome is typical of the gastric pathogen Helicobacter pylori. Such population-specific evolution could serve as a model for understanding host-pathogen interaction and the impact of genetic drift and recombination on insular populations. With a total of 320 isolates from six geographic regions (Japan, India, England, Spain, Ireland, Africa, and Peru) analyzed by enterobacterial repetitive intergenic consensus (ERIC)-based genotyping, we examined genetic affinities among various H. pylori populations in the world. Several strain-specific and region-specific differences were observed by ERIC-based typing. Polymorphic ERIC patterns indicated that the ERIC sequences are in fact dispersed in the H. pylori chromosome at different locations separated by various distances. Phylogenetic analysis of 61 representative isolates revealed three distinct genetic clusters populated by isolates with shared ERIC types independent of the cag right-junction motif type and vacA allele status. Among the notable genetic relationships were the genotypic similarities between Irish and Japanese and between Peruvian and Japanese isolates. Insular genotypic characteristics of Irish isolates amid genetic similarity to East Asian, as well as North European, strains have been once again proved in this study. Peruvian genotypes were more similar to those of Japanese isolates than to those of Iberian or European isolates. Given the current debate on the origin and age of present-day H. pylori, this is a significant finding that supports the possibility of ancient colonization of Amerindians with East Asian strains. Genotypic data presented here will be additionally helpful in realizing the importance of H. pylori geographical genomics in the development of gastroduodenal pathology.
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Affiliation(s)
- M Abid Hussain
- Pathogen Evolution Group, CDFD, ECIL Rd., Nacharam, Hyderabad 500 076, India
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21
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Englund S. IS900/ERIC-PCR as a tool to distinguish Mycobacterium avium subsp. paratuberculosis from closely related mycobacteria. Vet Microbiol 2003; 96:277-87. [PMID: 14559175 DOI: 10.1016/j.vetmic.2003.08.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
There is an increasing demand for fast and reliable methods to distinguish Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis) from closely related mycobacteria and also a need for rapid strain specific typing of clinical isolates for epidemiological reasons. In the present study, the potential of rep-PCR as a fingerprinting method for M. paratuberculosis was assessed and compared to conventional RFLP. A PCR assay was designed and optimised to obtain reproducible fingerprints of mycobacterial DNA with primers targeting the enterobacterial intergenic consensus (ERIC) sequence and the M. paratuberculosis specific insertion sequence IS900. Reproducible fingerprints were obtained with 60 strains of M. paratuberculosis, 16 strains of M. avium subsp. avium, 3 strains of M. intracellulare, and 11 other mycobacterial strains. A species-specific band pattern that was clearly distinguishable from that of other mycobacteria was obtained with M. paratuberculosis. The rep-PCR did not detect any differences among M. paratuberculosis strains of different RFLP types, and was therefore not considered as an alternative fingerprinting method. However, the species-specific band pattern make IS900/ERIC-PCR a suitable alternative for distinguishing M. paratuberculosis from other mycobacteria, especially in cases of IS900 PCR positive mycobacteria. The fingerprinting method reported was fast and easy to perform, and produced highly reproducible results.
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Affiliation(s)
- Stina Englund
- Department of Bacteriology, National Veterinary Institute, SE-751 89 Uppsala, Sweden.
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22
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Bruant G, Watt S, Quentin R, Rosenau A. Typing of nonencapsulated haemophilus strains by repetitive-element sequence-based PCR using intergenic dyad sequences. J Clin Microbiol 2003; 41:3473-80. [PMID: 12904341 PMCID: PMC179775 DOI: 10.1128/jcm.41.8.3473-3480.2003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intergenic dyad sequences (IDS) are short repeated elements that have been described for several Haemophilus genomes and for only two other bacterial genera. We developed a repetitive-element sequence-based PCR using an IDS-specific primer as a typing method (IDS-PCR) for nonencapsulated Haemophilus strains and compared this technique with pulsed-field gel electrophoresis (PFGE) of DNA restricted with SmaI. IDS-PCR was rapid, easy to perform, and reproducible, with a high discriminatory capacity for nontypeable Haemophilus influenzae (NTHI) strains. The 69 NTHI strains tested generated 65 different banding patterns. Epidemiologically related strains gave similar or identical fingerprints, and all of the unrelated strains except two showed different patterns. These results were in agreement with those obtained by PFGE. For 20 genital strains usually identified as being biotype IV NTHI and belonging to a cryptic genospecies of Haemophilus with remarkable genetic homogeneity, four bands were significantly present and six bands were significantly absent from the fingerprints. The 20 strains were gathered in 11 closely related profiles, whereas PFGE provided no band when DNA was treated with SmaI. IDS-PCR improved the differentiation previously obtained within this species by ribotyping and multilocus enzyme electrophoresis. Our findings suggest that IDS-PCR is a rapid, reliable, and discriminatory method for typing NTHI strains and is currently the most efficient method for distinguishing strains within the cryptic genospecies of HAEMOPHILUS:
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Affiliation(s)
- Guillaume Bruant
- Département de Microbiologie Médicale et Moléculaire, Unité de Bactériologie, Centre Hospitalo-Universitaire Bretonneau, 37044 Tours Cedex, France
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23
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Pinna A, Sechi LA, Zanetti S, Usai D, Delogu G, Cappuccinelli P, Carta F. Bacillus cereus keratitis associated with contact lens wear. Ophthalmology 2001; 108:1830-4. [PMID: 11581057 DOI: 10.1016/s0161-6420(01)00723-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE We report the first case of contact lens-related Bacillus cereus keratitis and ulcer associated with B. cereus contamination of the contact lens case. This is also the first study to investigate and establish the genetic identity of an organism isolated from the cornea and contact lens case in a patient with contact lens-associated keratitis. DESIGN Case report. INTERVENTION AND TESTING Conjunctival swabs and corneal scrapings from the left eye were inoculated for culture. The contact lens case was also cultured. Antibiotic susceptibility testing was determined by agar disk diffusion method. Initial treatment with topical ciprofloxacin and fortified tobramycin was given. Genetic analysis of the bacterial isolates was performed using polymerase chain reaction (PCR) with enterobacterial repetitive intergenic consensus primers (ERIC; ERIC-PCR). Susceptibility of B. cereus to heat and contact lens disinfecting solutions containing hydrogen peroxide, hydrogen peroxide-catalase, polyquaternium-1, and polyaminopropyl biguanide (PAPB) was tested. MAIN OUTCOME MEASURES Clinical features, culture results, and antibiotic susceptibility testing were analyzed. The ERIC-PCR amplification products were visualized in ethidium bromide-stained agarose gel. Bacterial growth after exposure to heat and contact lens disinfecting solutions was assessed on blood agar plates. RESULTS B. cereus was grown from the conjunctiva, corneal ulcer, and contact lens case. All isolates were sensitive to gentamicin, tobramycin, ciprofloxacin, clindamycin, and vancomycin. The corneal ulcer gradually healed over the next 6 days. Results of ERIC-PCR showed that the isolates from the cornea and contact lens case were indistinguishable, thus demonstrating the source of infecting organism to be the contaminated contact lens case. Exposure to a temperature of 80 degrees C for 20 minutes and incubation with hydrogen peroxide-catalase, polyquaternium-1, and PAPB for the minimum recommended time failed to kill B. cereus. Only exposure to hydrogen peroxide for 4 hours eradicated the organism. CONCLUSIONS B. cereus should be considered a possible etiologic agent of contact lens-associated keratitis. Heat and many types of contact lens disinfecting solutions may be ineffective in eradicating B. cereus from contaminated contact lens cases. Only prolonged exposure to hydrogen peroxide appeared to be sporicidal to B. cereus in this study.
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Affiliation(s)
- A Pinna
- Institute of Ophthalmology, University of Sassari, Sassari, Italy.
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24
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Ferreira AM, Suzart S, Vidotto O, Knowles DP, Vidotto MC. Use of repetitive DNA elements to define genetic relationships among Anaplasma marginale isolates. FEMS Microbiol Lett 2001; 197:139-43. [PMID: 11313126 DOI: 10.1111/j.1574-6968.2001.tb10595.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Anaplasma marginale genomic DNA was tested for the presence of repetitive extragenic palindromic (REP) and enterobacterial repetitive intergenic consensus (ERIC)-like sequences in order to evaluate the genetic diversity of multiple A. marginale isolates. A. marginale isolates were obtained from cattle of six different states of Brazil, from the US and an Anaplasma centrale strain was obtained from Uruguay. Patterns obtained from A. marginale isolates varied from 14 to 17 fragments by REP-polymerase chain reaction (PCR) and 6 to 14 fragments by ERIC-PCR. All A. marginale isolates presented a 0.75-kb fragment by REP and two common fragments (0.38 and 1.0 kb) by ERIC-PCR. These two fragments were not detectable in A. centrale. Both methods produced similar patterns (80%) among A. marginale isolates obtained from the same region, although some isolates within regions shared less similarity. Isolates from Parana and Pernambuco, were differentiated by these methods. The study demonstrates the presence of ERIC and REP-like elements in A. marginale isolates and shows that A. marginale isolates and strains can be differentiated by these methods.
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Affiliation(s)
- A M Ferreira
- Departamento de Microbiologia, Universidade Estadual de Londrina, PR, Brazil
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25
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Patton TG, Katz S, Sobieski RJ, Crupper SS. Genotyping of clinical Serratia marcescens isolates: a comparison of PCR-based methods. FEMS Microbiol Lett 2001; 194:19-25. [PMID: 11150660 DOI: 10.1111/j.1574-6968.2001.tb09440.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The polymerase chain reaction (PCR)-based procedures of randomly amplified polymorphic DNA (RAPD) and repetitive element (RE)-based PCR were used to amplify total DNA prepared from each of 62 clinical Serratia marcescens isolates. Three different random primers, designated 1060, 1254 and 1283, were used individually in RAPD-PCR. Primers representing enterobacterial repetitive intergenic consensus (ERIC) sequences, extragenic palindromic (REP) elements, and polymorphic GC-rich repetitive sequences (PGRS) constituted the repetitive element-PCR. We were able to generate 40, 40 and 58 genotypic groupings using the 1060, 1254 and 1283 RAPD primers, respectively. Using the ERIC, REP and PGRS primers, 19, 54 and 60 unique genotypic profiles were yielded, respectively. The PGRS primers, which were developed to amplify GC-rich repetitive sequences in the genome of Mycobacteria, were the most discriminatory. These data indicate that both of these PCR-based approaches are a valid means of discriminating strain differences among isolates of S. marcescens and the amount of differentiation depends on the primer used. These techniques should prove useful for routine surveillance or in examining outbreaks of S. marcescens in clinical settings.
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Affiliation(s)
- T G Patton
- Department of Biological Sciences, 1200 Commercial, Emporia State University, Emporia, KS 66801, USA
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26
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Van Soolingen D. Molecular epidemiology of tuberculosis and other mycobacterial infections: main methodologies and achievements. J Intern Med 2001; 249:1-26. [PMID: 11168781 DOI: 10.1046/j.1365-2796.2001.00772.x] [Citation(s) in RCA: 203] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In the last decade, DNA fingerprint techniques have become available to study the interperson transmission of tuberculosis and other mycobacterial infections. These methods have facilitated epidemiological studies at a population level. In addition, the species identification of rarely encountered mycobacteria has improved significantly. This article describes the state of the art of the main molecular typing methods for Mycobacterium tuberculosis complex and non-M. tuberculosis complex (atypical) mycobacteria. Important new insights that have been gained through molecular techniques into epidemiological aspects and diagnosis of mycobacterial diseases are highlighted.
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MESH Headings
- Animals
- Contact Tracing
- DNA Fingerprinting
- DNA, Bacterial/genetics
- Genetics, Microbial/trends
- Genotype
- Humans
- Molecular Epidemiology/methods
- Mycobacterium/classification
- Mycobacterium/genetics
- Mycobacterium/isolation & purification
- Mycobacterium Infections, Nontuberculous/epidemiology
- Mycobacterium Infections, Nontuberculous/genetics
- Mycobacterium Infections, Nontuberculous/transmission
- Mycobacterium tuberculosis/genetics
- Nontuberculous Mycobacteria/genetics
- Polymorphism, Restriction Fragment Length
- RNA, Bacterial/genetics
- Reproducibility of Results
- Sequence Analysis, DNA
- Sequence Analysis, RNA
- Transformation, Bacterial
- Tuberculosis/epidemiology
- Tuberculosis/genetics
- Tuberculosis/transmission
- Tuberculosis, Multidrug-Resistant/epidemiology
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Affiliation(s)
- D Van Soolingen
- Mycobacteria Reference Department, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment, Bilthoven, The Netherlands.
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27
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Sechi LA, Duprè I, Leori G, Fadda G, Zanetti S. Distribution of a specific 500-base-pair fragment in mycobacterium bovis isolates from Sardinian cattle. J Clin Microbiol 2000; 38:3837-9. [PMID: 11015414 PMCID: PMC87487 DOI: 10.1128/jcm.38.10.3837-3839.2000] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Amplification of a specific, 500-bp fragment from Mycobacterium bovis isolates and use of the fragment to differentiate between Mycobacterium tuberculosis and M. bovis was previously reported (J. G. Rodriguez, G. A. Meja, P. Del Portillo, M. E. Patarroyo, and L. A. Murillo, Microbiology 141:2131-2138, 1995). In the present study, 30 M. bovis isolates from Sardinian cattle were examined for the presence of this 500-bp fragment; 4 of the 30 isolates lacked the fragment. This result indicates that identification of M. bovis strains by amplification of the 500-bp sequence may lead to false-negative results.
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Affiliation(s)
- L A Sechi
- Dipartimento di Scienze Biomediche, Sezione di Microbiologia Sperimentale e Clinica, Università degli studi di Sassari, 07100 Sassari, Italy.
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28
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Shangkuan YH, Yang JF, Lin HC, Shaio MF. Comparison of PCR-RFLP, ribotyping and ERIC-PCR for typing Bacillus anthracis and Bacillus cereus strains. J Appl Microbiol 2000; 89:452-62. [PMID: 11021577 DOI: 10.1046/j.1365-2672.2000.01134.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
PCR-RFLP analysis of the vrrA gene and cerAB gene was used to investigate the genomic diversity in 21 strains of Bacillus anthracis and 28 strains of Bacillus cereus, and was compared with results obtained by ribotyping and enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) analysis. VrrA-typing divided the B. anthracis into four groups. Except for one Pasteur vaccine strain, the vrrA PCR-RFLP profiles of the B. anthracis were separated into three groups, which were different from those of the B. cereus strains. Ribotyping separated the B. anthracis isolates into seven ribotypes, and a common fragment of an approximately 850 bp band from the ERIC-PCR fingerprints separated most B. anthracis strains into two groups. VrrA/cerAB PCR-RFLP, ribotyping and ERIC-PCR generated 18, 22 and 23 types, respectively, from B. cereus strains. The results suggest that a combination of all three methods provides a high resolution typing method for B. anthracis and B. cereus. Compared with ribotyping and ERIC-PCR, PCR-RFLP is simple to perform and has potential as a rapid method for typing and discriminating B. anthracis strains from other B. cereus group bacteria.
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Affiliation(s)
- Y H Shangkuan
- Division of Bacteriology, Institute of Preventive Medicine, National Defense Medical Center, Taipei, Taiwan, Republic of China.
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29
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Bonora S, Gutierrez MC, Di Perri G, Brunello F, Allegranzi B, Ligozzi M, Fontana R, Concia E, Vincent V. Comparative evaluation of ligation-mediated PCR and spoligotyping as screening methods for genotyping of Mycobacterium tuberculosis strains. J Clin Microbiol 1999; 37:3118-23. [PMID: 10488164 PMCID: PMC85507 DOI: 10.1128/jcm.37.10.3118-3123.1999] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Spoligotyping has been suggested as a screening test in multistep genotyping of Mycobacterium tuberculosis strains. Relying on restriction fragment length polymorphism (RFLP) analysis with IS6110 (IS6110 RFLP analysis) as a "gold standard," we performed a comparative evaluation of spoligotyping and ligation-mediated PCR (LMPCR), a recently described PCR-based typing method, as rapid screening tests for fingerprinting of 158 M. tuberculosis strains collected in Verona, Italy. LMPCR seemed to be comparable to spoligotyping in terms both of feasibility with rapidly extracted DNA and of generation of software-analyzable images. Moreover, LMPCR grouped considerably fewer strains than spoligotyping (38 versus 67%) and was found to reduce the cluster overestimation rate (26.3 versus 58%) and to give a better discriminatory index (0.992 versus 0.970) compared to spoligotyping. In our geographical region, where there was no evidence of clustered strains carrying fewer than six IS6110 copies, LMPCR was found to be more discriminatory than spoligotyping. We also evaluated two models of three-step typing strategies, involving the use of spoligotyping and LMPCR as screening methods and IS6110 RFLP analysis as a further supporting test. LMPCR proved to be a more effective first-step test than spoligotyping, significantly reducing the need for subtyping. LMPCR should be considered an alternative to spoligotyping as a rapid screening method for M. tuberculosis fingerprinting, particularly in areas with a low prevalence of M. tuberculosis strains carrying few copies of IS6110.
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Affiliation(s)
- S Bonora
- Institute of Immunology and Infectious Diseases, University of Verona, 37126 Verona, Italy
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30
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Alam S, Brailsford SR, Whiley RA, Beighton D. PCR-Based methods for genotyping viridans group streptococci. J Clin Microbiol 1999; 37:2772-6. [PMID: 10449450 PMCID: PMC85375 DOI: 10.1128/jcm.37.9.2772-2776.1999] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/1999] [Accepted: 06/07/1999] [Indexed: 11/20/2022] Open
Abstract
Standard repetitive extragenic palindromic (REP)-PCR, enterobacterial repetitive intergenic consensus-PCR, and Salmonella enteritidis repetitive element-PCR methods for bacterial strain typing were performed with DNA extracted by boiling members of each of the currently recognized species of human viridans group streptococci. Each of the methods was reproducible. The unique isolates (n = 72) from 15 species of viridans group streptococci were readily distinguishable, with no two isolates showing greater than 90% per cent similarity. The majority of strains exhibited much less than 90% similarity. Isolates identical by REP-PCR were also identical by the other two methods. These PCR-based typing methods, although they do not permit determination of the species of the isolates, are simple to perform and are suitable for clinical and ecological investigations of viridans group streptococci.
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Affiliation(s)
- S Alam
- Joint Microbiology Research Unit, Guy's, King's and St. Thomas' Dental Institute, London SE5 9RW, England
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31
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Loubinoux J, Lozniewski A, Lion C, Garin D, Weber M, Le Faou AE. Value of enterobacterial repetitive intergenic consensus PCR for study of Pasteurella multocida strains isolated from mouths of dogs. J Clin Microbiol 1999; 37:2488-92. [PMID: 10405390 PMCID: PMC85264 DOI: 10.1128/jcm.37.8.2488-2492.1999] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fifty-six Pasteurella multocida strains (40 P. multocida subsp. septica and 16 P. multocida subsp. multocida strains) isolated from the mouths of 56 dogs among the 134 living in a French canine military training center (132e Groupe Cynophile de l'Armée de Terre, Suippes, France) were studied by use of enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) and restriction fragment length polymorphism (RFLP) techniques. Both techniques showed genomic heterogeneity of the strains studied. However, RFLP was more discriminatory than ERIC-PCR for differentiating P. multocida strains. All but three pairs of strains were discriminated by RFLP, suggesting a limited circulation of strains between these dogs living in proximity. Although ERIC-PCR is easier and faster to perform, it cannot be recommended for epidemiological studies of P. multocida strains.
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Affiliation(s)
- J Loubinoux
- Laboratoire de Virologie, CHU Nancy-Brabois, 54511 Vandoeuvre-lès-Nancy Cédex, France
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Sechi LA, Leori G, Lollai SA, Duprè I, Molicotti P, Fadda G, Zanetti S. Different strategies for molecular differentiation of Mycobacterium bovis strains isolated in Sardinia, Italy. Appl Environ Microbiol 1999; 65:1781-5. [PMID: 10103282 PMCID: PMC91252 DOI: 10.1128/aem.65.4.1781-1785.1999] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Different genetic markers were used to analyze 22 Mycobacterium bovis strains isolated from cattle in Sardinia and one human isolate. IS6110 DNA fingerprinting differentiated the strains into six patterns, whereas with enterobacterial repetitive consensus sequence primers produced seven clusters. PCR ribotyping followed by digestion with HaeIII and PvuII produced five and seven patterns, respectively. PCR with the (GTG)5 oligonucleotide primer showed the best discriminatory power, generating eight clusters among the strains analyzed.
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Affiliation(s)
- L A Sechi
- Dipartimento di Scienze Biomediche, Sezione di Microbiologia Sperimentale e Clinica, Università degli studi di Sassari, 07100 Sassari, Italy.
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Affiliation(s)
- N A Saunders
- Hepatitis and Retrovirus Laboratory, CPHL, London, UK
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Sechi LA, Zanetti S, Dupré I, Aceti A, Sanguinetti M, Fadda G. Genotypic changes in DNA fingerprinting patterns of Mycobacterium tuberculosis strains from HIV-positive persons in Sardinia. AIDS 1998; 12:2084-6. [PMID: 9814885 DOI: 10.1097/00002030-199815000-00028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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