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Evaluation of Genomic Typing Methods in the Salmonella Reference Laboratory in Public Health, England, 2012-2020. Pathogens 2023; 12:pathogens12020223. [PMID: 36839496 PMCID: PMC9966477 DOI: 10.3390/pathogens12020223] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/12/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
We aim to provide an evidence-based evaluation of whole genome sequence (WGS) methods, employed at the Salmonella reference laboratory in England, in terms of its impact on public health and whether these methods remain a fit for purpose test under UKAS ISO 15189. The evaluation of the genomic methods were mapped against the value of detecting microbiological clusters to support the investigation of food-borne outbreaks of Salmonella in England between 2012-2020. The analysis of WGS with both SNP- and allelic-based methods provided an unprecedented level of strain discrimination and detection of additional clusters when comparing to all of the previous typing methods. The robustness of the routine genomic sequencing at the reference laboratory ensured confidence in the microbiological identifications, even in large outbreaks with complex international food distribution networks. There was evidence that the phylogeny derived from the WGS data can be used to inform the provenance of strains and support discrimination between domestic and non-domestic transmission events. Further insight on the evolutionary context of the emerging pathogenic strains was enabled with a deep dive of the phylogenetic data, including the detection of nested clusters. The public availability of the WGS data linked to the clinical, epidemiological and environmental context of the sequenced strains has improved the trace-back investigations during outbreaks. The global expansion in the use of WGS-based typing in reference laboratories has shown that the WGS methods are a fit for purpose test in public health as it has ensured the rapid implementation of interventions to protect public health, informed risk assessment and has facilitated the management of national and international food-borne outbreaks of Salmonella.
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Chen JS, Hsu GJ, Hsu BM, Yang PY, Kuo YJ, Wang JL, Hussain B, Huang SW. Prevalence, virulence-gene profiles, antimicrobial resistance, and genetic diversity of human pathogenic Aeromonas spp. from shellfish and aquatic environments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 287:117361. [PMID: 34004475 DOI: 10.1016/j.envpol.2021.117361] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
Aeromonas are found in various habitats, particularly in aquatic environments. This study examined the presence of the most common human pathogenic Aeromonas species (Aeromonas caviae, A. hydrophila, and A. veronii) in surface water, sea water, and shellfish. The detection rates in fishing harbour seawater, shellfish farming seawater, and a river basin were 33.3%, 26.4%, and 29.4%, respectively, and high prevalence was observed in summer. The detection rates in shellfish procured from a fish market and shellfish farm were 34.9% and 13.3%, respectively. The most abundant species of human pathogenic Aeromonas detected via water sampling was A. caviae, whereas that obtained via shellfish sampling was A. veronii. The prevalence of human pathogenic Aeromonas in river water was lower in fishing harbours and in the estuary shellfish farming area. Here, 25 isolates of human pathogenic Aeromonas species were isolated from 257 samples and divided among 16 virulence profiles. The high virulence gene-carrying isolates (more than six genes) belonged to A. hydrophila. The shellfish-sourced isolates had the highest detection rates of act, aerA, and fla genes than of other virulence genes, and vice versa for seawater-sourced isolates. The Aeromonas isolates showed high levels of resistance to ampicillin-sulbactam; however, none were resistant to cefepime, ciprofloxacin, or gentamicin. The incidence of multiple drug resistance (MDR) in Aeromonas isolates was 20%. In this study, phylogenetic analysis with 16S rRNA sequencing, biochemical tests and enterobacterial repetitive intergenic consensus-polymerase chain reaction fingerprinting facilitated the distinct categorisation of three species of human pathogenic Aeromonas isolates. In addition, A. veronii isolates from the same geographical area were also concentrated in the same cluster. This study provides information on the risk of infection by Aeromonas with MDR and multiple virulence genes isolated from shellfish and aquatic environments.
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Affiliation(s)
- Jung-Sheng Chen
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Department of Medical Research, E-Da Hospital, Kaohsiung, Taiwan
| | - Gwo-Jong Hsu
- Division of Infectious Diseases, Ditmanson Medical Foundation, Chia-Yi Christian Hospital, Chiayi City, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Center for Innovative on Aging Society, National Chung Cheng University, Chiayi County, Taiwan.
| | - Pei-Yu Yang
- Department of Laboratory, Show Chwan Memorial Hospital, Changhua, Taiwan
| | - Yi-Jie Kuo
- Department of Orthopedic Surgery, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan; Department of Orthopedic Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Jiun-Ling Wang
- Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Shih-Wei Huang
- Center for Environmental Toxin and Emerging Contaminant Research, Cheng Shiu University, Kaohsiung, Taiwan; Super Micro Research and Technology Center, Cheng Shiu University, Kaohsiung, Taiwan
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Zhou W, Li Y, Li Z, Ma B, Jiang X, Hu C, Ai Y, Luo P. Genomic Changes and Genetic Divergence of Vibrio alginolyticus Under Phage Infection Stress Revealed by Whole-Genome Sequencing and Resequencing. Front Microbiol 2021; 12:710262. [PMID: 34671325 PMCID: PMC8521149 DOI: 10.3389/fmicb.2021.710262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 09/14/2021] [Indexed: 11/13/2022] Open
Abstract
Bacteriophages (phages) and their bacterial hosts were the most abundant and genetically highly diverse organisms on the earth. In this study, a series of phage-resistant mutant (PRM) strains derived from Vibrio alginolyticus were isolated and Infrequent-restriction-site PCR (IRS-PCR) was used to investigate the genetic diversity of the PRM strains. Phenotypic variations of eight PRM strains were analyzed using profiles of utilizing carbon sources and chemical sensitivity. Genetic variations of eight PRM strains and coevolved V. alginolyticus populations with phages were analyzed by whole-genome sequencing and resequencing, respectively. The results indicated that eight genetically discrepant PRM stains exhibited abundant and abundant phenotypic variations. Eight PRM strains and coevolved V. alginolyticus populations (VE1, VE2, and VE3) contained numerous single nucleotide variations (SNVs) and insertions/indels (InDels) and exhibited obvious genetic divergence. Most of the SNVs and InDels in coding genes were related to the synthesis of flagellar, extracellular polysaccharide (EPS), which often served as the receptors of phage invasion. The PRM strains and the coevolved cell populations also contained frequent mutations in tRNA and rRNA genes. Two out of three coevolved populations (VE1 and VE2) contained a large mutation segment severely deconstructing gene nrdA, which was predictably responsible for the booming of mutation rate in the genome. In summary, numerous mutations and genetic divergence were detected in the genomes of V. alginolyticus PRM strains and in coevolved cell populations of V. alginolyticus under phage infection stress. The phage infection stress may provide an important force driving genomic evolution of V. alginolyticus.
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Affiliation(s)
- Wenjie Zhou
- College of Animal Science, Jilin University, Changchun, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Yingying Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Geological Survey Institute of Guangzhou, Guangzhou, China
| | - Zhuobo Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Ma
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Jiang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Chaoqun Hu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yongxing Ai
- College of Animal Science, Jilin University, Changchun, China
| | - Peng Luo
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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Characterisation of Staphylococcus aureus isolates from bovine mastitis in Ningxia, Western China. J Glob Antimicrob Resist 2021; 25:232-237. [PMID: 33866044 DOI: 10.1016/j.jgar.2021.03.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/04/2021] [Accepted: 03/10/2021] [Indexed: 02/04/2023] Open
Abstract
OBJECTIVES The aim of this study was to explore the antimicrobial resistance, virulence genes and molecular characteristics of Staphylococcus aureus from bovine mastitis cases. METHODS A total of 125 non-duplicate S. aureus isolates from bovine mastitis cases in Ningxia, China, were characterised by antimicrobial susceptibility and molecular testing to determine the antimicrobial resistance, virulence genes and molecular characteristics. RESULTS All methicillin-resistant S. aureus (MRSA) isolates were resistant to ampicillin, oxacillin, ceftiofur, erythromycin, gentamicin and clindamycin, with resistance to nine different categories of antibiotics observed amongst the MRSA isolates. Of the methicillin-susceptible S. aureus (MSSA) isolates, 62.1% were resistant to ampicillin and sulfisoxazole. Nine clonal complexes (CCs) and 16 spa types were identified by multilocus sequence typing (MLST) and spa typing. The dominant CCs were CC97 (51.2%) and CC50 (30.4%), while t224 (30.4%), t518 (20.0%) and t359 (16.8%) were the most common spa types. A relatively high proportion (27.2%) of the S. aureus isolates belonged to ST4053, a novel sequence type identified in this study. In addition, two CC30 MSSA isolates and two CC59 MRSA isolates were positive for Panton-Valentine leukocidin, while one CC239 MRSA isolate and three CC5 MSSA isolates were positive for TSST-1. All MRSA isolates carried the immune evasion cluster (IEC) genes, including scn (100%; 9/9) and sak (100%; 9/9), which were classified into type E. CONCLUSION Our study indicates severe antibiotic resistance and complicated molecular characterisation of S. aureus causing bovine mastitis. Additional studies should be conducted to monitor infection and transmission of S. aureus.
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Current methodologies on genotyping for nosocomial pathogen methicillin-resistant Staphylococcus aureus (MRSA). Microb Pathog 2017; 107:17-28. [PMID: 28284852 DOI: 10.1016/j.micpath.2017.03.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 11/23/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a common pathogen in hospitals and the community. As the rapid spread and wide distribution of antimicrobial resistance (such as MRSA), treatment for infectious diseases caused by microorganisms has become a vital threat. Thus, early identification and genotyping are essential for further therapeutic treatment and the control of rapid expansion of MRSA. In combination with applications and data feedbacks, this review focused on the currently available molecular-based assays on their utility and performance for rapid typing of MRSA, especially on effective molecular-based methods. Besides, a common mobile element SCCmec and prevalence of HA-MRSA, LA-MRSA and CA-MRSA were introduced in this review in order to provide a more complete profile of MRSA.
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Rodriguez C, Van Broeck J, Taminiau B, Delmée M, Daube G. Clostridium difficile infection: Early history, diagnosis and molecular strain typing methods. Microb Pathog 2016; 97:59-78. [PMID: 27238460 DOI: 10.1016/j.micpath.2016.05.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/18/2016] [Accepted: 05/02/2016] [Indexed: 01/05/2023]
Abstract
Recognised as the leading cause of nosocomial antibiotic-associated diarrhoea, the incidence of Clostridium difficile infection (CDI) remains high despite efforts to improve prevention and reduce the spread of the bacterium in healthcare settings. In the last decade, many studies have focused on the epidemiology and rapid diagnosis of CDI. In addition, different typing methods have been developed for epidemiological studies. This review explores the history of C. difficile and the current scope of the infection. The variety of available laboratory tests for CDI diagnosis and strain typing methods are also examined.
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Affiliation(s)
- C Rodriguez
- Food Science Department, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
| | - J Van Broeck
- Belgian Reference Centre for Clostridium Difficile (NRC), Pôle de microbiologie médicale, Université Catholique de Louvain, Brussels, Belgium
| | - B Taminiau
- Food Science Department, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - M Delmée
- Belgian Reference Centre for Clostridium Difficile (NRC), Pôle de microbiologie médicale, Université Catholique de Louvain, Brussels, Belgium
| | - G Daube
- Food Science Department, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
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Huang PY, Hung MH, Shie SS, Su LH, Chen KY, Ye JJ, Chiang PC, Leu HS, Huang CT. Molecular concordance of concurrent Candida albicans candidemia and candiduria. Diagn Microbiol Infect Dis 2013; 76:382-4. [DOI: 10.1016/j.diagmicrobio.2013.03.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Revised: 03/13/2013] [Accepted: 03/13/2013] [Indexed: 10/26/2022]
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Byun JH, Yoo JH, Park C, Lee DG, Park SH, Choi SM, Choi JH, Kim SH, Kwon JC. Molecular Epidemiologic Analysis of Community-Onset Extended Spectrum Beta-Lactamase (ESBL) Producing Escherichia coliUsing Infrequent-Restriction-Site Polymerase Chain Reaction (IRS-PCR) with Comparison by Pulsed-Field Gel Electrophoresis (PFGE). Infect Chemother 2012. [DOI: 10.3947/ic.2012.44.1.5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Ji-Hyun Byun
- Department of Biomedical Science, The Catholic University of Korea, Graduate School, Seoul, Korea
| | - Jin-Hong Yoo
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Chulmin Park
- Catholic Research Institutes of Medical Science, The Catholic University of Korea, Seoul, Korea
| | - Dong-Gun Lee
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sun-Hee Park
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Su-Mi Choi
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jung-Hyun Choi
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Si-Hyun Kim
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jae-Cheol Kwon
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
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9
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Shin NY, Yoo JH, Park C, Lee DG, Choi SM, Kwon JC, Kim SH, Park SH, Choi JH. Application of Infrequent-Restriction-Site Polymerase Reaction (IRS-PCR) to the Molecular Epidemiologic Analysis of Methicillin Resistant Staphylococcus aureus(MRSA). Infect Chemother 2011. [DOI: 10.3947/ic.2011.43.5.396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Na-Young Shin
- Department of Biomedical Science, The Catholic University of Korea, Graduate School, Seoul, Korea
| | - Jin-Hong Yoo
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Chulmin Park
- Catholic Research Institutes of Medical Science, The Catholic University of Korea, Seoul, Korea
| | - Dong-Gun Lee
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Su-Mi Choi
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jae-Cheol Kwon
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Si-Hyun Kim
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sun-Hee Park
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jung-Hyun Choi
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Understanding the molecular epidemiology of the footrot pathogen Dichelobacter nodosus to support control and eradication programs. J Clin Microbiol 2010; 48:877-82. [PMID: 20071558 DOI: 10.1128/jcm.01355-09] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The Gram-negative anaerobe Dichelobacter nodosus is the primary etiologic agent of ovine footrot. Few studies of the genetic diversity and epidemiology of D. nodosus have been done, despite the economic cost and welfare implications of the disease. This study examined a large collection of Australian isolates; 735 isolates from footrot-infected sheep from 247 farms in Western Australia (WA) were tested by pulsed-field gel electrophoresis (PFGE), and a subset of 616 isolates was tested by infrequent restriction site PCR (IRS-PCR). The genetic diversity of WA isolates was compared to that of 61 isolates from three other Australian states. WA isolates were genetically diverse, with 181 molecular types resolved by PFGE, resulting in a simple diversity ratio (SDR) of 1:4 and a Simpson's index of discrimination value (D) of 0.98. IRS-PCR resolved 77 molecular types (SDR = 1:8 and D = 0.95). The isolates were grouped into 67 clonal groups by PFGE (SDR = 1:11, D = 0.90) and 36 clonal groups by IRS-PCR (SDR = 1:17, D = 0.87). Despite the high genetic diversity, three common clonal groups predominated in WA and were found in other Australian states. On some farms, molecular type was stable over a number of years, whereas on other farms genetically diverse isolates occurred within a flock of sheep or within a hoof. This study provides a large database from which to appropriately interpret molecular types found in epidemiological investigations and to identify common and unknown types that may compromise footrot eradication or control programs.
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Chuang YY, Huang YC, Lin CH, Su LH, Wu CT. Epidemiological investigation after hospitalising a case with pandrug-resistant Acinetobacter baumannii infection. J Hosp Infect 2009; 72:30-5. [DOI: 10.1016/j.jhin.2009.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 02/05/2009] [Indexed: 10/21/2022]
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Stepán J, Pantůcek R, Doskar J. Molecular diagnostics of clinically important staphylococci. Folia Microbiol (Praha) 2008; 49:353-86. [PMID: 15530002 DOI: 10.1007/bf03354664] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Bacterial species of the genus Staphylococcus known as important human and animal pathogens are the cause of a number of severe infectious diseases. Apart from the major pathogen Staphylococcus aureus, other species until recently considered to be nonpathogenic may also be involved in serious infections. Rapid and accurate identification of the disease-causing agent is therefore prerequisite for disease control and epidemiological surveillance. Modern methods for identification and typing of bacterial species are based on genome analysis and have many advantages compared to phenotypic methods. The genotypic methods currently used in molecular diagnostics of staphylococcal species, particularly of S. aureus, are reviewed. Attention is also paid to new molecular methods with the highest discriminatory power. Efforts made to achieve interlaboratory reproducibility of diagnostic methods are presented.
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Affiliation(s)
- J Stepán
- Department of Genetics and Molecular Biology, Faculty of Science, Masaryk University, 611 37 Brno, Czechia
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Ren C, Hu C, Luo P, Chen C, Jiang X, Wang Q. Genotyping of Vibrio alginolyticus isolates from Daya Bay by infrequent-restriction-site PCR and pulsed-field gel electrophoresis. Mol Cell Probes 2008; 22:267-71. [PMID: 18586455 DOI: 10.1016/j.mcp.2008.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2008] [Revised: 05/09/2008] [Accepted: 05/15/2008] [Indexed: 11/26/2022]
Abstract
Vibrio alginolyticus is a serious bacterial pathogen that hampered the whole industry of fish farming in Guangdong, China. In order to facilitate epidemiologic studies and improve the control of disease, we developed a highly efficient method of genotyping for V. alginolyticus using infrequent-restriction-site PCR (IRS-PCR) technology. With the enzyme combination of NotI-HhaI, optimized, unique, and easy-to-interpret patterns were generated. Forty-five V. alginolyticus isolates from aquatic animals and the marine environment in Daya Bay in Guangdong were fingerprinted by IRS-PCR and pulsed-field gel electrophoresis (PFGE). The reproducibility of the IRS-PCR method was high (100%) in conformity with PFGE. When primer PN-T or PN-G was used, IRS-PCR obtained the identical clustering as PFGE, producing 24 different patterns, respectively. Moreover, IRS-PCR presented a high discriminatory power (D=0.953) identical to that of PFGE. In conclusion, the IRS-PCR fingerprinting method using NotI-HhaI can provide a potentially useful tool for epidemiologic investigations of V. alginolyticus isolates.
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Affiliation(s)
- Chunhua Ren
- The Key Laboratory of Applied Marine Biology of Guangdong Province and Chinese Academy of Sciences, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, PR China
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Foley SL, Zhao S, Walker RD. Comparison of molecular typing methods for the differentiation of Salmonella foodborne pathogens. Foodborne Pathog Dis 2007; 4:253-76. [PMID: 17883310 DOI: 10.1089/fpd.2007.0085] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bacteria belonging to the genus Salmonella are among the leading causes of foodborne disease of bacterial etiology. These bacteria are also widely disseminated throughout the animal kingdom. The ability to identify the food source from which a human pathogen originated would be of great value in reducing the incidence of foodborne disease and the extent of disease outbreaks due to Salmonella. To date, efforts to identify the origin of these pathogens have centered on phenotypic and genotypic characterization of Salmonella isolates. This review focuses molecular or genotypic techniques that are currently being used for typing, and examines their strengths and weaknesses for determining the source of Salmonella foodborne infections.
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Affiliation(s)
- Steven L Foley
- National Farm Medicine Center, Marshfield Clinic Research Foundation, Marshfield, Wisconsin 54449, USA.
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Den Boer JW, Verhoef L, Bencini MA, Bruin JP, Jansen R, Yzerman EPF. Outbreak detection and secondary prevention of Legionnaires’ disease: A national approach. Int J Hyg Environ Health 2007; 210:1-7. [PMID: 16956792 DOI: 10.1016/j.ijheh.2006.07.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Revised: 07/03/2006] [Accepted: 07/03/2006] [Indexed: 11/30/2022]
Abstract
BACKGROUND To stop a possible outbreak of Legionnaires' disease (LD) at an early stage an outbreak detection programme was installed in The Netherlands. METHODS The programme consisted of sampling and controlling of potential sources to which LD patients had been exposed during their incubation period. Potential sources were considered to be true sources of infection if two or more LD patients (cluster) had visited them, or if available patients' isolates and environmental Legionella spp. were indistinguishable by amplified fragment length polymorphism genotyping. RESULTS Rapid sampling and genotyping as well as cluster recognition helped to target control measures. Despite these measures, two small outbreaks were only stopped after renewal of the water system. The combination of genotyping and cluster recognition lead to 29 of 190 (15%) patient-source associations. CONCLUSION Systematic sampling and cluster recognition can contribute to outbreak detection and lead to cost-effective secondary prevention of Legionnaires' disease.
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Affiliation(s)
- Jeroen W Den Boer
- Municipal Health Service Kennemerland, P.O. Box 5514, 2000 GM Haarlem, The Netherlands.
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16
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Lin PY, Chu C, Su LH, Huang CT, Chang WY, Chiu CH. Clinical and microbiological analysis of bloodstream infections caused by Chryseobacterium meningosepticum in nonneonatal patients. J Clin Microbiol 2004; 42:3353-5. [PMID: 15243115 PMCID: PMC446307 DOI: 10.1128/jcm.42.7.3353-3355.2004] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chryseobacterium meningosepticum bloodstream infections in 11 nonneonatal patients were reported. More than half of the infections were community acquired. PCR assays indicated that the organisms produced extended-spectrum beta-lactamases as well as metallo-beta-lactamases. Genotyping showed diverse fingerprints among the isolates. Six patients survived without appropriate antibiotic treatment. Host factors are the major determinant of the outcomes of C. meningosepticum infections.
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Affiliation(s)
- Pen-Yi Lin
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Children's Hospital, 5 Fu-Hsin St., Kweishan 333, Taoyuan, Taiwan
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Moissenet D, Vu-Thien H, Benzerara Y, Arlet G. DNA fingerprinting of Ralstonia paucula by infrequent-restriction-site PCR and randomly amplified polymorphic DNA analysis. J Clin Microbiol 2004; 41:5747-9. [PMID: 14662974 PMCID: PMC308977 DOI: 10.1128/jcm.41.12.5747-5749.2003] [Citation(s) in RCA: 4] [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
Ralstonia paucula (formerly CDC group IV c-2) is an environmental organism that can cause serious human infections, occasionally clusters of nosocomial infections. In the present work, 26 strains of R. paucula (4 from the American Centers for Disease Control and Prevention collection, 10 from the Belgian Laboratorium voor Microbiologie [LMG] collection, and 12 French clinical isolates) were analyzed with infrequent-restriction-site PCR and randomly amplified polymorphic DNA analysis. Both techniques accurately distinguished between collection strains. Two close patterns obtained for all the French isolates suggested a clonal strain. Two LMG collection strains originating from human sources in the United States also showed patterns close to those of French isolates.
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Affiliation(s)
- Didier Moissenet
- Service de Microbiologie, Hôpital d'enfants Armand-Trousseau AP-HP, Paris, France
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18
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Su LH, Ou JT, Leu HS, Chiang PC, Chiu YP, Chia JH, Kuo AJ, Chiu CH, Chu C, Wu TL, Sun CF, Riley TV, Chang BJ. Extended epidemic of nosocomial urinary tract infections caused by Serratia marcescens. J Clin Microbiol 2004; 41:4726-32. [PMID: 14532211 PMCID: PMC254321 DOI: 10.1128/jcm.41.10.4726-4732.2003] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In recent years a significant increase in the incidence of Serratia marcescens infections was noted at the Chang Gung Memorial Hospital, Taoyuan, Taiwan. A review of laboratory (1991 to 2002) and infection control (1995 to 2002) records showed the possibility of an extended epidemic of nosocomial urinary tract infections (UTIs) caused by S. marcescens. Therefore, in 1998 and 1999, 87 isolates were collected from patients with such infections and examined and another 51 isolates were collected in 2001 and 2002. The patients were mostly elderly or the infections were associated with the use of several invasive devices. S. marcescens was usually the only pathogen found in urine cultures in our study. Neither prior infections nor disseminated infections with the organism were observed in these patients. Resistance to most antibiotics except imipenem was noted. Two genotyping methods, pulsed-field gel electrophoresis and infrequent-restriction-site PCR, were used to examine the isolates. A total of 12 genotypes were identified, and 2 predominant genotypes were found in 72 (82.8%) of the 87 isolates derived from all over the hospital. However, 63.9% of the isolates of the two genotypes were from neurology wards. A subsequent intervention by infection control personnel reduced the infection rate greatly. The number and proportion of the two predominant genotypes were significantly reduced among the 51 isolates collected in 2001 and 2002. Thus, a chronic and long-lasting epidemic of nosocomial UTIs caused by S. marcescens was identified and a successful intervention was carried out. Both a cautious review of laboratory and infection control data and an efficient genotyping system are necessary to identify such a cryptic epidemic and further contribute to the quality of patient care.
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Affiliation(s)
- Lin-Hui Su
- Department of Clinical Pathology, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
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Masny A, Płucienniczak A. Ligation mediated PCR performed at low denaturation temperatures--PCR melting profiles. Nucleic Acids Res 2003; 31:e114. [PMID: 12954790 PMCID: PMC203340 DOI: 10.1093/nar/gng116] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We show that using low denaturation temperatures (80-88 degrees C) during ligation mediated PCR (LM PCR) of bacterial DNA leads to the amplification of limited sets of the less stable DNA fragments. A set of electrophoretic patterns of such fragments obtained at different denaturation temperatures forms the PCR melting profile (PCR MP). A single pattern obtained for a given temperature and a set of patterns arising after application of several denaturation temperatures (PCR MP) are very specific for the given bacterial genome and may be used for strain characterisation and differentiation. The method may also be used for amplification and isolation of the less stable DNA fragments in a genome.
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Affiliation(s)
- Aleksander Masny
- Institute of Biotechnology and Antibiotics, Staroscinska 5, 02-516 Warsaw, Poland.
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20
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Cloeckaert A, Grayon M, Grépinet O, Boumedine KS. Classification of Brucella strains isolated from marine mammals by infrequent restriction site-PCR and development of specific PCR identification tests. Microbes Infect 2003; 5:593-602. [PMID: 12787735 DOI: 10.1016/s1286-4579(03)00091-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Brucella strains have been isolated since the 1990s from a wide variety of marine mammals and represent potential zoonotic pathogens. They have distinctive phenotypic and molecular characteristics from the terrestrial mammal Brucella species, and two new species names have been previously proposed based on DNA polymorphism at the omp2 locus and their preferential host, i.e. Brucella cetaceae for cetacean isolates and Brucella pinnipediae for pinniped isolates. The results presented in this study on characterization of these strains by infrequent restriction site-PCR (IRS-PCR), taking into account the higher number of IS711 elements in their genome compared to terrestrial mammal Brucella species, supports this classification. The nucleotide sequences of specific DNA fragments detected by IRS-PCR were determined and used to develop PCR identification tests for either B. cetaceae or B. pinnipediae.
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Affiliation(s)
- Axel Cloeckaert
- Unité BioAgresseurs, Santé, Environnement, Institut National de la Recherche Agronomique, 37380, Nouzilly, France.
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21
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Su LH, Chiu CH, Wu TL, Chu C, Chia JH, Kuo AJ, Lee CC, Sun CF, Ou JT. Molecular epidemiology of Salmonella enterica serovar Enteritidis isolated in Taiwan. Microbiol Immunol 2003; 46:833-40. [PMID: 12597357 DOI: 10.1111/j.1348-0421.2002.tb02770.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Incidence of Salmonella enterica serovar Enteritidis infection seems to be on the rise in Taiwan, and therefore, the characteristics of the isolate, including genotypes, were epidemiologically investigated. Of the 71 clinical strains isolated in 1997-1999, 61 (86%) remained susceptible to the eight antibiotics tested, while the remaining ten, eight of which were isolated in 1999, were resistant to one to three of the agents including three multiply resistant strains. The majority, 69 or 97% of the isolates, harbored a 60-kb spvC gene-carrying virulence plasmid and 12 of them harbored one or two additional various-sized plasmids. Strains with more than one plasmid were isolated mostly in 1999. Pulse-field gel electrophoresis (PFGE) revealed three major genotypes (Types A, B and C), in which type A was the predominant type. Of the 68 Type A, which contained 8 subtypes, 59 (83%) belonged to only two subtypes. Similar results were obtained with a PCR-based typing method, the infrequent-restriction-site (IRS) PCR. All four methods detected types that were rarely seen before and most of these were of recent isolates, indicating that these unusual types were new or strains of foreign origin. Though all four methods discriminated types well, PFGE and IRS-PCR showed higher sensitivity for classification. Between the two, the latter, though less discriminatory than PFGE, seems the method of choice, since it is simpler, less time-consuming and above all easy to perform.
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Affiliation(s)
- Lin-Hui Su
- Department of Clinical Pathology, Chang Gung Memorial Hospital, Kweishan, 333, Taoyuan, Taiwan
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22
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van der Zee A, Steer N, Thijssen E, Nelson J, van't Veen A, Buiting A. Use of multienzyme multiplex PCR amplified fragment length polymorphism typing in analysis of outbreaks of multiresistant Klebsiella pneumoniae in an intensive care unit. J Clin Microbiol 2003; 41:798-802. [PMID: 12574286 PMCID: PMC149664 DOI: 10.1128/jcm.41.2.798-802.2003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We developed and optimized a new modified amplified fragment length polymorphism (AFLP) typing method to obtain a multibanding fingerprint that can be separated by agarose gel electrophoresis. Both to maximize the discriminatory power and to facilitate the computer-assisted analysis, bacterial DNA was digested with four different restriction enzymes. After ligation of adaptors to the DNA fragments, PCR testing of various single primers was performed. Two single primers that gave optimal results with regard to band resolution and discriminatory power were selected and combined. The computer-assisted analysis of fingerprint patterns was performed with Pearson's product-moment correlation values of densitometric curves, without assigning bands to peaks. Thus, the analysis is not subject to human interpretation errors. With this method, we investigated two outbreaks of multiresistant Klebsiella pneumoniae in an intensive care unit and various sporadic isolates of K. pneumoniae and Klebsiella oxytoca. Cluster analysis of isolates analyzed in different experiments and on different gels showed that fingerprint patterns clustered correctly according to subspecies or to the outbreaks. Multienzyme multiplex PCR AFLP revealed that the first outbreak was caused by two different types of strains. Outbreak two was caused by yet another strain of K. pneumoniae. In conclusion, the typing method used here is easy to perform and highly reproducible, and due to generation of complex banding patterns, it has a higher discriminatory power. Furthermore, the multienzyme multiplex PCR fingerprints are easy to analyze, and a reliable database can be stored in the computer to facilitate comparison of future isolates of Klebsiella spp. The method can be performed in every clinical microbiology laboratory.
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Affiliation(s)
- Anneke van der Zee
- Laboratory of Medical Microbiology, St Elisabeth Hospital, Tilburg, The Netherlands.
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23
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Salloum G, Meugnier H, Reyrolle M, Grimont F, Grimont PAD, Etienne J, Freney J. Identification of Legionella species by ribotyping and other molecular methods. Res Microbiol 2002; 153:679-86. [PMID: 12558187 DOI: 10.1016/s0923-2508(02)01381-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
There are currently more than 40 species of Legionella and the identification of most of them by standard methods is often technically difficult. The aim of this study was to use a ribotyping method with endonuclease HindIII and a probe consisting of a set of five oligonucleotides (referred to as OligoMix5). A total of 123 strains, including 78 type or reference strains corresponding to 44 species, eight clinical and 37 environmental isolates were tested. The usefulness of the method was demonstrated for the identification at the species level of all of the 123 Legionella isolates tested, with each species showing a specific profile. Among the 15 serogroups of Legionella pneumophila, eight patterns were obtained. For the 45 field strains, the randomly amplified polymorphic DNA (RAPD) technique and intergenic 16S-23S ribosomal spacer PCR analysis (ITS 16-23S) were also used. Altogether, these three methods allowed the identification of all of strains tested. However, ribotyping has proven to be more effective than the other methods.
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Affiliation(s)
- Gada Salloum
- Centre National de Référence des Legionella, Laboratoire de Bactériologie, EA 1655, Faculté de Médecine R.T.H. Laënnec, 69372 Lyon cedex 08, France
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24
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Huang YC, Su LH, Wu TL, Leu HS, Hsieh WS, Chang TM, Lin TY. Outbreak of Acinetobacter baumannii bacteremia in a neonatal intensive care unit: clinical implications and genotyping analysis. Pediatr Infect Dis J 2002; 21:1105-9. [PMID: 12488658 DOI: 10.1097/00006454-200212000-00004] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Outbreaks of sepsis associated with have been rarely reported in neonatal intensive care units (NICUs). We describe such an outbreak in a NICU, and the results of molecular epidemiologic investigations are presented. MATERIALS AND METHODS Between August and September 2000, 6 premature infants hospitalized in a pediatric NICU developed sepsis. Three additional cases had infections during November and December. For an environmental culture survey, 94 environmental specimens and hand washings of all 43 health care workers involved in this unit were examined for the presence of this organism. Two genotyping methods, pulsed field gel electrophoresis of genomic DNA digested with I and infrequent restriction site polymerase chain reaction, were used to analyze the 9 bacteremic isolates and any isolates obtained from the environmental survey and the hand washings. Another 3 bacteremic isolates of collected in the same NICU in 1999 were incorporated as controls. RESULTS The 9 infants were premature and had birth weights of <1,500 g. Before onset of sepsis 9 infants had received total parenteral nutrition, and 8 infants had had central venous catheters and received intrafat emulsion. Five (5.3%) environmental specimens and 10 (23.3%) hand washing specimens were positive for the organism. Except for the strain from Case 9, the results of both genotyping methods were concordant; 11 patterns were identified by infrequent restriction site polymerase chain reaction and 10 patterns by pulsed field gel electrophoresis. One major genotype was demonstrated in the first 6 bacteremic isolates as well as 3 hand washing isolates. The genotypes of the other 3 bacteremic isolates, the 3 control strains, the 5 environmental isolates and 7 other hand washing isolates were distinct from the genotype of outbreak strains. CONCLUSION An outbreak of bacteremia in a NICU was clearly demonstrated by the molecular epidemiologic investigation and was possibly transmitted via the hands of health care workers.
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Affiliation(s)
- Yhu-Chering Huang
- Division of Pediatric Infectious Disease, Taipei Branch, Chang Gung Children's Hospital, Taoyuan, Taiwan.
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25
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Wu TL, Su LH, Leu HS, Chiu CH, Chiu YP, Chia JH, Kuo AJ, Sun CF. Molecular epidemiology of nosocomial infection associated with multi-resistant Acinetobacter baumannii by infrequent-restriction-site PCR. J Hosp Infect 2002; 51:27-32. [PMID: 12009817 DOI: 10.1053/jhin.2002.1206] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Acinetobacter baumannii was considered endemic in a university-affiliated tertiary hospital. A significant increase was noted in the proportion of nosocomial infections associated with this micro-organism from 1996 to 1999, although no apparent clusters could be found. Between July 1998 and February 2000, 58 nosocomial isolates of A. baumannii were collected and characterized by antibiotyping and a genotyping method, infrequent-restriction-site PCR (IRS-PCR). High resistance to the 14 antimicrobial agents examined was observed among the isolates. Of the 13 antibiograms detected, eight were multi-resistant to gentamicin and almost all of the traditional and extended-spectrum beta-lactams. These multi-resistant strains consisted of 41 isolates (71%), distributed amongst different wards and intensive care units (ICUs). By IRS-PCR, 23 types were obtained, with one major type found among 28 (48%) isolates. All of these 28 isolates were collected from surgical ICUs. It appears that a single strain of multi-resistant A. baumannii was responsible for the prevalence of nosocomial infection amongst surgical patients, clearly differentiating this outbreak from the previous endemic situation. An efficient molecular typing method played a vital role in making this discrimination.
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Affiliation(s)
- T-L Wu
- Department of Clinical Pathology, Lin-Kou Medical Centre, Chang Gung Memorial Hospital, No. 5 Fu-Hsing Street, Kweishan, Taoyuan 333, Taiwan.
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26
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Chiu CH, Chu C, Su LH, Wu WY, Wu TL. Characterization of a laboratory-derived, high-level ampicillin-resistant Salmonella enterica serovar Typhimurium strain that caused meningitis in an infant. Antimicrob Agents Chemother 2002; 46:1604-6. [PMID: 11959613 PMCID: PMC127154 DOI: 10.1128/aac.46.5.1604-1606.2002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A Salmonella enterica serovar Typhimurium strain that harbored a plasmid carrying a TEM-1-type beta-lactamase gene was isolated from the blood and cerebrospinal fluid of an infant with meningitis. This 3.2-kb plasmid was further characterized to be a nonconjugative pGEM series cloning vector containing a foreign insert. The strain was likely laboratory derived and contaminated the environment before it caused the infection.
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Affiliation(s)
- Cheng-Hsun Chiu
- Department of Pediatrics, Chang Gung Children's Hospital, Kweishan 333, Taoyuan, Taiwan
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27
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Den Boer JW, Yzerman EPF, Schellekens J, Lettinga KD, Boshuizen HC, Van Steenbergen JE, Bosman A, Van den Hof S, Van Vliet HA, Peeters MF, Van Ketel RJ, Speelman P, Kool JL, Conyn-Van Spaendonck MAE. A large outbreak of Legionnaires' disease at a flower show, the Netherlands, 1999. Emerg Infect Dis 2002; 8:37-43. [PMID: 11749746 PMCID: PMC2730281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
In 1999, an outbreak of Legionnaires' disease affected many visitors to a flower show in the Netherlands. To identify the source of the outbreak, we performed an environmental investigation, as well as a case-control study among visitors and a serologic cohort study among exhibitors to measure exposure to possible sources. Of 77,061 visitors, 188 became ill (133 confirmed and 55 probable cases), for an attack rate of 0.23% for visitors and 0.61% for exhibitors. Two whirlpool spas in halls 3 and 4 of the exhibition and a sprinkler in hall 8 were culture positive for Legionella pneumophila. One of three genotypes found in both whirlpool spas was identical to the isolates from 28 of 29 culture-positive patients. Persons who paused at the whirlpool spa in hall 3 were at increased risk for becoming ill. This study illustrates that whirlpool spas may be an important health hazard if disinfection fails.
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Affiliation(s)
- Jeroen W Den Boer
- National Institute of Public Health and the Environment, Bilthoven, the Netherlands.
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28
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Boyd D, Peters GA, Cloeckaert A, Boumedine KS, Chaslus-Dancla E, Imberechts H, Mulvey MR. Complete nucleotide sequence of a 43-kilobase genomic island associated with the multidrug resistance region of Salmonella enterica serovar Typhimurium DT104 and its identification in phage type DT120 and serovar Agona. J Bacteriol 2001; 183:5725-32. [PMID: 11544236 PMCID: PMC95465 DOI: 10.1128/jb.183.19.5725-5732.2001] [Citation(s) in RCA: 317] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study describes the characterization of the recently described Salmonella genomic island 1 (SGI1) (D. A. Boyd, G. A. Peters, L.-K. Ng, and M. R. Mulvey, FEMS Microbiol. Lett. 189:285-291, 2000), which harbors the genes associated with the ACSSuT phenotype in a Canadian isolate of Salmonella enterica serovar Typhimurium DT104. A 43-kb region has been completely sequenced and found to contain 44 predicted open reading frames (ORFs) which comprised approximately 87% of the total sequence. Fifteen ORFs did not show any significant homology to known gene sequences. A number of ORFs show significant homology to plasmid-related genes, suggesting, at least in part, a plasmid origin for the SGI1, although some with homology to phage-related genes were identified. The SGI1 was identified in a number of multidrug-resistant DT120 and S. enterica serovar Agona strains with similar antibiotic-resistant phenotypes. The G+C content suggests a potential mosaic structure for the SGI1. Emergence of the SGI1 in serovar Agona strains is discussed.
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Affiliation(s)
- D Boyd
- National Microbiology Laboratory, Health Canada, Winnipeg, Manitoba R3E 3R2, Canada
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29
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Abstract
Klebsiella pneumoniae has been emerging as the leading cause of liver abscess in diabetic patients. Results of molecular typing of K. pneumoniae isolates from two siblings with liver abscess, their family members, and the environment suggest a possibility of cross infection of liver abscess by the fecal-oral route within diabetic patients.
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Affiliation(s)
- C H Chiu
- Divisions of Pediatric Infectious Diseases, Department of Medicine, Chang Gung Children's Hospital, 5 fu-hsin Street, Kweishan 333, Taoyuan, Taiwan.
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30
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Franciosa G, Tartaro S, Wedell-Neergaard C, Aureli P. Characterization of Listeria monocytogenes strains involved in invasive and noninvasive listeriosis outbreaks by PCR-based fingerprinting techniques. Appl Environ Microbiol 2001; 67:1793-9. [PMID: 11282635 PMCID: PMC92799 DOI: 10.1128/aem.67.4.1793-1799.2001] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2000] [Accepted: 01/22/2001] [Indexed: 11/20/2022] Open
Abstract
A total of 32 Listeria monocytogenes strains (16 from a recent outbreak of invasive listeriosis and 16 from two outbreaks of noninvasive listeriosis, all three occurring in Italy) were characterized by PCR-ribotyping, arbitrarily primed PCR (AP-PCR), and the recently developed infrequent-restriction-site PCR (IRS-PCR). The discriminatory ability of the techniques, first evaluated on 29 unrelated L. monocytogenes food isolates using Simpson's index of diversity, was 0.714 for PCR-ribotyping, 0.690 for AP-PCR, and 0.919 for IRS-PCR. IRS-PCR was also more capable of distinguishing among strains from the invasive listeriosis outbreak: three different clusters were identified by IRS-PCR compared to two clusters identified by both PCR-ribotyping and AP-PCR. Within each of the two outbreaks of noninvasive listeriosis, the patterns were practically identical, as demonstrated by all three techniques. Only IRS-PCR succeeded in clearly discriminating the strains related to noninvasive listeriosis from all of the other strains included in this study, including those from the outbreak of invasive listeriosis. This finding may suggest the presence of unique differences in their DNA sequences.
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Affiliation(s)
- G Franciosa
- Food Microbiology Laboratory, Food Department, Istituto Superiore di Sanità, 00161 Rome, Italy
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31
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Steinlein LM, Crawford JT. Reverse dot blot assay (insertion site typing) for precise detection of sites of IS6110 insertion in the Mycobacterium tuberculosis genome. J Clin Microbiol 2001; 39:871-8. [PMID: 11230397 PMCID: PMC87843 DOI: 10.1128/jcm.39.3.871-878.2001] [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: 11/20/2022] Open
Abstract
We have developed an amplification-based reverse dot blot assay for the detection of specific sites of insertion of the Mycobacterium tuberculosis insertion sequence IS6110. In this assay, a set of biotin-labeled amplicons representing the various copies of IS6110 and their flanking sequences is generated by linker-mediated PCR. The amplicons are then hybridized to immobilized oligonucleotide probes that are specific for known IS6110 insertion sites. The method was evaluated using an array of oligonucleotide probes corresponding to IS6110 insertion sites from M. tuberculosis strains CDC1551, Erdman, and H37Rv, and multidrug-resistant strain W. A set of 72 DNA samples from 60 M. tuberculosis clinical isolates was analyzed for the presence or absence of these insertion sites, and the assay was found to be highly reproducible. This method of identifying insertion sites has been named "insite" and can be used for the genotyping of M. tuberculosis complex strains based on IS6110 insertion site profiles.
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Affiliation(s)
- L M Steinlein
- Division of AIDS, STD, and TB Laboratory Research, National Center for Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30333, USA
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32
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Garaizar J, López-Molina N, Laconcha I, Lau Baggesen D, Rementeria A, Vivanco A, Audicana A, Perales I. Suitability of PCR fingerprinting, infrequent-restriction-site PCR, and pulsed-field gel electrophoresis, combined with computerized gel analysis, in library typing of Salmonella enterica serovar enteritidis. Appl Environ Microbiol 2000; 66:5273-81. [PMID: 11097902 PMCID: PMC92456 DOI: 10.1128/aem.66.12.5273-5281.2000] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2000] [Accepted: 10/03/2000] [Indexed: 11/20/2022] Open
Abstract
Strains of Salmonella enterica (n = 212) of different serovars and phage types were used to establish a library typing computerized system for serovar Enteritidis on the basis of PCR fingerprinting, infrequent-restriction-site PCR (IRS-PCR), or pulsed-field gel electrophoresis (PFGE). The rate of PCR fingerprinting interassay and intercenter reproducibility was low and was only increased when DNA samples were extracted at the same time and amplified with the same reaction mixtures. Reproducibility of IRS-PCR technique reached 100%, but discrimination was low (D = 0.52). The PFGE procedure showed an intercenter reproducibility value of 93.3%. The high reproducibility of PFGE combined with the previously determined high discrimination directed its use for library typing. The use of PFGE with enzymes XbaI, BlnI, and SpeI for library typing of serovar Enteritidis was assessed with GelCompar 4.0 software. Three computer libraries of PFGE DNA profiles were constructed, and their ability to recognize new DNA profiles was analyzed. The results obtained pointed out that the combination of PFGE with computerized analysis could be suitable in long-term epidemiological comparison and surveillance of Salmonella serovar Enteritidis, specially if the prevalence of genetic events that could be responsible for changes in PFGE profiles in this serovar was low.
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Affiliation(s)
- J Garaizar
- Department of Immunology, Microbiology and Parasitology, Basque Country University, 01080 Vitoria-Gasteiz, Spain.
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Su LH, Leu HS, Chiu YP, Chia JH, Kuo AJ, Sun CF, Lin TY, Wu TL. Molecular investigation of two clusters of hospital-acquired bacteraemia caused by multi-resistant Klebsiella pneumoniae using pulsed-field gel electrophoresis and in frequent restriction site PCR. Infection Control Group. J Hosp Infect 2000; 46:110-7. [PMID: 11049703 DOI: 10.1053/jhin.2000.0815] [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: 11/11/2022]
Abstract
Two molecular typing methods, DNA macrorestriction analysis with XbaI resolved by pulsed-field gel electrophoresis (PFGE) and infrequent restriction site PCR (IRS-PCR) assay with adapters designed for XbaI and HhaI restriction sites, were used to investigate two clusters of hospital-acquired bacteraemia associated with multi-resistant Klebsiella pneumoniae which occurred in a paediatric intensive care unit (PICU). A total of 56 K. pneumoniae isolates were analysed. These included 10 bacteraemic isolates from eight patients, 26 isolates obtained during an epidemiological survey, and 20 epidemiologically non-related isolates incorporated as controls. One major pattern was demonstrated in 22 of the 56 isolates analysed. These included nine of the 10 bacteraemic isolates, a single rectal isolate, two hand culture isolates and 10 sink isolates. All of these 22 isolates illustrated identical antibiograms, whilst the other 34 isolates shared six antibiograms and 31 unique patterns by either PFGE or IRS-PCR assay. The two clusters of bacteraemia appeared to be outbreaks induced by the same strain of K. pneumoniae which may have utilized sinks as reservoirs and been transmitted through the hands of medical personnel to patients. IRS-PCR demonstrates concordant results with PFGE analysis in studying the genetic relationships among K. pneumoniae isolates, and serves as an excellent epidemiological tool for this bacterium.
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Affiliation(s)
- L H Su
- Department of Clinical Pathology, Lin-Kou Medical Centre, Chang Gung Memorial Hospital, Kweishan, Taoyuan, Taiwan
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Handley SA, Regnery RL. Differentiation of pathogenic Bartonella species by infrequent restriction site PCR. J Clin Microbiol 2000; 38:3010-5. [PMID: 10921969 PMCID: PMC87173 DOI: 10.1128/jcm.38.8.3010-3015.2000] [Citation(s) in RCA: 23] [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
Infrequent restriction site PCR (IRS-PCR) is a recently described DNA fingerprinting technique based on selective amplification of restriction endonuclease-cleaved fragments. Bartonella isolates associated with human disease and related nonhuman isolates were analyzed by IRS-PCR genomic fingerprinting. Preparation of DNA templates began with double digestion using three different restriction endonuclease combinations. Combinations included the frequently cutting endonuclease HhaI in conjunction with an infrequently cutting endonuclease, EagI, SmaI, or XbaI. Digestion was followed by ligation of oligonucleotide adapters designed with ends complementary to the restriction endonuclease sites. Amplification of fragments flanked with an EagI, SmaI, or XbaI site in combination with an HhaI site produced a series of different-sized amplicons resolvable into patterns by polyacrylamide gel electrophoresis (PAGE). The pattern complexity was varied by the addition of selective nucleotides to the 3' ends of the EagI-, SmaI-, or XbaI-specific primers. Amplicons were also generated with fluorescently labeled primers and were subsequently resolved and detected by capillary electrophoresis. Analysis by traditional slab PAGE and capillary electrophoresis provided suitable resolution of patterns produced with the enzyme combinations EagI-HhaI and SmaI-HhaI. However, the combination of XbaI-HhaI produced too many fragments for sufficient resolution by traditional PAGE, thus requiring the better resolving properties of capillary electrophoresis. Due to the flexibility in modulating the pattern complexity and electrophoresis methods, these techniques allow for a high level of experimental optimization. The results provide evidence of the discriminatory power, ease of use, and flexibility of the IRS-PCR method as it applies to the identification of human-pathogenic Bartonella species.
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Affiliation(s)
- S A Handley
- Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
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35
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Jonas D, Meyer HG, Matthes P, Hartung D, Jahn B, Daschner FD, Jansen B. Comparative evaluation of three different genotyping methods for investigation of nosocomial outbreaks of Legionnaires' disease in hospitals. J Clin Microbiol 2000; 38:2284-91. [PMID: 10834990 PMCID: PMC86783 DOI: 10.1128/jcm.38.6.2284-2291.2000] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/1999] [Accepted: 04/10/2000] [Indexed: 11/20/2022] Open
Abstract
The increased incidence of nosocomial Legionnaires' disease in two hospitals prompted investigation of possible environmental sources. In the search for an effective DNA-typing technique for use in hospital epidemiology, the performance and convenience of three methods-SfiI macrorestriction analysis (MRA), amplified fragment length polymorphism (AFLP), and arbitrarily primed PCR (AP-PCR)-were compared. Twenty-nine outbreak-associated and eight nonassociated strains of Legionella pneumophila with 13 MRA types and subtypes were investigated. These strains comprised isolates from bronchoalveolar lavages, from environmental, patient-related sources, and type strains. All three typing methods detected one predominant genotype associated with the outbreaks in both hospitals. All of them correctly assigned epidemiologically associated, environmental isolates to their respective patient specimens. AP-PCR was the least discriminating and least reproducible technique. In contrast, AFLP was demonstrated as being the method with the best interassay reproducibility (90%) and concordance (94%) in comparison to the genotyping standard of MRA and the epidemiological data. Analysis of AFLP fragments revealed 12 different types and subtypes. Because of its simplicity and reproducibility, AFLP proved to be the most effective technique in outbreak investigation.
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Affiliation(s)
- D Jonas
- National Reference Centre of Hygiene and Institute of Environmental Medicine and Hospital Epidemiology, University Hospital Freiburg, 79106 Freiburg, Germany.
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36
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Yoo JH, Choi JH, Shin WS, Huh DH, Cho YK, Kim KM, Kim MY, Kang MW. Application of infrequent-restriction-site PCR to clinical isolates of Acinetobacter baumannii and Serratia marcescens. J Clin Microbiol 1999; 37:3108-12. [PMID: 10488162 PMCID: PMC85504 DOI: 10.1128/jcm.37.10.3108-3112.1999] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We applied infrequent-restriction-site PCR (IRS-PCR) to the investigation of an outbreak caused by 23 isolates of Acinetobacter baumannii in an intensive care unit from November 1996 to May 1997 and a pseudoepidemic caused by 16 isolates of Serratia marcescens in a delivery room from May to September 1996. In the epidemiologic investigation of the outbreak caused by A. baumannii, environmental sampling and screening of all health care workers revealed the same species from the Y piece of a mechanical ventilator and the hands of two health care personnel. IRS-PCR showed that all outbreak-related strains were genotypically identical and that three strains from surveillance cultures were also identical to the outbreak-related strains. In a pseudoepidemic caused by S. marcescens, IRS-PCR identified two different genotypes, and among them one genotype was predominant (15 of 16 [93.8%] isolates). Extensive surveillance failed to find any source of S. marcescens. Validation of the result of IRS-PCR by comparison with that of field inversion gel electrophoresis (FIGE) showed that they were completely concordant. These results suggest that IRS-PCR is comparable to FIGE for molecular epidemiologic studies. In addition, IRS-PCR was less laborious and less time-consuming than FIGE. To our knowledge, this is the first report of the application of IRS-PCR to A. baumannii and S. marcescens.
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Affiliation(s)
- J H Yoo
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.
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37
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Pestel-Caron M, Graff G, Berthelot G, Pons JL, Lemeland JF. Molecular analysis of Mycobacterium avium isolates by using pulsed-field gel electrophoresis and PCR. J Clin Microbiol 1999; 37:2450-5. [PMID: 10405383 PMCID: PMC85252 DOI: 10.1128/jcm.37.8.2450-2455.1999] [Citation(s) in RCA: 7] [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
Genetic relationships among 46 isolates of Mycobacterium avium recovered from 37 patients in a 2,500-bed hospital from 1993 to 1998 were assessed by pulsed-field gel electrophoresis (PFGE) and PCR amplification of genomic sequences located between the repetitive elements IS1245 and IS1311. Each technique enabled the identification of 27 to 32 different patterns among the 46 isolates, confirming that the genetic heterogeneity of M. avium strains is high in a given community. Furthermore, this retrospective analysis of sporadic isolates allowed us (i) to suggest the existence of two remanent strains in our region, (ii) to raise the question of the possibility of nosocomial acquisition of M. avium strains, and (iii) to document laboratory contamination. The methods applied in the present study were found to be useful for the typing of M. avium isolates. In general, both methods yielded similar results for both related and unrelated isolates. However, the isolates in five of the six PCR clusters were distributed among two to three PFGE patterns, suggesting that this PCR-based method may have limitations for the analysis of strains with low insertion sequence copy numbers or for resolution of extended epidemiologic relationships.
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Affiliation(s)
- M Pestel-Caron
- Groupe de Recherche sur les Antimicrobiens et les Micro-organismes (GRAM, EA 2656), 76000 Rouen, France.
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38
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Struelens MJ. Molecular epidemiologic typing systems of bacterial pathogens: current issues and perspectives. Mem Inst Oswaldo Cruz 1998; 93:581-5. [PMID: 9830521 DOI: 10.1590/s0074-02761998000500004] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The epidemiologic typing of bacterial pathogens can be applied to answer a number of different questions: in case of outbreak, what is the extent and mode of transmission of epidemic clone(s)? In case of long-term surveillance, what is the prevalence over time and the geographic spread of epidemic and endemic clones in the population? A number of molecular typing methods can be used to classify bacteria based on genomic diversity into groups of closely-related isolates (presumed to arise from a common ancestor in the same chain of transmission) and divergent, epidemiologically-unrelated isolates (arising from independent sources of infection). Ribotyping, IS-RFLP fingerprinting, macrorestriction analysis of chromosomal DNA and PCR-fingerprinting using arbitrary sequence or repeat element primers are useful methods for outbreak investigations and regional surveillance. Library typing systems based on multilocus sequence-based analysis and strain-specific probe hybridization schemes are in development for the international surveillance of major pathogens like Mycobacterium tuberculosis. Accurate epidemiological interpretation of data obtained with molecular typing systems still requires additional research on the evolution rate of polymorphic loci in bacterial pathogens.
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Affiliation(s)
- M J Struelens
- Service de Microbiologie, Hôpital Erasme, Bruxelles, Belgium.
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Gibson JR, Slater E, Xerry J, Tompkins DS, Owen RJ. Use of an amplified-fragment length polymorphism technique to fingerprint and differentiate isolates of Helicobacter pylori. J Clin Microbiol 1998; 36:2580-5. [PMID: 9705396 PMCID: PMC105166 DOI: 10.1128/jcm.36.9.2580-2585.1998] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Amplified-fragment length polymorphism (AFLP) analysis is the name given to a genotypic technique in which adapter oligonucleotides are ligated to restriction enzyme fragments and then used as target sites for primers in a PCR amplification process. The amplified fragments are electrophoretically separated to give strain-specific band profiles. We have developed a single-enzyme approach that did not require costly equipment or reagents for the fingerprinting of strains of Helicobacter pylori. The method was assessed with 46 isolates of H. pylori from 28 patients, and the results were compared with those from other genotypic tests. The AFLP profiles derived from HindIII fragments differentiated strains of H. pylori from unrelated individuals and confirmed the common origin of strains in some family members. AFLP analysis was also applied to investigate persistent infection following antibiotic therapy. Overall, the modified technique was relatively rapid and technically simple yet gave reproducible and discriminatory results. AFLP analysis samples variation throughout the genome and is a valuable addition to the existing genotypic fingerprinting methods for H. pylori.
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Affiliation(s)
- J R Gibson
- Helicobacter Reference Unit, Laboratory of Enteric Pathogens, Central Public Health Laboratory, London NW9 5HT, United Kingdom
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40
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Struelens MJ, De Gheldre Y, Deplano A. Comparative and Library Epidemiological Typing Systems: Outbreak Investigations versus Surveillance Systems. Infect Control Hosp Epidemiol 1998. [DOI: 10.2307/30141781] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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41
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Chang N, Chui L. A standardized protocol for the rapid preparation of bacterial DNA for pulsed-field gel electrophoresis. Diagn Microbiol Infect Dis 1998; 31:275-9. [PMID: 9597387 DOI: 10.1016/s0732-8893(98)00007-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A rapid method for the preparation of bacterial DNA for pulsed-field gel electrophoresis was developed for Gram-positive and Gram-negative bacteria. This method was accomplished by reducing the time for the cell lysis reaction, restriction endonuclease digestion, and electrophoresis to 1, 1.5, and 18 h, respectively. The whole procedure from the initial bacterial culture plate to the final analysis of restriction fragments can be completed within 24 h. This rapid method was successfully achieved for Staphylococcus aureus, Enterococcus faecalis, Neisseria gonorrhoeae, Salmonella typhimurium, Serratia marcescens, and Stenotrophomonas maltophilia.
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Affiliation(s)
- N Chang
- University of Alberta Hospital, University of Alberta, Edmonton, Canada
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42
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Sechi LA, Zanetti S, Dupré I, Delogu G, Fadda G. Enterobacterial repetitive intergenic consensus sequences as molecular targets for typing of Mycobacterium tuberculosis strains. J Clin Microbiol 1998; 36:128-32. [PMID: 9431935 PMCID: PMC124822 DOI: 10.1128/jcm.36.1.128-132.1998] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The presence of enterobacterial repetitive intergenic consensus (ERIC) sequences was demonstrated for the first time in the genome of Mycobacterium tuberculosis; these sequences have been found in transcribed regions of the chromosomes of gram-negative bacteria. In this study genetic diversity among clinical isolates of M. tuberculosis was determined by PCR with ERIC primers (ERIC-PCR). The study isolates comprised 71 clinical isolates collected from Sardinia, Italy. ERIC-PCR was able to identify 59 distinct profiles. The results obtained were compared with IS6110 and PCR-GTG fingerprinting. We found that the level of differentiation obtained by ERIC-PCR is greater than that obtained by IS6110 fingerprinting and comparable to that obtained by PCR-GTG. This method of fingerprinting is rapid and sensitive and can be applied to the study of the epidemiology of M. tuberculosis infections, especially when IS6110 fingerprinting is not of any help.
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Affiliation(s)
- L A Sechi
- Dipartimento di Scienze Biomediche, Sezione di Microbiologia Sperimentale e Clinica, Università degli studi di Sassari, Italy.
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43
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Riffard S, Lo Presti F, Vandenesch F, Forey F, Reyrolle M, Etienne J. Comparative analysis of infrequent-restriction-site PCR and pulsed-field gel electrophoresis for epidemiological typing of Legionella pneumophila serogroup 1 strains. J Clin Microbiol 1998; 36:161-7. [PMID: 9431941 PMCID: PMC124828 DOI: 10.1128/jcm.36.1.161-167.1998] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Two methods were compared for the analysis of 48 unrelated and epidemiologically related Legionella pneumophila serogroup 1 isolates. These are the infrequent-restriction-site PCR (IRS-PCR) assay with adapters designed for XbaI and PstI restriction sites and the pulsed-field gel electrophoresis (PFGE) analysis determined after DNA restriction with SfiI. Both methods demonstrated a high level of discrimination with a similar capacity for differentiating 23 of the 24 unrelated isolates. PFGE analysis and IRS-PCR assay were both able to identify epidemiologically related isolates of L. pneumophila from three outbreaks. Hence, IRS-PCR assay appears to be a reproducible (intergel reproducibility, 100%) and discriminative (discriminatory index, > or = 0.996) tool for typing of Legionella. Compared to PFGE, however, IRS-PCR presented an advantage through ease of performance and with attributes of rapidity and sensitivity of target DNA.
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Affiliation(s)
- S Riffard
- Centre National de Référence des Legionella, Laboratoire de Bactériologie, UPRES EA1655, Faculté de Médecine R.T.H. Laënnec, Lyon, France.
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44
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Prod'hom G, Guilhot C, Gutierrez MC, Varnerot A, Gicquel B, Vincent V. Rapid discrimination of Mycobacterium tuberculosis complex strains by ligation-mediated PCR fingerprint analysis. J Clin Microbiol 1997; 35:3331-4. [PMID: 9399550 PMCID: PMC230178 DOI: 10.1128/jcm.35.12.3331-3334.1997] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A ligation-mediated PCR (LMPCR) method for the amplification of sequences flanking the IS6110 of the Mycobacterium tuberculosis complex has been developed. The method uses one primer specific for IS6110 and a second specific for a linker ligated to SalI-restricted genomic DNA. LMPCR is a rapid screening method, valuable for the fingerprinting of M. tuberculosis complex strains.
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Affiliation(s)
- G Prod'hom
- Centre National de Référence des Mycobactéries, Institut Pasteur, Paris, France
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45
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Saulnier P, Andremont A. Les marqueurs moléculaires chez Staphylococcus aureus résistants à la méticilline. Analyse critique. Med Mal Infect 1997. [DOI: 10.1016/s0399-077x(97)80015-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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