451
|
Dawson SL, Fry JC, Dancer BN. A comparative evaluation of five typing techniques for determining the diversity of fluorescent pseudomonads. J Microbiol Methods 2002; 50:9-22. [PMID: 11943354 DOI: 10.1016/s0167-7012(02)00003-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Five typing methods were evaluated, utilising 63 strains of fluorescent pseudomonads, to assess their usefulness as tools to study the bacterial diversity within this complex group. The methods used were Biolog metabolic profiling, restriction fragment length polymorphism ribotyping, PCR ribotyping, and repetitive element sequence-based PCR (rep-PCR) utilising BOX and enterobacterial repetitive intergenic consensus (ERIC) primers. Cluster analysis of the results clearly demonstrated the considerable homogeneity of Pseudomonas aeruginosa isolates and, conversely, the heterogeneity within the other species, in particular P. putida and P. fluorescens, which need further taxonomic investigation. Biolog metabolic profiling enabled the best differentiation among the species. Rep-PCR proved to be highly discriminatory, more so than the other DNA fingerprinting techniques, demonstrating its suitability for the analysis of highly clonal isolates. RFLP ribotyping, PCR ribotyping, and rep-PCR produced specific clusters of P. aeruginosa isolates, which corresponded to their origins of isolation, hence we recommend these methods for intraspecific typing of bacteria.
Collapse
Affiliation(s)
- Shula L Dawson
- Cardiff School of Biosciences, Main Building, Cardiff University, P.O. Box 915, CF10 3TL, UK
| | | | | |
Collapse
|
452
|
Siafakas N, Markoulatos P, Stanway G, Tzanakaki G, Kourea-Kremastinou J. A reliable RT-PCR/RFLP assay for the molecular classification of enterovirus reference and wild type strains to either of the two genetic clusters on the basis of 5'-UTR. Mol Cell Probes 2002; 16:209-16. [PMID: 12144772 DOI: 10.1006/mcpr.2002.0414] [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: 11/22/2022]
Abstract
The available sequence data from a large segment of the 5'-UTR of all enterovirus reference and wild type strains were analysed in an attempt to discover possible restriction sites for reliable, serotypic identification of wild type isolates. No combination of restriction endonucleases, though, was found to produce serotype-, or group-specific haplotypes. Thirteen restriction enzymes were predicted to differentiate between representatives of the two enterovirus genetic clusters on the basis of 5'-UTR. One of these enzymes, BstOI, was tested in practice for the differentiation of 61 enterovirus reference strains from 56 different serotypes and 82 wild type strains which belong to the two genetic clusters on the basis of 5'-UTR. All the representatives of the two clusters were successfully differentiated with the specific restriction enzyme. Consequently, the simple RFLP-based assay presented here could be used as a very rapid and reliable means for the initial determination of whether a clinical isolate of unknown identity belongs to either of the 'poliovirus-like', or the 'CBV-like' genetic cluster on the basis of 5'-UTR classification of human enteroviruses.
Collapse
Affiliation(s)
- N Siafakas
- Virology Laboratory, Hellenic Pasteur Institute, 127, Vasilissis Sofias Avenue, Athens 115 21, Greece
| | | | | | | | | |
Collapse
|
453
|
Gilbert GL. Molecular diagnostics in infectious diseases and public health microbiology: cottage industry to postgenomics. Trends Mol Med 2002; 8:280-7. [PMID: 12067614 DOI: 10.1016/s1471-4914(02)02349-3] [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: 11/16/2022]
Abstract
Molecular methods have been used increasingly over the past ten years to improve the sensitivity and speed of diagnosis in infectious diseases. Although their routine use is still limited to the detection of pathogens that are difficult to culture in vitro,'real-time' methods, commercial kits, quantification and automation will increase potential applications. Molecular methods are now widely used for epidemiological fingerprinting of isolates of public health importance. Sequence-based identification and strain typing, together with the development of tools that can probe for thousands of markers, will allow detailed strain fingerprinting to assist in disease management and control.
Collapse
Affiliation(s)
- Gwendolyn L Gilbert
- Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology and Medical Research, University of Sydney, Westmead Hospital, Westmead, NSW 2145, Australia.
| |
Collapse
|
454
|
Montesinos I, Salido E, Delgado T, Cuervo M, Sierra A. Epidemiologic genotyping of methicillin-resistant Staphylococcus aureus by pulsed-field gel electrophoresis at a university hospital and comparison with antibiotyping and protein A and coagulase gene polymorphisms. J Clin Microbiol 2002; 40:2119-25. [PMID: 12037075 PMCID: PMC130756 DOI: 10.1128/jcm.40.6.2119-2125.2002] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A total of 124 methicillin-resistant Staphylococcus aureus (MRSA) isolates were ascertained at the University Hospital of the Canary Islands between January 1997 and April 2000. Genotyping included pulsed-field gel electrophoresis (PFGE) (SmaI digestion) and PCR-restriction fragment length polymorphism (PCR-RFLP) analysis for the coagulase (coa) and protein A (spa) genes. Antibiotic resistance was the main phenotypic marker correlated with genotyping results. Three main PFGE types were detected: A (with 12 subtypes), B (with 2 subtypes), and C. PFGE type A1 was the most commonly found (61% of isolates) and the one responsible for all the epidemic outbreaks. Other genetics markers used (coa and spa RFLPs) were significantly correlated with the PFGE types detected (P < 0.001). These PCR-RFLP assays were useful as molecular markers for a quick, preliminary study of MRSA outbreaks.
Collapse
Affiliation(s)
- I Montesinos
- Microbiology Laboratory, Hospital Universitario de Canarias, Tenerife, Canary Islands, Spain.
| | | | | | | | | |
Collapse
|
455
|
Ghaffar F, Muniz LS, Katz K, Smith JL, Shouse T, Davis P, McCracken GH. Effects of large dosages of amoxicillin/clavulanate or azithromycin on nasopharyngeal carriage of Streptococcus pneumoniae, Haemophilus influenzae, nonpneumococcal alpha-hemolytic streptococci, and Staphylococcus aureus in children with acute otitis media. Clin Infect Dis 2002; 34:1301-9. [PMID: 11981724 DOI: 10.1086/340054] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2001] [Revised: 12/27/2001] [Indexed: 11/03/2022] Open
Abstract
Prior use of antibiotics is associated with carriage of resistant bacteria. Colonization by Streptococcus pneumoniae, Haemophilus influenzae, nonpneumococcal alpha-hemolytic streptococci (NPAHS), and Staphylococcus aureus was evaluated in children receiving antibiotic therapy for acute otitis media and in untreated, healthy control subjects. Children were randomly assigned to receive either amoxicillin/clavulanate (90 mg/kg per day) or azithromycin. Swabs were obtained before initiating therapy and again 2 weeks and 2 months after initiating therapy. We also obtained swabs from control subjects at the time of enrollment and 2 weeks and 2 months after enrollment. The decrease in the rate of carriage of S. pneumoniae and H. influenzae at 2 weeks was significant only in the amoxicillin/clavulanate group (P<.001 and P=.005, respectively). The rate of nasopharyngeal colonization with NPAHS among treated patients increased from 23% to 39% at 2 months (P=.01). This increase was similar for both treatment groups. These results suggest that the competitive balance between organisms is altered by antibiotic therapy.
Collapse
Affiliation(s)
- Faryal Ghaffar
- Department of Pediatrics, Division of Infectious Disease, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA.
| | | | | | | | | | | | | |
Collapse
|
456
|
Houf K, De Zutter L, Van Hoof J, Vandamme P. Assessment of the genetic diversity among arcobacters isolated from poultry products by using two PCR-based typing methods. Appl Environ Microbiol 2002; 68:2172-8. [PMID: 11976086 PMCID: PMC127564 DOI: 10.1128/aem.68.5.2172-2178.2002] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) and randomly amplified polymorphic DNA PCR (RAPD-PCR) were optimized for characterization of Arcobacter butzleri, Arcobacter cryaerophilus, and Arcobacter skirrowii. In addition, a simple and rapid DNA extraction method was tested for use in both typing procedures. Both methods had satisfactory typeability and discriminatory power, but the fingerprints generated with ERIC-PCR were more reproducible and complex than those obtained with RAPD-PCR. The use of nondiluted boiled cell suspensions as DNA templates was found to be very useful in ERIC-PCR. Characterization of large numbers of Arcobacter isolates is therefore preferably performed by the ERIC-PCR procedure. Isolates for which almost identical ERIC fingerprints are generated may subsequently be characterized by RAPD-PCR, although adjustment and standardization of the amount of the DNA template are necessary. In the second part of this study, the genotypic diversity of arcobacters present on broiler carcasses was assessed by using both typing methods. A total of 228 cultures from 24 samples were examined after direct isolation and enrichment. The isolates were identified by using a multiplex PCR as A. butzleri (n = 182) and A. cryaerophilus (n = 46). A total of 131 types (91 A. butzleri types and 40 A. cryaerophilus types) were discerned without discordance between the two typing techniques. The analysis of the poultry isolates showed that poultry products may harbor not only more than one species but also multiple genotypes. All genotypes were confined to one poultry sample, and only three genotypes were found after simultaneous enrichment and direct isolation. These results demonstrate that different outcomes can be obtained in epidemiological studies depending on the isolation procedure used and the number of isolates characterized.
Collapse
Affiliation(s)
- Kurt Houf
- Department of Veterinary Food Inspection, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium.
| | | | | | | |
Collapse
|
457
|
Kudva IT, Evans PS, Perna NT, Barrett TJ, DeCastro GJ, Ausubel FM, Blattner FR, Calderwood SB. Polymorphic amplified typing sequences provide a novel approach to Escherichia coli O157:H7 strain typing. J Clin Microbiol 2002; 40:1152-9. [PMID: 11923324 PMCID: PMC140341 DOI: 10.1128/jcm.40.4.1152-1159.2002] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2001] [Revised: 10/17/2001] [Accepted: 01/04/2002] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli O157:H7 (O157) strains are commonly typed by pulsed-field gel electrophoresis (PFGE) following digestion of genomic DNA with the restriction enzyme XbaI. We have shown that O157 strains differ from each other by a series of discrete insertions or deletions, some of which contain recognition sites for XbaI, suggesting that these insertions and deletions are responsible for the differences in PFGE patterns. We have devised a new O157 strain typing protocol, polymorphic amplified typing sequences (PATS), based on this information. We designed PCR primer pairs to amplify genomic DNA flanking each of 40 individual XbaI sites in the genomes of two O157 reference strains. These primer pairs were tested with 44 O157 isolates, 2 each from 22 different outbreaks of infection. Thirty-two primer pairs amplified identical fragments from all 44 isolates, while eight primer pairs amplified regions that were polymorphic between isolates. The isolates could be differentiated solely on the basis of which of the eight polymorphic amplicons was detected. PATS correctly identified 21 of 22 outbreak pairs as being identical or highly related, whereas PFGE correctly identified 14 of the 22 outbreak pairs as being identical or highly related; PATS was also able to type isolates from three outbreaks that were untypeable by PFGE. However, PATS was less sensitive than PFGE in discriminating between outbreaks. These data suggest that typing by PATS may provide a simple procedure for strain typing of O157 and other bacteria and that further evaluation of the utility of this method for epidemiologic investigations is warranted.
Collapse
Affiliation(s)
- Indira T Kudva
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | | | | | | | | | | | | | | |
Collapse
|
458
|
Hardwick TH, Plikaytis B, Cassiday PK, Cage G, Peppler MS, Shea D, Boxrud D, Sanden GN. Reproducibility of Bordetella pertussis genomic DNA fragments generated by XbaI restriction and resolved by pulsed-field gel electrophoresis. J Clin Microbiol 2002; 40:811-6. [PMID: 11880398 PMCID: PMC120225 DOI: 10.1128/jcm.40.3.811-816.2002] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2001] [Revised: 06/19/2001] [Accepted: 12/10/2001] [Indexed: 11/20/2022] Open
Abstract
The intra- and interlaboratory variabilities of the molecular size measurements of each DNA fragment contributing to three pulsed-field gel electrophoresis (PFGE) profiles were assessed, as were the reproducibilities of the entire PFGE profiles for three Bordetella pertussis strains. The major source of variability within a laboratory occurred between subcultures rather than within gels or between gels. Each PFGE profile was generated reproducibly and was objectively defined by the molecular sizes of its composite fragments. A strain or profile most suitable for use as an internal reference standard was identified.
Collapse
Affiliation(s)
- Terri H Hardwick
- Meningitis and Special Pathogens Branch, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | | | | | | | | | | | | | | |
Collapse
|
459
|
Nallapareddy SR, Duh RW, Singh KV, Murray BE. Molecular typing of selected Enterococcus faecalis isolates: pilot study using multilocus sequence typing and pulsed-field gel electrophoresis. J Clin Microbiol 2002; 40:868-76. [PMID: 11880407 PMCID: PMC120268 DOI: 10.1128/jcm.40.3.868-876.2002] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The present study compared the recently developed multilocus sequence typing (MLST) approach with a well-established molecular typing technique, pulsed-field gel electrophoresis (PFGE), for subspecies differentiation of Enterococcus faecalis isolates. We sequenced intragenic regions of three E. faecalis antigen-encoding genes (ace, encoding a collagen and laminin adhesin; efaA, encoding an endocarditis antigen; and salA, encoding a cell wall associated antigen) and one housekeeping gene (pyrC) of 22 E. faecalis isolates chosen largely for their temporal and geographical diversity, but also including some outbreak isolates. MLST analysis of polymorphic regions of these four genes identified 13 distinct sequence types (STs) with different allelic profiles; the composite sequences generated from the four sequenced gene fragments of individual isolates showed 98.3 to 100% identity among the 22 isolates. We also found that the allelic profiles from two sequences, ace and salA, were sufficient to distinguish all 13 STs of this study. The 13 STs corresponded to 12 different PFGE types, with one previously designated PFGE clone (a widespread U.S. clone of beta-lactamase-producing isolates) being classified into two highly related STs which differed at 2 of 2,894 bases, both in the same allele. MLST also confirmed the clonal relationships among the isolates of two other PFGE clonal groups, including vancomycin resistant isolates. Thus, this pilot study with representative E. faecalis isolates suggests that, similar to PFGE, the sequence-based typing method may be useful for differentiating isolates of E. faecalis to the subspecies level in addition to identifying outbreak isolates.
Collapse
Affiliation(s)
- Sreedhar R Nallapareddy
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical School, Houston, Texas 77030, USA
| | | | | | | |
Collapse
|
460
|
Iwen PC, Hinrichs SH, Rupp ME. Utilization of the internal transcribed spacer regions as molecular targets to detect and identify human fungal pathogens. Med Mycol 2002; 40:87-109. [PMID: 11860017 DOI: 10.1080/mmy.40.1.87.109] [Citation(s) in RCA: 204] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Advances in molecular technology show great potential for the rapid detection and identification of fungi for medical, scientific and commercial purposes. Numerous targets within the fungal genome have been evaluated, with much of the current work using sequence areas within the ribosomal DNA (rDNA) gene complex. This section of the genome includes the 18S, 5.8S and 28S genes which code for ribosomal RNA (rRNA) and which have a relatively conserved nucleotide sequence among fungi. It also includes the variable DNA sequence areas of the intervening internal transcribed spacer (ITS) regions called ITS1 and ITS2. Although not translated into proteins, the ITS coding regions have a critical role in the development of functional rRNA, with sequence variations among species showing promise as signature regions for molecular assays. This review of the current literature was conducted to evaluate clinical approaches for using the fungal ITS regions as molecular targets. Multiple applications using the fungal ITS sequences are summarized here including those for culture identification, phylogenetic research, direct detection from clinical specimens or the environment, and molecular typing for epidemiological investigations. The breadth of applications shows that ITS regions have great potential as targets in molecular-based assays for the characterization and identification of fungi. Development of rapid and accurate amplification-based ITS assays to diagnose invasive fungal infections could potentially impact care and improve outcome for affected patients.
Collapse
Affiliation(s)
- P C Iwen
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha 68198-6495, USA.
| | | | | |
Collapse
|
461
|
Otman J, Cavassin ED, Perugini ME, Vidotto MC. An outbreak of extended-spectrum beta-lactamase-producing Klebsiella species in a neonatal intensive care unit in Brazil. Infect Control Hosp Epidemiol 2002; 23:8-9. [PMID: 11868896 DOI: 10.1086/503447] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
462
|
Gevers D, Huys G, Swings J. Applicability of rep-PCR fingerprinting for identification of Lactobacillus species. FEMS Microbiol Lett 2001; 205:31-6. [PMID: 11728712 DOI: 10.1111/j.1574-6968.2001.tb10921.x] [Citation(s) in RCA: 443] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
PCR amplification of repetitive bacterial DNA elements fingerprinting using the (GTG)(5) primer ((GTG)(5)-PCR) was proven to be useful for differentiation of a wide range of lactobacilli (i.e. 26 different (sub)species) at the species, subspecies and potentially up to the strain level. Using this rapid and reproducible genotypic technique, new Lactobacillus isolates recovered from different types of fermented dry sausage could be reliable identified at the (sub)species level. In conclusion, (GTG)(5)-PCR was found to be a promising genotypic tool for rapid and reliable speciation and typing of lactobacilli and other lactic acid bacteria important in food-fermentation industries.
Collapse
Affiliation(s)
- D Gevers
- Laboratory of Microbiology, Department of Biochemistry, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium.
| | | | | |
Collapse
|
463
|
Clementino MM, de Filippis I, Nascimento CR, Branquinho R, Rocha CL, Martins OB. PCR analyses of tRNA intergenic spacer, 16S-23S internal transcribed spacer, and randomly amplified polymorphic DNA reveal inter- and intraspecific relationships of Enterobacter cloacae strains. J Clin Microbiol 2001; 39:3865-70. [PMID: 11682499 PMCID: PMC88456 DOI: 10.1128/jcm.39.11.3865-3870.2001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PCR analysis of tRNA intergenic spacer (tDNA-PCR) and of the 16S-23S internal transcribed spacer (ITS-PCR) and random amplified polymorphic DNA (RAPD) analysis were evaluated for their usefulness in characterization of Enterobacter cloacae strains isolated from both clinical origins and vaccine microbial contamination. tDNA-PCR presented specific and reproducible patterns for Enterobacter sakazakii ATCC 29004, Enterobacter aerogenes ATCC 13048, and Enterobacter cloacae ATCC 13047 and 23355 that presented the same profile for all 16 E. cloacae isolates, offering an alternative tool for species-level identification. ITS-PCR and RAPD analysis yielded completely different banding patterns for the 20 strains studied, except for E. cloacae strains isolated from different batches of vaccine that exhibited a unique pattern, suggesting contamination by the same strain. The combined use of tDNA-PCR and ITS-PCR in a one-step protocol allows accurate identification and typing of E. cloacae strains a few hours after the colony has been isolated.
Collapse
Affiliation(s)
- M M Clementino
- Department of Microbiology, National Institute of Quality Control in Health, FIOCRUZ, Rio de Janeiro, Brazil.
| | | | | | | | | | | |
Collapse
|
464
|
Desai M, Logan JM, Frost JA, Stanley J. Genome sequence-based fluorescent amplified fragment length polymorphism of Campylobacter jejuni, its relationship to serotyping, and its implications for epidemiological analysis. J Clin Microbiol 2001; 39:3823-9. [PMID: 11682493 PMCID: PMC88450 DOI: 10.1128/jcm.39.11.3823-3829.2001] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The published genome sequence of Campylobacter jejuni strain NCTC 11168 was used to model an accurate and highly reproducible fluorescent amplified fragment length polymorphism (FAFLP) analysis. Predicted and experimentally observed amplified fragments (AFs) generated with the primer pair HindIII+A and HhaI+A were compared. All but one of the 61 predicted AFs were reproducibly detected, and no unpredicted fragments were amplified. This FAFLP analysis was used to genotype 74 C. jejuni strains belonging to the nine heat-stable (HS) serotypes most prevalent in human disease in England and Wales. The 74 C. jejuni strains exhibited 60 FAFLP profiles, and cluster analysis of them yielded a radial tree showing genetic relationships between and within 13 major clusters. Some clusters were related, and others were unrelated, to a single HS serotype. For example, all strains belonging to serotypes HS6 and HS19 grouped into corresponding single genotypic clusters, while strains of serotypes HS11 and HS18 each grouped into two genotypic clusters. Strains of HS50, the most prevalent serotype infecting humans, were found both in one large (multiserotype) cluster complex and dispersed throughout the tree. The strain genotypes within each FAFLP cluster were characterized by a particular combination of AFs, and among the cluster there were additional differential AFs. Identification of such AFs could act as a search tool to look for potential associations with disease or animal hosts, when applied to large number of human isolates. Genome-sequence based FAFLP, thus, has the potential to establish a genetic database for epidemiological investigations of Campylobacter.
Collapse
Affiliation(s)
- M Desai
- Molecular Biology Unit, Virus Reference Division, Central Public Health Laboratory, London NW9 5HT, United Kingdom.
| | | | | | | |
Collapse
|
465
|
Okatani AT, Uto T, Taniguchi T, Horisaka T, Horikita T, Kaneko K, Hayashidani H. Pulsed-field gel electrophoresis in differentiation of erysipelothrix species strains. J Clin Microbiol 2001; 39:4032-6. [PMID: 11682526 PMCID: PMC88483 DOI: 10.1128/jcm.39.11.4032-4036.2001] [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] [Received: 05/29/2001] [Accepted: 09/03/2001] [Indexed: 11/20/2022] Open
Abstract
We report here the first analysis of Erysipelothrix spp. using pulsed-field gel electrophoresis (PFGE). Seventy strains of Erysipelothrix spp. were analyzed. SmaI, AscI, and NotI were tested for the ability to cleave the DNA extracted from those strains, and among them, SmaI was the most reliable enzyme. Sixty-three distinct PFGE patterns were produced, and no DNA degradation was observed, allowing the identification of all of the strains. Based on these results and on those of a previous analysis using randomly amplified polymorphic DNA and ribotyping, PFGE with SmaI might be considered to be more sensitive than those methods and to be the best method for epidemiological studies of strains of this genus.
Collapse
Affiliation(s)
- A T Okatani
- Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | | | | | | | | | | | | |
Collapse
|
466
|
McAvin JC, Reilly PA, Roudabush RM, Barnes WJ, Salmen A, Jackson GW, Beninga KK, Astorga A, McCleskey FK, Huff WB, Niemeyer D, Lohman KL. Sensitive and specific method for rapid identification of Streptococcus pneumoniae using real-time fluorescence PCR. J Clin Microbiol 2001; 39:3446-51. [PMID: 11574554 PMCID: PMC88370 DOI: 10.1128/jcm.39.10.3446-3451.2001] [Citation(s) in RCA: 125] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Molecular surveillance of pathogens has shown the need for rapid and dependable methods for the identification of organisms of clinical and epidemiological importance. As the leading cause of community-acquired pneumonia, Streptococcus pneumoniae was used as a model organism to develop and refine a real-time fluorescence PCR assay and enhanced DNA purification method. Seventy clinical isolates of S. pneumoniae, verified by latex agglutination, were screened against 26 negative control clinical isolates employing a TaqMan assay on a thermocycler (LightCycler). The probe, constructed from the lytA gene, correctly detected all S. pneumoniae genomes without cross-reaction to negative controls. The speed and ease of this approach will make it adaptable to identification of many bacterial pathogens and provide potential for adaptation to direct detection from patient specimens.
Collapse
Affiliation(s)
- J C McAvin
- Molecular Epidemiology Branch, Air Force Institute for Environment and Occupational Health Risk Analysis/Epidemiology Surveillance Division, Brooks Air Force Base, San Antonio, Texas 78235, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
467
|
McLellan SL, Daniels AD, Salmore AK. Clonal populations of thermotolerant Enterobacteriaceae in recreational water and their potential interference with fecal Escherichia coli counts. Appl Environ Microbiol 2001; 67:4934-8. [PMID: 11571207 PMCID: PMC93254 DOI: 10.1128/aem.67.10.4934-4938.2001] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial strains were isolated from beach water samples using the original Environmental Protection Agency method for Escherichia coli enumeration and analyzed by pulsed-field gel electrophoresis (PFGE). Identical PFGE patterns were found for numerous isolates from 4 of the 9 days sampled, suggesting environmental replication. 16S rRNA gene sequencing, API 20E biochemical testing, and the absence of beta-glucuronidase activity revealed that these clonal isolates were Klebsiella, Citrobacter, and Enterobacter spp. In contrast, 82% of the nonclonal isolates from water samples were confirmed to be E. coli, and 16% were identified as other fecal coliforms. These nonclonal isolates produced a diverse range of PFGE patterns similar to those of isolates obtained directly from untreated sewage and gull droppings. beta-Glucuronidase activity was critical in distinguishing E. coli from other fecal coliforms, particularly for the clonal isolates. These findings demonstrate that E. coli is a better indicator of fecal pollution than fecal coliforms, which may replicate in the environment and falsely elevate indicator organism levels.
Collapse
Affiliation(s)
- S L McLellan
- Great Lakes WATER Institute, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53204, USA.
| | | | | |
Collapse
|
468
|
Coenye T, Vandamme P, Govan JR, LiPuma JJ. Taxonomy and identification of the Burkholderia cepacia complex. J Clin Microbiol 2001; 39:3427-36. [PMID: 11574551 PMCID: PMC88367 DOI: 10.1128/jcm.39.10.3427-3436.2001] [Citation(s) in RCA: 304] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- T Coenye
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan 48109-0646, USA.
| | | | | | | |
Collapse
|
469
|
D'Agata EM, Gerrits MM, Tang YW, Samore M, Kusters JG. Comparison of pulsed-field gel electrophoresis and amplified fragment-length polymorphism for epidemiological investigations of common nosocomial pathogens. Infect Control Hosp Epidemiol 2001; 22:550-4. [PMID: 11732783 DOI: 10.1086/501950] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
OBJECTIVE To compare molecular typing by amplified fragment-length polymorphism (AFLP) analysis with pulsed-field gel electrophoresis (PFGE) with respect to the ability to differentiate between epidemiologically related and unrelated isolates of common nosocomial pathogens recovered during a period of endemicity. DESIGN Retrospective laboratory analysis. SETTING Tertiary-care institution. METHODS 17 isolates of Acinetobacter baumannii, 22 isolates of Pseudomonas aeruginosa, and 22 vancomycin-resistant Enterococcusfaecium (VRE) were typed by both methods. RESULTS AFLP generated comparable results to PFGE for A baumannii and P aeruginosa isolates; both methods identified epidemiologically related and unrelated isolates. However, strain typing of VRE isolates produced discordant results between the two methods. PFGE identified 10 different strain types and differentiated between all epidemiologically related and unrelated isolates. In contrast, AFLP generated only five different strain types, three of which contained both epidemiologically related and unrelated isolates. CONCLUSION Molecular typing by AFLP is comparable to PFGE for A baumannii and P aeruginosa isolates. For VRE isolates, however, PFGE remains the method of choice.
Collapse
Affiliation(s)
- E M D'Agata
- Division of Infectious Diseases, Vanderbilt University, Nashville, Tennessee, USA
| | | | | | | | | |
Collapse
|
470
|
Clarke SC, Diggle MA, Edwards GF. Semiautomation of multilocus sequence typing for the characterization of clinical isolates of Neisseria meningitidis. J Clin Microbiol 2001; 39:3066-71. [PMID: 11526130 PMCID: PMC88298 DOI: 10.1128/jcm.39.9.3066-3071.2001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Scottish Meningococcus and Pneumococcus Reference Laboratory (SMPRL) provides a national service for the laboratory confirmation of meningococcal and pneumococcal disease in Scotland. Part of this service includes the serogrouping of meningococcal isolates followed by typing and subtyping. The procedures for this are labor-intensive but important for the identification of linked cases and the surveillance of disease so that effective public health measures can be taken. However, different strains of meningococci, such as those within the electrophoretic type 37 complex, occurring during case clusters of disease are now indistinguishable by current methods. The SMPRL has started using multilocus sequence typing (MLST) as a routine method for the characterization of isolates of Neisseria meningitidis. MLST produces nucleotide sequence data of seven housekeeping genes providing results that are useful for public health management. However, the method is laborious and time-consuming and therefore lends itself towards automation. The SMPRL therefore developed a semiautomated method for MLST using a 96-well format liquid handler and an automated DNA sequencer. Semiautomated MLST is now provided as a reference service for Scotland. This work describes the methodology required for the characterization of N. meningitidis and highlights its usefulness for public health intervention.
Collapse
Affiliation(s)
- S C Clarke
- Scottish Meningococcus and Pneumococcus Reference Laboratory, North Glasgow University Hospital NHS Trust, Stobhill Hospital, Glasgow, United Kingdom.
| | | | | |
Collapse
|
471
|
Krafft AE, Kulesh DA. Applying Molecular Biological Techniques to Detecting Biological Agents. Clin Lab Med 2001. [DOI: 10.1016/s0272-2712(18)30026-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
472
|
Benson JA, Ferrieri P. Rapid pulsed-field gel electrophoresis method for group B streptococcus isolates. J Clin Microbiol 2001; 39:3006-8. [PMID: 11474035 PMCID: PMC88282 DOI: 10.1128/jcm.39.8.3006-3008.2001] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2001] [Accepted: 05/28/2001] [Indexed: 11/20/2022] Open
Abstract
We developed a rapid pulsed-field gel electrophoresis (PFGE) method that required 3 days to complete, an improvement over the standard method that required as many as 8 days. The accuracy and reproducibility of the rapid method were verified by analysis of DNA band sizes of our control group B streptococcus isolate. The rapid method was superior to the standard method, providing more precise molecular sizing and gels of higher image quality. The reproducibility of rapid PFGE substantiated its value and continued use.
Collapse
Affiliation(s)
- J A Benson
- Department of Laboratory Medicine, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | | |
Collapse
|
473
|
Abstract
Whipple's disease is a rare bacterial infection that may involve any organ system in the body. It occurs primarily in Caucasian males older than 40 years. The gastrointestinal tract is the most frequently involved organ, with manifestations such as abdominal pain, malabsorption syndrome with diarrhea, and weight loss. Other signs include low-grade fever, lymphadenopathy, skin hyperpigmentation, endocarditis, pleuritis, seronegative arthritis, uveitis, spondylodiscitis, and neurological manifestations, and these signs may occur in the absence of gastrointestinal manifestations. Due to the wide variability of manifestations, clinical diagnosis is very difficult and is often made only years or even decades after the initial symptoms have appeared. Trimethoprim-sulfamethoxazole for at least 1 year is usually considered adequate to eradicate the infection. The microbiological diagnosis of this insidious disease is rendered difficult by the virtual lack of culture and serodiagnostic methods. It is usually based on the demonstration of periodic acid-Schiff-positive particles in infected tissues and/or the presence of bacteria with an unusual trilaminar cell wall ultrastructure by electron microscopy. Recently, the Whipple bacteria have been characterized at the molecular level by amplification of their 16S rRNA gene(s). Phylogenetic analysis of these sequences revealed a new bacterial species related to the actinomycete branch which was named "Tropheryma whippelli." Based on its unique 16S ribosomal DNA (rDNA) sequence, species-specific primers were selected for the detection of the organism in clinical specimens by PCR. This technique is currently used as one of the standard methods for establishing the diagnosis of Whipple's disease. Specific and broad-spectrum PCR amplifications mainly but not exclusively from extraintestinal specimens have significantly improved diagnosis, being more sensitive than histopathologic analysis. However, "T. whippelii" DNA has also been found in persons without clinical and histological evidence of Whipple's disease. It is unclear whether these patients are true asymptomatic carriers or whether differences in virulence exist among strains of "T. whippelii" that might account for the variable clinical manifestations. So far, six different "T. whippelii" subtypes have been found by analysis of their 16S-23S rDNA spacer region. Further studies of the pathogen "T. whippelii" as well as the host immune response are needed to fully understand this fascinating disease. The recent cultivation of the organisms is a promising major step in this direction.
Collapse
Affiliation(s)
- F Dutly
- Department of Medical Microbiology, University of Zürich, CH-8028 Zürich, Switzerland.
| | | |
Collapse
|
474
|
Palmer HM, Arnold C. Genotyping Neisseria gonorrhoeae using fluorescent amplified fragment length polymorphism analysis. J Clin Microbiol 2001; 39:2325-9. [PMID: 11376083 PMCID: PMC88137 DOI: 10.1128/jcm.39.6.2325-2329.2001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2001] [Accepted: 03/31/2001] [Indexed: 11/20/2022] Open
Abstract
An evaluation of fluorescent amplified fragment length polymorphism (FAFLP) for typing Neisseria gonorrhoeae using 52 isolates revealed that its discriminatory power approached that of Opa-typing in identifying epidemiologically linked isolates. Automated, accurate sizing of FAFLP amplified fragments permits objective data analysis and storage, making it an attractive method for large surveillance projects.
Collapse
Affiliation(s)
- H M Palmer
- Genitourinary Infections Reference Laboratory, Public Health Laboratory, Bristol Royal Infirmary, Bristol BS2 8HW, United Kingdom
| | | |
Collapse
|
475
|
Joo YS, Fox LK, Davis WC, Bohach GA, Park YH. Staphylococcus aureus associated with mammary glands of cows: genotyping to distinguish different strains among herds. Vet Microbiol 2001; 80:131-8. [PMID: 11295333 DOI: 10.1016/s0378-1135(00)00381-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The hypothesis that strains of Staphylococcus aureus are more likely to be unique to a herd than common to several herds was tested. Herds (n=28) from nine geographic areas of Korea, with elevated milk somatic cell counts (>500000 cells/ml) were enrolled in this study. Mammary quarter milk samples were aseptically collected from all lactating cows (n=616) with at least three functional quarters. Milk was cultured and S. aureus isolates were typed using pulse field gel electrophoresis of DNA SmaI digests. A total of 181 cows were identified as having S. aureus intramammary infections. A total of 52 different types of S. aureus were identified and 34 (65.4%) were associated with a single herd. A total of 18 types of S. aureus were found in multiple herds; 14 types were found in two herds, and four types were found in three herds. Herds with 1, 2, 3, and more than 3 types, were: four (14.3%); eight (28.6%); nine (32.1%); and seven (25.0%). The data indicate that the majority of strains were found in one herd only, and more than 90% were found in two or less herds, suggesting that strains of S. aureus are more likely to be restricted to a single herd, than found in multiple herds.
Collapse
Affiliation(s)
- Y S Joo
- Mastitis Research Laboratory, Bacteriology and Immunology Department, National Veterinary Research Institute, Kyunggi-do, South Korea
| | | | | | | | | |
Collapse
|
476
|
Luzzaro F, Mantengoli E, Perilli M, Lombardi G, Orlandi V, Orsatti A, Amicosante G, Rossolini GM, Toniolo A. Dynamics of a nosocomial outbreak of multidrug-resistant Pseudomonas aeruginosa producing the PER-1 extended-spectrum beta-lactamase. J Clin Microbiol 2001; 39:1865-70. [PMID: 11326005 PMCID: PMC88040 DOI: 10.1128/jcm.39.5.1865-1870.2001] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
From November 1998 to August 1999, a large outbreak occurred in the general intensive care unit of the Ospedale di Circolo in Varese (Italy), caused by Pseudomonas aeruginosa producing the PER-1 extended-spectrum beta-lactamase. A total of 108 clinical isolates of P. aeruginosa resistant to broad-spectrum cephalosporins were recovered from 18 patients. Epidemic isolates were characterized by synergy between clavulanic acid and ceftazidime, cefepime, and aztreonam. Isoelectric focusing of crude bacterial extracts detected two nitrocefin-positive bands with pI values of 8.0 and 5.3. PCR amplification and characterization of the amplicons by restriction analysis and direct sequencing indicated that the epidemic isolates carried a bla(PER-1) determinant. The outbreak was of clonal origin as shown by pulsed-field gel electrophoresis analysis. This technique also indicated that the epidemic strain was not related to three other PER-1-positive isolates obtained at the same hospital in 1997. Typing by enterobacterial repetitive intergenic consensus-PCR showed that minor genetic variations occurred during the outbreak. The epidemic strain was characterized by a multiple-drug-resistance phenotype that remained unchanged over the outbreak, including extended-spectrum cephalosporins, monobactams, aminoglycosides, and fluoroquinolones. Isolation of infected patients and appropriate carbapenem therapy were successful in ending the outbreak. Our report indicates that the bla(PER-1) resistance determinant may become an emerging therapeutic problem in Europe.
Collapse
Affiliation(s)
- F Luzzaro
- Laboratory of Microbiology, Ospedale di Circolo and University of Insubria, Viale Borri 57, 21100, Varese, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
477
|
Maruyama S, Kasten RW, Boulouis HJ, Gurfield NA, Katsube Y, Chomel BB. Genomic diversity of Bartonella henselae isolates from domestic cats from Japan, the USA and France by pulsed-field gel electrophoresis. Vet Microbiol 2001; 79:337-49. [PMID: 11267793 DOI: 10.1016/s0378-1135(00)00365-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genomic DNA diversity of 27 Bartonella henselae and three B. clarridgeiae isolates from 18 domestic cats from Japan, the USA and France was investigated by pulsed-field gel electrophoresis (PFGE) with NotI, AscI and SmaI restriction enzymes. A great diversity of genomic patterns was found for all B. henselae, but none for B. clarridgeiae isolates. The DNA size of B. henselae and B. clarridgeiae isolates were 1.7-2.9 and 1.7Mbp, respectively. All 13 Japanese cat isolates were identified as B. henselae type I. Furthermore, three of the four Japanese cats harbored genetically different B. henselae type I isolates, suggesting for the first time co-infection with various type I isolates. One French cat and one American cat were co-infected with B. henselae and B. clarridgeiae. B. henselae type I and type II were mainly grouped in two different clusters by PFGE using SmaI endonuclease in the dendrogram.
Collapse
Affiliation(s)
- S Maruyama
- Laboratory of Veterinary Public Health, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, 252-8510, Kanagawa, Japan.
| | | | | | | | | | | |
Collapse
|
478
|
Simpson KL, Pettersson B, Priest FG. Characterization of lactobacilli from Scotch malt whisky distilleries and description of Lactobacillus ferintoshensis sp. nov., a new species isolated from malt whisky fermentations. MICROBIOLOGY (READING, ENGLAND) 2001; 147:1007-1016. [PMID: 11283296 DOI: 10.1099/00221287-147-4-1007] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sixty-four strains of Lactobacillus were isolated from fermentation samples from 23 malt whisky distilleries located in the major whisky producing regions of Scotland. The strains were assigned to 26 ribotype patterns. Strains of some ribotype patterns were widely distributed and recovered from distilleries throughout Scotland, while strains representing other ribotypes were particular to a specific region or even a certain distillery. Repeated sampling of a single distillery over a 12 month period showed that the range of bacteria present, as indicated by ribotyping, was stable, but was influenced by changes in malt supply and the period of closure for annual maintenance. Partial 16S rDNA sequence analysis of ribotype representatives revealed Lactobacillus brevis, Lactobacillus fermentum, Lactobacillus paracasei and Lactobacillus pentosus as the major species present in the distilleries; however, four isolates could not be identified by this procedure. Determination of the full 16S rDNA gene sequence from one of these isolates (strain R7-84) revealed >98.5% similarity to Lactobacillus buchneri and its phylogenetic neighbours. DNA from two other strains showed greater than 70% hybridization to DNA from R7-84 under non-stringent renaturation conditions and DNA from strain R7-84 shared less than 65% hybridization with members of the L. buchneri group. It is proposed that these three strains should be placed in a new species for which the name Lactobacillus ferintoshensis represented by the type strain R7-84(T) is suggested.
Collapse
Affiliation(s)
- Kirsten L Simpson
- International Centre for Brewing & Distilling, Department of Biological Sciences, Heriot-Watt University, Edinburgh EH14 4AS, Scotland, UK1
| | - Bertil Pettersson
- Department of Biotechnology, Royal Institute of Technology,S-100 44 Stockholm, Sweden2
| | - Fergus G Priest
- International Centre for Brewing & Distilling, Department of Biological Sciences, Heriot-Watt University, Edinburgh EH14 4AS, Scotland, UK1
| |
Collapse
|
479
|
Tzanakaki G, Urwin R, Musilek M, Kriz P, Kremastinou J, Pangalis A, Blackwell CC, Maiden MC. Phenotypic and genotypic approaches to characterization of isolates of Neisseria meningitidis from patients and their close family contacts. J Clin Microbiol 2001; 39:1235-40. [PMID: 11283034 PMCID: PMC87917 DOI: 10.1128/jcm.39.4.1235-1240.2001] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2000] [Accepted: 01/12/2001] [Indexed: 11/20/2022] Open
Abstract
Characterization of isolates of Neisseria meningitidis obtained from patients with meningococcal disease or from pharyngeal swabs of asymptomatic carriers can be achieved by several approaches which provide different levels of discrimination. A total of 45 gram negative, oxidase-positive diplococcus strains isolated from 15 individuals with meningococcal disease and 30 of their family contacts were examined by three approaches: serological typing, multilocus enzyme electrophoresis (MLEE), and multilocus sequence typing (MLST). For 10 of the 15 patient and contact groups, all of the isolates were confirmed as meningococci, and the bacteria obtained from the patients and contacts, including their mother or principal caregiver in the case of children, were indistinguishable by all three methods. In the remaining five groups the isolates from the patients were distinct from those recovered from the contacts, and in three examples, in two separate groups, the contacts were shown by MLST to be carrying strains of Neisseria lactamica. The data obtained from the three techniques were consistent, although complete serological typing was possible for only a minority of isolates. Both MLEE and MLST established the genetic relationships of the isolates and identified members of known hypervirulent lineages, but MLST was faster than MLEE and had the additional advantages that it could be performed on noninfective material distributed by mail and that the results from different laboratories could be compared via the internet (http://mlst.zoo.ox.ac.uk).
Collapse
Affiliation(s)
- G Tzanakaki
- National Meningococcal Reference Laboratory, National School of Public Health, Athens, Greece
| | | | | | | | | | | | | | | |
Collapse
|
480
|
Quelle LS, Catalano M. Efficacy of two DNA fingerprinting methods for typing Acinetobacter baumannii isolates. Diagn Microbiol Infect Dis 2001; 39:215-23. [PMID: 11404063 DOI: 10.1016/s0732-8893(01)00238-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Performance of macrorestriction and repetitive extragenic palindromic DNA sequence-based PCR (REP-PCR) to type Acinetobacter baumannii isolates was quantitatively estimated using a test population of 54 outbreak-related, 29 endemic infection-related and 17 epidemiologically-unrelated isolates. Reproducibility and stability for macrorestriction were 100%, and REP-PCR showed only slightly lower stability. Macrorestriction resolved 18 fingerprints and REP-PCR 10 DNA patterns, forming eight and seven clusters at 75% of similarity level, respectively. Intercluster band variation was > 7 bands for both methods. Although, all endemic isolates, except one, were concordantly grouped by both methods, macrorestriction distinguished a greater number of subtypes over one year study. For outbreaks, the epidemiologic concordance for both methods was 88%. The discriminatory index for macrorestriction and REP-PCR was 0.884 and 0.877, respectively. In conclusion, both methods showed similar efficacy as epidemiological markers, and by concordance, this study demonstrated that for REP-PCR typing, a > or = 7 bands difference seemed an appropriate threshold to identify unrelated strains.
Collapse
Affiliation(s)
- L S Quelle
- Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | |
Collapse
|
481
|
Velappan N, Snodgrass JL, Hakovirta JR, Marrone BL, Burde S. Rapid identification of pathogenic bacteria by single-enzyme amplified fragment length polymorphism analysis. Diagn Microbiol Infect Dis 2001; 39:77-83. [PMID: 11248519 DOI: 10.1016/s0732-8893(00)00235-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Despite major progress in their treatment and prevention, bacterial infections remain a significant cause of morbidity and mortality worldwide. In responding to a disease outbreak, rapid and accurate identification of the bacterial species involved is of paramount importance. Strain level discrimination is desirable to allow selection of treatment modalities, and in the case of a deliberate release, for identification of the source. Single-enzyme amplified fragment length polymorphism (SE-AFLP) analysis was used to perform species and strain identification of subgroup I Bacilli, Yersinia, Staphylococci and Escherichia coli. By careful selection of AFLP primers, it was possible to obtain reproducible and sensitive identification to strain level, even within the highly monomorphic species Bacillus anthracis. SE-AFLP fragments can be analyzed using standard gel electrophoresis, and can be easily scored by visual inspection, due to the low complexity of the fingerprint obtained by this method. These features make SE-AFLP suitable for use in either field or laboratory applications.
Collapse
Affiliation(s)
- N Velappan
- Los Alamos National Laboratory, Bioscience Division, P.O. Box 1663, MS M888, Los Alamos, NM 87545, USA
| | | | | | | | | |
Collapse
|
482
|
Vrioni G, Matsiota-Bernard P. Molecular typing of Candida isolates from patients hospitalized in an intensive care unit. J Infect 2001; 42:50-6. [PMID: 11243754 DOI: 10.1053/jinf.2000.0778] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVES The aim of our study was the molecular typing of 40 clinical isolates of Candida spp. obtained from patients with burns or trauma hospitalized in the intensive care unit of a general hospital. METHODS Isolates were recovered from blood, deep trauma, urine, sputum or from environment within a short period of time (4 months). The yeasts were identified using commercial yeast identification kits as C. albicans (17 isolates), C. tropicalis (16 isolates) and C. parapsilosis (10 isolates). The epidemiological relation of the isolates was tested with the Random Amplified Polymorphic DNA assay using three or four arbitrary chosen primers. RESULTS All C. albicans isolates presented distinct RAPD profiles, C. tropicalis isolates presented both the same and distinct RAPD patterns and the C. parapsilosis isolates presented the same RAPD pattern. All the environmental isolates were identified as C. parapsilosis and they had the same RAPD pattern as C. parapsilosis clinical isolates. Candida parapsilosis delineation was confirmed with PFGE. CONCLUSIONS The colonization/infection with C. albicans was endogenous, the C. tropicalis colonization/infection was both endogenous and exogenous, and the C. parapsilosis colonization/infection had an environmental origin.
Collapse
Affiliation(s)
- G Vrioni
- Laboratoire de Microbiologie, Hôpital Raymond Poincaré, 92380 Garches, France
| | | |
Collapse
|
483
|
Su X, Lind I. Molecular basis of high-level ciprofloxacin resistance in Neisseria gonorrhoeae strains isolated in Denmark from 1995 to 1998. Antimicrob Agents Chemother 2001; 45:117-23. [PMID: 11120953 PMCID: PMC90248 DOI: 10.1128/aac.45.1.117-123.2001] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Denmark surveillance of the in vitro susceptibility to ciprofloxacin of Neisseria gonorrhoeae was established in 1990. The proportion of N. gonorrhoeae strains with decreased susceptibility or resistance to ciprofloxacin (MIC >/= 0.06 microg/ml) was low (0.3 to 2.3%) up to 1995. Between 1995 and 1998 the rate of less-susceptible and resistant strains rose from 6.9 to 13.2%. Among ciprofloxacin-resistant strains (MIC >/= 1 microg/ml), 81% were highly resistant (MIC >/= 4 microg/ml). Thirty-five N. gonorrhoeae strains (40 isolates) for which ciprofloxacin MICs were 4 to 32 microg/ml were investigated for the frequency and patterns of mutations within the gyrA and parC genes. The quinolone resistance-determining regions of the gyrA and parC genes were amplified by PCR, and the amplicons were directly sequenced. Alterations at Ser-91 and Asp-95 in GyrA and a single or double alteration in ParC were identified in 32 strains (91%). Ser-91-to-Phe and Asp-95-to-Gly alterations in GyrA were detected in 28 strains (80%). The most common ParC alteration, Asp-86 to Asn, was found in 19 strains (54%). The strains were analyzed for genetic relationship by pulsed-field gel electrophoresis (PFGE). The analysis showed that nine strains with the same mutation pattern in the gyrA and parC genes, originating from different geographical areas over 3 years, had the same PFGE patterns after SpeI as well as NheI digestion (only one strain with one band difference in the NheI pattern), suggesting that a resistant clone had spread worldwide. The results from this study strongly suggest that double gyrA mutations plus a parC mutation(s) play an important role in the development of high-level fluoroquinolone resistance in N. gonorrhoeae.
Collapse
Affiliation(s)
- X Su
- Neisseria Unit, Department of Respiratory Infections, Meningitis and STIs, Statens Serum Institut, Copenhagen, Denmark
| | | |
Collapse
|
484
|
Goulding JN, Hookey JV, Stanley J, Olver W, Neal KR, Ala'Aldeen DA, Arnold C. Fluorescent amplified-fragment length polymorphism genotyping of Neisseria meningitidis identifies clones associated with invasive disease. J Clin Microbiol 2000; 38:4580-5. [PMID: 11101599 PMCID: PMC87640 DOI: 10.1128/jcm.38.12.4580-4585.2000] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fluorescent amplified-fragment length polymorphism (FAFLP), a genotyping technique with phylogenetic significance, was applied to 123 isolates of Neisseria meningitidis. Nine of these were from an outbreak in a British university; 9 were from a recent outbreak in Pontypridd, Glamorgan; 15 were from sporadic cases of meningococcal disease; 26 were from the National Collection of Type Cultures; 58 were carrier isolates from Ironville, Derbyshire; 1 was a disease isolate from Ironville; and five were representatives of invasive clones of N. meningitidis. FAFLP analysis results were compared with previously published multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) results. FAFLP was able to identify hypervirulent, hyperendemic lineages (invasive clones) of N. meningitidis as well as did MLST. PFGE did not discriminate between two strains from the outbreak that were classified as similar but distinct by FAFLP. The results suggest that high resolution of N. meningitidis for outbreak and other epidemiological analyses is more cost efficient by FAFLP than by sequencing procedures.
Collapse
Affiliation(s)
- J N Goulding
- Molecular Biology Unit, SBVL, Central Public Health Laboratory, London, UK
| | | | | | | | | | | | | |
Collapse
|
485
|
Smith D, Willshaw G, Stanley J, Arnold C. Genotyping of verocytotoxin-producing Escherichia coli O157: comparison of isolates of a prevalent phage type by fluorescent amplified-fragment length polymorphism and pulsed-field gel electrophoresis analyses. J Clin Microbiol 2000; 38:4616-20. [PMID: 11101605 PMCID: PMC87646 DOI: 10.1128/jcm.38.12.4616-4620.2000] [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
We applied the high-resolution genotyping technique fluorescent amplified-fragment length polymorphism (FAFLP) analysis to 71 isolates of a single phage type (PT8) of pulsed-field gel electrophoresis (PFGE)-characterized verocytotoxin-producing Escherichia coli O157. Twenty-seven similar, but not identical, groupings were defined by both FAFLP analysis and the PFGE profiles. Given the FAFLP analysis conditions described here, these two methods exhibited equivalent discriminatory powers.
Collapse
Affiliation(s)
- D Smith
- Molecular Biology Unit, Virus Reference Division, Central Public Health Laboratory, London NW9 5HT, United Kingdom
| | | | | | | |
Collapse
|
486
|
Bedendo J, Pignatari AC. Typing of Enterococcus faecium by polymerase chain reaction and pulsed field gel electrophoresis. Braz J Med Biol Res 2000; 33:1269-74. [PMID: 11050655 DOI: 10.1590/s0100-879x2000001100002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Polymerase chain reaction (PCR) with JB1 or REP consensus oligonucleotides and pulsed field gel electrophoresis (PFGE) were used to study genomic DNA extracted from 31 strains of enterococci. Eleven ATCC strains, representative of 11 species of Enterococcus, were initially tested by JB1-PCR, revealing that Enterococcus malodoratus and Enterococcus hirae presented identical banding patterns. Eight Enterococcus faecium isolates from Stanford University and 12 from São Paulo Hospital were studied by JB1-PCR, REP-PCR (1/2)R and PFGE. Among the isolates from Stanford University, 5 genotypes were defined by JB1-PCR, 7 by REP-PCR (1/2)R and 4 by PFGE. Among the isolates from São Paulo Hospital, 9 genotypes were identified by JB1-PCR, 6 by REP-PCR and 5 by PFGE. The three methods identified identical genotypes, but there was not complete agreement among them.
Collapse
Affiliation(s)
- J Bedendo
- Departamento de Enfermagem, Centro de Ciências da Saúde, Universidade Estadual de Maringá, Maringá, PR, Brasil.
| | | |
Collapse
|
487
|
Wang X, Maegawa T, Karasawa T, Kozaki S, Tsukamoto K, Gyobu Y, Yamakawa K, Oguma K, Sakaguchi Y, Nakamura S. Genetic analysis of type E botulinum toxin-producing Clostridium butyricum strains. Appl Environ Microbiol 2000; 66:4992-7. [PMID: 11055954 PMCID: PMC92410 DOI: 10.1128/aem.66.11.4992-4997.2000] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Type E botulinum toxin (BoNT/E)-producing Clostridium butyricum strains isolated from botulism cases or soil specimens in Italy and China were analyzed by using nucleotide sequencing of the bont/E gene, random amplified polymorphic DNA (RAPD) assay, pulsed-field gel electrophoresis (PFGE), and Southern blot hybridization for the bont/E gene. Nucleotide sequences of the bont/E genes of 11 Chinese isolates and of the Italian strain BL 6340 were determined. The nucleotide sequences of the bont/E genes of 11 C. butyricum isolates from China were identical. The deduced amino acid sequence of BoNT/E from the Chinese isolates showed 95.0 and 96.9% identity with those of BoNT/E from C. butyricum BL 6340 and Clostridium botulinum type E, respectively. The BoNT/E-producing C. butyricum strains were divided into the following three clusters based on the results of RAPD assay, PFGE profiles of genomic DNA digested with SmaI or XhoI, and Southern blot hybridization: strains associated with infant botulism in Italy, strains associated with food-borne botulism in China, and isolates from soil specimens of the Weishan lake area in China. A DNA probe for the bont/E gene hybridized with the nondigested chromosomal DNA of all toxigenic strains tested, indicating chromosomal localization of the bont/E gene in C. butyricum. The present results suggest that BoNT/E-producing C. butyricum is clonally distributed over a vast area.
Collapse
Affiliation(s)
- X Wang
- Department of Bacteriology, School of Medicine, Kanazawa University, Kanazawa 920-8640, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
488
|
Johansson A, Ibrahim A, Göransson I, Eriksson U, Gurycova D, Clarridge JE, Sjöstedt A. Evaluation of PCR-based methods for discrimination of Francisella species and subspecies and development of a specific PCR that distinguishes the two major subspecies of Francisella tularensis. J Clin Microbiol 2000; 38:4180-5. [PMID: 11060087 PMCID: PMC87560 DOI: 10.1128/jcm.38.11.4180-4185.2000] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous studies have demonstrated that the four subspecies of the human pathogen Francisella tularensis, despite showing marked variations in their virulence for mammals and originating from different regions in the Northern Hemisphere, display a very close phylogenetic relationship. This property has hampered the development of generally applicable typing methods. To overcome this problem, we evaluated the use of PCR for discrimination of the subspecies using various forms of long arbitrary primers or primers specific for repetitive extragenic palindromic sequences (REP) or enterobacterial repetitive intragenic consensus (ERIC) sequences. Patterns generated by use of REP, ERIC, or long arbitrary primers allowed differentiation at the species level and of the four subspecies of F. tularensis. With each of these three methods, similar or identical clustering of strains was found, and groups of strains of different geographical origins or differing in virulence showed distinct patterns. The discriminatory indices of the methods varied from 0.57 to 0.65; thus, the patterns were not sufficiently discriminatory to distinguish individual strains. The sequence of a fragment generated by amplification with an arbitrary primer was determined, and a region showing interstrain heterogeneity was identified. Specific primers were designed, and a PCR was developed that distinguished strains of F. tularensis subsp. holarctica from strains of other F. tularensis subspecies, including strains of the highly virulent F. tularensis subsp. tularensis. Notably, one European isolate showed the genetic pattern typical of the highly virulent F. tularensis subsp. tularensis, generally believed to exist only in North America. It is proposed that a combination of the specific PCR together with one method generating subspecies-specific patterns is suitable as a rapid and relatively simple strategy for discrimination of Francisella species and subspecies.
Collapse
Affiliation(s)
- A Johansson
- Infectious Diseases, Umeå University, and Department of Microbiology, Defence Research Establishment, Sweden
| | | | | | | | | | | | | |
Collapse
|
489
|
Kunishima S, Inoue C, Nishimoto Z, Kamiya T, Ozawa K. Application of 16S ribosomal RNA gene amplification to the rapid identification of bacteria from blood culture bottles. Transfusion 2000; 40:1420-1. [PMID: 11099676 DOI: 10.1046/j.1537-2995.2000.40111420.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
490
|
Nielsen EM, Engberg J, Fussing V, Petersen L, Brogren CH, On SL. Evaluation of phenotypic and genotypic methods for subtyping Campylobacter jejuni isolates from humans, poultry, and cattle. J Clin Microbiol 2000; 38:3800-10. [PMID: 11015406 PMCID: PMC87479 DOI: 10.1128/jcm.38.10.3800-3810.2000] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Six methods for subtyping of Campylobacter jejuni were compared and evaluated with a collection of 90 isolates from poultry, cattle, and sporadic human clinical cases as well as from a waterborne outbreak. The applied methods were Penner heat-stable serotyping; automated ribotyping (RiboPrinting); random amplified polymorphic DNA typing (RAPD); pulsed-field gel electrophoresis (PFGE); restriction fragment length polymorphisms of the flagellin gene, flaA (fla-RFLP); and denaturing gradient gel electrophoresis of flaA (fla-DGGE). The methods were evaluated and compared on the basis of their abilities to identify isolates from one outbreak and discriminate between unrelated isolates and the agreement between methods in identifying clonal lines. All methods identified the outbreak strain. For a collection of 80 supposedly unrelated isolates, RAPD and PFGE were the most discriminatory methods, followed by fla-RFLP and RiboPrinting. fla-DGGE and serotyping were the least discriminative. All isolates included in this study were found to be typeable by each of the methods. Thirteen groups of potentially related isolates could be identified using a criterion that at least four of the methods agreed on clustering of isolates. None of the subtypes could be related to only one source; rather, these groups represented isolates from different sources. Furthermore, in two cases isolates from cattle and human patients were found to be identical according to all six methods.
Collapse
Affiliation(s)
- E M Nielsen
- Danish Veterinary Laboratory, 1790 Copenhagen, Denmark.
| | | | | | | | | | | |
Collapse
|
491
|
Ghaffar F, Muniz LS, Katz K, Reynolds J, Smith JL, Davis P, Friedland IR, McCracken GH. Effects of amoxicillin/clavulanate or azithromycin on nasopharyngeal carriage of Streptococcus pneumoniae and Haemophilus influenzae in children with acute otitis media. Clin Infect Dis 2000; 31:875-80. [PMID: 11049764 DOI: 10.1086/318160] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/1999] [Indexed: 11/03/2022] Open
Abstract
The effect of antibiotic therapy on nasopharyngeal colonization by Streptococcus pneumoniae and Haemophilus influenzae was evaluated in children diagnosed with acute otitis media. Children were randomly assigned to receive either amoxicillin/clavulanate or azithromycin therapy, and nasopharyngeal swabs were obtained for culture before and after starting therapy. Amoxicillin/clavulanate therapy eradicated or suppressed all strains of S. pneumoniae susceptible to penicillin, 75% of strains with intermediate resistance, and 40% of strains resistant to penicillin. Azithromycin therapy cleared two-thirds of azithromycin-susceptible strains of S. pneumoniae but none of azithromycin-nonsusceptible strains. Selection for antibiotic-resistant strains in individual children was not observed in children who received amoxicillin/clavulanate therapy but was observed in 2 children who received azithromycin therapy. Carriage of H. influenzae was also reduced by antimicrobial therapy but more so by amoxicillin/clavulanate. Antibiotic therapy does not directly increase the number of resistant strains in the population but, by eradicating susceptible strains, allows greater opportunity for carriage and spread of resistant strains.
Collapse
Affiliation(s)
- F Ghaffar
- Dept. of Pediatrics, Division of Infectious Disease, University of Texas Southwestern Medical Center, Dallas, TX 75235-9063, USA.
| | | | | | | | | | | | | | | |
Collapse
|
492
|
McKee KT, Shields TM, Jenkins PR, Zenilman JM, Glass GE. Application of a geographic information system to the tracking and control of an outbreak of shigellosis. Clin Infect Dis 2000; 31:728-33. [PMID: 11017823 DOI: 10.1086/314050] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/1999] [Revised: 02/29/2000] [Indexed: 11/03/2022] Open
Abstract
A personal computer-based commercial geographic information system (GIS) was applied to an outbreak of Shigella sonnei infection at Fort Bragg, North Carolina. We used a database consisting of demographic, temporal, and home-address information for all recognized cases of S. sonnei that occurred among health care beneficiaries from 23 May 1997 through 14 August 1997. We imported this database into the GIS, which contained a digitized basemap of the local community. Through simultaneous examination of temporal and spatial distribution of the 59 identified cases of S. sonnei, a focus of infection in a single housing area was identified. Targeted education among residents of the neighborhood in which there was intense transmission was associated with prompt extinction of the epidemic. A GIS offers an efficient and practical way to directly visualize the dynamics of transmission of infectious diseases in the setting of a community outbreak.
Collapse
Affiliation(s)
- K T McKee
- US Army Medical Research Institute of Infectious Diseases, Medical Division, Fort Detrick, MD 21702-5011, USA.
| | | | | | | | | |
Collapse
|
493
|
Bi K, Shi L, Maehara Y, Miyoshi S, Tomochika K, Shinoda S. Analysis of Vibrio mimicus clinical strains by arbitrarily primed polymerase chain reaction. Microbiol Immunol 2000; 44:149-53. [PMID: 10803502 DOI: 10.1111/j.1348-0421.2000.tb01258.x] [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: 11/29/2022]
Abstract
A total of 51 Vibrio mimicus clinical strains from different geographic locations were examined by arbitrarily primed polymerase chain reaction (AP-PCR). The primer VMH-3 divided them into 28 groups, although 18 groups consisted of a single strain at present. All groups had a common 1.0-kb amplification fragment. Most of the groups consisted of strains from same region, although two exceptional groups showed a few amplification fragments including strains from different regions. AP-PCR groups were not consistently associated with serogroups. AP-PCR is thought to be a valuable and easy method for the epidemiological study of V. mimicus.
Collapse
Affiliation(s)
- K Bi
- Faculty of Pharmaceutical Sciences, Okayama University, Japan.
| | | | | | | | | | | |
Collapse
|
494
|
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.
Collapse
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
| | | |
Collapse
|
495
|
Millemann Y, Gaubert S, Remy D, Colmin C. Evaluation of IS200-PCR and comparison with other molecular markers To trace Salmonella enterica subsp. enterica serotype typhimurium bovine isolates from farm to meat. J Clin Microbiol 2000; 38:2204-9. [PMID: 10834977 PMCID: PMC86765 DOI: 10.1128/jcm.38.6.2204-2209.2000] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/1999] [Accepted: 03/25/2000] [Indexed: 11/20/2022] Open
Abstract
A procedure that uses an original molecular marker (IS200-PCR) and that is based on the amplification of DNA with outward-facing primers complementary to each end of IS200 has been evaluated with a collection of 85 Salmonella enterica subsp. enterica serotype Typhimurium isolates. These strains were isolated from a group of 10 cows at different stages: during transportation between the farm and the slaughterhouse, on the slaughter line, from the environment, and from the final product (ground beef). The 85 isolates were characterized by their antibiotic resistance patterns and were compared by IS200-PCR and by use of four other genotypic markers. Those markers included restriction profiles for 16S and 23S rRNA (ribotypes) and amplification profiles obtained by different approaches: random amplified polymorphic DNA analysis, enterobacterial repetitive intergenic consensus PCR, and PCR ribotyping. The results of the IS200-PCR were in accordance with those of other molecular typing methods for this collection of isolates. Five different genotypes were found, which made it possible to refine the hypotheses on transmission obtained from phenotypic results. The genotyping results indicated the massive contamination of the whole group of animals and of the environment by one clonal strain originally recovered from one cow that excreted the strain. On the other hand, a few animals and their environment appeared to be simultaneously contaminated with genetically different strains.
Collapse
Affiliation(s)
- Y Millemann
- Epidémiologie et Analyse des Risques, Ecole Nationale Vétérinaire d'Alfort, F-94704 Maisons-Alfort Cedex, France.
| | | | | | | |
Collapse
|
496
|
Abstract
DNA fingerprinting methods have evolved as major tools in fungal epidemiology. However, no single method has emerged as the method of choice, and some methods perform better than others at different levels of resolution. In this review, requirements for an effective DNA fingerprinting method are proposed and procedures are described for testing the efficacy of a method. In light of the proposed requirements, the most common methods now being used to DNA fingerprint the infectious fungi are described and assessed. These methods include restriction fragment length polymorphisms (RFLP), RFLP with hybridization probes, randomly amplified polymorphic DNA and other PCR-based methods, electrophoretic karyotyping, and sequencing-based methods. Procedures for computing similarity coefficients, generating phylogenetic trees, and testing the stability of clusters are then described. To facilitate the analysis of DNA fingerprinting data, computer-assisted methods are described. Finally, the problems inherent in the collection of test and control isolates are considered, and DNA fingerprinting studies of strain maintenance during persistent or recurrent infections, microevolution in infecting strains, and the origin of nosocomial infections are assessed in light of the preceding discussion of the ins and outs of DNA fingerprinting. The intent of this review is to generate an awareness of the need to verify the efficacy of each DNA fingerprinting method for the level of genetic relatedness necessary to answer the epidemiological question posed, to use quantitative methods to analyze DNA fingerprint data, to use computer-assisted DNA fingerprint analysis systems to analyze data, and to file data in a form that can be used in the future for retrospective and comparative studies.
Collapse
|
497
|
Carroll NM, Jaeger EE, Choudhury S, Dunlop AA, Matheson MM, Adamson P, Okhravi N, Lightman S. Detection of and discrimination between gram-positive and gram-negative bacteria in intraocular samples by using nested PCR. J Clin Microbiol 2000; 38:1753-7. [PMID: 10790093 PMCID: PMC86579 DOI: 10.1128/jcm.38.5.1753-1757.2000] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/1999] [Accepted: 02/22/2000] [Indexed: 11/20/2022] Open
Abstract
A nested PCR protocol has been developed for the detection of and discrimination between 14 species of gram-positive and -negative bacteria in samples of ocular fluids. First-round PCR with pan-bacterial oligonucleotide primers, based on conserved sequences of the 16S ribosomal gene, was followed by a gram-negative-organism-specific PCR, which resulted in a single 985-bp amplification product, and a multiplex PCR which resulted in two PCR products: a 1,025 bp amplicon (all bacteria) and a 355 bp amplicon (gram-positive bacteria only). All products were detected by gel electrophoresis. The sensitivity of the assay was between 10 fg and 1 pg of bacterial DNA, depending on the species tested, equivalent to between 24 and 4 live bacteria spiked in water. The identification was complete in 3.5 h. The molecular techniques were subsequently applied to four samples of intraocular fluid, (three vitreous and one aqueous) from three patients with clinical signs of bacterial endophthalmitis (test samples) and two samples of vitreous from a patient with chronic intraocular inflammation (control samples). In all culture-positive samples (two of three vitreous and one of one aqueous), a complete concordance was observed between molecular methods and culture results. PCR correctly identified the gram stain classification of the organisms. The bacterial etiology was also identified in a culture-negative patient with clinical history and signs highly suggestive of bacterial endophthalmitis. Furthermore, control samples from a patient with chronic intraocular inflammation remained PCR negative. In summary, this protocol has demonstrated potential as a rapid diagnostic test in confirming the diagnosis of infection and also determining the Gram status of bacteria with high specificity and sensitivity.
Collapse
Affiliation(s)
- N M Carroll
- Department of Clinical Ophthalmology, The Institute of Ophthalmology, London EC1V 9EL, United Kingdom
| | | | | | | | | | | | | | | |
Collapse
|
498
|
Monnet DL. [Antibiotic use and bacterial resistance]. ANNALES FRANCAISES D'ANESTHESIE ET DE REANIMATION 2000; 19:409-17. [PMID: 10874442 DOI: 10.1016/s0750-7658(00)90211-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
The relationships between antibiotic use and bacterial resistance are not so easy to demonstrate. However, the evidence is abundant and mostly consistent. In this review, we will consider and discuss the different levels of evidence models: biological, consistent associations, dose-effect relationship, and concomitant variations. Decision-making is dependent of the local conditions. In the hospital, establishing an epidemiological diagnosis is a prerequisite to any decision, including restriction of antibiotic use.
Collapse
Affiliation(s)
- D L Monnet
- Department of Research and Development, Statens Serum Institut, Copenhague, Danemark
| |
Collapse
|
499
|
Abstract
DNA fingerprinting methods have evolved as major tools in fungal epidemiology. However, no single method has emerged as the method of choice, and some methods perform better than others at different levels of resolution. In this review, requirements for an effective DNA fingerprinting method are proposed and procedures are described for testing the efficacy of a method. In light of the proposed requirements, the most common methods now being used to DNA fingerprint the infectious fungi are described and assessed. These methods include restriction fragment length polymorphisms (RFLP), RFLP with hybridization probes, randomly amplified polymorphic DNA and other PCR-based methods, electrophoretic karyotyping, and sequencing-based methods. Procedures for computing similarity coefficients, generating phylogenetic trees, and testing the stability of clusters are then described. To facilitate the analysis of DNA fingerprinting data, computer-assisted methods are described. Finally, the problems inherent in the collection of test and control isolates are considered, and DNA fingerprinting studies of strain maintenance during persistent or recurrent infections, microevolution in infecting strains, and the origin of nosocomial infections are assessed in light of the preceding discussion of the ins and outs of DNA fingerprinting. The intent of this review is to generate an awareness of the need to verify the efficacy of each DNA fingerprinting method for the level of genetic relatedness necessary to answer the epidemiological question posed, to use quantitative methods to analyze DNA fingerprint data, to use computer-assisted DNA fingerprint analysis systems to analyze data, and to file data in a form that can be used in the future for retrospective and comparative studies.
Collapse
Affiliation(s)
- D R Soll
- Department of Biological Sciences, University of Iowa, Iowa City, IA 52242, USA.
| |
Collapse
|
500
|
de la Puente-Redondo VA, del Blanco NG, Gutiérrez-Martín CB, García-Peña FJ, Rodríguez Ferri EF. Comparison of different PCR approaches for typing of Francisella tularensis strains. J Clin Microbiol 2000; 38:1016-22. [PMID: 10698989 PMCID: PMC86326 DOI: 10.1128/jcm.38.3.1016-1022.2000] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we evaluated three PCR methods for epidemiological typing of Francisella tularensis: repetitive extragenic palindromic element PCR (REP-PCR), enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR), and random amplified polymorphic DNA (RAPD) assay with both M13 and T3-T7 primers. The analysis was performed with 40 strains of F. tularensis isolated from hares, humans, ticks, and a vole. On the basis of the combination of REP, ERIC, and RAPD fingerprints, F. tularensis strains were divided into 17 genetic groups (designated A to Q), and one Francisella novicida strain was classified in group R. The F. novicida strain is of special concern, since previous genetic methods have been unable to clearly distinguish between F. tularensis and F. novicida. The F. tularensis isolates recovered from hares were included in groups A to J, M, and P; those recovered from humans were included in groups A, D, G, J, L, O, and N; those isolated from ticks were included in groups B and Q; and that recovered from a vole was in group K. The diversities calculated for the 40 F. tularensis isolates, according to Simpson's index, were 0.14 for REP-PCR, 0.52 for ERIC-PCR, 0.39 for RAPD assay with the M13 primer (RAPD/M13-PCR), and 0.65 for RAPD/T3-T7-PCR, and the diversity increased up to 0.90 when ERIC-PCR, RAPD/M13-PCR, and RAPD/T3-T7-PCR were combined. Our results suggest that although limited genetic heterogeneity among F. tularensis strains was observed, this small variation is enough to validate the PCR methods used in this study and their combinations, because they can provide safe, useful, and rapid tools for the typing of F. tularensis.
Collapse
Affiliation(s)
- V A de la Puente-Redondo
- Section of Microbiology and Immunology, Department of Animal Health, Faculty of Veterinary Medicine, León, Spain
| | | | | | | | | |
Collapse
|