Journal of Clinical Microbiology
1098-660X
0095-1137
Mỹ
Cơ quản chủ quản: American Society for Microbiology , AMER SOC MICROBIOLOGY
Lĩnh vực:
Microbiology (medical)
Các bài báo tiêu biểu
Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing
Tập 33 Số 9 - Trang 2233-2239 - 1995
Chỉ số định lượng khả năng phân biệt của các hệ thống phân loại: ứng dụng chỉ số đa dạng Simpson Một chỉ số định lượng về khả năng phân biệt của các phương pháp phân loại được miêu tả, dựa trên khả năng hai chủng không liên quan nào đó được xác định là cùng loại. Chỉ số này có thể được sử dụng để so sánh các phương pháp phân loại và chọn ra hệ thống có khả năng phân biệt tốt nhất.
Tập 26 Số 11 - Trang 2465-2466 - 1988
#phân loại #khả năng phân biệt #chỉ số Simpson #sự đa dạng #chỉ số định lượng #chủng không liên quan #hệ thống phân loại
Multilocus Sequence Typing for Characterization of Methicillin-Resistant and Methicillin-Susceptible Clones of<i>Staphylococcus aureus</i> ABSTRACT A multilocus sequence typing (MLST) scheme has been developed forStaphylococcus aureus . The sequences of internal fragments of seven housekeeping genes were obtained for 155S. aureus isolates from patients with community-acquired and hospital-acquired invasive disease in the Oxford, United Kingdom, area. Fifty-three different allelic profiles were identified, and 17 of these were represented by at least two isolates. The MLST scheme was highly discriminatory and was validated by showing that pairs of isolates with the same allelic profile produced very similarSma I restriction fragment patterns by pulsed-field gel electrophoresis. All 22 isolates with the most prevalent allelic profile were methicillin-resistantS. aureus (MRSA) isolates and had allelic profiles identical to that of a reference strain of the epidemic MRSA clone 16 (EMRSA-16). Four MRSA isolates that were identical in allelic profile to the other major epidemic MRSA clone prevalent in British hospitals (clone EMRSA-15) were also identified. The majority of isolates (81%) were methicillin-susceptibleS. aureus (MSSA) isolates, and seven MSSA clones included five or more isolates. Three of the MSSA clones included at least five isolates from patients with community-acquired invasive disease and may represent virulent clones with an increased ability to cause disease in otherwise healthy individuals. The most prevalent MSSA clone (17 isolates) was very closely related to EMRSA-16, and the success of the latter clone at causing disease in hospitals may be due to its emergence from a virulent MSSA clone that was already a major cause of invasive disease in both the community and hospital settings. MLST provides an unambiguous method for assigning MRSA and MSSA isolates to known clones or assigning them as novel clones via the Internet.
Tập 38 Số 3 - Trang 1008-1015 - 2000
Defining the Normal Bacterial Flora of the Oral Cavity ABSTRACT
More than 700 bacterial species or phylotypes, of which over 50% have not been cultivated, have been detected in the oral cavity. Our purposes were (i) to utilize culture-independent molecular techniques to extend our knowledge on the breadth of bacterial diversity in the healthy human oral cavity, including not-yet-cultivated bacteria species, and (ii) to determine the site and subject specificity of bacterial colonization. Nine sites from five clinically healthy subjects were analyzed. Sites included tongue dorsum, lateral sides of tongue, buccal epithelium, hard palate, soft palate, supragingival plaque of tooth surfaces, subgingival plaque, maxillary anterior vestibule, and tonsils. 16S rRNA genes from sample DNA were amplified, cloned, and transformed into
Escherichia coli
. Sequences of 16S rRNA genes were used to determine species identity or closest relatives. In 2,589 clones, 141 predominant species were detected, of which over 60% have not been cultivated. Thirteen new phylotypes were identified. Species common to all sites belonged to the genera
Gemella
,
Granulicatella
,
Streptococcus
, and
Veillonella
. While some species were subject specific and detected in most sites, other species were site specific. Most sites possessed 20 to 30 different predominant species, and the number of predominant species from all nine sites per individual ranged from 34 to 72. Species typically associated with periodontitis and caries were not detected. There is a distinctive predominant bacterial flora of the healthy oral cavity that is highly diverse and site and subject specific. It is important to fully define the human microflora of the healthy oral cavity before we can understand the role of bacteria in oral disease.
Tập 43 Số 11 - Trang 5721-5732 - 2005
Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology Widespread use of DNA restriction fragment length polymorphism (RFLP) to differentiate strains of Mycobacterium tuberculosis to monitor the transmission of tuberculosis has been hampered by the need to culture this slow-growing organism and by the level of technical sophistication needed for RFLP typing. We have developed a simple method which allows simultaneous detection and typing of M. tuberculosis in clinical specimens and reduces the time between suspicion of the disease and typing from 1 or several months to 1 or 3 days. The method is based on polymorphism of the chromosomal DR locus, which contains a variable number of short direct repeats interspersed with nonrepetitive spacers. The method is referred to as spacer oligotyping or "spoligotyping" because it is based on strain-dependent hybridization patterns of in vitro-amplified DNA with multiple spacer oligonucleotides. Most of the clinical isolates tested showed unique hybridization patterns, whereas outbreak strains shared the same spoligotype. The types obtained from direct examination of clinical samples were identical to those obtained by using DNA from cultured M. tuberculosis. This novel preliminary study shows that the novel method may be a useful tool for rapid disclosure of linked outbreak cases in a community, in hospitals, or in other institutions and for monitoring of transmission of multidrug-resistant M. tuberculosis. Unexpectedly, spoligotyping was found to differentiate M. bovis from M. tuberculosis, a distinction which is often difficult to make by traditional methods.
Tập 35 Số 4 - Trang 907-914 - 1997
Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology DNA fingerprinting of Mycobacterium tuberculosis has been shown to be a powerful epidemiologic tool. We propose a standardized technique which exploits variability in both the number and genomic position of IS6110 to generate strain-specific patterns. General use of this technique will permit comparison of results between different laboratories. Such comparisons will facilitate investigations into the international transmission of tuberculosis and may identify specific strains with unique properties such as high infectivity, virulence, or drug resistance.
Tập 31 Số 2 - Trang 406-409 - 1993
Adherence of coagulase-negative staphylococci to plastic tissue culture plates: a quantitative model for the adherence of staphylococci to medical devices The adherence of coagulase-negative staphylococci to smooth surfaces was assayed by measuring the optical densities of stained bacterial films adherent to the floors of plastic tissue culture plates. The optical densities correlated with the weight of the adherent bacterial film (r = 0.906; P less than 0.01). The measurements also agreed with visual assessments of bacterial adherence to culture tubes, microtiter plates, and tissue culture plates. Selected clinical strains were passed through a mouse model for foreign body infections and a rat model for catheter-induced endocarditis. The adherence measurements of animal passed strains remained the same as those of the laboratory-maintained parent strain. Spectrophotometric classification of coagulase-negative staphylococci into nonadherent and adherent categories according to these measurements had a sensitivity, specificity, and accuracy of 90.6, 80.8, and 88.4%, respectively. We examined a previously described collection of 127 strains of coagulase-negative staphylococci isolated from an outbreak of intravascular catheter-associated sepsis; strains associated with sepsis were more adherent than blood culture contaminants and cutaneous strains (P less than 0.001). We also examined a collection of 84 strains isolated from pediatric patients with cerebrospinal fluid (CSF) shunts; once again, pathogenic strains were more adherent than were CSF contaminants (P less than 0.01). Finally, we measured the adherence of seven endocarditis strains. As opposed to strains associated with intravascular catheters and CSF shunts, endocarditis strains were less adherent than were saprophytic strains of coagulase-negative staphylococci. The optical densities of bacterial films adherent to plastic tissue culture plates serve as a quantitative model for the study of the adherence of coagulase-negative staphylococci to medical devices, a process which may be important in the pathogenesis of foreign body infections.
Tập 22 Số 6 - Trang 996-1006 - 1985
16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls
Tập 45 Số 9 - Trang 2761-2764 - 2007
Phát hiện và phân loại nhanh virus dengue từ mẫu bệnh phẩm lâm sàng bằng phản ứng chuỗi polymerase sao chép ngược Chúng tôi báo cáo về việc phát triển và ứng dụng của một phương pháp kiểm tra nhanh để phát hiện và phân loại virus dengue. Các mồi oligonucleotide đồng thuận đã được thiết kế để gắn kết với bất kỳ trong bốn loại virus dengue nào và khuếch đại một sản phẩm 511-bp trong một phản ứng chuỗi polymerase sao chép ngược (PCR). Đầu tiên, chúng tôi đã tạo ra một bản sao cDNA của một phần của bộ gen virus trong một phản ứng sao chép ngược với sự hiện diện của mồi D2 và sau đó thực hiện một PCR tiêu chuẩn (35 chu kỳ biến tính nhiệt, gắn kết và kéo dài mồi) với sự bổ sung của mồi D1. Sản phẩm DNA sợi kép kết quả từ RT-PCR đã được phân loại bằng hai phương pháp: lai chấm của sản phẩm 511-bp đã được khuếch đại với các đầu dò đặc thù loại virus dengue hoặc một đợt PCR khuếch đại thứ hai (PCR lồng) với các mồi đặc thù theo loại, tạo ra sản phẩm DNA có kích thước duy nhất chẩn đoán được cho từng kiểu huyết thanh của virus dengue. Dữ liệu tích lũy đã cho thấy rằng virus dengue có thể được phát hiện và phân loại chính xác từ các mẫu huyết thanh người đang trong giai đoạn viremia.
Tập 30 Số 3 - Trang 545-551 - 1992
#phát hiện nhanh #dengue #PCR #sao chép ngược #phân loại virus #huyết thanh người #viremia
Polymerase chain reaction amplification and typing of rotavirus nucleic acid from stool specimens The rotavirus gene segment coding for the major outer capsid glycoprotein vp7 was amplified directly from stool specimens by the polymerase chain reaction (PCR). Double-stranded RNA extracted from stool samples was used as the template for reverse transcription, which was followed immediately and in the same reaction mix with amplification, using the Taq polymerase. Various conditions were examined to optimize the yield of the amplified gene. The concentrations of MgCl2, dimethyl sulfoxide, and template RNA were critical. The choice of primer pairs allowed amplification of the entire segment or specific portions. By using type-specific primers derived from distinct regions on the gene, we devised a PCR typing method in which each human serotype virus produced a characteristic segment size, readily identifiable in agarose gels. The PCR typing method was applied to 10 rotavirus reference strains, including all 6 known human serotypes (serotypes 1, 2, 3, 4, 8, and 9), and to 34 stool specimens previously serotyped by an enzyme immunoassay with monoclonal antibodies. An absolute correlation was found between the molecular and serologic methods. In addition, 14 stool specimens nonserotypable by an enzyme immunoassay with monoclonal antibodies could be typed by the PCR method. Besides the application for rotavirus detection and typing directly from stools, the PCR method provides a rapid and efficient means of obtaining large quantities of cDNA suitable for sequencing, cloning, and other genetic studies, precluding the need for cell culture and virus purification.
Tập 28 Số 2 - Trang 276-282 - 1990