This article reports the development of a method for genotyping Chlamydia trachomatis, using PCR and sequencing of omp1, supplemented with three new variable number tandem repeat (VNTR) loci of C. trachomatis. Typeability, reproducibility and discriminatory power were assessed using four groups of samples: two groups (I and II) of C. trachomatis-positive patients and their positive partner(s), one group (III) of patients with recurrent or persistent C. trachomatis infections, and one group (IV) comprising samples containing a newly discovered mutant strain with a 377-bp deletion in the cryptic plasmid, the new variant C. trachomatis (nvCT). The VNTR loci (designated CT1335, CT1299, and CT1291) were all single nucleotide repeats chosen for maximal mutability and variation. In the study material, nine variants of CT1335, eight variants of CT1299 and five variants of CT1291 were found. The discriminatory power (D) of omp1 in the present material was D(omp1) = 0.69. Ds for VNTRs CT1335, CT1299 and CT1291 were 0.53, 0.74 and 0.74, respectively. The resolution power of the omp1-VNTR assay was 0.94. Stability over time of the VNTRs was investigated and found to be adequate for epidemiological studies. Using this genotyping assay, it was confirmed that the nvCT strain was indeed a clone. These results indicate that, with this novel method, strains of C. trachomatis can be individually identified, and epidemiological associations established.

Patients with short QT syndrome (SQTS) may present with syncope, ventricular fibrillation or sudden cardiac death. Six SQTS susceptibility genes, encoding cation channels, explain <25% of SQTS cases. Here we identify a missense mutation in the anion exchanger (AE3)-encoding SLC4A3 gene in two unrelated families with SQTS. The mutation causes reduced surface expression of AE3 and reduced membrane bicarbonate transport. Slc4a3 knockdown in zebrafish causes increased cardiac pHi, short QTc, and reduced systolic duration, which is rescued by wildtype but not mutated SLC4A3. Mechanistic analyses suggest that an increase in pHi and decrease in [Cl−]i shortened the action potential duration. However, other mechanisms may also play a role. Altered anion transport represents a mechanism for development of arrhythmia and may provide new therapeutic possibilities.

A historical review is provided of the various methods used for half a century to differentiate and type Chlamydia trachomatis strains. Typing of C. trachomatis is an important tool for revealing transmission patterns in sexual networks, and enabling association with clinical manifestations and pathogenicity. Serotyping using the major outer membrane protein (MOMP) has been the mainstay of epidemiological work for several decades. However, the development of nucleic acid amplification techniques (NAAT) and easy access to sequencing have shifted the focus from MOMP serotypes to omp1 genotypes. However, insufficient epidemiological resolution is achieved by characterization of both MOMP and omp1. This calls for new high-resolution genotyping methods applying for example a multilocus variable number tandem repeat assay (MLVA) or multilocus sequence typing (MLST). The futuristic nanotechnology already seems at hand to further simplify and automate the high-resolution genotyping method based on NAAT and sequencing of various targets in the C. trachomatis genome. Thereby, a high throughput can be achieved and more epidemiological information can be obtained. However, it is important to realize that culture of C. trachomatis may still be needed to detect and characterize new variants of C. trachomatis.

We here report on the development of a novel multiplex PCR with product detection in a Luminex 100 suspension array system. The assay covers the nine most important bacterial and viral pathogens found in Danish meningitis patients. The microorganisms include Neisseria meningitidis, Streptococcus pneumoniae, Escherichia coli, Staphylococcus aureus, Listeria monocytogenes, Streptococcus agalactiae, herpes simplex virus types 1 and 2, and varicella-zoster virus. The study was based on 1,187 samples, of which 55 were found to be positive by PCR. The assay was found to have an excellent sensitivity and an excellent specificity compared to the results of a "gold standard," defined by routine laboratory tests, for the two most important pathogens, S. pneumoniae (95 and 99.1%, respectively) and N. meningitidis (100 and 99.7%, respectively). The method provides a valuable supplement to the traditional microscopy and culture of cerebrospinal fluid (CSF) samples in a routine diagnostic setting, and results can be available within 1 workday. The method is suitable for use for the initial screening and identification of nine important microorganisms in CSF samples from patients with suspected meningitis. Compared to microscopy and culture of CSF, this rapid and sensitive method will support physicians with the selection of the appropriate antimicrobial agents and the initiation of timely treatment in the absence of live microorganisms in the CSF.Bacterial meningitis is an infectious disease with a high rate of mortality and many cases of severe sequelae (4,5,23). Since the early administration of antibiotics correlates with reduced rates of morbidity and mortality, it is of crucial importance to initiate relevant treatment as soon as possible (10,11,13,19,22). The administration of antibiotics to patients with suspected meningitis before hospital admission and the collection of a cerebrospinal fluid (CSF) sample have become common practice (19). This practice may correspondingly impair microbiological diagnosis by culture of the bacteria responsible for the infection. The focus in recent years has therefore been on the development of alternative methods that can be used to obtain an etiological diagnosis, e.g., PCR. The use of broadrange 16S rRNA gene PCR with subsequent sequencing has been reported (1,20,24). This approach can be difficult to handle in a routine laboratory due to the presence of interfering bacterial or viral DNA, which may easily be added during sample handling, or, importantly, due to the presence of traces of bacterial DNA in the enzymes and mixtures used for PCR. The method also lacks speed because of the requisite sequencing step. Alternatively, species-specific real-time PCR (3, 21) has the advantage that rapid and high throughput is possible, but due to the limited number of detection channels of most real-time instruments, only a very limited number of different targets can be analyzed at a time.We chose to develop a system that uses a species-specific multiplex PCR focused on the bacterial and vira...

The aim was to evaluate "16S rDNA PCR and sequencing" (PCR) for identification of bacterial DNA in heart valves in routine diagnosis of infective endocarditis (IE). Heart valves from 74 patients with suspected infective endocarditis, and 16 controls were analysed by histology, culture and PCR. Results from blood culture served as the gold standard. Patients were classified according to the Duke criteria. The final classification resulted in 57 definitive cases of IE, 7 possible, and 10 cases without IE. Sensitivity of valve culture was 26% and specificity 62%. Sensitivity of PCR was 72% and specificity 100%. In patients who had received antibiotic treatment for less than 5 days before surgery, sensitivity of culture and PCR were comparable. In patients who had received antibiotic treatment for more than 5 days, sensitivity of valve culture was markedly reduced compared to sensitivity of PCR. In three of seven blood-culture-negative cases PCR was positive, including two cases with non-cultivable bacteria. No PCR samples were contaminated, whereas 35% of valve-culture samples were contaminated. PCR is more sensitive and specific than valve culture, and a valuable supplement to the existing analyses of valve tissue. PCR is necessary to identify the full spectrum of pathogens causing IE. In contrast to sensitivity of culture, sensitivity of PCR was independent of length of antibiotic treatment before surgery.