Routine Clinical Diagnostic Laboratories Research Articles

Implementation of an ISO15189 accredited next-generation sequencing service with the fully automated Ion Torrent Genexus: the experience of a clinical diagnostic laboratory

AimsNext-generation sequencing (NGS) is integral to the delivery of personalised medicine for targeted cancer therapy. Average turnaround times (TAT) from reference laboratories with advanced expertise in sequencing are typically 2–3...

Simple, fast and inexpensive quantification of glycolate in the urine of patients with primary hyperoxaluria type 1

In primary hyperoxaluria type 1 excessive endogenous production of oxalate and glycolate leads to increased urinary excretion of these metabolites. Although genetic testing is the most definitive and preferred diagnostic method, quantification of these metabolites is important for the diagnosis and evaluation of potential therapeutic interventions. Current metabolite quantification methods use laborious, technically highly complex and expensive liquid, gas or ion chromatography tandem mass spectrometry, which are available only in selected laboratories worldwide. Incubation of ortho-aminobenzaldehyde (oABA) with glyoxylate generated from glycolate using recombinant mouse glycolate oxidase (GO) and glycine leads to the formation of a stable dihydroquinazoline double aromatic ring chromophore with specific peak absorption at 440 nm. The urinary limit of detection and estimated limit of quantification derived from eight standard curves were 14.3 and 28.7 µmol glycolate per mmol creatinine, respectively. High concentrations of oxalate, lactate and L-glycerate do not interfere in this assay format. The correlation coefficient between the absorption and an ion chromatography tandem mass spectrometry method is 93% with a p value < 0.00001. The Bland–Altmann plot indicates acceptable agreement between the two methods. The glycolate quantification method using conversion of glycolate via recombinant mouse GO and fusion of oABA and glycine with glyoxylate is fast, simple, robust and inexpensive. Furthermore this method might be readily implemented into routine clinical diagnostic laboratories for glycolate measurements in primary hyperoxaluria type 1.

A Rapid Method for Determination of Serum Methotrexate Using Ultra-High-Performance Liquid Chromatography-Tandem Mass Spectrometry and Its Application in Therapeutic Drug Monitoring.

Objectives Methotrexate (MTX) has anticancer therapeutic potential with multiple doses-related adverse effects and toxicities. Immunoassays for therapeutic monitoring of serum MTX have their own limitations. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is considered as the reference method; however, commercially availability of them is limited. We aimed to adapt/develop an in-house LC-MS/MS method for therapeutic monitoring of serum MTX. Materials and Methods Serum protein precipitation was performed using acetonitrile-water containing 250 μM solution of aminoacetophenone as internal standard (IS). Chromatographic separation was achieved on a C18 column with mobile phase of 0.1% solution of formic acid (solvent A) and acetonitrile (solvent B) at a flow rate of 0.4 mL/min. MS was performed under positive ion mode with mass transition for MTX and IS as m/z 455.1→308.1 and 136.2→94.1, respectively. The method was validated by following Bioanalytical Method Validation Guidance for Industry, 2018 and applied on leukemia patients' samples on MTX therapy. Results The correlation coefficient of eight serially diluted calibration standards of 0.09 to 12.5 μM was >0.99 and had linearity with > 95% precision and accuracy at analytical quality control levels. The lower limit of MTX quantification achieved was 0.09 μM with good intensity and sharp peak as compared with blank sample. The total run time of the assay was 5 minutes. The serum MTX levels obtained by this method in leukemia patients exhibited clinical correlation and an excellent agreement with commercial immunoassay used in parallel. Conclusion We were able to develop a rapid, sensitive, and cost-effective LC-MS/MS method suitable for therapeutic drug monitoring of MTX in routine clinical diagnostic laboratories.

CalmBelt: Rapid SARS-CoV-2 Genome Characterization for Outbreak Tracking.

Background: The ongoing COVID-19 pandemic is a global health crisis caused by the spread of SARS-CoV-2. Establishing links between known cases is crucial for the containment of COVID-19. In the healthcare setting, the ability to rapidly identify potential healthcare-associated COVID-19 clusters is critical for healthcare worker and patient safety. Increasing sequencing technology accessibility has allowed routine clinical diagnostic laboratories to sequence SARS-CoV-2 in clinical samples. However, these laboratories often lack specialized informatics skills required for sequence analysis. Therefore, an on-site, intuitive sequence analysis tool that enables clinical laboratory users to analyze multiple genomes and derive clinically relevant information within an actionable timeframe is needed.Results: We propose CalmBelt, an integrated framework for on-site whole genome characterization and outbreak tracking. Nanopore sequencing technology enables on-site sequencing and construction of draft genomes for multiple SARS-CoV-2 samples within 12 h. CalmBelt's interactive interface allows users to analyse multiple SARS-CoV-2 genomes by utilizing whole genome information, collection date, and additional information such as predefined potential clusters from epidemiological investigations. CalmBelt also integrates established SARS-CoV-2 nomenclature assignments, GISAID clades and PANGO lineages, allowing users to visualize relatedness between samples together with the nomenclatures. We demonstrated multiple use cases including investigation of potential hospital transmission, mining transmission patterns in a large outbreak, and monitoring possible diagnostic-escape.Conclusions: This paper presents an on-site rapid framework for SARS-CoV-2 whole genome characterization. CalmBelt interactive web application allows non-technical users, such as routine clinical laboratory users in hospitals to determine SARS-CoV-2 variants of concern, as well as investigate the presence of potential transmission clusters. The framework is designed to be compatible with routine usage in clinical laboratories as it only requires readily available sample data, and generates information that impacts immediate infection control mitigations.

Assessment of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF- MS) for Accurate Bacterial Identification in Clinical Labs

Abstract Introduction/Objective On behalf of the diagnostic Medical Laboratory rapid, and accurate identification of bacteria with their one-to-one anti-microbial susceptibility outlines is of ultimate importance for the management of infected patients. Contemporary microbial identification methods employed in routine clinical diagnostic laboratories relies on the use of conventional phenotypic methods. Phenotypic methods are time consuming with minimum turn-around times of at least 24 hrs and in many occurrences of 48hrs. With the intention of accelerate laboratory processes the MALDI-TOF MS was familiarized. MALDI-TOF MS is established on proteomic profiling and permits for rapid identification of bacteria. This technology has not been widely used in Egypt, but has been regularly used in Europe for the past few years. Methods Two hundred forty three positive non duplicate blood cultures were accrued over a period of six months. Experimental aliquots were taken from excess sample material that was collected as part of routine clinical care. 105 were positive for Gram negative bacilli, 123 were positive for Gram positive cocci, 3 positive for Gram positive bacilli, and 7 were positive for yeast. MALDI-TOF identification was compared to conventional identification. Conventional identification consisted of a combination of MALDI-TOF identification of a subcultures colony by direct smear, biochemical reactions, Vitek 2, and molecular identification. Results Ninety seven of the one hundred and five blood cultures positive for Gram negative bacilli were monomicrobial. The majority of these were identified as Escherichia coli by conventional methods, followed by Klebsiella pneumoniae and Pseudomonas aeruginosa. Eighty-four of these monomicrobial cultures were identified by MALDI-TOF to the species level. Eighty-one of the eighty-four were concordant with the conventional identification (96.4%). Conclusion The MALDI-TOF proved to be useful for the rapid and reliable identification of g-ve bacteria from the clinical specimens. The difference in turnaround time for bacterial identification was significant between MALDI-TOF MS and VITEK 2 with minimal preparation for the blood cultures.

A high performance liquid chromatography fluorescence method for the analysis of both pyridoxal-5-phosphate and thiamine pyrophosphate in whole blood

Background and aimsThe active coenzymes of the water soluble vitamins B1 and B6 (thiamine pyrophosphate (TPP) and pyridoxal-5-phosphate (P5P) respectively) play an important role in numerous bodily functions. The simultaneous analysis of both these analytes is limited to either mass spectrometry based methods or commercial kit suppliers. In this study we developed a novel method for analysis of both TPP and P5P by fluorescence detection. MethodsBriefly, whole blood samples are precipitated by trichloroacetic acid, and P5P and TPP are both derivatised before separation on a C18-PFP column. The new assay’s performance was compared against a recent cycle from an external quality assurance program (RCPAQAP) and the current only existing commercial kit (n = 76). ResultsLinearity for both analytes was above 0.99 (r2) up to a concentration range of: 4000 nmol/L (P5P) and 2000 nmol/L (TPP). Precision of the method (intra-day and inter-day) compared against commercial quality control material was below 6% (coefficient of variation). Recovery of both compounds exceeded 90%. Accuracy of the protocol displayed satisfactory results in proficiency testing and had an acceptable level of agreement with the existing current kit method. ConclusionsOverall, this method provides an economical alternative in routine clinical diagnostic laboratories wishing to perform P5P and TPP analysis.

Condensation of delta-1-piperideine-6-carboxylate with ortho-aminobenzaldehyde allows its simple, fast, and inexpensive quantification in the urine of patients with antiquitin deficiency.

Antiquitin (ATQ) deficiency leads to tissue, plasma, and urinary accumulation of alpha‐aminoadipic semialdehyde (AASA) and its Schiff base delta‐1‐piperideine‐6‐carboxylate (P6C). Although genetic testing of ALDH7A1 is the most definitive diagnostic method, quantifications of pathognomonic metabolites are important for the diagnosis and evaluation of therapeutic and dietary interventions. Current metabolite quantification methods use laborious, technically highly complex, and expensive liquid chromatography‐tandem mass spectro‐metry, which is available only in selected laboratories worldwide. Incubation of ortho‐aminobenzaldehyde (oABA) with P6C leads to the formation of a triple aromatic ring structure with characteristic absorption and fluorescence properties. The mean concentration of P6C in nine urine samples from seven ATQ‐deficient patients under standard treatment protocols was statistically highly significantly different (P < .001) compared to the mean of 74 healthy controls aged between 2 months and 57 years. Using this limited data set the specificity and sensitivity is 100% for all tested age groups using a P6C cut‐off of 2.11 μmol/mmol creatinine, which represents the 99% prediction interval of the P6C concentrations in 17 control urine samples from children below 6 years of age. Plasma P6C concentrations were only elevated in one ATQ subject, possibly because P6C is trapped by pyridoxal‐5‐phosphate (PLP) blocking fusing with oABA. Nevertheless, both urine and plasma samples were amenable to the quantification of exogenous P6C with high response rates. The P6C quantification method using fusion of oABA with P6C is fast, simple, and inexpensive and might be readily implemented into routine clinical diagnostic laboratories for the early diagnosis of neonatal pyridoxine‐dependent epilepsy.

Establishing Campylobacter culture methods in a clinical diagnostic laboratory and the first report of Campylobacter species isolation in northern Sri Lanka

Introduction: The Enteric Reference Laboratory of the Medical Research Institute (ERL/MRI), Colombo is the only public sector laboratory in Sri Lanka that performs Campylobacter cultures. Due to logistic limitations involving specimen transport from distant sites, efforts were taken to establish Campylobacter culture facilities in our local clinical microbiology laboratory. Methods: A blood-free charcoal-based selective agar medium (Karmali medium) was chosen based on performance characteristics and quality control (QC)/verification performed at the ERL/MRI. A suitable incubating method was assessed and chosen, and QC was performed in our laboratory. A technical staff member of our local laboratory received capacity building training at the ERL/MRI. Results: The quality control/verification process of the Karmali medium was satisfactory. The variable atmospheric incubator was chosen as the incubating method as it was shown to be more economical in the long-term given the anticipated work load and the QC was satisfactory. Following a satisfactory verification process, Campylobacter culture method was introduced in our laboratory. Five C. jejuni and one hippurate-negative C. jejuni/C. coli was detected in faecal specimens of six paediatric patients between May-December 2018. The isolation rate was 2.25% (6/267). Ciprofloxacin resistance was detected in four out of five C. jejuni isolates. Conclusion: Establishing Campylobacter culture methods in a routine clinical diagnostic laboratory will be beneficial in regions with high prevalence of diarrhoeal disease and with logistic limitations for specimen transport to the central reference laboratory. This is the first report of isolation and antimicrobial susceptibility of Campylobacter species from patients in northern Sri Lanka.

EGFR mutations in non-small cell lung cancer: an audit from West China Hospital

ABSTRACTObjectives: To discover the incidence and characteristics of EGFR mutations in non-small cell lung cancer (NSCLC) in a single, large cohort as a part of routine diagnostic investigations.Methods: We reviewed EGFR mutations investigated by Amplification Refractory Mutation System (ARMS) PCR (covering 29 known mutations) using DNA samples from FFPE tissue or cell clot specimens in a total of 3894 cases of NSCLC analysed between 2012-2014.Results: EGFR mutations are preferentially associated with adenocarcinomaand adenosquamous histology, particularly those well to moderately differentiated, and were significantly more common in female than male patients irrespective of histological subtypes. Exon 19 deletion (45.7%) and exon 21 L858R (45.6%) accounted for the vast majority of the EGFR mutations detected, with the remaining mutations being infrequent (<2%). Compound mutations were seen in 51 (3%) of the mutant cases, the combination of these compound mutations could be classified into three subgroups according to the potential impact of individual mutations on EGFR TKI therapy. Accordingly, 7 cases had both sensitive mutations, 4 cases harboured one sensitive and one less responsive /uncertain mutation, 19 cases contained one sensitive and one resistant change, and a further 21 cases had two less responsive /uncertain mutations.Conclusion: Our data represents the largest EGFR mutation survey based on routine clinical diagnostic laboratory data from a single institution, it confirms the incidence and characteristics of EGFR mutations in NSCLC seen in Asian patients, and also unravels the combinatorial nature of rare compound EGFR mutations.

Urinary Glycosaminoglycan Electrophoresis With Optimized Keratan Sulfate Separation Using Peltier System for the Screening of Mucopolysaccharidoses

The purpose of this communication is to indicate a simple and rapid method with a small volume of urine sample to detect urine glycosaminoglycan (GAG) and serve as a screening procedure for mucopolysaccharidoses (MPSs). Total GAG measurement for patients with MPS disorders is considered to be the first step in diagnosis of those heterogeneous group of lysosomal storage disorders presenting clinical phenotype. In this study, modified 9-dimethylmethylene blue method is used for total GAG measurement. Following GAG quantitation, the procedure described here allows GAG isolation from a very a small volume of urine sample and subjected to high-resolution GAG electrophoresis, which can be easily performed in routine clinical diagnostic laboratories. Glycosaminoglycan precipitation is a modified method based on total GAG concentration in the urine. For optimized isolation of total GAG for electrophoresis, instead of considering the urine creatinine concentration, 300 μg/mL GAG containing urine is considered to be the target concentration for the best precipitation with 1000 μL cetylpyridinium chloride (CPC)/citrate buffer. Glycosaminoglycan concentration-based precipitation of urine with CP Ca llows the laboratory to be able to work with as mall volume of urine sample by keeping the precipitating ratio with CPC constant for samples that contain GAG less than 300 μg/mL. Based on the effect of cold buffer using low voltage, GAGs high-resolution electrophoresis banding patterns described here enable a clear separation of keratan sulfate from chondroitin sulfate as well as dermatan sulfate (DS1 and DS2) and heparan sulfate. By this procedure, GAG patterns are more clear, easily identified, and provide a guide for the enzyme analysis deficient in the MPS disorders.

ADAMTS-13 in the Diagnosis and Management of Thrombotic Microangiopathies.

Thrombotic microangiopathies (TMAs) comprise a group of distinct disorders characterized by microangiopathic hemolytic anemia, thrombocytopenia, and microvascular thrombosis. For many years distinction between these TMAs, especially between thrombotic thrombocytopenic purpura (TTP) and hemolytic uremic syndrome (HUS), remained purely clinical and hard to make. Recent discoveries shed light on different pathogenesis of TTP and HUS. Ultra-large von Willebrand factor (UL-VWF) platelet thrombi, resulting from the deficiency of cleavage protease which is now known as ADAMTS-13 (a disintegrin and metalloproteinase with a thrombospondin type 1 motif, member 13), were found to cause TTP pathology, while Shiga toxins or abnormalities in regulation of the complement system cause microangiopathy and thrombosis in HUS. TMAs may appear in various conditions such as pregnancy, inflammation, malignancy, or exposure to drugs. These conditions might cause acquired TTP, HUS, or other TMAs, or might be a trigger in individuals with genetic predisposition to ADAMTS-13 or complement factor H deficiency. Differentiation between these TMAs is highly important for urgent initiation of appropriate therapy. Measurement of ADAMTS-13 activity and anti-ADAMTS-13 antibody levels may advance this differentiation resulting in accurate diagnosis. Additionally, assessment of ADAMTS-13 levels can be a tool for monitoring treatment efficacy and relapse risk, allowing consideration of therapy addition or change. In the past few years, great improvements in ADAMTS-13 assays have been made, and tests with increased sensitivity, specificity, reproducibility, and shorter turnaround time are now available. These new assays enable ADAMTS-13 measurement in routine clinical diagnostic laboratories, which may ultimately result in improvement of TMA management.

Diagnostic validity of the chemiluminescent method compared to polymerase chain reaction for hepatitis B virus detection in the routine clinical diagnostic laboratory.

Background:Hepatitis B virus (HBV) is the most common significant chronic viral infection world-wide. Hepatitis B surface antigen (HBsAg) has been the principal target for laboratory testing to identify active infection by HBV. We aimed to find out diagnostic validity of the Liaison chemiluminescent method compared to the polymerase chain reaction (PCR) method for HBV detection in the routine clinical diagnostic laboratory.Materials and Methods:From 350 patients suspicious of having infection with HBV, serum samples were separated and used for testing HBsAg by two methods of Liaison chemiluminescent immunoassay, with HBsAg confirmatory test and PCR method.Results:According to the PCR results as assumed as gold standard method with 100% sensitivity and specificity, detection rate sensitivity of chemiluminescent with confirmatory test was 96% and its specificity was 100%, and for chemiluminescent without confirmatory test sensitivity and specificity were 100% and 70%, respectively. Also for chemiluminescent with confirmatory test, positive predictive value (PPV) was 100% and its negative predictive value (NPV) was 97%, compared to chemiluminescent without confirmatory test with PPV and NPV equal to 71% and 100%, respectively.Conclusions:It is possible to conclude that in the majority of the HBV cases, the diagnostic value of chemiluminescent method compared to the PCR method is acceptable, except in low indexes positive cases that need further investigation with the PCR method.

Diagnostic validity of Liaison chemiluminescent method compare to PCR for Hepatitis B virus detection in the routine clinical diagnostic laboratory

obtained 100 ng/ml. Subsequently melatonin was conjugated to biotin, after that a competitive ELISA was designed and detection limit was 10 ng/ml. In order to increase sensitivity, different combinations of blockers and working buffers at different pH were investigated. According to final data, a competitive ELISA was designed by melatonin-HRP as tracer, direct coating and skim milk as the protein composition of blocker and working buffer at pH=7. The calibration curvewas constructed and sensitivity rangewas from500 pg/ml to 1 μg/ ml. Conclusion: The results of different combination of blockers and working buffers at different pH, indicate the influence of protein composition and pH of buffer on antibody and antigen interaction.

Microarray‐based genomic profiling as a diagnostic tool in acute lymphoblastic leukemia

In acute lymphoblastic leukemia (ALL) specific genomic abnormalities provide important clinical information. In most routine clinical diagnostic laboratories conventional karyotyping, in conjunction with targeted screens using e.g., fluorescence in situ hybridization (FISH), is currently considered as the gold standard to detect such aberrations. Conventional karyotyping, however, is limited in its resolution and yield, thus hampering the genetic diagnosis of ALL. We explored whether microarray-based genomic profiling would be feasible as an alternative strategy in a routine clinical diagnostic setting. To this end, we compared conventional karyotypes with microarray-deduced copy number aberration (CNA) karyotypes in 60 ALL cases. Microarray-based genomic profiling resulted in a CNA detection rate of 90%, whereas for conventional karyotyping this was 61%. In addition, many small (< 5 Mb) genetic lesions were encountered, frequently harboring clinically relevant ALL-related genes such as CDKN2A/B, ETV6, PAX5, and IKZF1. From our data we conclude that microarray-based genomic profiling serves as a robust tool in the genetic diagnosis of ALL, outreaching conventional karyotyping in CNA detection both in terms of sensitivity and specificity. We also propose a practical workflow for a comprehensive and objective interpretation of CNAs obtained through microarray-based genomic profiling, thereby facilitating its application in a routine clinical diagnostic setting.

Establishment of a semi-automated pathogen DNA isolation from whole blood and comparison with commercially available kits

Molecular methods for bacterial pathogen identification are gaining increased importance in routine clinical diagnostic laboratories. Achieving reliable results using DNA based technologies is strongly dependent on pre-analytical processes including isolation of target cells and their DNA of high quality and purity. In this study a fast and semi-automated method was established for bacterial DNA isolation from whole blood samples and compared to different commercially available kits: Looxster, MolYsis kit, SeptiFast DNA isolation method and standard EasyMAG protocol. The newly established, semi-automated method utilises the EasyMAG device combined with pre-processing steps comprising human cell lysis, centrifugation and bacterial pellet resuspension. Quality of DNA was assessed by a universal PCR targeting the 16S rRNA gene and subsequent microarray hybridisation. The DNA extractions were amplified using two different PCR-mastermixes, to allow comparison of a commercial mastermix with a guaranteed bacterial DNA free PCR mastermix. The modified semi-automated EasyMAG protocol and the Looxster kit gave the most sensitive results. After hybridisation a detection limit of 10 1 to 10 2 bacterial cells per mL whole blood was achieved depending on the isolation method and microbial species lysed. Human DNA present in the isolated DNA suspension did not interfere with PCR and did not lead to non-specific hybridisation events.

Microbead-based technologies in diagnostic autoantibody detection

There is a rapid proliferation of new technologies to identify a spectrum of autoantibodies in medical conditions that range from organ-specific autoimmune diseases to systemic rheumatic diseases. Although many laboratories have adopted high-throughput diagnostic platforms such as enzyme linked immunoassays (ELISA), other technologies such as microbead-based assays are emerging as an alternative diagnostic platform. To understand the performance and importance of bead based immunoassays in clinical diagnostics and therapeutics. Current literature was reviewed using the PubMed search engine combining keywords of immunoassay and Luminex, as well as a personal literature database. Included in the evaluation and commentary are bead-based assays such as addressable laser bead immunoassays and related magnetic bead assays. Comparison with other conventional technologies has indicated that laser microbead immunoassays are reliable, accurate, cost-effective, highly sensitive and have rapid turn around time for results. While there are advantages to this diagnostic platform, there are challenges that must be addressed before wider acceptance or long-term use of this technology platform in the routine clinical diagnostic laboratory.

High-Resolution Identification of Chromosomal Abnormalities Using Oligonucleotide Arrays Containing 116,204 SNPs

Mutation of the human genome ranges from single base-pair changes to whole-chromosome aneuploidy. Karyotyping, fluorescence in situ hybridization, and comparative genome hybridization are currently used to detect chromosome abnormalities of clinical significance. These methods, although powerful, suffer from limitations in speed, ease of use, and resolution, and they do not detect copy-neutral chromosomal aberrations--for example, uniparental disomy (UPD). We have developed a high-throughput approach for assessment of DNA copy-number changes, through use of high-density synthetic oligonucleotide arrays containing 116,204 single-nucleotide polymorphisms, spaced at an average distance of 23.6 kb across the genome. Using this approach, we analyzed samples that failed conventional karyotypic analysis, and we detected amplifications and deletions across a wide range of sizes (1.3-145.9 Mb), identified chromosomes containing anonymous chromatin, and used genotype data to determine the molecular origin of two cases of UPD. Furthermore, our data provided independent confirmation for a case that had been misinterpreted by karyotype analysis. The high resolution of our approach provides more-precise breakpoint mapping, which allows subtle phenotypic heterogeneity to be distinguished at a molecular level. The accurate genotype information provided on these arrays enables the identification of copy-neutral loss-of-heterozygosity events, and the minimal requirement of DNA (250 ng per array) allows rapid analysis of samples without the need for cell culture. This technology overcomes many limitations currently encountered in routine clinical diagnostic laboratories tasked with accurate and rapid diagnosis of chromosomal abnormalities.

Use of DNA microarrays for rapid genotyping of TEM beta-lactamases that confer resistance.

Standard clinical procedures for pathogen resistance identification are laborious and usually require 2 days of cultivation before the resistance can be determined unequivocally. In contrast, clinicians and patients face increasing threats from antibiotic-resistant pathogenic bacteria in terms of their frequencies and levels of resistance. A major class of microbial resistance stems from the occurrence of beta-lactamases, which, if mutated, can cause the severe extended-spectrum beta-lactamase (ESBL) or inhibitor-resistant TEM (IRT) phenotype, which cause resistance to extended-spectrum cephalosporins, monobactams, and beta-lactamase inhibitors. We describe an oligonucleotide microarray for identification of the single nucleotide polymorphisms (SNPs) of 96% of the TEM beta-lactamase variants described to date which are related to the ESBL and/or IRT phenotype. The target DNA, originating from Escherichia coli, Enterobacter cloacae, and Klebsiella pneumoniae cells isolated from clinical samples, was amplified and fluorescently labeled by PCR with consensus primers in the presence of cyanine 5-labeled nucleotides. The total assay, including PCR, hybridization, and image analysis, could be performed in 3.5 h. The microarray results were validated by standard clinical procedures. The microarray outperformed the standard procedures in terms of assay time and the depth of information provided. In conclusion, this array offers an attractive option for the identification and epidemiologic monitoring of TEM beta-lactamases in the routine clinical diagnostic laboratory.

PCR assay or culture for diagnosis of Bordetella pertussis in the routine diagnostic laboratory?

A nested PCR method was compared with culture for the detection of Bordetella pertussis in a routine clinical diagnostic laboratory. A total of 241 clinical nasopharyngeal aspirates were examined in parallel in the laboratory. Both methods were positive for 75 samples (31%), eight samples were positive by nested PCR only (3.3%), and one sample was positive by culture only (0.4%). The mean time actually required in the clinical laboratory (not operating with pertussis diagnosis during weekends) from the day of arrival to the diagnosis of a positive or negative sample by the nested PCR assay was 1.8 +/- 1.3 days (mean +/- SD), for positive culture 4.5 +/- 1.4 days and for negative culture 10.5 +/- 1.0 days. The hands-on time in the laboratory to perform the nested PCR was 2 h, for a positive culture 25 min, and for a negative culture 15 min. The cost analysis of the methods, when running one sample at a time, showed that the laboratory cost for PCR was six times higher than culture. When running four samples together the cost for PCR was three times higher than culture. In conclusion, the nested PCR is the more rapid and sensitive method compared to culture. With the present design, the PCR-protocol involves higher material expenditure and claims more hands-on time.

Non-radioactive in situ hybridization for the detection of cytomegalovirus infections.

Acetylaminofluorene (AAF) modified cytomegalovirus (CMV) DNA probes have been applied for the rapid detection of CMV genomes by non-radioactive in situ hybridization in routinely obtained pathological material. To establish proper protocols, AAF modified mouse satellite DNA and mouse liver were used to investigate the procedural variables. Among these were type and time of fixation, glass slide coating for improved tissue adherence, protease permeabilization of sections, type and time of denaturation and hybridization, probe concentration, post-hybridization washing conditions and immunocytochemical detection. This research has led to a user-friendly procedure which, in addition to cells displaying a cytopathological effect typical for CMV infection, detects with high sensitivity CMV carrying cells that show no histo-pathological alterations. It can be readily applied in routine clinical-diagnostic laboratories.