Specimen Contamination Research Articles

Melanoma and Human Papillomaviruses: Is There an Outlook for Study?

Melanoma is one of the most aggressive human malignant tumors. Its incidence and mortality are growing steadily. Ultraviolet irradiation is the main risk factor for melanoma involved in melanomagenesis. The probability of viral etiology of melanoma has been discussed. Human papillomaviruses (HPV) have been mentioned among candidates for its etiologic agents because some HPV types are the powerful carcinogens causing cervical cancer and other cancers. The review analyses the literature data on the association of melanoma with HPV Several groupsfound HPVin skin melanomas as well as in mucosa; viruses of high oncogenic risk were detected in some cases. For some organs the etiological role of high-risk HPV as inducers of invasive carcinomas is confirmed. These organs require special mention: cervix uteri, vulva, vagina, penis, anal region, and oral cavity. However in the majority of the studies in which viral DNA-positive melanomas were found, testing for viral genome expression was not done while this is the fact of primary importance. HPVare found in normal skin and mucous membranes thus creating justifiable threat of tumor specimen contamination with viral DNA in vivo. There are limited data on aggravation of the disease prognosis in papillomavirus-positive melanomas. However, any systematic observation of a sizeable patient group distinguished by that tumor type has not been performed yet. Viral E6 and E7 oncogenes of high-risk papillomaviruses were shown to be able to transform normal human melanocytes in vitro experiments. Thus, we can assume the presence of the association of melanoma with oncogenic HPV. The clinical significance of this problem is indisputable under the conditions of the steady increase in melanoma incidence and mortality rates in Russia and abroad. The problem requires further study.

Does Your SEM Really Tell the Truth?-How Would You Know? Part 4: Charging and its Mitigation.

This is the fourth part of a series of tutorial papers discussing various causes of measurement uncertainty in scanned particle beam instruments, and some of the solutions researched and developed at NIST and other research institutions. Scanned particle beam instruments, especially the scanning electron microscope (SEM), have gone through tremendous evolution to become indispensable tools for many and diverse scientifc and industrial applications. These improvements have significantly enhanced their performance and made them far easier to operate. But, the ease of operation has also fostered operator complacency. In addition, the user-friendliness has reduced the apparent need for extensive operator training. Unfortunately, this has led to the idea that the SEM is just another expensive "digital camera" or another peripheral device connected to a computer and that all of the problems in obtaining good quality images and data have been solved. Hence, one using these instruments may be lulled into thinking that all of the potential pitfalls have been fully eliminated and believing that, everything one sees on the micrograph is always correct. But, as described in this and the earlier papers, this may not be the case. Care must always be taken when reliable quantitative data are being sought. The first paper in this series discussed some of the issues related to signal generation in the SEM, including instrument calibration, electron beam-sample interactions and the need for physics-based modeling to understand the actual image formation mechanisms to properly interpret SEM images. The second paper has discussed another major issue confronting the microscopist: specimen contamination and methods to eliminate it. The third paper discussed mechanical vibration and stage drift and some useful solutions to mitigate the problems caused by them, and here, in this the fourth contribution, the issues related to specimen "charging" and its mitigation are discussed relative to dimensional metrology.

Occult Specimen Contamination in Routine Clinical Next-Generation Sequencing Testing.

To evaluate the extent of human-to-human specimen contamination in clinical next-generation sequencing (NGS) data. Using haplotype analysis to detect specimen admixture, with orthogonal validation by short tandem repeat analysis, we determined the rate of clinically significant (>5%) DNA contamination in clinical NGS data from 296 consecutive cases. Haplotype analysis was performed using read haplotypes at common, closely spaced single-nucleotide polymorphisms in low linkage disequilibrium in the population, which were present in regions targeted by the clinical assay. Percent admixture was estimated based on frequencies of the read haplotypes at loci that showed evidence for contamination. We identified nine (3%) cases with at least 5% DNA admixture. Three cases were bone marrow transplant patients known to be chimeric. Six admixed cases were incidents of contamination, and the rate of contamination was strongly correlated with DNA yield from the tissue specimen. Human-human specimen contamination occurs in clinical NGS testing. Tools for detecting contamination in NGS sequence data should be integrated into clinical bioinformatics pipelines, especially as laboratories trend toward using smaller amounts of input DNA and reporting lower frequency variants. This study provides one estimate of the rate of clinically significant human-human specimen contamination in clinical NGS testing.

Nanomanufacturing Concerns about Measurements Made in the SEM Part IV: Charging and its Mitigation.

This is the fourth part of a series of tutorial papers discussing various causes of measurement uncertainty in scanned particle beam instruments, and some of the solutions researched and developed at NIST and other research institutions. Scanned particle beam instruments especially the scanning electron microscope (SEM) have gone through tremendous evolution to become indispensable tools for many and diverse scientific and industrial applications. These improvements have significantly enhanced their performance and made them far easier to operate. But, the ease of operation has also fostered operator complacency. In addition, the user-friendliness has reduced the apparent need for extensive operator training. Unfortunately, this has led to the idea that the SEM is just another expensive "digital camera" or another peripheral device connected to a computer and that all of the problems in obtaining good quality images and data have been solved. Hence, one using these instruments may be lulled into thinking that all of the potential pitfalls have been fully eliminated and believing that, everything one sees on the micrograph is always correct. But, as described in this and the earlier papers, this may not be the case. Care must always be taken when reliable quantitative data are being sought. The first paper in this series discussed some of the issues related to signal generation in the SEM, including instrument calibration, electron beam-sample interactions and the need for physics-based modeling to understand the actual image formation mechanisms to properly interpret SEM images. The second paper has discussed another major issue confronting the microscopist: specimen contamination and methods to eliminate it. The third paper discussed mechanical vibration and stage drift and some useful solutions to mitigate the problems caused by them, and here, in this the fourth contribution, the issues related to specimen "charging" and its mitigation are discussed relative to dimensional metrology.

Evaluation of a multiplex polymerase chain reaction for early diagnosis of ventriculostomy-related infections.

Diagnosis of ventriculostomy-related infections (VRIs) is challenging due to the lack of rapid, sensitive assays for pathogen detection. The authors report the development of a multiplex polymerase chain reaction (PCR) assay for differential diagnosis of common VRI pathogens. MassTag PCR was used to develop a multiplex assay for detection of 11 VRI pathogens. The assay was established and optimized using cloned template standards and spiked samples and was then evaluated on CSF specimens from ventricular drains. Subjects were grouped into definite VRI, possible VRI, or no VRI based on conventional microbiology, CSF evaluation, and clinical parameters. CSF specimens were obtained from 45 subjects (median age 49 years, interquartile range 32-63 years; 51% were male). The assay detected 10-100 genome copies. It detected a pathogen in 100% (6 of 6) of definite VRI cases in which a pathogen targeted by the assay was present; these represented 67% of all definite VRIs (6 of 9). Among subjects with a possible VRI, the assay detected a pathogen in 29% (5 of 17). In subjects without overt infection the presence of a pathogen was detected in 32% of subjects (6 of 19), albeit with lower signal compared with the VRI group. MassTag PCR enabled parallel testing of CSF specimens for 11 pathogens of VRI. The high sensitivity of PCR combined with possible device colonization, specimen contamination, and concurrent antibiotic treatments limit the clinical value of the assay, similar to other current diagnostic approaches. With further optimization, multiplex PCR may provide timely identification of multiple possible VRI pathogens and guide management, complementing classic culture approaches.

May Latent Bacterial Infection Provoke Degenerative Disc Disease?

Introduction As a chronic condition, the degenerative disc disease is a significant health problem. Several factors, such as genetics, mechanical stress, inflammatory and biochemical changes, vascular aspects, as well as infection may initiate degenerative processes, most commonly affecting the nucleus pulposus. It has been proposed that disc degeneration might be initiated by possible long-lasting low-grade infection. Materials and Methods The aim of the study was to assess the incidence of bacterial infection in the lumbar intervertebral disc specimens obtained from patients with disc herniation. In a prospective study, 62 patients were included (49% women and 51% men, average age 56 years, range 22–83 years). No experience of previous invasive spinal diagnostic procedures was reported. Disc specimens from levels L1 to S1 were collected during discectomies and microbiologically tested on blood, thioglycolate, and nutrient agars. MRI and CT were used as diagnostic methods and comparison of microbiological results to clinical signs and imaging was done. Results In included patients, affected discs were removed. All microbiological cultures of disc specimens remained sterile after 1 week. Clinically, no signs of discitis were observed. The absence of an acute infection was confirmed by routine laboratory tests. Although clinical signs corresponded well to the MRI and CT imaging results, no connection with microbiological tests was found. Conclusion The exact pathobiology of degenerative disc disease is unknown. According to some studies, intradiscal bacteria may initiate a low-grade infection, playing a role in intervertebral disc degeneration. Our observations do not support this fact. Microbiological samples remained sterile in all patients, meaning that intervertebral disc is a sterile environment and bacterial infection is unlikely the cause of degeneration. Positive disc cultures in other studies may have resulted from specimen contamination after disc removal. However, the hypothesis of disc infection cannot completely be excluded because of slow growing and special growth conditions requiring bacteria that were not tested in our study. The potential role of low-grade bacterial infection contributing to the pathogenesis of degenerative disc disease thus remains uncertain. The genesis of disc degeneration might originate in the immune system and repeated episodes of injury and reparation that could culminate to progressive tissue damage.

Can bacterial infection by low virulent organisms be a plausible cause for symptomatic disc degeneration? A systematic review.

Systematic review and meta-analysis. To review and assess the current evidence from the literature on the potential association between disc infection with the development of symptomatic degenerative disc disease. The potential relationship between disc infection- and disc degeneration-related symptoms remains controversial, with contradictory evidence available in the literature. Several studies have demonstrated the presence of infected extruded nucleus tissue from first-time disc herniations, implicating the role of disc microbial infection as a pathway for disc degeneration. In contrast, other studies reported very low prevalence of bacterial infection in samples from patients with sciatica, quoting contamination as the predominant source. To summarize the available evidence to date, a systematic review and meta-analysis was conducted. A comprehensive search from 6 electronic databases was performed for studies investigating the potential relationship between disc infection as a cause for degenerative disc disease and symptomatic neck/back pain or radiculopathy. Random-effects meta-analysis of proportions and odds ratio with 95% confidence intervals was used to pool the available evidence. Nine relevant studies involving 602 patients with degenerative disc disease or pain were identified. From 6 studies supporting the role of infection in the pathophysiology of disc degeneration, the pooled infection prevalence was 45.2% (34.5%-56.0%). Overall pooled prevalence in all studies was 36.2% (24.7%-47.7%). Proportion of disc infections was higher in patients with symptomatic disc disease than in patients without (37.4% vs. 5.9%; odds ratio, 6.1; 95% confidence intervals, 1.426-25.901). The majority of infections were due to Propionibacterium acnes in 59.6% (43.2%-76.1%). From the limited evidence available, the possibility that disc infection may be linked with disc degeneration should not be ruled out. There is a need to investigate this further through larger, adequately powered multi-institutional studies with contaminant arm to control for specimen contamination. 2.

Comparative analysis of hospital and forensic laboratory ethanol concentrations: A 15 month investigation of antemortem specimens

Quantitative serum alcohol concentrations from regional hospitals (from specimens collected at time of hospital admission) were compared to results from whole blood (from specimens collected at the time of hospital admission) concentrations measured at the San Diego County Medical Examiner's Office (SDCMEO). Over a 15 month period (January 2012 to March 2013), the postmortem forensic toxicology laboratory analyzed a total of 2,321 cases. Of these, 280 were hospital cases (antemortem) representing 12% of the overall Medical Examiner toxicology casework. 59 of the 280 hospital cases (or 21%) screened positive for alcohol (ethanol). 39 of these 59 cases were included in the study based on available specimens for quantitative analyses. This investigation indicated that serum hospital ethanol concentrations correlated well (R2 = 0.942) with ethanol values determined at SDCMEO (generally measured in whole blood). There was an observed negative bias with an average of −14.1%. A paired t-test was applied to the data and it was shown that this observed bias is statistically significant. These differences in ethanol concentrations could result from differences in specimen, analytical techniques, and/or calibration. The potential for specimen contamination is also discussed.

Diagnosing inflammation and infection in the urinary system via proteomics.

BackgroundCurrent methodology for the diagnosis of diseases in the urinary system includes patient symptomology, urine analysis and urine culture. Asymptomatic bacteriuria from urethral colonization or indwelling catheters, sample contamination from perineal or vaginal sources, and non-infectious inflammatory conditions can mimic UTIs, leading to uncertainty on medical treatment decisions.MethodsInnovative shotgun metaproteomic methods were used to analyze urine sediments from 120 patients also subjected to conventional urinalysis for various clinical reasons including suspected UTIs. The proteomic data were simultaneously searched for the presence of microbial agents, inflammation, immune responses against pathogens, and evidence of urothelial tissue injury. Hierarchical clustering analysis was performed to identify host protein patterns discerning UTI from urethral colonization and vaginal contamination of urine samples.ResultsOrganisms causing more than 98% of all UTIs and commensal microbes of the urogenital and perineal area were identified from 76 urine sediments with detection sensitivities estimated to be similar to urine culture. Proteomic data permitted a thorough evaluation of inflammatory and antimicrobial immune responses. Hierarchical clustering of the data revealed that high abundances of proteins from activated neutrophils were associated with pathogens in most cases, and correlated well with leukocyte esterase activities and leukocyte counts via microscopy. Proteomic data also allowed assessments of urothelial injury, by quantifying proteins highly expressed in red blood cells and contributing to the acute phase response. Lactobacillus and Gardnerella vaginalis were frequently identified suggesting urethral colonization and/or vaginal contamination of urine.ConclusionsA metaproteomic approach of interest for routine urine clinical diagnostics is presented. As compared to urinalysis and urine culture methods, the data are derived from a single experiment for a given sample and provide additional insights into presence or absence of inflammatory responses and vaginal contamination of urine specimens.Electronic supplementary materialThe online version of this article (doi:10.1186/s12967-015-0475-3) contains supplementary material, which is available to authorized users.

Contamination mitigation strategies for scanning transmission electron microscopy

Modern scanning transmission electron microscopy (STEM) enables imaging and microanalysis at very high magnification. In the case of aberration-corrected STEM, atomic resolution is readily achieved. However, the electron fluxes used may be up to three orders of magnitude greater than those typically employed in conventional STEM. Since specimen contamination often increases with electron flux, specimen cleanliness is a critical factor in obtaining meaningful data when carrying out high magnification STEM. A range of different specimen cleaning methods have been applied to a variety of specimen types. The contamination rate has been measured quantitatively to assess the effectiveness of cleaning. The methods studied include: baking, cooling, plasma cleaning, beam showering and UV/ozone exposure. Of the methods tested, beam showering is rapid, experimentally convenient and very effective on a wide range of specimens. Oxidative plasma cleaning is also very effective and can be applied to specimens on carbon support films, albeit with some care. For electron beam-sensitive materials, cooling may be the method of choice. In most cases, preliminary removal of the bulk of the contamination by methods such as baking or plasma cleaning, followed by beam showering, where necessary, can result in a contamination-free specimen suitable for extended atomic scale imaging and analysis.

Development and clinical application of an InvaderPlus® assay for the detection of genital mycoplasmas.

We developed a PCR-based assay involving Invader® technology for detection of the genital mycoplasmas of Mycoplasma genitalium, Mycoplasma hominis, Ureaplasma urealyticum, and Ureaplasma parvum. We compared its performance with that of a PCR-microtiter plate hybridization assay, which we developed previously, in detecting genital mycoplasmas in first-voided urine (FVU) specimens from men with non-gonococcal urethritis. The tests targeting each of the genital mycoplasmas were specific for the respective species and could detect as few as 10 copies of the plasmids containing the target genes of each of the genital mycoplasmas per reaction. The assay using the InvaderPlus® method (InvaderPlus® assay) showed very similar performance to that of the PCR-microtiter plate hybridization assay for detecting the genital mycoplasmas in the FVU specimens. In addition, the PCR and endonuclease reaction in the InvaderPlus® assay were carried out simultaneously in one procedure, thus simplifying the assay, leading to time- and labor-savings and a decrease in the risk of specimen contamination. The InvaderPlus® assay could be useful in diagnosing genitourinary tract infections caused by the genital mycoplasmas.

Measurement of Total and Free Urinary Phenol and Paraben Concentrations over the Course of Pregnancy: Assessing Reliability and Contamination of Specimens in the Norwegian Mother and Child Cohort Study.

BackgroundExposures to environmental phenols and parabens may be harmful, especially in utero. Prior studies have demonstrated high within-person variability of urinary concentrations across pregnancy.ObjectivesWe sought to measure phenol and paraben biomarker concentrations for the Norwegian Mother and Child Cohort (MoBa) study, assess within-person variability, and investigate any possible external phenol or paraben contamination of specimens.MethodsWe collected three spot urine samples at approximately 17, 23, and 29 weeks gestation in a hospital setting and added a preservative containing ethyl paraben. We measured urinary concentrations and within-person variability for phenols and parabens in a MoBa sample (n = 45), including a subgroup of 15 participants previously randomly selected for a bisphenol A (BPA) exposure study who had unusually high total BPA concentrations. Additionally, we compared reliability results for total, conjugated, and free concentrations of phenolic compounds.ResultsWe detected total and free BPA, butyl paraben, propyl paraben, and methyl paraben in 100% of samples, total benzophenone-3 in 95% of samples, and infrequently detected free benzophenone-3 and total and free 2,4-dichlorophenol and 2,5-dichlorophenol. Intraclass correlation coefficients (ICCs) for total, conjugated, and free concentrations ranged from relatively low for BPA to moderate for propyl paraben. ICCs were generally similar overall and by subgroup.ConclusionsUsing conjugated concentrations improved reliability estimates only for BPA. Measuring total and free concentrations, an approach that may be useful for future studies, allowed us to identify likely BPA and butyl paraben contamination of archived MoBa urine specimens.CitationGuidry VT, Longnecker MP, Aase H, Eggesbø M, Zeiner P, Reichborn-Kjennerud T, Knudsen GP, Bertelsen RJ, Ye X, Calafat AM, Engel SM. 2015. Measurement of total and free urinary phenol and paraben concentrations over the course of pregnancy: assessing reliability and contamination of specimens in the Norwegian Mother and Child Cohort Study. Environ Health Perspect 123:705–711; http://dx.doi.org/10.1289/ehp.1408325

Assessment of the Bacteriological Quality of Food Samples May Offer Clues the Antibiotic Resistance Pattern

Background: Foodborne illnesses continue to be a leading cause of morbidity and mortality worldwide; however, the burden of diseases caused by food-borne pathogens remains largely unknown. Objectives: The aim of the present study was to culture-confirmed the bacterial profile and their antibiotic resistant pattern in Food and Drug Laboratory, Alborz University of Medical Sciences, Karaj, Iran. Patients and Methods: A total of 22 bacteria including of Staphylococcus aureus, Klebsiella spp and E. coli were presumptive isolated from the traditional ice cream, cream pastries, sausage, and salami by the Official Food Microbiology Laboratory, Deputy of Food and Drug Administration, Alborz University of Medical Sciences, Karaj, Iran, and sent to the Research Center Laboratory, Alborz University of Medical Sciences, to confirm the bacterial spp by multiplex polymerase chain reaction. These isolates were also checked for their antimicrobial resistance pattern according to CLSI guideline. Results: The highest rate of contamination was with Klebsiella spp 09 (40.9%), followed by S. aureus 07 (31.8%), E. coli 06 (27.27%), as reported by the Official Food Microbiology Laboratory of Alborz University of Medical Sciences. Gel electrophoresis of the isolates shows the 600bp bp and 80 bp gene among S. aureus and E. coli respectively. The antibiotic resistant pattern in case of Klensiella spp showed that 6 (66.6%) Klensiella spp were resistant to Penicillin and Cotrimoxazole. Similarly, penicillin and amoxicillin were found the highest resistant antibiotic against 83.3% E. coli, however, ceftriaxone showed the highest sensitivity against 100% E. coli isolates. Conclusions: In conclusion, Klebsiella spp, S. aureus and E. coli are contaminants of food specimens obtained from food industries in Karaj, Iran; they constitute a serious health risk for human population. Moreover, the principal purpose of this study is to increase awareness of the antibiotic resistance of these bacteria poses threat.

Low rate of Propionibacterium acnes in arthritic shoulders undergoing primary total shoulder replacement surgery using a strict specimen collection technique

Propionibacterium acnes is a recognized pathogen in postoperative shoulder infections. A recent study reported growth of P acnes in 42% of glenohumeral joints in primary shoulder arthroplasty, concluding that P acnes may cause shoulder osteoarthritis. Whether these results reflect true bacterial infection or specimen contamination is unclear. Our prospective study aimed to determine the rate of P acnes infection in arthritic shoulders using a strict specimen collection technique. We used modified Oxford protocol to collect tissue specimens from the glenohumeral joint of 32 consecutive patients undergoing primary shoulder arthroplasty. Specimens were cultured specifically for P acnes. Diagnosis of P acnes infection required 2 or more positive cultures and histopathology compatible with infection. Three of 32 patients had a positive culture for P acnes. Overall, 3.125% of specimens grew P acnes without histologic evidence of infection. There were no patients with P acnes infection. The difference in culture rates between patients with idiopathic osteoarthritis and those with a predisposing cause for osteoarthritis was not significant. We found a low rate of positive cultures for P acnes, but no P acnes infection and no difference between types of osteoarthritis. These results do not support a cause-and-effect relationship between P acnes and osteoarthritis. The differing results from previous studies are likely explained by our strict specimen collection technique, reflecting different rates of contamination rather than infection. That P acnes contamination occurs in primary shoulder arthroplasty is concerning. Further studies are needed to assess the rates of contamination in shoulder surgery, its clinical effect, and to determine optimal antibiotic prophylaxis.

Nucleic acid contamination in sexual health clinics.

This review explores the potential for nucleic acid contamination with gonorrhoea or chlamydia within healthcare settings, the implications that this has for the transmission of infection and the potential for contamination to cause false positive test results in patients. Contamination with Chlamydia trachomatis and Neisseria gonorrhoeae nucleic acid on hard surfaces and examination equipment is common particularly in areas where urine samples are being taken. The quantity of material which can be detected is low and unlikely to lead to transmission of infection, but does present a potential risk for contamination of patient samples leading to false positive results. Attempts to reduce contamination through cleaning and improved infection control have been unsuccessful. Clinicians involved in taking specimens for sexually transmitted infections should be aware of the risk of surface contamination, and the potential for specimen contamination. As patients increasingly take their own genital specimens rather than it being done by doctors or nurses, patients need to be given appropriate advice to minimize the risk of contamination.

Prevention of DNA contamination during forensic medical examinations in a clinical forensic medical service: A best practice implementation project.

Contamination of forensic specimens can have significant and detrimental effects on cases presented in court. In 2010 a wrongful conviction in Australia resulted in an inquiry with 25 recommendations to minimize the risk of DNA contamination of forensic specimens. DNA decontamination practices in a clinical forensic medical service currently attempt to comply with these recommendations. Evaluation of these practices has not been undertaken. The aim of this project was to audit the current DNA decontamination practices of forensic medical and nursing examiners in the forensic medical examination process and implement changes based on the audit findings. A re-audit following implementation would be undertaken to identify change and inform further research. The Joanna Briggs Institute's Practical Application of Clinical Evidence System and Getting Research into Practice were used as the audit tool in this project. A baseline audit was conducted; analysis of this audit process was then undertaken. Following education and awareness training targeted at clinicians, a re-audit was completed. There were a total of 24 audit criteria; the baseline audit reflected 20 of these criteria had 100% compliance. The remaining 4 audit criteria demonstrated compliance between 65% and 90%. Education and awareness training resulted in improved compliance in 2 of the 4 audit criteria, with the remaining 2 having unchanged compliance. The findings demonstrated that education and raising awareness can improve clinical practice; however there are also external factors outside the control of the clinicians that influence compliance with best practice.

Measurement of Total and Free Urinary Phenol and Paraben Concentrations over the Course of Pregnancy: Assessing Reliability and Contamination of Specimens in the Norwegian Mother and Child Cohort Study

Measurement of Total and Free Urinary Phenol and Paraben Concentrations over the Course of Pregnancy: Assessing Reliability and Contamination of Specimens in the Norwegian Mother and Child Cohort Study

DNA and the minimum requirements for dna decontamination from a clinical forensic perspective

Forensic DNA testing has had a significant impact upon the investigation of crimes and the process has attained infallibility status in the minds of many involved in the medico-legal system. This has led to some significant miscarriages of justice both in Australia and abroad. DNA fingerprinting, despite becoming increasingly sensitive, is not infallible and is open to error at numerous points during the process of specimen collection, testing, interpretation and application. To minimise the risk of unintentional contamination of biological specimens collected, the clinical forensic practitioner must implement appropriate cleaning and DNA decontamination of clinical examination areas and of the equipment used during any clinical examination. Mindful that cleaning, sterilisation and DNA decontamination are each different processes, a generic DNA decontamination process is proposed that is applicable across jurisdictions and in both dedicated and non-dedicated forensic clinical examination suites. This process is based on the understanding that, in the clinical setting, DNA contamination may only be minimised, not eliminated. There are four basic elements to the process: cleaning, selection of disposables, protection of permanent clinical equipment, and limiting contamination from the examiner. These processes are discussed from an evidentiary basis.

Matrix-assisted laser desorption ionization time of flight mass spectrometry and diagnostic testing for prosthetic joint infection in the clinical microbiology laboratory

Identification of pathogen(s) associated with prosthetic joint infection (PJI) is critical for patient management. Historically, many laboratories have not routinely identified organisms such as coagulase-negative staphylococci to the species level. The advent of matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) has enhanced clinical laboratory capacity for accurate species-level identification. The aim of this study was to describe the species-level identification of microorganisms isolated from periprosthetic tissue and fluid specimens using MALDI-TOF MS alongside other rapid identification tests in a clinical microbiology laboratory. Results of rapid identification of bacteria isolated from periprosthetic joint fluid and/or tissue specimens were correlated with clinical findings at Mayo Clinic, Rochester, Minnesota, between May 2012 and May 2013. There were 178 PJI and 82 aseptic failure (AF) cases analyzed, yielding 770 organisms (median, 3/subject; range, 1–19/subject). MALDI-TOF MS was employed for the identification of 455 organisms (59%) in 197 subjects (123 PJIs and 74 AFs), with 89% identified to the species level using this technique. Gram-positive bacteria accounted for 68% and 93% of isolates in PJI and AF, respectively. However, the profile of species associated with infection compared to specimen contamination differed. Staphylococcus aureus and Staphylococcus caprae were always associated with infection, Staphylococcus epidermidis and Staphylococcus lugdunensis were equally likely to be a pathogen or a contaminant, whereas the other coagulase-negative staphylococci were more frequently contaminants. Most streptococcal and Corynebacterium isolates were pathogens. The likelihood that an organism was a pathogen or contaminant differed with the prosthetic joint location, particularly in the case of Propionibacterium acnes. MALDI-TOF MS is a valuable tool for the identification of bacteria isolated from patients with prosthetic joints, providing species-level identification that may inform culture interpretation of pathogens versus contaminants.

The Clinical and Economic Implications of Specimen Provenance Complications in Diagnostic Prostate Biopsies

Inaccurate diagnoses of prostate cancer can result from transposition or contamination of patient biopsy specimens, which are known as specimen provenance complications. We assessed the clinical and economic burden of specimen provenance complications in prostate biopsies in the United States. We performed a comprehensive, systematic review of the literature to approximate the effect of specimen provenance complications on direct medical costs, patient QALYs and medicolegal costs. Data were extracted from published studies on specimen provenance complications rates, prostate cancer treatment efficacy, treatment cost, litigation/settlement costs after false diagnoses of prostate biopsies and patient quality of life. Sensitivity analysis was done to identify factors that most influenced the outcomes and assess the robustness of the findings. Of the estimated 806,251 primary and secondary prostate biopsies performed annually in the United States 20,322 specimen provenance complications were projected to result in 4,570 clinically meaningful false diagnoses and an expected loss of 634 QALYs. The total burden of specimen provenance complications was projected to exceed $879.9 million or $3,776 per positive cancer diagnosis. This estimate was most sensitive to the indemnity cost per false-positive case and the rate of transpositions at independent reference laboratories. The societal burden of specimen provenance complications in patients who undergo prostate biopsy exceeds $880 million annually in the United States. This analysis framework may be useful as policy makers, health organizations and researchers seek to decrease false diagnoses of prostate cancer and the consequent effects of delayed or unnecessary treatment. Further study is warranted to quantify the economic burden among additional diseases.