Practical Guidance for Clinical Microbiology Laboratories: Mycobacteria.

Mycobacteria are the causative organisms for diseases such as tuberculosis (TB), leprosy, Buruli ulcer, and pulmonary nontuberculous mycobacterial disease, to name the most important ones. In 2015, globally, almost 10 million people developed TB, and almost half a million patients suffered from its multidrug-resistant form. In 2016, a total of 9,287 new TB cases were reported in the United States. In 2015, there were 174,608 new case of leprosy worldwide. India, Brazil, and Indonesia reported the most leprosy cases. In 2015, the World Health Organization reported 2,037 new cases of Buruli ulcer, with most cases being reported in Africa. Pulmonary nontuberculous mycobacterial disease is an emerging public health challenge. The U.S. National Institutes of Health reported an increase from 20 to 47 cases/100,000 persons (or 8.2% per year) of pulmonary nontuberculous mycobacterial disease among adults aged 65 years or older throughout the United States, with 181,037 national annual cases estimated in 2014. This review describes contemporary methods for the laboratory diagnosis of mycobacterial diseases. Furthermore, the review considers the ever-changing health care delivery system and stresses the laboratory's need to adjust and embrace molecular technologies to provide shorter turnaround times and a higher quality of care for the patients who we serve.

A review of the current state of digital plate reading of cultures in clinical microbiology.

Digital plate reading (DPR) is increasingly being adopted as a means to facilitate the analysis and improve the quality and efficiency within the clinical microbiology laboratory. This review discusses the role of DPR in the context of total laboratory automation and explores some of the platforms currently available or in development for digital image capturing of microbial growth on media. The review focuses on the advantages and challenges of DPR. Peer-reviewed studies describing the utility and quality of these novel DPR systems are largely lacking, and professional guidelines for DPR implementation and quality management are needed. Further development and more widespread adoption of DPR is anticipated.

Infants 1-90 days old hospitalized with human rhinovirus infection.

BACKGROUND: Human rhinovirus (HRV) is a common cause of respiratory illness in children. The impact of HRV infection on 1- to 90-day-old infants is unclear. We hypothesized that HRV infection would be clinically similar to respiratory syncytial virus (RSV) infection in the hospitalized infants. METHODS: We conducted a retrospective study of hospitalized infants, who were 1-90 days old, with HRV or RSV within the Southern California Kaiser Permanente network over a 1-year period (August 2010 to October 2011). RESULTS: We identified 245 hospitalized infants who underwent respiratory virus testing. HRV was found in 52 infants (21%) compared to 79 infants (32%) with RSV (P = 0.008). Infants with HRV infection experienced longer hospital stays compared to those with RSV (median length of stay 4 days vs. 3 days, P = 0.009) and had fewer short hospital stays ≤3 days (P = 0.029). There was a trend in infants with HRV infection to be younger (P = 0.071) and have more fevers (P = 0.052). CONCLUSIONS: Recent advances in diagnostics allow for identification of a broad range of viral pathogens in infants. Compared to RSV, HRV was associated with longer hospital stays. Additional studies and improved, more specific testing, methods are needed to further define the effects of HRV infection in infants 1-90 days old.

Automation in the clinical microbiology laboratory.

Imagine a clinical microbiology laboratory where a patient's specimens are placed on a conveyor belt and sent on an automation line for processing and plating. Technologists need only log onto a computer to visualize the images of a culture and send to a mass spectrometer for identification. Once a pathogen is identified, the system knows to send the colony for susceptibility testing. This is the future of the clinical microbiology laboratory. This article outlines the operational and staffing challenges facing clinical microbiology laboratories and the evolution of automation that is shaping the way laboratory medicine will be practiced in the future.

Rimonabant-mediated changes in intestinal lipid metabolism and improved renal vascular dysfunction in the JCR:LA-cp rat model of prediabetic metabolic syndrome.

Rimonabant (SR141716) is a specific antagonist of the cannabinoid-1 receptor. Activation of the receptor initiates multiple effects on central nervous system function, metabolism, and body weight. The hypothesis that rimonabant has protective effects against vascular disease associated with the metabolic syndrome was tested using JCR:LA-cp rats. JCR:LA-cp rats are obese if they are cp/cp, insulin resistant, and exhibit associated micro- and macrovascular disease with end-stage myocardial and renal disease. Treatment of obese rats with rimonabant (10 mg.kg(-1).day(-1), 12-24 wk of age) caused transient reduction in food intake for 2 wk, without reduction in body weight. However, by 4 wk, there was a modest, sustained reduction in weight gain. Glycemic control improved marginally compared with controls, but at the expense of increased insulin concentration. In contrast, rimonabant normalized fasting plasma triglyceride and reduced plasma plasminogen activator inhibitor-1 and acute phase protein haptoglobin in cp/cp rats. Furthermore, these changes were accompanied by reduced postprandial intestinal lymphatic secretion of apolipoprotein B48, cholesterol, and haptoglobin. While macrovascular dysfunction and ischemic myocardial lesion frequency were unaffected by rimonabant treatment, both microalbuminuria and glomerular sclerosis were substantially reduced. In summary, rimonabant has a modest effect on body weight in freely eating obese rats and markedly reduces plasma triglyceride levels and microvascular disease, in part due to changes in intestinal metabolism, including lymphatic secretion of apolipoprotein B48 and haptoglobin. We conclude that rimonabant improves renal disease and intestinal lipid oversecretion associated with an animal model of the metabolic syndrome that appears to be independent of hyperinsulinemia or macrovascular dysfunction.

Pig preovulatory oocytes modulate cumulus cell protein and gene expression in vitro.

This study investigated the changes in protein and gene expression in oocytectomized cumulus cells (OOX) of medium-sized follicles from gilts, cultured with or without denuded oocytes isolated from large oestrogenic sow follicles. Proteomic analysis identified 14 proteins that were differentially expressed in OOX, of which the protein 14-3-3 eta, a signal transduction pathway modulator, was down-regulated in the presence of oocytes. Oocyte co-culture also down-regulated FSHR mRNA expression in OOX, as measured by real-time PCR, and FSHR and 14-3-3 eta mRNA abundance were positively correlated. The oocyte also up-regulated HSD3B mRNA, suggesting an effect on cumulus cell progesterone synthesis. Together with data on gene expression in granulosa cells during the follicular phase of the sow oestrous cycle, this study suggests that modulation of the expression of steroidogenesis related proteins and genes in cumulus cells by the porcine preovulatory oocyte reflects the specific physiological requirements of the preovulatory follicle.

Seminal plasma proteins as potential markers of relative fertility in boars.

This study investigated whether specific proteins from distinct seminal plasma fractions of boars could be related to in vivo fertility. Nine boars with acceptable sperm motility and morphology for use in artificial insemination demonstrated major differences in total number born and pregnancy rate when low sperm doses (1.5 billion sperm) were used to breed a minimum of 50 gilts per boar. The 2 lowest-fertility and 2 highest-fertility boars were chosen for evaluation of specific seminal plasma proteins. On 4 occasions, semen was collected and separated into 3 fractions based on sperm concentration (Sperm-Peak, Sperm-Rich, and Sperm-Free), and the fractions were analyzed for total protein concentration and abundance of major seminal plasma glycoprotein (PSP-I), AWN-1, and osteopontin protein using Western blotting techniques. The concentrations of these seminal plasma proteins were lower in the Sperm-Peak fractions compared with the Sperm-Free fractions (P < .05). Seminal plasma from the pooled Sperm-Rich fraction used for artificial insemination was also subjected to two-dimensional gel electrophoresis to investigate novel protein markers related to in vivo fertility. Total piglets born (r = -0.76, P = .01) and sperm motility at day 7 (r = -0.74, P = .037) were again negatively correlated with a 22-kDa protein identified by mass spectrometry as PSP-I. However, fertility index and farrowing rate tended to be positively correlated (P < .10) with a 25-kDa protein, identified as glutathione peroxidase (GPX5), an antioxidant enzyme that may protect sperm membranes from oxidative damage. These candidate proteins merit further investigation as markers of fertility in boars.

Temporal regulation of BMP2, BMP6, BMP15, GDF9, BMPR1A, BMPR1B, BMPR2 and TGFBR1 mRNA expression in the oocyte, granulosa and theca cells of developing preovulatory follicles in the pig.

This study aimed to describe the abundance and localization of BMP2, BMP6, BMP15, GDF9, BMPR1A, BMPR1B, BMPR2 and TGFBR1 mRNA during pig preovulatory follicular development and to evaluate their implication in improving follicular maturity in the preovulatory period preceding the second versus first post-weaning oestrus. Oocytes, granulosa (GC) and theca cells (TC) were recovered from antral follicles of primiparous sows at day 1, 2 and 4 after weaning and at day 14, 16 and 20 of their subsequent oestrous cycle. Real-time PCR analysis revealed that with the exception of BMP6 mRNA, which was absent in GC, all genes were expressed in every cell type. Although BMP6, BMP15 and GDF9 mRNA were most abundant in the oocyte, their expression remained relatively constant during follicular development. By contrast, receptor BMPR1B and TGFBR1 expressions in the GC and TC were temporally regulated. BMPR1B mRNA abundance was positively correlated with plasma oestradiol (E2) suggesting that its regulation by oestrogen may be implicated in normal folliculogenesis. Interestingly, the increase in BMPR1B mRNA and protein abundance during the periovulatory period in GC and TC suggests a role for bone morphogenetic protein (BMP) 15 in the ovulatory process. Finally, expression of these ligands and receptors was not associated with potential differences in follicle maturity observed during the second versus first post-weaning preovulatory follicular wave. In conclusion, our results clearly demonstrate the presence of a complex signalling system within the pig follicle involving the transforming growth factor-beta superfamily and their receptors, and provide evidence to support a role for BMP15 and BMPR1B during ovulation.

Performance of the GeneXpert enterovirus assay for detection of enteroviral RNA in cerebrospinal fluid.

BACKGROUND: The GeneXpert Dx System allows for automated extraction, processing, amplification and real-time detection of target nucleic acids. OBJECTIVES: To evaluate the performance of the Cepheid Xpert enterovirus (EV) assay for detection of EV RNA compared to a nucleic acid sequence based amplification (NASBA) assay and a user-developed TaqMan RT-PCR assay. STUDY DESIGN: Assays were evaluated using a 12-member proficiency panel and up to 138 CSF specimens. Samples in which EV RNA was detected by two or more assays were considered true positives. RESULTS: The GeneXpert, NASBA, and TaqMan assays correctly identified 10, 8, and 7 of 12 proficiency panel members, respectively. For detection of EV RNA in CSF, the sensitivities of the GeneXpert, NASBA, and TaqMan were 100%, 87.5%, and 96%, respectively. There were no false positives. Two samples tested by GeneXpert and NASBA yielded indeterminate or invalid results and could not be resolved. CONCLUSIONS: The Xpert EV assay is a sensitive and specific method for detection of EV RNA in CSF specimens. The ease of use, random access capability, and minimal hands-on time with the automated GeneXpert system affords laboratories with little molecular diagnostics expertise an opportunity to complete a clinically useful testing within 2.5 h.

Identification of porcine oocyte proteins that are associated with somatic cell nuclei after co-incubation.

Relatively little is known with respect to the oocyte proteins that are involved in nuclear reprogramming of somatic cells in mammals. The aim of the present study was to use a cell-free incubation system between porcine oocyte proteins and somatic cell nuclei and to identify oocyte proteins that remain associated with these somatic cell nuclei. In two separate experiments, porcine oocytes were either labeled with biotin to label total proteins at the germinal vesicle stage or metaphase II stage or they were labeled with 0.1 mM (35)S-methionine either during the first 6 h or 22-28 h of in vitro maturation to characterize protein synthesis during two distinct phases. To determine which oocyte proteins associate with somatic nuclei, labeled proteins were incubated in a collecting buffer and energy-regenerating system with isolated ovarian epithelial-like cell nuclei. After incubation, the nuclei were subjected to a novel affinity-binding system to recover biotin-labeled oocyte proteins or two-dimensional SDS-PAGE for separation and visualization of radiolabeled proteins. Proteins of interest were sent for identification using either matrix-assisted laser desorption/ionization time of flight or liquid chromatography-tandem mass spectrometry. Of the proteins that remain associated with isolated nuclei after incubation, 4 were identified using the affinity-binding system and 24 were identified using mass spectrometry and the two-dimensional gel interface. This study has identified porcine oocyte proteins that associate with somatic cell nuclei in a cell-free system using proteomics techniques, providing a novel way to identify oocyte proteins potentially functionally involved in nuclear reprogramming.

Comparison of bulk enucleation methods for porcine oocytes.

Cloning of mammalian oocytes requires that the recipient oocyte is enucleated to remove all genetic material associated with the chromosomes. The procedure currently used in most species requires careful micromanipulation of oocytes treated with cytochalasin B to prevent structural damage. Although functional, this procedure requires time and limits the number of oocytes available for cloning, and our ability to understand the mechanisms of nuclear reprogramming. Therefore, this study aimed at evaluating different procedures to enucleate large pools of oocytes in a time-efficient manner. Two different approaches were tested. The first approach involved centrifugation of zona-free oocytes through a percoll gradient to separate the portion containing the chromatin from the cytoplasmic portion. The second used etoposide to prevent chromatin segregation at first metaphase and resulting in the expulsion of all chromosomes in the polar body. Using the chemical approach an average enucleation rate of 39.4 +/- 7.5% was obtained, while the centrifugation approach resulted in an average enucleation rate of 66.9 +/- 6. In terms of time efficiency, the control manipulation method takes 0.11 min and the centrifugation took an average of 0.52 min per oocyte. The MPF activity at the end of procedure was estimated through the measurement of H1 activity and as expected, the etoposide-cycloheximide treated oocytes had lower H1 activity which was restored by further incubation in the maturation medium for 5 hr while the centrifugation gave a nonsignificant intermediary result. In conclusion, the results presented suggest that both the chemical and the mechanical methods are usable alternatives to micromanipulation of oocytes to generate a large number of chromosome free cytoplasm for biochemical analysis. Mol. Reprod. Dev. 67: 70-76, 2004.

Commercial assay for detection of Giardia lamblia and Cryptosporidium parvum antigens in human fecal specimens by rapid solid-phase qualitative immunochromatography.

The ImmunoCard STAT! Cryptosporidium/Giardia rapid assay (Meridian Bioscience, Inc.) is a solid-phase qualitative immunochromatographic assay that detects and distinguishes between Giardia lamblia and Cryptosporidium parvum in aqueous extracts of human fecal specimens (fresh, frozen, unfixed, or fixed in 5 or 10% formalin or sodium acetate-acetic acid-formalin). By using specific antibodies, antigens specific for these organisms are isolated and immobilized on a substrate. After the addition of appropriate reagents, a positive test is detected visually by the presence of a gray-black color bar (regardless of the intensity) next to the organism name printed on the test device. A control is included in the device. Steps include tube preparation (buffer, patient specimen, conjugates A and B), testing (addition of sample onto the test device), and visual reading (total time, 12 min). Test performance was evaluated with known positive and negative stool specimens (170 specimens positive for Giardia and 231 specimens negative for Giardia) (85 specimens positive for Cryptosporidium and 316 specimens negative for Cryptosporidium); they were tested with trichrome, iron-hematoxylin, or modified acid-fast stains or the Meridian Bioscience, Inc., Giardia/Cryptosporidium Merifluor combination reagent; specimens with discrepant results were retested by using the Merifluor combination reagent. On the basis of the results of the reference methods, the sensitivities, specificities, and positive and negative predictive values were as follows: for G. lamblia, 93.5, 100, 100, and 95.5%, respectively; for C. parvum, 98.8, 100, 100, and 99.7%, respectively. False-negative results for G. lamblia were obtained with specimens with low parasite numbers (n = 7) or specimens containing trophozoites only (n = 3); one specimen with a false-negative result contained numerous cysts. The one specimen false negative for C. parvum was confirmed to be positive by immunofluorescence. No cross-reactivity was seen with 10 different protozoa (152 challenges), nine different helminths (35 challenges), or human cells (4 challenges) found in fecal specimens. This rapid test system may be very beneficial in the absence of trained microscopists; however, for patients who remain symptomatic after a negative result, the ova and parasite examination and special stains for other coccidia and the microsporidia should always remain options.

Comparison of two signal-amplification DNA tests for high-risk HPV as an aid to colposcopy.

OBJECTIVE: To compare Hybrid Capture Tube (HCT) and the second-generation Hybrid Capture II (HC II) test for detection of high-risk human papillomavirus (HPV) DNA at the time of colposcopy. STUDY DESIGN: Colposcopy and HPV testing were performed by HCT and HC II on 1,309 women for evaluation of abnormal Pap smears. Differences in the proportions were tested with chi 2 and 95% CI calculations. RESULTS: When compared to HCT, HC II was more often positive in women with any abnormal Pap smear (44% [95% CI 41-46%] vs. 34% [31-37%], P < .005) and in the subset of women with atypical squamous cells of undetermined significance Pap smears (32% [29-35%] vs. 24% [22-27%], P < .005). HC II was more sensitive in detecting cervical intraepithelial neoplasia (CIN) 2 or worse (93% [88-97%] vs. 78% [70-84%], P < .005) and had a lower rate of undetected > or = CIN 2 in HPV test-negative subjects (1.5% [0.7-2.7%]) vs. 4.3% [3.0-5.9%], P < .005). HC II was also more often positive in women with negative colposcopic evaluations (29% [25.7-32.4%] vs. 20% [17.6-23.5%], P < .005). The specificity of HC II in detection of > or = CIN 2 was lower than that for HCT (63% [60.5-66.2%] vs. 73% [69.5-74.8%], P < .005).

Regulation of IGF-I and porcine oviductal secretory protein (pOSP) secretion into the pig oviduct in the peri-ovulatory period, and effects of previous nutrition.

The mechanisms regulating oviduct function were investigated. In Experiment 1, porcine oviductal secretory protein (pOSP) mRNA, and pOSP and insulin-like growth factor (IGF-I) in oviductal flushings, decreased through the peri-ovulatory period. In Experiment 2, higher plasma steroids in oviductal veins, ipsilateral (INT), rather than contralateral (OVX), to the remaining ovary in unilaterally ovariectomized gilts, were associated with higher pOSP in INT oviductal flushings. In Experiment 3, oviduct function was assessed as part of a collaborative study in cyclic gilts. Feed restriction in the late, compared to the early, luteal phase reduced estradiol concentrations in oviductal plasma, pOSP mRNA in oviductal tissue, and IGF-I concentrations and pOSP abundance in oviduct flushings. Previous insulin treatment differentially affected oviduct function. These data provide the first direct evidence for effects of previous feed restriction and insulin treatment on the oviduct environment in the peri-ovulatory period, which may contribute to nutritional effects on embryonic survival.