Employment of broad-range 16S rRNA PCR to detect aetiological agents of infection from clinical specimens in patients with acute meningitis--rapid separation of 16S rRNA PCR amplicons without the need for cloning

AIMS: The aim of this study was to develop a polyacrylamide gel electrophoresis (PAGE) method for the rapid separation of 16S rRNA PCR amplicons from aetiological agents of acute meningitis. METHODS AND RESULTS: Blood samples from 40 patients with suspected acute meningococcal meningitis were examined for the presence of causal agents, including Neisseria meningitidis employing two methods: (i) broad-range 16S rRNA PCR in conjunction with PAGE and automated sequencing and (ii) species-specific PCR employing ABI TaqMan technology for N. meningitidis. Analysis of clinical specimens employing 16S rRNA PCR yielded 33/40 (82.5%) positive for the presence of bacterial DNA. Species-specific PCR yielded 30/40 (75%) clinical specimens positive for N. meningitidis. Prior to separation by PAGE, only 6/33 (18.2%) amplicons were able to be identified by sequence analysis, the remaining amplicons (n=27) did not yield an identification due to the presence of mixed 16S rRNA PCR amplicons. Following separation, amplicons were re-amplified and sequenced, yielding 24/27 (88.9%) positive for N. meningitidis and three specimens positive for Acinetobacter sp., Staphylococcus aureus and Streptococcus pneumoniae. One specimen was positive for both N. meningitidis and Streptococcus spp. and another specimen was positive for N. meningitidis and Pseudomonas sp., by broad-range PCR. Seven clinical specimens were negative for N. meningitidis and other eubacteria using both detection techniques. CONCLUSIONS: Clinical specimens including blood and cerebrospinal fluid from patients with suspected acute bacterial meningitis, may become contaminated with commensal skin flora, resulting in difficulties in downstream sequencing of pathogen plus contaminant DNA. This study allows for the rapid separation of amplified pathogen from contaminant DNA. SIGNIFICANCE AND IMPACT OF STUDY: This study demonstrated the usefulness of the rapid separation of multiple 16S rRNA PCR amplicons using a combination of PAGE and automated sequencing, without the need of cloning. Adoption of this technique is therefore proposed when trying to rapidly identify pathogens in clinical specimens employing broad-range 16S rRNA PCR.     

Automated fluorescence image cytometry. DNA quantification and detection of chlamydial infections

Digitized fluorescence microscopy in conjunction with automated image segmentation is a promising approach for screening clinical specimens quickly and reliably. This paper describes the hardware and software of a prototype image-based cytometer that can identify fluorescent objects, discriminate true objects from artifacts and divide overlapping pairs of objects. The use of this image cytometer is discussed for: (1) the measurement of the DNA ploidy distribution of isolated mature rat liver nuclei labeled with 4',6-diamidine-2-phenylindole; (2) the comparison of the DNA ploidy distributions of the same samples measured by image cytometry (ICM) and flow cytometry (FCM); and (3) the quantification of chlamydial infection by double labeling cells with antichlamydiae antibody and Hoechst 33258 for nuclear DNA analysis. Ploidy distributions measured by the automated image cytometer compared favorably to those obtained by FCM. All pairs of overlapping nuclei were automatically detected by an additional computer algorithm, and those pairs that were clearly more than one nucleus by visual inspection were correctly divided. The irregular morphology of the chlamydiae-infected cells meant that 26% of them were not correctly identified in the fluorescein-stained images (as judged by manual inspection), but all cells were nevertheless detected correctly from the images of the Hoechst-stained samples. Automated fluorescence ICM yielded results similar to those obtained with FCM and had the additional benefit of maintaining cell and tissue architecture while preserving the opportunity for subsequent manual inspection of the specimen.     

Automated sperm head morphology analyzer for open-source software

Sperm head morphology has been identified as a characteristic that can be used to predict a male's semen quality. In the present study, we have developed an automated sperm head morphology analysis (ASMA) plug-in for open-source ImageJ software (http://rsbweb.nih.gov/ij/). We describe the plug-in's functionality, and confirm its validity for sperm head morphology analysis using fish sperm. Sperm head morphological measurements (length and width) made with the ASMA plug-in did not differ from manual measurements. Using the plug-in to measure sperm head-shaped objects of known size, the associated plug-in error rate was < 0.5%. Brightness and contrast ratios influenced sperm head measurements, suggesting the need for standardized protocols. This plug-in was effective at measuring elliptical (i.e., Atlantic cod) as well as slightly irregular (i.e., Chinook salmon) shaped sperm heads. In conclusion, our ASMA plug-in represents a versatile alternative to costly sperm morphology software.     

Apport de deux techniques d’analyse automatisées des examens [F] FDG TEP dans la discrimination des patients déments frontotemporaux et malades d’Alzheimer

Introduction

In younger patients, the in vivo clinical diagnosis of Alzheimer's disease (AD) and of the frontotemporal type (FTD) may be cumbersome. The gold standard diagnostic proof is currently still based upon pathology examination. It is crucial to find reliable techniques to make an accurate in vivo diagnosis and to differentiate the etiology of the dementia.

Patients and method

Twenty-four patients bearing clinically diagnosed AD (n = 16) and FTD (n = 8) underwent [¹⁸F] FDG-PET/CT brain scan. Four nuclear medicine physicians with varying expertise in neuroimaging read each scan according to: visual analysis; automated analysis computed by BRASS^® Hermes^® software; automated analysis computed by Cortex ID^® General Electric^® software. Interpretation aimed at assessing the global scan aspect, the cerebral metabolism per hemisphere (in five relevant regions) and the diagnostic degree of confidence. Diagnostic interpretations derived from visual and automated analyses were compared to clinical diagnosis. Inter-observer agreement and Kappa scores were calculated.

Results

Kappa analyses showed a gain in diagnostic accuracy for a nonexpert physician, a gain in diagnostic confidence with Cortex ID^® and a gain in interobserver diagnostic agreement with BRASS^®.

Conclusion

Using automated software such as Cortex ID^® or BRASS^® helps standardizing the interpretation of [¹⁸F] FDG distribution pattern in AD or FTD.     

Enhanced detection of cytomegalovirus in shell vial cell culture monolayers by preinoculation treatment of urine with low-speed centrifugation

In an effort to reduce the number of unreadable MRC-5 cell culture monolayers (i.e., monolayers that are obscured by an opaque film or are detached from their coverslips), urine specimens were subjected to low-speed (500 g for 10 min at 4°C) centrifugation prior to their inoculation into shell vials for the detection of cytomegalovirus (CMV). A total of 182 urine specimens obtained from patients suffering from ARC or AIDS were subjected to routine centrifugation culture and to preinoculation centrifugation. Cytomegalovirus recovery among the two specimen-treatment procedures was determined by counting the number of immunofluorescent MRC 5-positive cells. Eleven of 19 positive specimens were in accord in both systems. However, routinely treated (i.e., without preinoculation centrifugation) specimens were difficult to read specifically among those specimens that were cloudy or opaque. Cytome-galovirus was recovered in 18 of the 19 positive specimens that were subjected to the preinoculation centrifugation procedure. Only 12 of 19 positive specimens were identified following direct inoculation of untreated urine into shell vials. The additional preinoculation centrifugation step is appropriate for the removal of obfuscating amorphous substances from the assay system without compromising CMV detection rates.     

Cost Analysis of a Nucleic Acid Amplification Test in the Diagnosis of Pulmonary Tuberculosis at an Urban Hospital with a High Prevalence of TB/HIV

Introduction

The Centers for Disease Control and Prevention has recommended using a nucleic acid amplification test (NAAT) for diagnosing pulmonary tuberculosis (TB) but there is a lack of data on NAAT cost-effectiveness.

Methods

We conducted a prospective cohort study that included all patients with an AFB smear-positive respiratory specimen at Grady Memorial Hospital in Atlanta, GA, USA between January 2002 and June 2008. We determined the sensitivity, specificity, and positive and negative predictive value of a commercially available and FDA-approved NAAT (amplified MTD, Gen-Probe) compared to the gold standard of culture. A cost analysis was performed and included costs related to laboratory tests, hospital charges, anti-TB medications, and contact investigations. Average cost per patient was calculated under two conditions: (1) using a NAAT on all AFB smear-postive respiratory specimens and (2) not using a NAAT. One-way sensitivity analyses were conducted to determine sensitivity of cost difference to reasonable ranges of model inputs.

Results

During a 6 1/2 year study period, there were 1,009 patients with an AFB smear-positive respiratory specimen at our public urban hospital. We found the NAAT to be highly sensitive (99.6%) and specific (99.1%) on AFB smear-positive specimens compared to culture. Overall, the positive predictive value (PPV) of an AFB smear-positive respiratory specimen for culture-confirmed TB was 27%. The PPV of an AFB smear-positive respiratory specimen for culture-confirmed TB was significantly higher for HIV-uninfected persons compared to those who were HIV-seropositive (152/271 [56%] vs. 85/445 [19%]; RR = 2.94, 95% CI 2.36–3.65, p<0.001). The cost savings of using the NAAT was $2,003 per AFB smear-positive case.

Conclusions

Routine use of the NAAT on AFB smear-positive respiratory specimens was highly cost-saving in our setting at a U.S. urban public hospital with a high prevalence of TB and HIV because of the low PPV of an AFB smear for culture-confirmed TB.     

Human cytomegalovirus glycoprotein B genotyping from bronchoalveolar lavage specimens

The genes encoding glycoprotein complexes of human cytomegalovirus are often polymorphic; in particular, glycoprotein B (gB), which is essential for both in vivo and in vitro replication, is encoded by the highly polymorphic gene UL55. In this study, the distribution of gB genotypes was investigated in 44 bronchoalveolar lavage specimens from adult patients positive for human cytomegalovirus DNA by a multiplex nested fast PCR able to amplify 5 gB genotypes (gB1-gB5). The distribution of gB genotypes was as follows: 12 (27.3%) gB1, 11 (25%) gB2, 9 (20.4%) gB3, 4 (9.1%) gB4, 0 gB5, and 8 (18.2%) mixed genotypes. No difference in prevalence was found in relation to clinical features, including immunological status, non-transplant or transplant condition, and type of transplanted organ, or in follow-up specimens; while gB4 and gB3 were shown to be significantly more prevalent in patients with respiratory insufficiency, and gB4 and gB2 in those with pneumonia. The prevalence of gB genotypes in the lower respiratory tract was similar to that previously reported using other specimen types and patients, with gB1 found to be the most prevalent. The association of gB genotypes with specific clinical features should be further investigated.     

Automated experimental system capturing three behavioral components during murine forced swim test

AimsAn automated experimental system applying a commercially available video image analyzer was developed for the simultaneous detection and measurement of three behavioral components; immobility, swimming (horizontal movements) and climbing (vertical movements) that occur in the murine forced swim test (FST). The system was validated using four typical antidepressants.Main methodsSystem validity was confirmed by demonstrating no significant difference in 6 min time course of control group and imipramine-dosed group (30 mg/kg) between manual examinations and automated digital analysis for all the three behaviors (i.e., correlation coefficients were 0.96, 0.83 and 0.94 for immobility, swimming and climbing, respectively). The effects of acute single treatment with four antidepressants in clinical use, i.e., imipramine, desipramine, bupropion and fluvoxamine were evaluated at doses of 15, 30 and 60 mg/kg using the system.Key findingsIn 2–4 min time span analysis, all four antidepressants reduced immobility and increased climbing significantly, desipramine and bupropion increased swimming significantly, while imipramine and fluvoxamine did not.SignificanceThe automated experimental system enabled efficient and accurate analysis of the three murine behaviors during FST at once. Climbing could be more sensitive parameter to detect anti-depressant-like effect than immobility in this system.     

Efficacy of Conventional Endoscopic Disinfection and Sterilization Methods Against Helicobacter pylori Contamination

Background. Iatrogenic transmission of Helicobacter pylori via contaminated endoscopic devices is well documented. Despite the prevalence of this infectious agent, few controlled studies have investigated the major factors that impact on reprocessing of endoscopes contaminated with H. pylori. Materials and Methods. An endoscope (Pentax) was contaminated with 10⁸ cfu/ml of H. pylori in 5% bovine calf serum as standardized inoculum. The endoscope then was passed through one of eight arms (five repetitions per arm = 40 total runs), as follows: 1, recovery control (no cleaning or disinfection); 2, manual cleaning alone; 3–5, manual precleaning followed by either 10-, 20-, or 45-minute exposure to 2% glutaraldehyde and ethanol (ETOH) drying; 6, manual cleaning followed by automated reprocessing by STERIS System; 7 and 8, automated reprocessing by STERIS with and without active peracetic acid sterilant (wash-off control). Suction-biopsy channels and air-water channels were harvested for microbiological culture. Results. Control runs recovered more than 1 × 10⁶ cfu per site, confirming the viability of the test organism and the adequacy of the biological burden for challenge. When instruments underwent manual cleaning alone (without subsequent disinfection), test organisms remained in 40% of runs at the air-water site. Manual cleaning followed by 10-, 20-, or 45-minute glutaraldehyde exposure and ETOH drying removed all test organisms from all sites in all runs (i.e., 100% disinfection). The automated STERIS system with or without active peracetic acid sterilant also removed all test organisms from all sites in all runs, as did manual cleaning followed by STERIS use. Conclusion. Manual cleaning alone does not effectively remove H. pylori from an endoscope. Current joint association recommendations for minimal disinfection (manual cleaning followed by at least 20 minutes of immersion in glutaraldehyde and ETOH drying) are effective in preventing cross-transmission of H. pylori. Reprocessing using the automated STERIS system according to manufacturer's recommendations also is highly effective in sterilizing endoscopes contaminated with H. pylori.     

Rapid detection of influenza A virus in clinical samples using an ion channel switch biosensor

This report describes the fabrication and successful use of the ion channel switch biosensor (ICSB) for rapid point-of-care detection of influenza A in different types of respiratory specimens. Virus culture -- regarded as the "gold standard" -- and an immunochromatographic rapid point-of-care test for influenza A virus were compared with the biosensor. The ICSB rapid test provided an objective readout within 10 min of specimen inoculation into the ICSB chamber wells, without the need for chemical or other pretreatments. Construction of the ICSB with specific antibodies also enables rapid detection and identification of appropriate influenza A subtypes.     

858例血感染患者病原菌分布及耐药情况

目的:通过对某地区中心医院收集的临床血感染患者感染病原菌的分析,了解该地区血感染患者病原菌构成、分布及耐药特点,为临床治疗提供参考和指导。方法:收集2012年6月至2013年8月期间在某院就诊的858例血感染患者血液标本,采用BACTEC9050全自动血培养仪培养,采用VITEK 2 Compack系统和K-B琼脂纸片扩散法对阳性标本进行菌种鉴定和药敏检测。结果:血培养结果显示,在858份血培养标本中共检出阳性标本109份,每份标本都只检出一种病菌,总检出率为12.7%,革兰阳性菌占64.22%(70/109),革兰阴性菌占33.03%(36/109),真菌占0.35%%(3/109);药物敏感试验结果显示:葡萄球菌对青霉素、红霉素和复方新诺明耐药率40%;肠杆菌科细菌对氨苄西林和氯霉素耐药率40%;非发酵菌科细菌对氨苄西林,头孢他啶,头孢噻肟和氯霉素耐药率40%。结论:目前本地区临床血感染患者革兰阳性菌感染率高,以金黄色葡萄球菌和凝固酶阴性葡萄球菌为主,治疗可以首选糖肽类抗菌药物;革兰阴性菌以大肠杆菌和绿脓杆菌为主,对氨苄西林、氯霉素耐药率高,大肠杆菌对头孢类抗生素的耐受较绿脓杆菌低,两种细菌感染治疗可以考虑选择单环-内酰胺类抗生素。及时准确的血培养结果及药敏试验可为临床合理选择抗菌药物提供重要依据。     

Automated sperm head morphology analyzer for open-source software

Sperm head morphology has been identified as a characteristic that can be used to predict a male's semen quality. In the present study, we have developed an automated sperm head morphology analysis (ASMA) plug-in for open-source ImageJ software (http://rsbweb.nih.gov/ij/). We describe the plug-in's functionality, and confirm its validity for sperm head morphology analysis using fish sperm. Sperm head morphological measurements (length and width) made with the ASMA plug-in did not differ from manual measurements. Using the plug-in to measure sperm head-shaped objects of known size, the associated plug-in error rate was < 0.5%. Brightness and contrast ratios influenced sperm head measurements, suggesting the need for standardized protocols. This plug-in was effective at measuring elliptical (i.e., Atlantic cod) as well as slightly irregular (i.e., Chinook salmon) shaped sperm heads. In conclusion, our ASMA plug-in represents a versatile alternative to costly sperm morphology software.     

Inoculation with a Mixed Degrading Culture Improves the Pesticide Removal of an On-Farm Biopurification System

To investigate whether the pesticide removal in on-farm biopurification systems (BPS) filled with two different types of substrata (biomix and plastic carriers) is affected by inoculation with a pesticide-degrading strain or mixed culture, lab-scale BPS used to treat chloropropham point source contaminations were bioaugmented with either a specialized chloropropham-degrading strain or a chloropropham-degrading enrichment culture. Application of both inoculum types leads to an accelerated degradation activity in the columns filled with plastic carriers. For both substratum types, inoculation with the mixed culture resulted in a lower breakthrough of the toxic intermediate 3-chloroaniline at high hydraulic loads, compared to inoculation with the pure isolate and no inoculation. This study suggests that the use of plastic carrier materials could be a proficient alternative to the use of a conventional biomix as a substratum in on-farm BPS and that inoculation with a mixed degrading culture can reduce the leaching of more mobile toxic intermediates.     

Protamine, a substrate for thrombolytic agents and enzymes of similar specificity.

Protamine, a highly purified basic polypeptide of 4000 molecular weight containing 80–85% arginine, is a useful substrate for the assay of plasmin, activated plasminogen, and enzymes of similar specificity, e.g., urokinase, coagulation factor Xa, trypsin, and thrombin, and is also an excellent secondary substrate for activator assays of urokinase and streptokinase. The assays were performed manually, and also automated procedures for continuous multiple sample analyses were used. The relative sensitivities for various plasmin-like enzymes were: trypsin > plasmin > urokinase > factor Xa > thrombin. Using protamine with manual assay procedures, the amino-terminal groups of the enzyme-degraded protamine digestion products were detected and quantitated by the colorimetric ninhydrin or the fluorometric fluorescamine procedures, and using protamine with an automated system the ninhydrin method was used. Assigning the CTA casein assay for plasmin a nominal sensitivity of 0.1 (for 0.1 CTA unit of plasmin), the sensitivities of the various assay methods were casein, automated protamine, and manual protamine with ninhydrin, 0.1; manual protamine-trichloroacetic acid with fluorescamine, 0.005; and manual protamine direct fluorescamine, 0.0005. A unit of plasmin, based on the uptake of 1 μequiv base/min during hydrolysis of 0.4% protamine sulfate under standard conditions, is equal to approximately 1.7 × 10³ RFI units or 2.9 CTA units; or, 1 CTA unit of plasmin resulted in an average uptake of 0.346 μmol of base or equivalent bonds split per minute.     

Multiple initial culture conditions enhance the establishment of cell lines from primary ovarian cancer specimens

Summary To increase the efficiency of stable cell line establishment from primary ovarian cancer specimens, we simultaneously initiated cultures under, multiple conditions, varying extracellular matrices and the inclusion of supplements (e.g., serum or serum albumin), while minimizing exposure to xenogeneic antigens (e.g., fetal calf serum). Primary cultures were initiated from 30 specimens; cell lines were established from 10 of these for a success rate of 33%. In some instances, multiple cell lines were established from the same specimen. Five lines were characterized extensively with respect to growth properties, antigen expression, and genomic alterations. Although these lines are all low-passage, marked heterogeneity was observed, even between lines derived from the same specimen. The culture approach outlined herein will facilitate generation of reagents useful for many aspects of ovarian cancer biology. Equal contribution.     

Protective efficacy of IgA monoclonal antibodies to O and H antigens in a mouse model of intranasal challenge with Salmonella enterica serotype Enteritidis

Protective properties of immunoglobulin A (IgA) monoclonal antibodies (MAbs) directed against O and H antigens of Salmonella enterica serotype Enteritidis (S. enteritidis) were evaluated in a model of generalized infection after intranasal (i.n.) inoculation of BALB/c mice. Passive i.n. instillation of antibodies 1 h before i.n. challenge did not prevent infection, and mice developed rapid inflammatory response in the lower respiratory tract. The passive systemic immunization was partially protective and a single intravenous (i.v.) injection of both O and H antigen specific IgA antibodies prolonged survival period of the infected animals. Permanent secretion of O:9 specific IgA MAb 177E6 into the respiratory tract in a "backpack" tumor model protected 50% of animals infected i.n. with a high dose of virulent S. enteritidis strain. Thus, secretory IgA (S-IgA) directed against O:9 antigen alone can prevent bacterial invasion in the respiratory epithelium.     

感染耐亚胺培南鲍曼不动杆菌临床分布情况及耐药性分析

目的:探讨感染耐亚胺培南(IPM)鲍曼不动杆菌临床分布情况及耐药性。方法:回顾性分析2013~2015年榆林市中医院患者感染鲍曼不动杆菌的临床分布,并对耐亚胺培南鲍曼不动杆菌进行培养、鉴定及药敏试验,分析其耐药情况。结果:2013~2015年我院共分离培养出鲍曼不动杆菌185株,其中IPM耐药99株(53.51%),IPM敏感86株(46.49%)。绝大部分菌株分离自痰液标本(138株,74.59%),其次是血液标本(14株,7.57%)与尿液标本(12株,6.49%);来自ICU送检标本菌株数量最多(84株,45.41%),其次是呼吸内科标本(53株,28.65%)与神经内科标本(30株,16.22%)。不同标本类型及科室中IPM耐药及IPM敏感鲍曼不动杆菌占比无显著差异(P0.05)。IPM耐药鲍曼不动杆菌对抗菌药物耐药性均较高,其中以头孢哌酮/舒巴坦(CSL)敏感性最高(50.51%);IPM敏感鲍曼不动杆菌对部分抗菌药物耐药性尚可,其中以IPM敏感性最高(93.02%)。结论:耐亚胺培南鲍曼不动杆菌临床分布广泛,多重耐药性严重甚至出现泛耐药,应当对患者进行药敏试验,以药敏结果选择合适的抗菌药物进行使用。     

Collecting in collections: a PCR strategy and primer set for DNA barcoding of decades‐old dried museum specimens

Natural history museums are vastly underutilized as a source of material for DNA analysis because of perceptions about the limitations of DNA degradation in older specimens. Despite very few exceptions, most DNA barcoding projects, which aim to obtain sequence data from all species, generally use specimens collected specifically for that purpose, instead of the wealth of identified material in museums, constrained by the lack of suitable PCR methods. Any techniques that extend the utility of museum specimens for DNA analysis therefore are highly valuable. This study first tested the effects of specimen age and PCR amplicon size on PCR success rates in pinned insect specimens, then developed a PCR primer set and amplification strategy allowing greatly increased utilization of older museum specimens for DNA barcoding. PCR success rates compare favourably with the few published studies utilizing similar aged specimens, and this new strategy has the advantage of being easily automated for high‐throughput laboratory workflows. The strategy uses hemi‐nested, degenerate, M13‐tailed PCR primers to amplify two overlapping amplicons, using two PCRs per amplicon (i.e. four PCRs per DNA sample). Initial PCR products are reamplified using an internal primer and a M13 primer. Together the two PCR amplicons yield 559 bp of the COI gene from Coleoptera, Lepidoptera, Diptera, Hemiptera, Odonata and presumably also other insects. BARCODE standard‐compliant data were recovered from 67% (56 of 84) of specimens up to 25 years old, and 51% (102 of 197) of specimens up to 55 years old. Given the time, cost and specialist expertise required for fieldwork and identification, ‘collecting in collections’ is a viable alternative allowing researchers to capitalize on the knowledge captured by curation work in decades past.