Community-acquired pneumonia in adult patients with special reference to rapid methods for etiological diagnosis

Aikuispotilaan kotisyntyisen keuhkokuumeen etiologinen diagnostiikka mikrobiologisilla pikamenetelmillä Tausta. Keuhkokuume on vakava sairaus, johon sairastuu Suomessa vuosittain n. 60 000 aikuista. Huolimatta siitä, että taudin hoito on kehittynyt, siihen liittyy yhä merkittävä, 6-15%:n kuolleisuus. Alahengitystieinfektion aiheuttajamikrobien tunnistaminen on myös edelleen haasteellista. Tavoitteet. Tämän työn tavoitteena oli tutkia Turun yliopistollisessa keskussairaalassa hoidettujen aikuispotilaiden keuhkokuumeen etiologiaa sekä selvittää uusien mikrobiologisten pikamenetelmi¬en hyödyllisyyttä taudinaiheuttajan toteamisessa. Aineisto. Osatöiden I ja III aineisto koostui 384 Turun yliopistollisen keskussairaalaan infektio-osastolla hoidetusta keuhkokuumepotilaasta. Osatyössä I tutkittiin keuhkokuumeen aiheuttaja¬mikrobeja käyttämällä perinteisten menetelmien lisäksi antigeeniosoitukseen ja PCR-tekniikkaan perustuvia pikamenetelmiä. Osatyö II käsitti 231 potilaasta koostuvan alaryhmän, jossa tutkittiin potilaiden nielun limanäytteestä rinovirusten ja enterovirusten esiintyvyyttä. Osatyössä III potilailta tutkittiin plasman C-reaktiivisen proteiinin (CRP) pitoisuus ensimmäisten viiden sairaalahoitopäi¬vän aikana. Laajoja tilastotieteellisiä analyysejä käyttämällä selvitettiin CRP:n käyttökelpoisuutta sairauden vaikeusasteen arvioinnissa ja komplikaatioiden kehittymisen ennustamisessa. Osatyössä IV 68 keuhkokuumepotilaan sairaalaan tulovaiheessa otetuista näytteistä määritettiin neutrofiilien pintareseptorien ekspressio. Osatyössä V analysoitiin sisätautien vuodeosastoilla vuosina 1996-2000 keuhkokuumepotilaille tehtyjen keuhkohuuhtelunäytteiden laboratoriotutkimustulokset. Tulokset. Keuhkokuumeen aiheuttaja löytyi 209 potilaalta, aiheuttajamikrobeja löydettiin kaikkiaan 230. Näistä aiheuttajista 135 (58.7%) löydettiin antigeenin osoituksella tai PCR-menetelmillä. Suu¬rin osa, 95 (70.4%), todettiin pelkästään kyseisillä pikamenetelmillä. Respiratorinen virus todettiin antigeeniosoituksella 11.1% keuhkokuumepotilaalla. Eniten respiratorisia viruksia löytyi vakavaa keuhkokuumetta sairastavilta potilailta (20.3%). 231 keuhkokuumepotilaan alaryhmässä todettiin PCR-menetelmällä picornavirus 19 (8.2%) potilaalla. Respiratorinen virus löytyi tässä potilasryh¬mässä kaiken kaikkiaan 47 (20%) potilaalta. Näistä 17:llä (36%) löytyi samanaikaisesti bakteerin aiheuttama infektio. CRP-tasot olivat sairaalaan tulovaiheessa merkitsevästi korkeammat vakavaa keuhkokuumetta (PSI-luokat III-V) sairastavilla potilailla kuin lievää keuhkokuumetta (PSI-luokat I-II) sairastavilla potilailla (p <0.001). Yli 100 mg/l oleva CRP-taso neljän päivän kuluttua sairaa¬laan tulosta ennusti keuhkokuumeen komplikaatiota tai huonoa hoitovastetta. Neutrofiilien komple¬menttireseptorin ekspressio oli pneumokokin aiheuttamaa keuhkokuumetta sairastavilla merkitse¬västi korkeampi kuin influenssan aiheuttamaa keuhkokuumetta sairastavilla. BAL-näytteistä vain yhdessä 71:stä (1.3%) todettiin diagnostinen bakteerikasvu kvantitatiivisessa viljelyssä. Uusilla menetelmilläkin keuhkokuumeen aiheuttaja löytyi vain 9.8% BAL-näytteistä. Päätelmät. Uusilla antigeeniosoitus- ja PCR-menetelmillä keuhkokuumeen etiologia voidaan saada selvitettyä nopeasti. Lisäksi näitä menetelmiä käyttämällä taudin aiheuttajamikrobi löytyi huomattavasti suuremmalta osalta potilaista kuin pelkästään tavanomaisia menetelmiä käyttämällä. Pikamenetelmien hyödyllisyys vaihteli taudin vaikeusasteen mukaan. Respiratorinen virus löytyi huomattavan usein keuhkokuumetta sairastavilta potilailta, ja näiden potilaiden taudinkuva oli usein vaikea. Tulovaiheen korkeaa CRP-tasoa voidaan käyttää lisäkeinona arvioitaessa keuhkokuumeen vaikeutta. CRP on erityisen hyödyllinen arvioitaessa hoitovastetta ja riskiä komplikaatioiden ke¬hittymiseen. Neutrofiilien komplementtireseptorin ekspression tutkiminen näyttää lupaavalta pi¬kamenetelmältä erottamaan bakteerien ja virusten aiheuttamat taudit toisistaan. Antimikrobihoitoa saavilla potilailla BAL-tutkimuksen löydökset olivat vähäiset ja vaikuttivat hoitoon vain harvoin.

Rapid methods for the chemical analysis of special steels, steel-making alloys, their ores and graphites,

Table on lining-paper.

Evaluation of rapid alternative methods for drug susceptibility testing in clinical isolates of Mycobacterium tuberculosis

A study was carried out to compare the performance of a commercial method (MGIT) and four inexpensive drug susceptibility methods: nitrate reductase assay (NRA), microscopic observation drug susceptibility (MODS) assay, MTT test, and broth microdilution method (BMM). A total of 64 clinical isolates of Mycobacterium tuberculosis were studied. The Lowenstein-Jensen proportion method (PM) was used as gold standard. MGIT, NRA, MODS, and MTT results were available on an average of less than 10 days, whereas BMM results could be reported in about 20 days. Most of the evaluated tests showed excellent performance for isoniazid and rifampicin, with sensitivity and specificity values > 90%. With most of the assays, sensitivity for ethambutol was low (62-87%) whereas for streptomycin, sensitivity values ranged from 84 to 100%; NRA-discrepancies were associated with cultures with a low proportion of EMB-resistant organisms while most discrepancies with quantitative tests (MMT and BMM) were seen with isolates whose minimal inhibitory concentrations fell close the cutoff. MGIT is reliable but still expensive. NRA is the most inexpensive and easiest method to perform without changing the organization of the routine PM laboratory performance. While MODS, MTT, and BMM, have the disadvantage from the point of view of biosafety, they offer the possibility of detecting partial resistant strains. This study shows a very good level of agreement of the four low-cost methods compared to the PM for rapid detection of isoniazid, rifampicin and streptomycin resistance (Kappa values > 0.8); more standardization is needed for ethambutol.

Evaluation of rapid techniques for the detection of mycobacteria in sputum with scanty bacilli or clinically evident, smear negative cases of pulmonary and extra-pulmonary tuberculosis

The objective of the current study was to compare two rapid methods, the BBL Mycobacteria Growth Indicator Tube (MGIT TM) and Biotec FASTPlaque TB TM (FPTB) assays, with the conventional Löwenstein-Jensen (LJ) media assay to diagnose mycobacterial infections from paucibacillary clinical specimens. For evaluation of the clinical utility of the BBL MGIT TM and FPTB assays, respiratory tract specimens (n = 208), with scanty bacilli or clinically evident, smear negative cases and non-respiratory tract specimens (n = 119) were analyzed and the performance of each assay was compared with LJ media. MGIT and FPTB demonstrated a greater sensitivity (95.92% and 87.68%), specificity (94.59% and 98.78%), positive predictive value (94.91% and 99.16%) and negative predictive value (96.56% and 90.92%), respectively, compared to LJ culture for both respiratory tract and non-respiratory tract specimens. However, the FPTB assay was unable to detect nontuberculous mycobacteria and few Mycobacterium tuberculosis complex cases from paucibacillary clinical specimens. It is likely that the analytical sensitivity of FPTB is moderately low and may not be useful for the direct detection of tuberculosis in paucibacillary specimens. The current study concluded that MGIT was a dependable, highly efficient system for recovery of M. tuberculosis complexes and nontuberculous mycobacteria from both respiratory and non-respiratory tract specimens in combination with LJ media.

Use of three rapid detection systems to evaluate the prevalence and dissemination of Salmonella in a Brazilian poultry slaughterhouse

Prevalence and dissemination of Salmonella in a Brazilian poultry slaughterhouse were evaluated by three rapid detection systems (SS/SV(TM), VICAM, OSRT(TM), Unipath/Oxoid, and REVEAL(TM), Neogen), plus the conventional procedure. The carcasses were sampled after bleeding (P1), defeathering (P2), evisceration (P3), washing (P4), chilling (P5) and the packaged end-product (P6). In the first set of carcasses, the Salmonella incidence determined by the conventional method was 38.3% and 22.5% by SS/SV(TM). In the set for evaluation of OSRT(TM), the number of positive samples was the same detected by the cultural procedure (49.0%). In the third set, the positivity by the conventional procedure was 33.3%, and 5.0% by REVEAL(TM). The comparisons of positives in the first and third sets of carcasses were significantly different (P < 0.05). The positivity for Salmonella, in carcasses at P1 to P6, as determined by at least one of the methods, was 47.5%, 47.5%, 32.5%, 30.0%, 30.0% and 37.7%, respectively.

Microbiological quality and safety of minimally processed vegetables marketed in Campinas, SP-Brazil, as assessed by traditional and alternative methods

In this study, a total of 172 samples of minimally processed vegetables (MPV) were collected from supermarkets in the city of Campinas, Brazil. The MPV were analyzed using traditional and/or alternative methods for total aerobic mesophilic bacteria, total coliforms, Escherichia coil, coagulase positive staphylococci, Salmonella and Listeria monocytogenes. All the MPV analyzed presented populations of aerobic mesophilic microorganisms and total coliforms were >4 log(10) CFU/g and 1.0-3.4 log(10) CFU/g, respectively. E. coil was enumerated in only 10 samples out of 172 collected, while none of the 172 samples of MPV presented contamination by coagulase positive Staphylococcus (<10(1) CFU/g). Among the four methods used for detection of Salmonella in MPV (Vidas, 1,2 Test, Reveal, and Traditional), when Reveal was used a total of 29 positive samples were reported. For L monocytogenes, the four methods tested (Vidas, Vip, Reveal, and traditional) performed similarly. The presence of Salmonella and L monocytogenes in MPV was confirmed in one (watercress) and two samples (watercress and escarole), respectively. In conclusion, it has been observed that the microbiological quality of MPV commercialized in Campinas is generally satisfactory. Besides, the choice of microbiological method should be based not only on resource and time issues, but also on parameters such as sensitivity and specificity for the specific foods under ahalysis. (C) 2012 Elsevier Ltd. All rights reserved.

Performance of a chromogenic medium for the isolation of Listeria monocytogenes in food

According to the producers, CHROMagar (TM) Listeria medium comes to facilitate the detection, differentiating Listeria monocytogenes from the other species, directly on the isolation process, allowing final results in 72 h, while the traditional method takes up to 10 days. A total of 120 food samples of sliced cooked ham, ground beef and frankfurters was analyzed. From 151 colonies presenting typical L. monocytogenes characteristics on CHROMagar (TM) Listeria (bluish, surrounded by a white halo), only 95 (62.9%) were confirmed as L. monocytogenes. The medium was highly sensitive to detect L. monocytogenes in ground beef and frankfurter, but not in sliced ham. (c) 2007 Elsevier Ltd. All rights reserved.

Performance of Petrifilm Aerobic Count plates on enumeration of lactic acid bacteria in fermented milks

This study aimed to compare Petrifilm Aerobic Count (AC) plates and the conventional pour plate methodology using the de Man-Rogosa-Sharpe (MRS) agar for the enumeration of lactic acid bacteria (LAB) in fermented milks (FMs), with different starter cultures added. FM samples (n = 66) were collected and plated on both methodologies, with incubation under anaerobic conditions at 35C for 48 h. The count results were compared by analysis of variance (P <= 0.05) and regression analysis. No differences between the mean counts obtained by both methodologies were observed, even when distinct FMs were compared. Considering all samples, a high correlation level was obtained between Petrifilm AC and MRS agar (r = 0.92), but these indexes were lower in FMs with Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus (r = 0.90) and Lactobacillus fortis (r = 0.81). Despite some slight interferences, Petrifilm AC has proven to be a convenient methodology on enumerating LAB in FM.

Iron oxide/gold core/shell nanomagnetic probes and CdS biolabels for amplified electrochemical immunosensing of Salmonella typhimurium

There is an imminent need for rapid methods to detect and determine pathogenic bacteria in food products as alternatives to the laborious and time-consuming culture procedures. In this work, an electrochemical immunoassay using iron/gold core/shell nanoparticles (Fe@Au) conjugated with anti-Salmonella antibodies was developed. The chemical synthesis and functionalization of magnetic and gold-coated magnetic nanoparticles is reported. Fe@Au nanoparticles were functionalized with different self-assembled monolayers and characterized using ultraviolet-visible spectrometry, transmission electron microscopy, and voltammetric techniques. The determination of Salmonella typhimurium, on screen-printed carbon electrodes, was performed by square-wave anodic stripping voltammetry through the use of CdS nanocrystals. The calibration curve was established between 1×101 and 1×106 cells/mL and the limit of detection was 13 cells/mL. The developed method showed that it is possible to determine the bacteria in milk at low concentrations and is suitable for the rapid (less than 1 h) and sensitive detection of S. typhimurium in real samples. Therefore, the developed methodology could contribute to the improvement of the quality control of food samples.

Blood culture-based diagnosis of bacteraemia: state of the art.

Blood culture remains the best approach to identify the incriminating microorganisms when a bloodstream infection is suspected, and to guarantee that the antimicrobial treatment is adequate. Major improvements have been made in the last years to increase the sensitivity and specificity and to reduce the time to identification of microorganisms recovered from blood cultures. Among other factors, the introduction in clinical microbiology laboratories of the matrix-assisted laser desorption ionization time-of-flight mass spectrometry technology revolutionized the identification of microorganisms whereas the introduction of nucleic-acid-based methods, such as DNA hybridization or rapid PCR-based test, significantly reduce the time to results. Together with traditional antimicrobial susceptibility testing, new rapid methods for the detection of resistance mechanisms respond to major epidemiological concerns such as methicillin-resistant Staphylococcus aureus, extended-spectrum β-lactamase or carbapenemases. This review presents and discusses the recent developments in microbial diagnosis of bloodstream infections based on blood cultures.

Childhood community-acquired pneumonia

Background: Community-acquired pneumonia is a leading cause of morbidity and mortality in children worldwide. New, rapid methods are needed to improve the microbiologic diagnosis of pneumonia in clinical practice. The increasing incidence of parapneumonic empyema in children accentuates the importance of the identification of the causative agent and clinical predictors of empyema. Aims and methods: Two prospective studies were conducted to find feasible diagnostic methods for the detection of causative agents of pneumonia. The usefulness of pneumolysin-targeted real-time PCR in the diagnosis of pneumococcal disease was studied in children with pneumonia and empyema, and the clinical utility of induced sputum analysis in the microbiologic diagnosis of pneumonia was investigated in children with pneumonia. In addition, two retrospective clinical studies were performed to describe the frequency and clinical profile of influenza pneumonia in children and the frequency, clinical profile and clinical predictors of empyema in children. Results: Pneumolysin-PCR in pleural fluid significantly improved the microbiologic diagnosis of empyema by increasing the detection rate of pneumococcus almost tenfold to that of pleural fluid culture (75 % vs. 8 %). In whole blood samples, PCR detected pneumococcus in only one child with pneumonia and one child with pneumococcal empyema. Sputum induction provided good-quality sputum specimens with high microbiologic yield. Streptococcus pneumoniae (46 %) and rhinovirus (29 %) were the most common microbes detected. The quantification results of the paired sputum and nasopharyngeal aspirate specimens provided support that the majority of the bacteria (79 %) and viruses (55 %) found in sputum originated from the lower airways. Pneumonia was detected in 14 % of children with influenza infection. A history of prolonged duration of fever, tachypnea, and pain on abdominal palpation were found to be independently significant predictors of empyema. Conclusions: Pneumolysin-targeted real-time PCR is a useful and rapid method for the diagnosis of pneumococcal empyema in children. Induced sputum analysis with paired nasopharyngeal aspirate analysis can be of clinical value in the microbiologic diagnosis of pneumonia. Influenza pneumonia is an infrequent and generally benign disease in children with rare fatalities. Repeat chest radiograph and ultrasound imaging are recommended in children with pneumonia presenting with clinical predictors of empyema and in children with persistent fever and high CRP levels during hospitalization.

Evaluation of the BAX® system for the detection of Salmonella spp. in naturally contaminated chicken meat

The aim of this study was to verify the efficiency of the BAX® system for the detection of Salmonella spp. in raw chicken meat. The conventional culture method (IN 62, MAP) was used as a reference method. A total of 8,813 chicken carcass samples were analyzed. In the first part of the study, 1,200 samples were analyzed using the BAX® System and the conventional culture method. In the second part, 7,613 samples were analyzed by the BAX® system, and the conventional method was used only for samples that tested positive for Salmonella spp. by the BAX® system. The sensitivity, specificity, relative accuracy, positive predictive value, and negative predictive value obtained in the first part of this study were 100%, 92.3%, 96.4%, 53.3% and 100%, respectively. The BAX® system showed no false-negative results and reduced the time to obtain presumptive positive results. It is a suitable method for use in laboratories that perform a large number of food samples analyses daily. However, the conventional method is still required to confirm the presence of Salmonella spp. in samples that test positive using the BAX® system.

Estudio de las comunidades microbianas de embutidos fermentados ligeramente acidificados mediante técnicas moleculares. Estandarización, seguridad y mejora tecnológica.

Los embutidos fermentados ligeramente acidificados son un grupo de productos tradicionales mediterráneos, caracterizados por un pH superior a 5,3. Para un control eficiente de la seguridad microbiológica de los embutidos se necesitan técnicas rápidas para la identificación y recuento de los microorganismos patógenos a estudiar. En el presente trabajo, se desarrolló una técnica para la enumeración de L. monocytogenes que combinó el método del número más probable y la identificación mediante PCR específica. Para la detección de Salmonella spp. y L. monocytogenes se desarrolló un sistema de PCR-multiplex que permitió la identificación de ambos patógenos de forma simultánea en una sola reacción. El estudio de la calidad microbiológica de los embutidos fermentados ligeramente acidificados se completó con la caracterización de las comunidades microbianas más importantes en estos productos. Se identificaron a nivel de especie los aislados de bacterias del ácido láctico (BAL), de enterococos y de cocos gram-positivos catalasa-positivos (CGC+). Posteriormente se realizó una tipificación molecular de los mismos mediante RAPD y análisis del perfil plasmídico y se estudiaron las principales características de interés higiénico-sanitario y tecnológico de las cepas. Mediante PCR se identificó Lactobacillus sakei como la especie predominante (74%), seguida por Lactobacillus curvatus (21,2%). La actividad aminoácido-descarboxilasa se asoció a la especie L. curvatus (el 66% de los aislados presentaron esta actividad). La identificación de los enterococos se realizó mediante PCR-multiplex y por secuenciación del gen sodA. Enterococcus faecium fue la especie de enterococos predominante (51,9%) seguida por Enterococcus faecalis (14,2%). Todas las cepas de E. faecalis presentaron genes asociados a factores de virulencia. E. faecalis presentó mayor resistencia a antibióticos que el resto de las especies de enterococos estudiadas. Tan sólo una cepa de E. faecium presentó el genotipo vanA (que confiere resistencia de alto nivel a la vancomicina). La identificación de los aislados de CGC+ (mediante PCR específica y amplificación de la región intergénica 16S-23S ARNr) demostró que Staphylococcus xylosus es la especie predominante en los embutidos fermentados ligeramente acidificados (80,8%). La amina biógena más común en los CGC+ fue la feniletilamina, producida por un 10,8% de aislados. Un pequeño porcentaje de aislados fueron mecA+ (4,6%), presentando además resistencia a múltiples antibióticos. El potencial enterotoxigénico de las cepas de CGC+ fue muy reducido (3,3% de los aislados), detectándose únicamente el gen entC. El estudio pormenorizado de las comunidades bacterianas de interés permitió la selección de 2 cepas de L. sakei y 2 cepas de S. xylosus con características tecnológicas e higiénico-sanitarias óptimas. Para evaluar su efectividad como cultivos iniciadores se elaboraron dos tipos de embutidos ligeramente ácidos, chorizo y fuet, inoculados con microorganismos patógenos (Salmonella spp., L. monocytogenes y S. aureus). El uso de cultivos iniciadores permitió el control de L. monocytogenes, Enterobacteriaceae y Enterococcus así como del contenido en aminas biógenas. Los recuentos de Salmonella spp. disminuyeron de forma significante durante la maduración de los embutidos, independientemente del uso de cultivos iniciadores. El uso del tratamiento de alta presión (400 MPa) en los embutidos madurados consiguió la ausencia de Salmonella spp. en los lotes tratados.

Detection of Listeria sp in meat and meat products using TECRA Listeria visual immunoassay and biocontrol visual immunoprecipitate assay for Listeria immunoassays and a cultural procedure

The routine methods for detecting Listeria sp. in foods are time consuming and involve using selective enrichments and plating on agars. In this study, the presence of Listeria sp. in 120 meat and meat product samples was investigated by two rapid immunoassays (TECRA Listeria Visual Immunoassay [VIA] and BioControl Visual Immunoprecipitate Assay [VIP] for Listeria) and a cultural procedure. The cultural method of detecting Listeria sp. followed Canada's Health Protection Branch Method, and the rapid tests followed the manufacturers' instructions. The agreement between the cultural and the rapid tests was established at a confidence limit of 95%. Seventy-nine samples (65.8%) were Listeria sp. positive in at least one of the three tests. There was no statistically significant difference between the cultural procedure and any of the rapid immunoassays. The agreement rates between the VIA and the cultural method and between the VIP and the cultural method were 87 and 84%, respectively. Both tests - the VIA and VIP - proved to be rapid, efficient and easy to perform.