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Objectives: To quantify the workload and cost overload that the COVID-19 pandemic has meant for a Clinical Microbiology laboratory in a real-life scenario., Methods: We compared the number of samples received, their distribution, the human resources, and the budget of a Microbiology laboratory in the COVID pandemic (March-December 2020) with the same months of the previous year., Results: the total number of samples processed in the Clinical Microbiology laboratory in March to December 2020 increased 96.70% with respect to 2019 (from 246,060 to 483,993 samples), reflecting an increment of 127.50% when expressed as samples/1000 admissions (from 6057 to 13,780). The increase in workload was mainly at the expense of the virology (+2058%) and serology (+86%) areas. Despite additional personnel hiring, the samples processed per technician increased 12.5%. The extra cost attributed to Microbiology amounts to 6,616,511 euros (114.8%)., Conclusions: This is the first study to provide quantitative figures about workload and cost increase caused by the COVID-19 in a Microbiology laboratory., Competing Interests: Declaration of Competing Interests The authors report no conflicts of interest relevant to this article., (Copyright © 2021 Elsevier Inc. All rights reserved.)

SARS-CoV-2 pandemic shows the importance of having efficient virus diagnosis, especially in groups of particular relevance such as health care professionals, without involving a large economic expense. This is a prevalence study carried out in 7400 health care professionals in a 1350-bed hospital in Madrid, Spain. Pools of 10 samples were performed, using the Xpert® Xpress SARS-CoV-2 test for the diagnosis from clinical samples of nasopharyngeal exudate. A previous study was performed to evaluate the effect of the dilution in terms of sensitivity. The estimated sensitivity was over 95%. A total of 740 pools were performed, with a final result of 218 health care professionals being positive. Using the pooling system, the reagent cost reduction to the institution was 75.3%. It can be concluded that the described sample pooling system is a useful and efficient tool in the diagnosis of SARS-CoV-2 in certain groups, assuming a cost reduction without reducing the sensitivity., (Copyright © 2021. Published by Elsevier Inc.)

Clostridium difficile (CD) diagnosis is very varied and under discussion. Different research groups disagree on the clinical significance of patients with negative direct toxin and positive polymerase chain reaction (PCR) or even more with direct toxin and glutamate dehydrogenase (GDH) both negatives, but CD detected by toxigenic culture (TC). The objective was to analyze the characteristics of patients with 3 different diagnostic criteria. We compared these 3 groups of patients: group 1: (GDH+/direct toxin+/PCR+), group 2: (GDH+/direct toxin-/PCR+) and group 3: (GDH-/direct toxin-/PCR not done/TC+). The proportion of patients with CD infection (CDI) (not colonization) for groups 1 to 3 was, respectively, 90.3%, 95.4%, and 59.1%. No differences between severity (40.8%, 38.5%, 27.3%), recurrence (20.3%, 24.1%, 7.6%), or related mortality (12.5%, 5.2%, 0%) were found within the 3 groups of patients. Laboratory clinical results should not be used as the only tool to differentiate CDI versus colonization or severity. We recommend that PCR or a second-look TC be performed on all patients., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Background: Clostridium difficile infection (CDI) causes increased morbidity and mortality. Clinical data cannot clearly predict poor CDI outcome. Data on the value of microbiological predictors is scarce., Objective: To identify early predictors of poor outcome of CDI., Methods: We prospectively included patients with CDI aged >2years. Clinical, immunological (Toxin B IgG/Ig A and Toxin A IgG/Ig A), microbiological factors (bacterial load, toxin quantification, sporulation, germination, and metronidazole susceptibility) were evaluated to identify early independent predictors of poor outcome., Results: We identified 204 cases of CDI; outcome was poor in 22.1%. Advanced age, presence of comorbidities, leukocytosis and high toxigenic C. difficile load were independently associated with poor outcome. We could not demonstrate this correlation for antitoxin antibodies., Conclusion: We identified high bacterial load as a microbiological predictor of poor outcome. We propose this factor to be included in combined clinical and microbiological prediction rules of poor outcome in CDI., (Copyright © 2017 Elsevier Inc. All rights reserved.)

We compared in an vitro model the yields of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and conventional culture (CC) for the detection of catheter colonization with superficial catheter samples (SS). We used blood culture bottles (BCB) with an inserted cannula and incubated at 37 °C. The BCB were manipulated with different contaminations and when a BCB turned positive, SS were obtained to perform both techniques. To compare both techniques we analyzed the mean time to colonization (MTC) and the mean time to a result (MTR). The MTC (SD, days) by CC and MALDI-TOF was as follows: hub, 0.59 (0.79) versus 1.07 (1.39), P=0.06; surface: 0.62 (0.67) versus 0.82 (0.81), P<0.001. The MTR (SD, days) of CC and MALDI-TOF was as follows: hub: 1.58 (0.79) versus 2.25 (1.48), P=0.04; surface: 1.62 (0.67) versus 1.95 (0.80), P<0.001. In general, the use of MALDI-TOF performed directly with SS was no better than CC and did not anticipate colonization results., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Present guidelines recommend culturing only central venous catheter (CVC) tips from patients with suspected catheter-related bloodstream infection (CR-BSI). However, a high proportion of these suspicions are not confirmed. Moreover, CVC tip culture increases laboratory workload, and reports of colonization may be meaningless or misleading for the clinician. Our working hypothesis was that CVC tips should be refrigerated and cultured only in patients with positive blood cultures. We evaluated the effect of 6-day refrigeration of 215 CVC tips. We selected all the catheters with a significant count according to the Maki's roll-plate technique and randomly assigned them to 2 groups. In group A, the catheters were recultured after 24 h of refrigeration, and in group B, the catheters were recultured after 6 days more of refrigeration, so that the refrigeration time evaluated would be of 6 days. The yield of refrigerated CVC tips that grow significant colony counts of primary culture in group B was compared with the yield of refrigerated catheter tips in group A. The difference showed that 6-day refrigeration reduced the number of significant CVCs by 15.2%. Only 61 CVCs were obtained from patients with CR-BSI, and in most of them, blood cultures were already positive before CVC culture, so only 0.91% of the CR-BSI episodes would have been misdiagnosed as culture negative after refrigeration. Refrigeration of CVC tips sent for culture and culturing only those from patients with positive blood cultures reduce the workload in the microbiology laboratory without misdiagnosing CR-BSI.

The in vitro activities of amphotericin B, itraconazole, and voriconazole against 283 clinical isolates of Aspergillus fumigatus were studied by comparing the E test method with the reference procedure NCCLS (CLSI) M-38A. The methods were considered to agree when the results of the MICs by E test were within +/-2 dilutions of the MICs obtained by CLSI M-38 A. Agreement of readings at 24, 48, and 72 h of incubation was as follows: amphotericin B: 4.2%, 98%, and 40.6%; itraconazole: 92.5%, 100%, and 89.9%; and voriconazole: 98.9%, 100%, and 99.7%. The correlation between methods to classify the strains as "susceptible" or "resistant" was very good for itraconazole and voriconazole after 48 h of incubation, but 23% of the strains were incorrectly classified by E test for amphotericin B. The E test is an efficacious method for antifungal susceptibility testing in A. fumigatus for itraconazole and voriconazole when the plates are read after 48 h of incubation. The use of the E test to study the activity of amphotericin B should be avoided.

The aim of the study was to assess of the role of intraoperative cultures taken at the end of major heart surgery (MHS) in the prediction of postoperative mediastinitis (PM) in patients undergoing MHS over a 6-month period in a tertiary university hospital. Just before wound closure, a sample of the sternal border was taken, swabbing back and forth the sternal border and the subcutaneous tissues. A second sample was taken after irrigation of the deep mediastinal structures with 10 mL of Ringer lactate. Swabs were processed semiquantitatively and the mediastinal fluid with a quantitative technique. The observation of one or more colonies per plate was considered a positive culture. Cultures obtained at the end of 229 surgical interventions (227 patients) were positive with the semiquantitative or with the quantitative procedures in 31.0% (95% confidence interval [CI], 25.1-37.4%) and 34.5% (95% CI, 28.4-41.0%) of the times, respectively (P = NS). The number of microorganisms isolated in the wound swab or mediastinal fluid was 91 and 110, respectively. Of the 227 patients, 7 developed an episode of PM (3.1%; 95% CI, 1.2-6.2%) after a median time of 11 days (range, 5-19 days). The microorganisms causing the 7 cases of mediastinitis were not isolated in the intraoperative cultures in any of the cases. The value of intraoperative cultures as a test for prediction of PM depending on the breakpoint chosen were as follows: sensitivity (0%), specificity (66.2-97.3%), and positive (0%) and negative predictive values (96.8-98.0%). We recommend against surveillance cultures taken intraoperatively in patients undergoing MHS.

This study compared the acridine orange and Gram stains of an external smear of intravascular catheter-tip segments with the culture results obtained 24 to 48 h later. Both staining techniques were randomly assigned to be performed either before (group A) or after (group B) rolling on the agar plate. Of the 425 catheter tips processed, 25.7% were significantly colonized and 6.1% were from patients with catheter-related bloodstream infections (CRBSIs). The yield of group A was superior to that of group B for the prediction of colonization (sensitivity, 94.3%/69.6%; specificity, 92.4%/96.2%; positive predictive value (PPV), 80.6%/86.7%; negative predictive value (NPV), 98.0%/90.0%; and full concordance, 91.9%/89.3%). The values for the prediction of CRBSIs were as follows for group A and group B: sensitivity, 100%/69.2%; specificity, 96.3%/100%; PPV, 86.7%/100.0%; NPV, 100%/93.9%; and full concordance, 97.0%/94.7%. Catheter-tip staining before culture is an easy-to-perform, cheap, and effective procedure to anticipate catheter colonization and rule out CRBSIs.

The in vitro activities of amphotericin B, itraconazole, and voriconazole against 279 clinical isolates of Aspergillus fumigatus were studied by comparing Sensititre YeastOne with the reference method NCCLS (CLSI) M38-A. The methods were considered to agree when the results of the MICs by Sensititre were within 2 dilutions of the MICs obtained by NCCLS M38-A. Agreement of readings at 24, 48, and 72 h was as follows: amphotericin B (0%, 31.5%, 82.1%), itraconazole (86.7%, 98.3%, 98.2%), and voriconazole (92.8%, 98.3%, 98.9%). Sensititre YeastOne is a suitable alternative for the determination of the MICs of itraconazole and voriconazole against A. fumigatus when results are read at 48 h of incubation.

We compared the efficiency of Czapeck agar and Sabouraud dextrose agar irradiated to detect Aspergillus conidia in air. Both media were equally suitable. Czapeck agar should be used in institutions interested only in Aspergillus surveys, and Sabouraud agar should be used in those institutions interested in all sorts of filamentous fungi.

The level of procalcitonin is undetectable in healthy individuals and slightly increased in viral infections and noninfectious inflammatory responses. It has been described to be notably increased in bacterial, parasitic, or fungal infections. Procalcitonin has been reported to be a reliable marker for severe bacterial infections, although it has mainly been studied in specific entities or in selected groups of patients. We prospectively determined the procalcitonin level in 103 unselected febrile hospitalized patients. Most of them had a proven (39) or probable bacterial infection (44). Procalcitonin was more frequently positive in bacteremic patients (p = 0.01), in patients with a proven bacterial infection (p < 0.01), and in those with a high sepsis score (p < 0.005), however; when cases with proven bacterial infection were considered as a reference, the sensitivity of the test was only 54% and the specificity 70%. Procalcitonin determination should not be included systematically in the screening of febrile hospitalized patients.

Reduced susceptibility to fluconazole (RSF) is relatively common in non-albicans Candida isolates and in Candida albicans recovered from HIV-infected patients with relapsing Candida stomatitis or esophagitis. However, little clinical data on bloodstream infections caused by C. albicans with RSF is available. We analyzed 116 episodes of C. albicans fungemia detected over an 11-year period. Four patients (3.4%) had a blood isolate of C. albicans with RSF. Fluconazole MICs were 16 (3 SDD strains) and 128 microg/ml (1 resistant strain), respectively. Three of the patients were HIV (+) and the fourth was a liver transplant recipient. All of them had been previously treated with an azole compound. The liver recipient had breakthrough fungemia while being treated with 400 mg of preemptive fluconazole despite having an MIC of 16 microg/ml. Fluconazole clinical failure was documented in two of the remaining three cases. Only five other patients with C. albicans fungemia caused by fluconazole-resistant strains (>or=64 microg/ml) are described in the literature. Candida albicans fungemia produced by strains with RSF is still uncommon. It should be suspected in patients previously treated with azole agents or with breakthrough fungemia. In our experience, fluconazole remains a safe option for the treatment of most C. albicans fungemias, although surveillance seems advisable.

We evaluated the upgraded Amplified Mycobacterium Tuberculosis Direct Test kit (AMTD) (Gen-Probe Inc.) for the direct detection of Mycobacterium tuberculosis in respiratory and non-respiratory specimens, and compared the results between the traditional 30,000 RLUs cutoff criteria (C) and three equivocal ranges (30,000-100,000, R1; 30,000-500,000, R2; and 30,000-1,000,000, R3). We tested 663 respiratory and 238 non-respiratory samples from 464 patients. The gold standard was considered to be the combination of culture and clinical data. One hundred and nineteen samples were from 56 patients with pulmonary tuberculosis, and 36 samples were from 19 patients with extrapulmonary tuberculosis. When C criteria was applied, the sensitivity and specificity values were 90.8 and 93.0% for respiratory specimens, while they were 88.9 and 92.1% for non-respiratory specimens (p = NS). The sensitivity was significantly higher in smear-positive specimens (96.7%) than in smear-negative ones (81.0%) (p < 0.05). When compared with C criteria, the overall sensitivity was maintained at 90.3% for R1 criteria, and slightly decreased to 89.7% for R2 and R3 criteria (p = NS). Overall, specificity increased significantly from 92.9% (C) to 97.5% (R1), 99.1% (R2), and 99.2% (R3). Application of R2 or R3 criteria improved significantly the specificity of the test with little decrease in sensitivity.

This study aims to evaluate the performance of a new vial (Myco/F Lytic) for the detection of mycobacteria from blood specimens. This vial is monitored in the BACTEC 9000 blood culture system. We compared it with the traditional method routinely used in our laboratory, which is a lysis-centrifugation based procedure. Of 275 samples tested in parallel by both methods, 23 from 20 patients grew mycobacteria (18 Mycobacterium avium complex, 4 M. tuberculosis and 1 M. simiae); 11 isolates were recovered using both systems, 12 were isolated with the Myco/F Lytic medium only, and none were isolated using the traditional method only (p < 0.05). Blood was the diagnostic sample for 12 patients with the Myco/F Lytic system and only 7 with the traditional system. The mean time to detection of mycobacteria with Myco/F Lytic medium was 17 days, whereas it was 44 days with the traditional method (p < 0.001). Identification by DNA probes was performed directly from the Myco/F Lytic bottle. Myco/F Lytic is a rapid, simple, safe and highly reliable diagnostic method for the detection of mycobacteria in blood.

The novel 8-methoxyquinolone, moxifloxacin (Bay 12-8039), was compared with ciprofloxacin and eight other antimicrobials for activity against 425 strains Gram-positive clinical isolates, including 73 methicillin-resistant staphylococci, 35 vancomycin-resistant enterococci, and 80 penicillin- or eythromycin-resistant streptococci. Overall, 82% of the strains were inhibited at < or = 2 micrograms/mL. Moxifloxacin was more active than ciprofloxacin against staphylococci (8- to 32-fold), enterococci (0- to 16-fold), pneumococci (16-fold) and other streptococci (4- to 16-fold) when MIC90 results were compared. Moxifloxacin demonstrated good activity against all Gram-positive isolates tested except for ciprofloxacin-resistant enterococci (MIC90, 32 micrograms/mL) and methicillin-resistant staphylococci (MIC90, 8 micrograms/mL). Clinical trials should be initiated to define the role of this new quinolone.