Rapid identification,fluconazole and micafungin susceptibility testing of Candida species from blood culture by a short incubation method.

This study aimed to develop and validate a rapid method for identification by MALDI-TOF system and determination of the susceptibility to Fluconazole and Micafungin by broth microdilution among Candidaspecies causing bloodstream infections. Subcultures from blood culture bottles were incubated for 5 hours (+/- 1h) and used to perform the tests, so that the turnaround time of rapid identification and susceptibility profile was about 5 and 24 hours, respectively. The rapid identification showed agreement of 92.05 %. Regarding the rapid broth microdilution for Fluconazole and Micafungin, the agreement was 97.06 % (p<0.001) and 100 % (p<0.001), and the Kappa coefficient was 0.91 (p<0.001) and 1.0 (p<0.001), respectively. To conclude, both rapid methods showed to be reproducible, inexpensive, easy to perform and time-saving. Thus, these methodologies could be useful to guide and adjust empirical antifungal therapy.

Evaluation of clinical and microbiological factors related to mortality in patients with Gram-negative bacterial infections treated with ceftazidime-avibactam: A prospective multicentric cohort study.

OBJECTIVES: This study aimed to evaluate the clinical and microbiological risk factors associated with mortality in patients treated with ceftazidime-avibactam for carbapenem-resistant Gram-negative bacterial infections. METHODS: This multicentric prospective cohort study included hospitalized adult patients with a microbiologically confirmed infection treated with ceftazidime-avibactam for ≥48 hours. The clinical and microbiological risk factors for 30-day mortality were evaluated using a Cox regression model. RESULTS: Of the 193 patients evaluated from the five tertiary hospitals, 127 were included in the study. Thirty-five patients (27.6%) died within 30 days. Infections with AmpC beta-lactamase-carrying bacteria were independently related to 30-day mortality (adjusted hazard ratio [aHR] 2.49, 95% confidence interval [CI] 1.28-4.84, P < 0.01) after adjusting for time from infection to antimicrobial prescription (P = 0.04). Further, these bacterial infections were also related to higher in-hospital mortality (aHR 2.17, 95% CI 1.24-3.78, P < 0.01). Only one patient developed resistance to ceftazidime-avibactam during treatment. CONCLUSIONS: Treatment with ceftazidime-avibactam had worse clinical outcomes in patients with infections with bacteria with chromosomally encoded AmpC beta-lactamase. However, these findings should be confirmed in future studies.

Rapid bacterial identification by MALDI-TOF MS directly from blood cultures and rapid susceptibility testing: A simple approach to reduce the turnaround time of blood cultures.

Antimicrobial treatment of patients with bloodstream infections (BSI) is time-sensitive. In an era of increasing antimicrobial resistance, rapid detection and identification of bacteria with antimicrobial susceptibility are critical for targeted therapy early in the disease course. This study describes the performance of a rapid method for identifying and testing antimicrobial susceptibility of Gram-negative bacteria performed directly from blood culture bottles in a routine microbiology laboratory. A total of 284, 120, and 24 samples were analyzed by rapid identification (Rid), rapid susceptibility testing (RAST), and rapid broth microdilution for polymyxin B (rMIC), respectively, and compared with standard methods. Our protocol was able to identify 93% of isolates at the species level using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). We obtained 100% agreement for RAST compared to the standard method and 96% agreement for rMIC. Our protocol has proven to be an excellent tool for rapid identification of Gram-negative bacilli causing BSIs. It can also be used in microbiology laboratory routine along with RAST and faster polymyxin microdilution, especially for carbapenemase-producing bacteria, allowing for rapid, simple, accurate, and cost-effective diagnosis.

Rapid bacterial identification by MALDI-TOF MS directly from blood cultures and rapid susceptibility testing: A simple approach to reduce the turnaround time of blood cultures

Abstract Antimicrobial treatment of patients with bloodstream infections (BSI) is time-sensitive. In an era of increasing antimicrobial resistance, rapid detection and identification of bacteria with antimicrobial susceptibility are critical for targeted therapy early in the disease course. This study describes the performance of a rapid method for identifying and testing antimicrobial susceptibility of Gram-negative bacteria performed directly from blood culture bottles in a routine microbiology laboratory. A total of 284, 120, and 24 samples were analyzed by rapid identification (Rid), rapid susceptibility testing (RAST), and rapid broth microdilution for polymyxin B (rMIC), respectively, and compared with standard methods. Our protocol was able to identify 93% of isolates at the species level using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). We obtained 100% agreement for RAST compared to the standard method and 96% agreement for rMIC. Our protocol has proven to be an excellent tool for rapid identification of Gram-negative bacilli causing BSIs. It can also be used in microbiology laboratory routine along with RAST and faster polymyxin microdilution, especially for carbapenemase-producing bacteria, allowing for rapid, simple, accurate, and cost-effective diagnosis.

Evaluation of filter paper to transport oro/nasopharyngeal samples to detect SARS-CoV-2 by RT-qPCR.

PURPOSE: To evaluate filter paper as a means to transport oro/nasopharyngeal samples from laboratories with few resources for SARS-CoV-2 detection by RT-qPCR in a central laboratory that usually performs this technique as routine. METHODS: A total of 40 specimens were evaluated in parallel by RT-qPCR carried out after RNA extraction using two different protocols: direct RNA extraction (Protocol A - reference method) and RNA extraction after impregnation in filter paper (Protocol B). RESULTS: The RT-qPCR for SARS-CoV-2 using Protocol B presented 97.22% (35/36) of agreement for SARS-CoV-2-positive samples when compared to the reference method (Protocol A), even for specimens with low viral load (increased Ct values). Noteworthy, three clinical specimens which were categorized as inconclusive by Protocol A presented amplification of both N1 and N2 targets using Protocol B, presenting positive results for SARS-CoV-2. CONCLUSION: The use of filter paper to transport oro/nasopharyngeal clinical samples presented very satisfactory results to detect SARS-CoV-2 by RT-qPCR. In addition, it proved to be a feasible and sensitive approach, being able to generate the detection of SARS-CoV-2 even at low concentrations, without presenting false-negative results.

Evaluation of Identification and Susceptibility for Candida Spp. Isolated Directly from Positive Blood Culture Bottles.

Determination of the susceptibility profile of isolates of Candida from blood culture bottles is extremely important for correctly guiding patient pharmacotherapy. The aim of this study was to compare the results of analysis of Candida isolated directly from blood culture bottles by the VITEK MS MALDI-TOF identification system and the fluconazole disk diffusion assay with those of standard identification methods. Testing directly from the bottle allowed results 24 to 48 hours quicker than the standard method. There was a categorical agreement of 51.64% (47 of 91 samples) between the results of analysis directly from the bottle and analysis by the standard method. Regarding species identification, there was 96.15% agreement for Candida parapsilosis (25 of 26 samples). Categorical agreement between the rapid and standard disk diffusion methods was 95%, and the agreement between the rapid disk diffusion method and the broth microdilution method was 97%. Only minor errors in the rapid method were observed: 3 (5%) in the standard disk diffusion method and 2 (3%) in the broth microdilution method. Our study concluded that the rapid disk diffusion method for fluconazole is a fast, easy, reproducible, and consistent method. Its timely implementation for testing antifungal agents in the clinical microbiology laboratory can help reduce profile release times, thus helping to determine the most appropriate antifungal treatment.

Rapid antimicrobial susceptibility of Enterobacteriaceae by disk diffusion directly from blood culture bottles using the EUCAST RAST breakpoints.

OBJECTIVES: To evaluate the disk diffusion technique after 4 and 6 h directly from positive blood culture bottles of Enterobacteriaceae using the rapid antimicrobial susceptibility test (RAST) breakpoints established by The European Committee on Antimicrobial Susceptibility Testing (EUCAST). METHODS: A total of 61 isolates of Escherichia coli and Klebsiella spp. were selected. The results were assessed using the RAST breakpoints (4-6h) as well as the standard breakpoints (18h) from EUCAST. RESULTS: The vast majority of the zone diameters of E. coli and Klebsiella spp. were optimally readable after 6 h of incubation. RAST at 6 h presented best results of categorical agreement (CA) and errors (CA = 94.4%, minor errors [mE] = 4.3%, major errors [ME] = 0.8% and very major errors [VME] = 0.4%) compared to RAST at 4 h (CA = 84.3%, mE = 13.0%, ME = 3.2% and VME = 0.4%). The proportion of results in the area of technical uncertainty decreased over time: from 13.8% at 4 h to 6.8% at 6 h. According to the U.S. Food and Drug Administration and ISO criteria, early readings at 6 h using the RAST breakpoints provided acceptable results (CA > 90%), whereas accuracy of results at 4 h was unacceptable (CA < 90%). CONCLUSION: These data indicate that the early readings at 6 h using the RAST breakpoints for all antibiotics tested in this study (except amikacin) may be used in the clinical microbiology laboratory to anticipate the antimicrobial susceptibility test results of blood cultures. Early readings at 4 h (RAST breakpoints) may also be used, but not for all antibiotics.

Integrating Bacterial Identification and Susceptibility Testing: A Simple and Rapid Approach to Reduce the Turnaround Time in the Management of Blood Cultures.

We evaluated a rapid bacterial identification (rID) and a rapid antimicrobial susceptibility testing by disk diffusion (rAST) from positive blood culture to overcome the limitations of the conventional methods and reduce the turnaround time in bloodstream infection diagnostics. The study included hemocultures flagged as positive by bacT/ALERT®, identification by MALDI-TOF MS, and rAST. The results were compared to identification and antimicrobial susceptibility testing (AST) results by current standard methods, after 24 h incubation. For rAST categorical agreement (CA), very major errors (VME), major errors (ME), and minor errors (mE) were calculated. A total of 524 bacterial samples isolated from blood cultures were obtained, including 246 Gram-negative (GN) and 278 Gram-positive (GP) aerobes. The overall concordance of rID was 88.6%, and it was highest among GN (96%). A total of 2196 and 1476 antimicrobial agent comparisons were obtained for GN and GP, respectively. Evaluation of rAST, CA, VME, ME, and mE disclosed 97.7, 0.7, 0.5, and 1.1% for GN and 98.0, 0.5, 0.7, and 0.8% for GP, respectively. Meropenem CA, VME, and ME were 98.3, 0.5, and 0.5%, respectively; mE was not observed. Oxacillin CA, ME, and mE were 97.4, 1.6, and 0.6%, respectively; VME was not observed. Overall, kappa scores of the results of the comparisons demonstrated the high agreement between rAST and the standard method. Identification and AST of aerobic bacteria from positive blood cultures after a short period of incubation on solid blood agar is a fast and reliable method that may improve the management of bloodstream infections.

Association between Accessory Gene Regulator Polymorphism and Mortality among Critically Ill Patients Receiving Vancomycin for Nosocomial MRSA Bacteremia: A Cohort Study.

Background. Polymorphism of the accessory gene regulator group II (agr) in methicillin-resistant Staphylococcus aureus (MRSA) is predictive of vancomycin failure therapy. Nevertheless, the impact of group II agr expression on mortality of patients with severe MRSA infections is not well established. Objective. The goal of our study was to evaluate the association between agr polymorphism and all-cause in-hospital mortality among critically ill patients receiving vancomycin for nosocomial MRSA bacteremia. Methods. All patients with documented bacteremia by MRSA requiring treatment in the ICU between May 2009 and November 2011 were included in the study. Cox proportional hazards regression was performed to evaluate whether agr polymorphism was associated with all-cause in-hospital mortality. Covariates included age, APACHE II score, initial C-reactive protein plasma levels, initial serum creatinine levels, vancomycin minimum inhibitory concentration, vancomycin serum levels, and time to effective antibiotic administration. Results. The prevalence of group I and group II agr expression was 52.4% and 47.6%, respectively. Bacteremia by MRSA group III or group IV agr was not documented in our patients. The mean APACHE II of the study population was 24.3 (standard deviation 8.5). The overall cohort mortality was 66.6% (14 patients). After multivariate analysis, initial plasma C-reactive protein levels (P = 0.01), initial serum creatinine levels (P = 0.008), and expression of group II agr (P = 0.006) were positively associated with all-cause in-hospital mortality. Patients with bacteremia by MRSA with group II agr expression had their risk of death increased by 12.6 times when compared with those with bacteremia by MRSA with group I agr expression. Conclusion. Group II agr polymorphism is associated with an increase in mortality in critically ill patients with bacteremia by MRSA treated with vancomycin.

Synthesis of isosteric triterpenoid derivatives and antifungal activity.

Dermatomycoses are among the most widespread and common superficial and cutaneous fungal infections in humans. There is an urgent need to develop efficient and non-toxic antimycotic agents with a specific spectrum of activity. Triterpenes have been demonstrated to exhibit a wide range of biological activities, including antifungal activities. In this study, through hemisynthesis, we aimed to obtain triterpene-isosteric molecules from betulinic and ursolic acids to improve the antifungal activity and spectrum of action of these compounds. Six compounds were resynthesized and tested against eleven mucocutaneous and cutaneous mycotic agents. The results of the susceptibility assays were expressed as the minimal inhibitory concentration (MIC). The MIC values of the piperazinyl derivatives of ursolic and betulinic acids that were active against pathogenic yeasts were in the range of 16-32 µg/mL and 4-16 µg/mL, respectively, whereas fungicidal effects were observed at concentrations ranging from 16 to 128 µg/mL and 8 to 128 µg/mL, respectively. The piperazinyl derivative of betulinic acid exhibited an antifungal profile similar to that of terbinafine and was the most effective derivative against dermatophytes. This strategy led to a promising candidate for the development of a new antifungal agent.

Hypermutable Pseudomonas aeruginosa in Cystic fibrosis patients from two Brazilian cities.

Hypermutable (HPM) strains of Pseudomonas aeruginosa have been found at high frequencies in cystic fibrosis (CF) patients in Europe. We report the results of testing for HPM frequencies, mutator genotype, and antimicrobial resistance of P. aeruginosa strains from Brazilian CF patients. A modified disk diffusion technique was used to quantify antibiotic-resistant subpopulations of an isolate, and estimations of the frequency of mutation to rifampin resistance were determined for 705 isolates from 149 patients attending clinics in two Brazilian cities. Mutations in the mutS gene were detected by sequencing assays. We found 194 (27.5%) HPM isolates in samples from 99 (66.4%) patients. Thirty-five HPM isolates (18.0%) from 31 (31.3%) patients exhibited a high increased spontaneous mutation rate compared with controls, and eight isolates from six patients displayed a defective mutS gene. The dominant HPM population was associated with very low antibiotic resistance levels, while HPM subpopulations were generally more resistant to antimicrobials. A relatively high prevalence of HPM P. aeruginosa in CF patients was associated with surprisingly low antibiotic resistance levels, in contrast to some earlier studies.

Macrolides decrease the minimal inhibitory concentration of anti-pseudomonal agents against Pseudomonas aeruginosa from cystic fibrosis patients in biofilm.

BACKGROUND: Biofilm production is an important mechanism for bacterial survival and its association with antimicrobial resistance represents a challenge for the patient treatment. In this study we evaluated the in vitro action of macrolides in combination with anti-pseudomonal agents on biofilm-grown Pseudomonas aeruginosa recovered from cystic fibrosis (CF) patients. RESULTS: A total of 64 isolates were analysed. The biofilm inhibitory concentration (BIC) results were consistently higher than those obtained by the conventional method, minimal inhibitory concentration, (MIC) for most anti-pseudomonal agents tested (ceftazidime: P = 0.001, tobramycin: P = 0.001, imipenem: P < 0.001, meropenem: P = 0.005). When macrolides were associated with the anti-pseudomonal agents, the BIC values were reduced significantly for ceftazidime (P < 0.001) and tobramycin (P < 0.001), regardless the concentration of macrolides. Strong inhibitory quotient was observed when azithromycin at 8 mg/L was associated with all anti-pseudomonal agents tested in biofilm conditions. CONCLUSIONS: P. aeruginosa from CF patients within biofilms are highly resistant to antibiotics but macrolides proved to augment the in vitro activity of anti-pseudomonal agents.

A six-year epidemiological survey of vulvovaginal candidiasis in cytopathology reports in the state of Rio Grande do Sul, Brazil

Candidíase Vulvovaginal (CVV) é uma infecção vaginal comum. O constante aumento da incidência da doença pode estar associado a fatores como idade, infecção por HIV, diabetes, uso de métodos hormonais de contracepção e alterações citopatológicas. O objetivo deste estudo foi avaliar a prevalência de Candida sp. em amostras de secreção vaginal no estado do Rio Grande so Sul, no período de 2005 a 2010. Trata-se de um estudo retrospectivo e observacional, por meiodo qual foram avaliados 121.328 relatórios médicos de citopatologia num período de seis anos. Foram constatados 8.582 (7,1por cento) casos positivos de Candida sp.. A idade média das pacientes era de 35 anos. Mais da metade das pacientes (53por cento) usavam anticoncepcional oral e, em 49por cento dos casos, verificou-se a existência de alterações no colo do útero. A continuidade da investigaçãoepidemiológica é necessária para o acompanhamento das tendências ao longo dos anos e para uma melhor compreensão dos fatores que predispõem à CVV no Brasil.

Microbiological quality of minimally processed vegetables sold in Porto Alegre, Brazil

Minimally processed vegetables go through various steps during their preparation, with many modifications to their natural structure. However, they must maintain the same quality as the fresh produce. The aim of the present study was to quantify mesophilic and psychrotrophic microorganisms and total and faecal coliforms, and to assess the presence of Escherichia coli, parasites, and dirt material in ready-to-eat minimally processed vegetables. Fifty-six samples of minimally processed vegetables were analysed for the presence of mesophilic and psychrotrophic microorganisms by the plate-count method. Monthly means ranged from 4.7x10(5) to 1.6x10(8) CFU/g and from 7.9x10(6) to 2.7x10(8) CFU/g, respectively for mesophilic and psychrotrophic microorganisms. Coliforms were analysed by the multiple-tube method; total coliforms ranged from <3 to ³ 2.4x10(4) MPN/g and faecal coliforms from <3 to 1.1x10(4) MPN/g. Escherichia coli was detected in eight samples. Out of 52 samples, eight (15.3 percent) contained oocysts of Eimeria spp.. Dirt matter, such as insect body parts and young mites, was also found. Contamination of faecal origin was observed in these samples, suggesting that either the sanitisation of the product was unsuccessful, or soil or irrigation water could be the source of these microorganisms.

Hortaliças minimamente processadas passam por várias etapas durante seu processamento, no qual ocorrem várias modificações de sua estrutura natural, todavia elas devem manter a mesma qualidade do produto não processado. O objetivo deste estudo foi quantificar microrganismos mesófilos e psicrótróficos, coliformes totais e fecais e verificar a presença de E. coli, parasitas e sujidades em hortaliças minimamente processadas prontas para consumo. Foram analisadas 56 amostras para mesófilos e psicrotróficos pelo método de contagem em placas, com média mensal 4,7x10(5) a 1,6x10(8) UFC/g e de 7,9x10(6) a 2,7x10(8) UFC/g, respectivamente. Os coliformes foram analisados pela técnica dos tubos múltiplos, onde coliformes totais variaram de <3 a ³ 2,4x10(4) NMP/g e coliformes fecais, de <3 a 1,1x10(4) NMP/g, e E. coli foi observada em oito amostras. De 52 amostras, 8 (15,3 por cento) apresentaram oocistos de Eimeria spp. Sujidades, como fragmentos de insetos e ácaros jovens foram encontrados. Contaminação de origem fecal foi verificada no presente estudo, sugerindo falhas nas etapas do processamento das hortaliças, ou que o solo ou a água de irrigação também poderiam ser fontes de disseminação destes microrganismos.