Search

Purpose: Blood culture (BC) is the gold standard for diagnosing blood stream infections (BSI) but is limited by long turnaround times (TAT) and low detection rate. The T2 Magnetic Resonance method (T2MR) offers a rapid, culture-independent alternative. The objective of this study was to compare the performance of the T2Bacteria assay to BCs in a real-world setting. Methods: Retrospective comparative study consisting of T2Bacteria samples and BCs sampled within 72 h from the T2Bacteria sample. The primary outcome was detections by BC and T2Bacteria, respectively. The secondary outcome was difference in TAT. Results: In total, 640 episodes were included, consisting of 640 T2Bacteria samples and 2,117 BCs. A median of three BCs was collected for each T2Bacteria sample. Overall positivity was 101 (15.8%) by either method. In 29 (28.7%) episodes, both T2Bacteria and BC were concordantly positive. In discordant episodes, 46/101 (45.5%) episodes were T2Bacteria positive/BC negative and 26/101 (25.7%) were T2Bacteria negative/BC positive (McNemar χ2, p < 0,05). In T2Bacteria positive/BC negative episodes, eight had growth of the same microorganism in a non-BC culture. Median (IQR) TAT for BC was 35 h and 30 min (25 h 50 min − 45 h 24 min), compared to 21 h and 3 min (17 h 6 min − 27 h 30 m) for T2Bacteria (p < 0.001), with longer delays for samplings occurring outside work hours. Conclusions: The study highlights a high discordance between T2Bacteria and BC and suggests complementary roles of the methods in BSI diagnostics. Furthermore, it is crucial to improve TAT by reducing preanalytical delays. [ABSTRACT FROM AUTHOR]

Rapid identification and antimicrobial susceptibility testing remain a crucial step for early efficient therapy of bloodstream infections. Traditional methods require turnaround times of at least 2 days, while rapid procedures are often associated with extended hands-on time. The Accelerate Pheno™ System provides microbial identification results within 90 min and susceptibility data in approximately 7 h directly from positive blood cultures with only few minutes of hands-on time. The aim of this study was, therefore, to evaluate the performance of the Accelerate Pheno™ System in identification and antimicrobial susceptibility testing of both Gram-positive and Gram-negative bacteria directly from clinical blood culture samples. We analyzed 108 and 67 blood culture bottles using the Accelerate PhenoTest™ BC kit with software version v1.0 and the FDA-cleared version v1.2, respectively. Reliable identification was achieved for Enterobacteriaceae, staphylococci, and enterococci, with 76/80 (95%), 42/46 (91%), and 10/11 (91%) correct identifications. Limitations were observed in the identification of streptococci, including Streptococcus pneumoniae and Streptococcus pyogenes, and coagulase-negative staphylococci. Antimicrobial susceptibility results for Enterobacteriaceae, for amikacin, ertapenem, ciprofloxacin, gentamicin, meropenem, and piperacillin-tazobactam ranged between 86 and 100% categorical agreement. Using v1.2, results for ceftazidime showed 100% concordance with the reference method. For staphylococci, the overall performance reached 92% using v1.2. Qualitative tests for detection of methicillin or macrolide-lincosamide-streptogramin B (MLSB) resistance caused major and very major errors for isolates. Overall, the present data show that the Accelerate Pheno™ system can, in combination with Gram stain, be used as a rapid complementation to standard microbial diagnosis of bloodstream infections. [ABSTRACT FROM AUTHOR]

Summary: The aim of this study was to estimate the annual burden of fungal infections in Sweden using data mainly from 2016. Data on specific populations were obtained from Swedish national data registries. Annual incidence and prevalence of fungal disease was calculated based on epidemiological studies. Data on infections due to Cryptococcus sp., Mucorales, Histoplasma capsulatum, Coccidioides immitis and Pneumocystis jirovecii were retrieved from Karolinska University Laboratory and covers only 25% of Swedish population. In 2016, the population of Sweden was 9 995 153 (49.8% female). The overall burden of fungal infections was 1 713 385 (17 142/100 000). Superficial fungal infections affect 1 429 307 people (1429/100 000) based on Global Burden of Disease 14.3% prevalence. Total serious fungal infection burden was 284 174 (2843/100 000) in 2016. Recurrent Candida vulvovaginitis is common; assuming a 6% prevalence in women. Prevalence of allergic bronchopulmonary aspergillosis and severe asthma with fungal sensitisation were estimated to be 20 095 and 26 387, respectively. Similarly, chronic pulmonary aspergillosis was estimated to affect 490 patients after tuberculosis, sarcoidosis and other conditions. Candidemia incidence was estimated to be 500 in 2016 (4.7/100 000) and invasive aspergillosis 295 (3.0/100 000). In Stockholm area, Mucorales were reported in three patients in 2015, while Cryptococcus spp. were reported in two patients. In 2016, there were 297 patients PCR positive for P jirovecii. The present study shows that the overall burden of fungal infections in Sweden is high and affects 17% of the population. The morbidity, mortality and the healthcare‐related costs due to fungal infections warrant further studies. [ABSTRACT FROM AUTHOR]

Identification of anaerobic bacteria causing blood stream infections (BSI) is challenging. This study describes the epidemiology of anaerobic BSI at a tertiary care hospital and the performance of a rapid method for identification of anaerobic bacteria from blood cultures over three years, between June 2015 and June 2018. Short-term culturing is a low-cost user-friendly method and may be used for rapid identification of bacteria from positive blood cultures by matrix-associated laser desorption ionization time of flight (MALDI-TOF). Short-term culturing is performed after Gram staining on all positive blood culture bottles (BCBs) before 10:30 a.m. in our laboratory. Successful short-term cultures were defined as growth and reliable MALDI-TOF result in maximum 8 h after culture positivity. Data pertaining to unique anaerobic episodes and short-term cultures was collected retrospectively from our laboratory information system. Overall, during the three-year period, 692 unique anaerobic episodes (including Propionibacterium spp) were isolated. A total of 17 anaerobic bacterial genera were isolated in our laboratory, with 5 GNB genera and 12 GPB genera. The most prevalent bacteria were Bacteroides spp. 266/692 (38%) , Propionibacterium spp. 128/692 (18%), Clostridium spp. 103/692 (15%) , Fusobacterium spp. 34/692 (5%), and Actinomyces spp. 34/692 (5%). We performed short-term cultures on 270/564 (48%) clinically relevant episodes (excluding Propionibacterium spp) on chocolate agar plates. Growth within 8 h from culture positivity was detected in 33/270 (12%) short-term cultures. There were 22/33 (67%) gram negative (GNB) and 11/33 (33%) gram positive bacteria (GPB). Only two genera were identified: Bacteroides spp 22/33 (67%) and Clostridium spp 11/33 (33%). Thus, short-term culturing can function as a low-cost add-on to already existing protocols involving MALDI-TOF, where both GNB and GPB can be identified. • Bacteroides spp. (38%), Propionibacterium spp. (18%) and Clostridium spp (15%) were most common. • Short-term culture followed by MALDI-TOF MS can function as an add-on to conventional methods. • The method could identify 67% of Bacteroides spp. and 33% of Clostridium spp. within 8 h. [ABSTRACT FROM AUTHOR]

Invasive mold infections are life-threatening complications in patients with hematological malignancies. Conventional microbiological methods for diagnosing invasive pulmonary mold infections have low sensitivity, and molecular methods are being developed. Detection of molds using PCR with a narrow spectrum has been reported, but data with broad-spectrum PCR are lacking. In this study, the diagnostic performance and utility of a broad-spectrum PCR (broad-spectrum PCR with subsequent electrospray ionization-mass spectrometry, PCR/ESI-MS) for detection of molds in bronchoalveolar lavage (BAL) in 27 hematological patients with a new pulmonary infiltrate was analyzed. Using the revised EORTC/MSG criteria, PCR/ESI-MS was the only positive microbiological test in patients with proven invasive mold infection (n = 2) and correctly identified all cases of probable invasive pulmonary aspergillosis (n = 5). In patients with a possible invasive mold infection (n = 5), PCR/ESI-MS was positive in three patients. Mucorales was identified with PCR/ESI-MS in four patients that were all culture negative. The PCR/ESI-MS results had a clinical impact on antifungal therapy in 12 (44%) of the patients: modification of treatment in 6 (22%) patients and discontinuation in 6 (22%) patients. This study provides proof of concept that routine use of a broad-spectrum PCR for molds in bronchoalveolar lavage in immunocompromised patients is sensitive, fast, and has an impact on clinical decision-making [ABSTRACT FROM AUTHOR]

Antimicrobial chemotherapy for septic patients begins with empirical therapy and can be subsequently revised when the results of microbiological testing become available. In recent years, a number of novel technologies for the microbiological diagnosis of sepsis have been developed that return results in a shorter timeframe compared with conventional diagnostic approaches. These novel technologies aid antimicrobial stewardship when treating septic patients by reducing the time to appropriate antimicrobial chemotherapy. Advantages and limitations of these technologies should be well understood upon their introduction in the diagnostic workflow. Increasingly popular DNA-based technologies primarily focus on the rapid identification of pathogens, but information on antimicrobial susceptibility is lacking or limited to a few clinically relevant resistance markers. Thus, DNA-based molecular techniques can complement conventional technologies but cannot replace them. On the other hand, a novel technology that provides both rapid identification of bacterial pathogens and a rapid phenotypic antibiogram with MIC values, and which starts from positive blood cultures, is a very promising approach for fast diagnosis of sepsis. To fully leverage the advantages offered by novel diagnostic technologies for sepsis requires a careful introduction into the laboratory workflow, following an evaluation by a health technology assessment approach. It may also require some reshaping of the workflow (e.g. to process the positive blood cultures on a 24/7 schedule) and of the laboratory organization (e.g. by creating a laboratory subsection for fast diagnosis of sepsis). [ABSTRACT FROM AUTHOR]

Although there are several US Food and Drug Administration (FDA)-approved/cleared molecular microbiology diagnostics for direct analysis of patient samples, all are single target or panel-based tests. There is no FDA-approved/cleared diagnostic for broad microbial detection. Polymerase chain reaction (PCR)/electrospray ionization-mass spectrometry (PCR/ESI-MS), commercialized as the IRIDICA system (Abbott) and formerly PLEX-ID, had been under development for over a decade and had become CE-marked and commercially available in Europe in 2014. Capable of detecting a large number of microorganisms, it was under review at the FDA when, in April 2017, Abbott discontinued it. This turn of events represents not only the loss of a potential diagnostic tool for infectious diseases but may be a harbinger of similar situations with other emerging and expensive microbial diagnostics, especially genomic tests. [ABSTRACT FROM AUTHOR]

Many strategies and technologies are available to improve blood culture (BC)-based diagnostics. The ideal approach to BCs varies between healthcare institutions. Institutions need to examine clinical needs and practices in order to optimize BC-based diagnostics for their site. Before laboratories consider offering rapid matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) or expensive rapid panel-based molecular BC diagnostics, they should optimize preanalytical, analytical, and postanalytical processes and procedures surrounding BC systems. Several factors need to be considered, including local resistance rates, antibiotic prescribing patterns, patient- and provider-types, laboratory staffing, and personnel available to liaise with clinicians to optimize antibiotic use. While there is much excitement surrounding new high-technology diagnostics, cost-neutral benefits can be realized by optimizing existing strategies and using available tools in creative ways. Rapid BC diagnostics should be implemented in a manner that optimizes impact. Strategies to optimize these BC diagnostics in individual laboratories are presented here. [ABSTRACT FROM AUTHOR]

Cancer patients with advanced disease display signs of immune suppression, which constitute a major obstacle for effective immunotherapy. Both T cells and NK cells are affected by a multitude of mechanisms of which the generation of reactive oxygen species is of major importance. Therefore, we hypothesized that two weeks of high-dose treatment with the anti-oxidant vitamin E may enhance NK cell function in cancer patients by protecting from oxidative stress. Seven patients with colorectal cancer (Dukes stage C and D) received a daily dose of 750 mg of vitamin E during a period of two weeks and the function, phenotype and receptor expression of NK cells were analyzed. The short-term vitamin E treatment significantly improved NK cell cytolytic activity in six out of the seven patients analyzed. The increased NK cell activity in patients’ PBMC was not due to increased numbers of NK cells or an increase in the proportion of the CD56dim NK cell subpopulation. Furthermore, neither an increased perforin expression nor an enhanced ability of NK cells to produce IFN-γ was observed as a result of vitamin E treatment. Finally, vitamin E treatment was associated with a minor, but consistent, induction of NKG2D expression in all patients analyzed. In conclusion, this pilot study demonstrates that vitamin E may boost NK cell function in patients with colorectal cancer. Further studies are warranted to explore the potential of vitamin E as an adjuvant for immunotherapy against cancer and to determine the underlying mechanism(s) behind vitamin E induced NK cell activation. [ABSTRACT FROM AUTHOR]

Dendritic cells (DC) are antigen-presenting cells (APC) that most efficiently initiate and control immune responses. Migration processes of blood DC are crucial to exert their professional antigen-presenting functions. Matrix-degrading metalloproteinases (MMP) are proteolytic enzymes, which are considered to be key enzymes in extracellular matrix (ECM) turnover and mediators of cell migration. Tissue inhibitors of metalloproteinases (TIMP) are important regulators of MMP activity. Here we investigate whether blood monocyte-derived immature DC (iDC) and mature DC (mDC) express, produce and secrete functionally active MMP-1, -2, -3 and -9 and their inhibitors TIMP-1 and -2, and examine their involvement in multiple sclerosis (MS). On mRNA level, we observed high numbers of MMP-2 and TIMP-2 mRNA expressing iDC in MS. On protein level, high percentages of MMP-1, -2 and -9 expressing iDC by flow cytometry, and high MMP-1 secretion by Western blot together with high MMP-2 and -9 activities in iDC supernatants as studied with zymography were observed. Similarly, MS is associated with high percentages of MMP-2 and -3 and of TIMP-1 expressing mDC by flow cytometry together with high MMP-3 secretion and high MMP-9 activity in culture supernatants. Spontaneous migratory capacity of both iDC and mDC over ECM-coated filters was higher in MS compared to healthy controls (HC).In conclusion, blood monocyte-derived iDC and mDC express, produce and secrete several MMP and TIMP. Alterations in these molecules as observed in MS may be functionally important for DC functioning. [Copyright &y& Elsevier]

A medical report is present on Earlier and more targeted treatment of neonatal sepsis. The article mentions about the mortality rates due to neonatal infections are unacceptably high; samples with a limited number of viable microorganisms due to slow-growing bacteria or pre-emptive antibiotic treatment may lead to false-negative results and detrimental effects.

Background: The prevalence of fungal bloodstream infections (BSI), especially candidaemia, has been increasing globally during the last decades. Fungal diagnosis is still challenging due to the slow growth of fungal microorganisms and need for special expertise. Fungal polymicrobial infections further complicate the diagnosis and extend the time required. Epidemiological data are vital to generate effective empirical treatment strategies. Objectives: The overall aim of this project is to describe the epidemiology of monomicrobial candidaemia and polymicrobial BSI, both with mixed fungaemia and with mixed Candida/bacterial BSIs. Methods: We conducted a single‐centre retrospective epidemiological study that encompasses 950,161 blood cultures during the years 2010 to 2020. The epidemiology of monomicrobial and polymicrobial candidaemia episodes were investigated from the electronic records. Results: We found that 1334 candidaemia episodes were identified belonging to 1144 individual patients during 2010 to 2020. Candida albicans was the most prevalent species detected in candidaemia patients, representing 57.7% of these episodes. Nakaseomyces (Candida) glabrata and Candida parapsilosis complex showed an increasing trend compared to previous studies, whereas Candida albicans demonstrated a decrease. 19.8% of these episodes were polymicrobial and 17% presented with mixed Candida/bacterial BSIs while 2.8% were mixed fungaemia. C. albicans and N. glabrata were the most common combination (51.4%) in mixed fungaemia episodes. Enterococcus and Lactobacillus spp. were the most common bacteria isolated in mixed Candida/bacterial BSIs. Conclusions: Polymicrobial growth with candidaemia is common, mostly being mixed Candida/bacterial BSIs. C. albicans was detected in more than half of all the candidaemia patients however showed a decreasing trend in time, whereas an increase is noteworthy in C. parapsilosis complex and N. glabrata. [ABSTRACT FROM AUTHOR]

Knowledge of infective endocarditis (IE) caused by Streptococcus dysgalactiae (SD) is limited. This study aimed to identify the clinical and microbiological features of SD-caused IE and to investigate any possible synergy between penicillin and gentamicin on SD isolates. Cases of IE 2008-2016 due to SD reported to the Swedish Registry of Infective Endocarditis (SRIE) were identified. Isolates were emm typed and synergy between antibiotics was determined in time-kill experiments. Medical records were reviewed and SD-cases were compared to cases of IE due to other pathogens reported to the SRIE. Fifty cases of SD-caused IE were confirmed. emm types stC74a, stG62647, and stG643 were most commonly encountered. The patients had a median age of 74 years (range 38-93) and were significantly older compared to patients with Staphylococcus aureus-caused IE, (65 years (p = 0.003)). The median time to diagnosis from symptom onset was 1 day for patients with SD-caused IE which was less compared to patients with IE due to the other pathogens (2-15 days). Embolization was seen in 46% and the in-hospital mortality was 8%. Etest-based methods did not indicate any synergy between penicillin and gentamicin whereas synergy was noted for four out of nine isolates applying time-kill assays. This is the largest study of SD-caused IE, a condition with an acute onset predominantly affecting elderly people. Synergy between penicillin and gentamicin against some SD isolates was distinguished but the potential benefit of this must be weighed against the risk of aminoglycoside side effects. [ABSTRACT FROM AUTHOR]

The European Confederation of Medical Mycology (ECMM) collected data on epidemiology, risk factors, treatment, and outcomes of patients with culture-proven candidaemia across Europe to assess how adherence to guideline recommendations is associated with outcomes. In this observational cohort study, 64 participating hospitals located in 20 European countries, with the number of eligible hospitals per country determined by population size, included the first ten consecutive adults with culture-proven candidaemia after July 1, 2018, and entered data into the ECMM Candida Registry (FungiScope Candi Reg). We assessed ECMM Quality of Clinical Candidaemia Management (EQUAL Candida) scores reflecting adherence to recommendations of the European Society of Clinical Microbiology and Infectious Diseases and the Infectious Diseases Society of America guidelines. 632 patients with candidaemia were included from 64 institutions. Overall 90-day mortality was 43% (265/617), and increasing age, intensive care unit admission, point increases in the Charlson comorbidity index score, and Candida tropicalis as causative pathogen were independent baseline predictors of mortality in Cox regression analysis. EQUAL Candida score remained an independent predictor of mortality in the multivariable Cox regression analyses after adjusting for the baseline predictors, even after restricting the analysis to patients who survived for more than 7 days after diagnosis (adjusted hazard ratio 1·08 [95% CI 1·04–1·11; p<0·0001] in patients with a central venous catheter and 1·09 [1·05–1·13; p<0·0001] in those without one, per one score point decrease). Median duration of hospital stay was 15 days (IQR 4–30) after diagnosis of candidaemia and was extended specifically for completion of parenteral therapy in 100 (16%) of 621 patients. Initial echinocandin treatment was associated with lower overall mortality and longer duration of hospital stay among survivors than treatment with other antifungals. Although overall mortality in patients with candidaemia was high, our study indicates that adherence to clinical guideline recommendations, reflected by higher EQUAL Candida scores, might increase survival. New antifungals, with similar activity as current echinocandins but with longer half-lives or oral bioavailability, are needed to reduce duration of hospital stay. Scynexis. [ABSTRACT FROM AUTHOR]

The T2Bacteria panel is a direct-from-blood assay that delivers rapid results, targeting E. coli, S. aureus, K. pneumoniae, A. baumanii, P. aeruginosa, and E. faecium (ESKAPE pathogens). In this study, T2Bacteria and T2Candida (targeting C. albicans/C. tropicalis, C. glabrata/C. krusei, and C. parapsilosis) were evaluated in parallel with blood cultures in 101 consecutive surgical patients with suspected intra-abdominal infection admitted to the intensive care unit or high dependency unit. Fifteen patients had bacteremia, with T2Bacteria correctly identifying all on-panel (n = 8) pathogens. T2Bacteria was positive in 19 additional patients, 11 of whom had supportive cultures from other normally sterile sites (newly inserted drains, perioperative cultures or blood cultures) within seven days. Six of these eleven patients (55%) received broad-spectrum antibiotics at the sampling time. T2Candida identified the two cases of blood-culture-positive candidemia and was positive in seven additional patients, three of whom were confirmed to have intra-abdominal candidiasis. Of four patients with concurrent T2Bacteria and T2Candida positivity, only one patient had positive blood cultures (candidemia), while three out of four patients had supporting microbiological evidence of a mixed infection. T2Bacteria and T2Candida were fast and accurate in diagnosing on-panel bloodstream infections, and T2Bacteria was able to detect culture-negative intra-abdominal infections. [ABSTRACT FROM AUTHOR]

OBJECTIVES: Ventilator-associated lower respiratory tract infections (VA-LRTIs) are associated with prolonged length of stay and increased mortality. We aimed to investigate the occurrence of bacterial VA-LRTI among mechanically ventilated COVID-19 patients and compare these findings to non-COVID-19 cohorts throughout the first and second wave of the pandemic. DESIGN: Retrospective cohort study. SETTING: Karolinska University Hospital, Stockholm, Sweden. PATIENTS: All patients greater than or equal to 18 years treated with mechanical ventilation between January 1, 2011, and December 31, 2020. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: The cohort consisted of 20,223 ICU episodes (479 COVID-19), with a VA-LRTI incidence proportion of 30% (129/426) in COVID-19 and 18% (1,081/5,907) in non-COVID-19 among patients ventilated greater than or equal to 48 hours. The median length of ventilator treatment for COVID-19 patients was 10 days (interquartile range, 5–18 d), which was significantly longer than for all other investigated specific diagnoses. The VA-LRTI incidence rate per 1,000 ventilator days at risk was 31 (95% CI, 26–37) for COVID-19 and 34 (95% CI, 32–36) for non-COVID-19. With COVID-19 as reference, adjusted subdistribution hazard ratios for VA-LRTI was 0.29–0.50 (95% CI, < 1) for influenza, bacterial pneumonia, acute respiratory distress syndrome, and severe sepsis, but 1.38 (95% CI, 1.15–1.65) for specific noninfectious diagnoses. Compared with COVID-19 in the first wave of the pandemic, COVID-19 in the second wave had adjusted subdistribution hazard ratio of 1.85 (95% CI, 1.14–2.99). In early VA-LRTI Staphylococcus aureus was more common and Streptococcus pneumoniae , Haemophilus influenzae , and Escherichia coli less common in COVID-19 patients, while Serratia species was more often identified in late VA-LRTI. CONCLUSIONS: COVID-19 is associated with exceptionally long durations of mechanical ventilation treatment and high VA-LRTI occurrence proportions. The incidence rate of VA-LRTI was compared with the pooled non-COVID-19 cohort, however, not increased in COVID-19. Significant differences in the incidence of VA-LRTI occurred between the first and second wave of the COVID-19 pandemic. [ABSTRACT FROM AUTHOR]

Background: Sepsis is associated with substantial mortality rates. Antibiotic treatment is crucial, but global antibiotic resistance is now classified as one of the top ten global public health risks facing humanity. Ozone (O3) is an inorganic molecule with no evident function in the body. We investigated the bactericide properties of ozone, using a novel system of extracorporeal ozone blood treatment. We hypothesized that ozone would decrease the concentration of viable Escherichia coli (E. coli) in human whole blood and that the system would be technically feasible and physiologically tolerable in a clinically relevant model of E. coli sepsis in swine. Methods: The E. coli strain B09-11822, a clinical isolate from a patient with septic shock was used. The in vitro study treated E. coli infected human whole blood (n = 6) with ozone. The in vivo 3.5-h sepsis model randomized swine to E. coli infusion and ozone treatment (n = 5) or E. coli infusion and no ozone treatment (n = 5). Live E. coli, 5 × 107 colony-forming units (CFU/mL) was infused in a peripheral vein. Ozone treatment was initiated with a duration of 30 min after 1.5 h. Results: The single pass in vitro treatment decreased E. coli by 27%, mean 1941 to 1422 CFU/mL, mean of differences − 519.0 (95% CI − 955.0 to − 82.98, P = 0.0281). pO2 increased (95% CI 31.35 to 48.80, P = 0.0007), pCO2 decreased (95% CI − 3.203 to − 1.134, P = 0.0069), oxyhemoglobin increased (95% CI 1.010 to 3.669, P = 0.0113). Methemoglobin was not affected. In the sepsis model, 9/10 swine survived. One swine randomized to ozone treatment died from septic shock before initiation of the treatment. Circulatory, respiratory, and metabolic parameters were not affected by the ozone treatment. E. coli in arterial blood, in organs and in aerobic and anaerobic blood cultures did not differ. Hemoglobin, leucocytes, and methemoglobin were not affected by the treatment. Conclusions: Ozone decreased the concentration of viable E. coli in human whole blood. The system was technically feasible and physiologically tolerable in porcine sepsis/septic shock and should be considered for further studies towards clinical applications. [ABSTRACT FROM AUTHOR]

The aim of the present study is to analyse the secondary bacterial infections in a large group of patients with seasonal influenza A and influenza A(H1N1) pdm09. Patients diagnosed with seasonal influenza A and influenza A(H1N1) pdm09 between 2005 and 2009 were enrolled in the study. Data was retrieved from medical records and laboratory information systems (LIS). In total, 1094 patients with laboratory confirmed influenza were studied. There were 352 patients with seasonal influenza A and 742 patients with influenza A(H1N1) pdm09. The patients with influenza A were older and had higher comorbidity than patients with influenza A(H1N1) pdm09 (P<0.001 and P<0.05, resp.). Hospital admission was higher in influenza A group (P = 0.01). In contrast, ICU admission was higher in patients with influenza A(H1N1) pdm09 than influenza A patients (P<0.05). There were higher numbers of bacterial samples taken and culture positivity in patients with influenza A than patients with influenza A(H1N1) pdm09 (P<0.0001 and P = 0.01, resp.). In both groups, the majority of the patients with positive bacterial cultures had underlying diseases. The present study shows that the patient characteristics and the frequency of secondary bacterial infections were different in patients with seasonal influenza A and in patients with influenza A(H1N1) pdm09. [ABSTRACT FROM AUTHOR]

Bloodstream infections (BSIs) are related to high mortality and morbidity. Rapid administration of effective antimicrobial treatment is crucial for patient survival. Recently developed rapid methods to identify pathogens directly from blood culture bottles speed up diagnosis of BSIs. The present study compares the performance of two rapid identification methods, FilmArray and direct MALDI‐TOF MS, on identifying microorganisms directly from positive blood culture bottles with polymicrobial growth. FilmArray and direct MALDI‐TOF MS were performed directly on positive clinical and simulated polymicrobial blood culture bottles. Assay results were compared with standard culture methods. In total, 110 polymicrobial blood culture samples, of which 96 samples contained two microorganisms while 14 samples contained three microorganisms, were studied. FilmArray was able to identify 215/234 (92.0%) of isolates detected by the standard culture method and successfully identified all microorganisms in 88/110 (80.0%) of blood culture bottles. In contrast, direct MALDI‐TOF MS was only able to identify 65/234 (27.8%) of isolates and managed to identify all microoganisms in 2/110 (2.1%) of blood culture bottles. FilmArray is a rapid method for direct identification of polymicrobial blood culture samples that can complement the conventional identification methods. Direct MALDI‐TOF MS has low performance with polymicrobial samples. [ABSTRACT FROM AUTHOR]

Short-term culture followed by MALDI-TOF MS is one of the most widely used methods for fast identification of microorganisms from blood cultures. The method identifies the vast majority of bloodstream infection pathogens in 2–6 h after positive blood culture. Transport time of blood culture bottles to laboratories is a major problem affecting total turnaround time. Therefore, many central laboratories establish satellite blood culture systems in other clinics and hospitals to allow blood culture bottles to be incubated immediately after sampling. However, positive blood culture bottles still need to be transported to the clinical microbiology laboratory for analysis. The aim of this study was to investigate how delayed analysis of positive blood culture bottles would affect the short-term culture followed by MALDI-TOF MS method. To simulate the effect of transportation and delayed analysis of blood culture bottles, 51 simulated blood culture bottles were incubated for 0, 2, 4 and 24 h at room temperature. After each time interval, a 2 to 4 h short-term culture followed by MALDI-TOF MS was performed. In addition, 257 prospective clinical positive blood culture bottles were analysed with the same method after a 24 h incubation at room temperature. In simulated samples, all (120/120) Gram-negative bacteria and 77/84 (91.6%) Gram-positive bacteria were accurately identified at species-level after a 2 h short-term culture, regardless of the duration of simulated transport time. In the clinical samples, 100/116 (86.2%) Gram-negative, and 44/141 (31.2%) Gram-positive bacteria were accurately identified at species-level after a 2 h short-term culture. After contaminants were excluded, 39/71 (54.9%) Gram-positive bacteria could be identified after 2 h. After a 4 h short-term culture, 112/116 (96.6%) Gram-negative, and 108/141 (76.6%) Gram-positive bacteria were accurately identified at species-level. Of the clinically relevant Gram-positive bacteria, 68/71 (95.8%) were identified at species-level after 4 h. Short-term culture followed by MALDI-TOF MS can provide fast and accurate results for identification of clinically relevant bacteria, despite long transportation times from satellite laboratories. The present data shows that the method can be used for identification of microorganisms from positive blood cultures transported from satellite blood culture systems. • Impact of transport time on rapid identification of positive blood cultures. • Most bacteria were reliably identified despite long transport times. • Gram-negative bacteria were identified more reliably than Gram-positive bacteria. [ABSTRACT FROM AUTHOR]

Purpose: In the management of COVID-19, knowledge is lacking on the frequency of secondary bacterial infections and on how empirical antibiotic therapy should be used. In the present study, we aimed to compare blood culture (BC) results of a COVID-19 patient cohort with two cohorts of patients without detected COVID-19. Methods: Using a retrospective cohort study design of patients subjected to BC in six tertiary care hospitals, SARS-CoV-2 positive patients from March 1 to April 30 in 2020 (COVID-19 group) were compared to patients without confirmed SARS-CoV-2 during the same period (control group-2020) and with patients sampled March 1 to April 30 in 2019 (control group-2019). The outcomes studied were proportion of BC positivity, clinically relevant growth, and contaminant growth. Results: In total 15,103 patients and 17,865 BC episodes were studied. Clinically relevant growth was detected in 197/3,027 (6.5%) BC episodes in the COVID-19 group compared to 717/6,663 (10.8%) in control group-2020 (p<0.0001) and 850/8,175 (10.4%) in control group-2019 (p<0.0001). Contamination was present in 255/3,027 (8.4%) BC episodes in the COVID-19 group compared to 330/6,663 (5.0%) in control group-2020 (p<0.0001) and 354/8,175 (4.3%) in control group-2019 (p<0.0001). Conclusion: In COVID-19 patients, the prevalence of bloodstream bacterial infection is low and the contamination rate of BC is high. This knowledge should influence guidelines regarding blood culture sampling and empirical antibiotic therapy in COVID-19 patients. [ABSTRACT FROM AUTHOR]

There are several approaches available for purifying microorganisms prior to matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) analysis. In the present study, rapid BACpro® II (Nittobo Medical Co., Ltd., Tokyo, Japan), a new application, has been compared with Sepsityper® kit (Bruker Daltonics, Billerica, USA) and an in-house method. Samples were also tested with two modules, standard and Sepsityper®, identified in the Bruker MALDI-TOF MS. The bottles having monomicrobial growth were included in the study according to Gram staining results. In total, two hundred blood culture bottles were included but there was no growth in one of the subcultures so 199 blood culture bottles were studied prospectively. With the standard MALDI-TOF MS analysis, rapid BACpro® II could successfully identify microorganisms in 174/199 (87.4%) of the bottles where Sepsityper® kit and in-house method were successful in 136/199 (68.3%) and 114/199 (57.3%), respectively. When the MALDI-TOF MS data were analysed by Sepsityper® module, the identification rates were increased to 94.4%, 82.1% and 69.8% (p < 0.001), respectively. In the Sepsityper® module, 72/73 (98.6%) of Gram-negative and 97/106 (91.5%) of Gram-positive microorganisms were detected by rapid BACpro® II method. The present study shows that rapid BACpro® II is a reliable preparation procedure and has higher rates of identification compared with Sepsityper® kit and in-house method. The use of the Sepsityper® module in blood cultures increases the chance of identification for all three methods studied. [ABSTRACT FROM AUTHOR]

Cystic fibrosis (CF) patients become colonized by pathogenic bacteria as well as by Candida species. The interplay between different microorganisms may play a key role in the prognosis of CF. The aim of the study was to analyze the coexistence patterns of bacteria and Candida spp. in sputum samples of patients with CF and to compare these patterns with the results of patients with other respiratory disorders (ORD). Sputum samples from 130 patients with CF and 186 patients with ORD were cultured on six different agar plates promoting the growth of bacteria and yeasts. Bacterial and Candida species were identified with MALDI-TOF MS. Pathogenic bacteria were found in 69.2% of the sputum samples of the CF patients, and in 44.1% the patients with ORD. CF patients tended to have growth of Pseudomonas aeruginosa and Staphylococcus aureus in sputum more often than patients with ORD. Overall, there was no difference in the coexistence of pathogenic bacteria and Candida spp. in these patient groups. However, when analyzed at the species level, P. aeruginosa and S. aureus coexisted with Candida spp. more frequently in sputum samples of CF patients compared with patients with ORD. Also, when analyzed according to age, it was shown that the adult (≥ 18 years) CF patients had a higher rate of coexistence of any pathogenic bacteria and Candida spp. than the children with CF and the adult patients with ORD. The rate for colonization with Candida together with pathogenic bacteria is increased in adult patients with CF. [ABSTRACT FROM AUTHOR]

[Display omitted] • This study provided the first species-level characterization of OFIs in HNC patients receiving RT using MALDI-TOF MS technology. • Five species including C. albicans , C. glabrata , P. kudriavzevii , C. parapsilosis , and C. tropicalis , were commonly detected in both ongoing- and post-RT patients and appeared to be the core mycobiota of OFIs in HNC. • HNC patients under ongoing-RT had more complex co-occurrence of fungal species than post-RT patients. • Despite the newly emergence of F. solani and C. jadinii , C. albicans remained the most prevalent OFIs pathogen in HNC patients. Head and neck cancer (HNC) impairs patient immunity and increases susceptibility to oral fungal infections (OFIs). Effectively treating such infections requires accurate identification of the causative pathogens. This study aimed to characterize the mycobiota profile of OFIs in HNC patients undergoing radiation treatment (RT). A 6-year retrospective analysis of oral mucosal samples from HNC patients with a history of RT and OFIs between 2014 and 2019 was conducted using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) profiling. Samples from the Clinical Microbiology Laboratory at Karolinska University Hospital were evaluated for mycobiota diversity and species co-occurrence patterns in the ongoing-RT and post-RT groups. A total of 190 oral fungi (88% Candida , 5% Pichia) were isolated from 162 HNC patients receiving RT. In the ongoing-RT group, the emergent non-albicans Candida (NAC) species; F. solani and C. jadinii , were detected for the first time. The dominant pathogens in both ongoing and post-RT groups were C. albicans , C. glabrata , P. kudriavzevii , C. parapsilosis , and C. tropicalis , as shown by Venn analysis. Network analysis revealed greater fungi diversity and multi-species co-occurrence in the ongoing-RT group. C. albicans commonly co-occurred with C. glabrata in both ongoing-RT (21%) and post-RT groups (30%). MALDI-TOF MS identified a wide range of oral fungal species in HNC patients receiving RT. While C. albicans remains the most prevalent OFIs pathogen, multi-species co-occurrence and novel NACs were noted. Understanding the ecological interactions among these causative pathogens could significantly advance the development of effective therapeutics for treating OFIs in HNC patients. [ABSTRACT FROM AUTHOR]

Summary: Objectives: To identify the epidemiology and antifungal susceptibilities of Candida spp. among blood culture isolates to identify the epidemiology and antifungal susceptibilities of Candida spp. among blood culture isolates in Sweden. Methods: The study was a retrospective, observational nationwide laboratory‐based surveillance for fungaemia and fungal meningitis and was conducted from September 2015 to August 2016. Results: In total, 488 Candida blood culture isolates were obtained from 471 patients (58% males). Compared to our previous study, the incidence of candidaemia has increased from 4.2/100 000 (2005‐2006) to 4.7/100 000 population/year (2015‐2016). The three most common Candida spp. isolated from blood cultures were Candida albicans (54.7%), Candida glabrata (19.7%) and species in the Candida parapsilosis complex (9.4%). Candida resistance to fluconazole was 2% in C. albicans and between 0% and 100%, in non‐albicans species other than C. glabrata and C. krusei. Resistance to voriconazole was rare, except for C. glabrata, C. krusei and C. tropicalis. Resistance to anidulafungin was 3.8% while no Candida isolate was resistant to amphotericin B. Conclusions: We report an overall increase in candidaemia but a minor decrease of C. albicans while C. glabrata and C. parapsilosis remain constant over this 10‐year period. [ABSTRACT FROM AUTHOR]

Summary: We evaluated the performance of Yeast Traffic Light PNA FISH (YTL PNA FISH) in identification of Candida spp. from blood cultures. A total of 200 new episodes of candidaemia were analysed prospectively. The YTL PNA FISH results were reported to the clinicians and data on antifungal therapy were documented. In total, there were 164/200 (82%) positive blood culture bottles with monomicrobial growth. Coverage of monomicrobial yeast was 150/164 (91.5%). YTL PNA FISH could identify 23/24 (95.8%) Candida spp. in bottles with concomitant growth of bacteria and one yeast. Growth of two or more different yeast was observed in 12/200 (6%) blood culture bottles and the method could identify all yeast in 8/12 (66.7%). Data on antifungal treatment were available for 181/200 patients (90.5%). In 132/137 (96.4%) samples from patients without antifungal treatment, YTL PNA FISH could identify the Candida spp. or gave a negative result for yeast not included in panel, and based on the result guide appropriate antifungal therapy the same day when the blood culture bottle signalled positive. This study shows that YTL PNA FISH is a rapid, reliable diagnostic method which significantly reduces time delay for choice of appropriate antifungal therapy for critically ill patients. [ABSTRACT FROM AUTHOR]

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and chromogenic media are widely used in clinical microbiology laboratories to facilitate the rapid selection and identification of pathogens. The aim of this study was to evaluate whether usage of chromogenic media limits the diagnostic performance of MALDI-TOF MS for microbial identification. A total of 386 microorganisms collected and analyzed at five laboratories were included. Isolates were cultured on relevant chromogenic media and non-selective agar plates in parallel and identified using the Bruker MALDI-TOF MS. Among the tested isolates, no misidentification was recorded and there was no medium-related difference in the identification level. However, score values were overall slightly but significantly lower for isolates grown on chromogenic media. In conclusion, the use of chromogenic culture media tested here had no relevant impact on MALDI-TOF MS performance for diagnostic purposes. [ABSTRACT FROM AUTHOR]

The clinical demand on rapid microbiological diagnostic is constantly increasing. PCR coupled to electrospray ionization-mass spectrometry, PCR/ESI-MS, offers detection and identification of over 750 bacteria and Candida species directly from clinical specimens within 6 hours. In this study, we investigated the clinical performance of the IRIDICA BAC LRT Assay for detection of bacterial pathogens in 121 bronchoalveolar lavage (BAL) samples that were received consecutively at our bacterial laboratory for BAL culture. Commensal or pathogenic microorganisms were detected in 118/121 (98%) BAL samples by PCR/ESI-MS, while in 104/121 (86%) samples by routine culture (P<0.01). Detection of potentially pathogenic microorganisms by PCR/ESI-MS was evaluated in comparison with conventional culture-based or molecular methods. The agreement between positive findings was overall good. Most Staphylococcus aureus-positive PCR/ESI-MS results were confirmed by culture or species-specific PCR (27/33, 82%). The identity of Streptococcus pneumoniae could however be confirmed for only 6/17 (35%) PCR/ESI-MS-positive samples. Non-cultivable and fastidious pathogens, which were not covered by standard culture procedures were readily detected by PCR/ESI-MS, including Legionella pneumophila, Bordetella pertussis, Norcadia species and Mycoplasma pneumoniae. In conclusion, PCR/ESI-MS detected a broad range of potential pathogens with equal or superior sensitivity compared to conventional methods within few hours directly from BAL samples. This novel method might thus provide a relevant tool for diagnostics in critically ill patients. [ABSTRACT FROM AUTHOR]

National data from Denmark, Finland, Norway and Sweden demonstrate remarkable differences in candidaemia epidemiology. Only Denmark has reported a high incidence of 10 per 100 000 inhabitants and a species shift towards increased C. glabrata candidaemias. The reasons for this development remain unclear. The aim of this study was to explore possible contributing factors for the differences in Candida epidemiology in the Nordic countries. We used public data from 2011 from Denmark, Finland, Norway and Sweden on epidemiology, demographics, health facilities, predisposing risk factors, consumption of antimicrobial drugs and fungicides in agricultural industry. Only the prevalence of haematological malignancies ( P < 0.001) was significantly higher in Denmark compared to the other Nordic countries. The antibacterial drug use of metronidazole, piperacillin-tazobactam, ciprofloxacin, colistin and carbapenems, and antifungal use of fluconazole in humans ( P < 0.001), were significantly higher in Denmark compared to the other Nordic countries (all P < 0.001). Our findings suggest haematological malignancy, the use of certain antibacterial drugs and azoles in humans as possible contributing factors for the differences in Candida epidemiology. However, our results should be interpreted with caution due to the lack of long-term, case-specific data. Further studies are needed. [ABSTRACT FROM AUTHOR]

We studied the diagnostic performance of the IRIDICA PCR/electrospray ionization–mass spectrometry (PCR/ESI-MS) assay applied on bronchoalveolar lavage (BAL) samples, from 51 mechanically ventilated patients with suspected pneumonia, in a prospective study. In 32 patients with X-ray verified pneumonia, PCR/ESI-MS was positive in 66% and BAL culture was positive in 38% (p = 0.045), and either of the methods was positive in 69%. The following BAL result combinations were noted: PCR/ESI-MS+/culture+, 34%; PCR/ESI-MS+/culture-, 31%; PCR/ESI-MS-/culture+, 3.1%; PCR/ESI-MS-/culture-, 31%; kappa 0.36 (95% confidence interval (CI), 0.10–0.63). In pneumonia patients without prior antibiotic treatment, optimal agreement was noted with 88% PCR/ESI-MS+/culture+ and 12% PCR/ESI-MS-/culture- (kappa 1.0). However, in patients with prior antibiotic treatment, the test agreement was poor (kappa 0.16; 95% CI, -0.10–0.44), as 10 patients were PCR/ESI-MS+/culture-. In 8/10 patients the pathogens detected by PCR/ESI-MS could be detected by other conventional tests or PCR tests on BAL. Compared with BAL culture, PCR/ESI-MS showed specificities and negative predictive values of ≥87% for all individual pathogens, an overall sensitivity of 77% and positive predictive value (PPV) of 42%. When other conventional tests and PCR tests were added to the reference standard, the overall PPV increased to 87%. The PCR/ESI-MS semi-quantitative level tended to be higher for PCR/ESI-MS positive cases with pneumonia compared with cases without pneumonia (p = 0.074). In conclusion, PCR/ESI-MS applied on BAL showed a promising performance and has potential to be clinically useful in mechanically ventilated patients with suspected pneumonia. The usefulness of the method for establishment of pneumonia etiology and selection of antibiotic therapy should be further studied. [ABSTRACT FROM AUTHOR]

Eggerthella lenta is a Gram-positive anaerobic bacillus. Improved diagnostics and increased awareness of rare pathogens have revealed its potential to cause serious invasive infections. In this study, 18 clinical E. lenta isolates derived from positive blood cultures were included. Underlying problems of the patients were in the majority of cases related to the gastrointestinal tract. The performance of two MALDI-TOF MS systems, i.e. Bruker and Vitek MS, in identification of E. lenta was analyzed. In addition, the minimal inhibitory concentrations for clinically relevant antimicrobial agents were determined by routine procedures using E-test. 17 of the 18 E. lenta isolates investigated in this study were correctly identified to species level by the Bruker MS system, while the Vitek MS system identified all 18 isolates. Antimicrobial sensitivity towards the tested agents was in general good. However, high resistance rates were observed for penicillin G and piperacillin-tazobactam based on EUCAST breakpoints. [ABSTRACT FROM AUTHOR]

Detection and identification of anaerobic bacteria in blood cultures (BC) is a well-recognized challenge in clinical microbiology. We studied 100 clinical anaerobic BC isolates to evaluate the performance of BacT/ALERT-FN, -FN Plus (BioMérieux), BACTEC-Plus and -Lytic (Becton Dickinson BioSciences) BC bottles in detection and time to detection (TTD) of anaerobic bacteria. BACTEC Lytic had higher detection rate (94/100, 94%) than BacT/ALERT FN Plus (80/100, 80%) (p<0.01) in the studied material. There was no significant difference in detection of anaerobic bacteria among the remaining bottle types. The 67 anaerobic bacteria that signalled positive in all four bottle types were analyzed to compare the time to detection (TTD) and isolates were directly identified by MALDI-TOF MS. There was a significant difference in TTD among the four bottle types (p<0.0001). The shortest median TTD was 18 h in BACTEC Lytic followed by BacT/ALERT FN (23.5 h), BACTEC Plus (27 h) and finally BacT/ALERT FN Plus (38 h) bottles. In contrast, MALDI-TOF MS performed similarly in all bottle types with accurate identification in 51/67 (76%) BacT/ALERT FN, 51/67 (76%) BacT/ALERT FN Plus, 53/67 (79%) BACTEC Plus and 50/67 (75%) BACTEC Lytic bottles. In conclusion, BACTEC Lytic bottles have significantly better detection rates and shorter TTD compared to the three other bottle types. The anaerobic BC bottles are equally suitable for direct MALDI-TOF MS for rapid and reliable identification of common anaerobic bacteria. Further clinical studies are warranted to investigate the performance of anaerobic BC bottles in detection of anaerobic bacteria and identification by direct MALDI-TOF MS. [ABSTRACT FROM AUTHOR]

Knowledge of photo-oxidative stress responses in bacteria that survive antimicrobial photodynamic therapy (aPDT) is scarce. Whereas aPDT is attracting growing clinical interest, subsequent stress responses are crucial to evaluate as they may lead to the up-regulation of pathogenic traits. Here, we aimed to assess transcriptional responses to sublethal aPDT-stress and identify potential connections with virulence-related genes. Six Enterococcus faecalis strains were investigated; ATCC 29212, three dental root-canal isolates labelled UmID1, UmID2 and UmID3 and two vancomycin-resistant isolates labelled A1 and A2. TMPyP was employed as a photosensitiser. A viability dose-response curve to increasing concentrations of TMPyP was determined by culture plating. Differential expression of genes involved in oxidative stress responses (dps and hypR), general stress responses (dnaK , sigma-factorV and relA), virulence-related genes (ace , fsrC and gelE) and vancomycin-resistance (vanA) was assessed by reverse-transcription qPCR. TMPyP-mediated aPDT inactivated all strains with comparable efficiencies. TMPyP at 0.015 μM was selected to induce sublethal photo-oxidative stress. Despite heterogeneities in gene expression between strains, transcriptional profiles revealed up-regulations of transcripts dps , hypR as well as dnaK and sigma factorV after exposure to TMPyP alone and to light-irradiated TMPyP. Specifically, the alternative sigma factorV reached up to 39 ± 113-fold (median ± IQR) (p = 0.0369) in strain A2. Up-regulation of the quorum sensing operon, fsr , and its downstream virulence-related gelatinase gelE were also observed in strains ATCC-29212, A1, A2 and UmID3. Finally, photo-oxidative stress induced vanA-type vancomycin-resistance gene in both carrier isolates, reaching up to 3.3 ± 17-fold in strain A2 (p = 0.015). These findings indicate that, while aPDT successfully inactivates vancomycin-resistant and naïve strains of E. faecalis , subpopulations of surviving cells respond by co-ordinately up-regulating a network of genes involved in stress survival and virulence. This includes the induction of vancomycin-resistance genes in carrier isolates. These data may provide the mechanistic basis to circumvent bacterial responses and improve future clinical protocols. • Light-activated TMPyP efficiently kills vancomycin-resistant E. faecalis strains. • Ensuing photo-oxidative stress responses enhance survival abilities and virulence. • Sublethal photo-oxidative stress induces vanA-type vancomycin-resistance gene. [ABSTRACT FROM AUTHOR]

The clonal dissemination of VanB-type vancomycin-resistant Enterococcus faecium (VREfm) strains in three Swedish hospitals between 2007 and 2011 prompted further analysis to reveal the possible origin and molecular characteristics of the outbreak strain. A representative subset of VREfm isolates (n = 18) and vancomycin-susceptible E. faecium (VSEfm, n = 2) reflecting the spread in time and location was approached by an array of methods including: selective whole genome sequencing (WGS; n = 3), multi locus sequence typing (MLST), antimicrobial susceptibility testing, virulence gene profiling, identification of mobile genetic elements conferring glycopeptide resistance and their ability to support glycopeptide resistance transfer. In addition, a single VREfm strain with an unrelated PFGE pattern collected prior to the outbreak was examined by WGS. MLST revealed a predominance of ST192, belonging to a hospital adapted high-risk lineage harbouring several known virulence determinants (n≥10). The VREfm outbreak strain was resistant to ampicillin, gentamicin, ciprofloxacin and vancomycin, and susceptible to teicoplanin. Consistently, a vanB2-subtype as part of Tn1549/Tn5382 with a unique genetic signature was identified in the VREfm outbreak strains. Moreover, Southern blot hybridisation analyses of PFGE separated S1 nuclease-restricted total DNAs and filter mating experiments showed that vanB2-Tn1549/Tn5382 was located in a 70-kb sized rep17/pRUM plasmid readily transferable between E. faecium. This plasmid contained an axe-txe toxin-antitoxin module associated with stable maintenance. The two clonally related VSEfm harboured a 40 kb rep17/pRUM plasmid absent of the 30 kb vanB2-Tn1549/Tn5382 gene complex. Otherwise, these two isolates were similar to the VREfm outbreak strain in virulence- and resistance profile. In conclusion, our observations support that the origin of the multicentre outbreak was caused by an introduction of vanB2-Tn1549/Tn5382 into a rep17/pRUM plasmid harboured in a pre-existing high-risk E. faecium ST192 clone. The subsequent dissemination of VREfm to other centres was primarily caused by clonal spread rather than plasmid transfer to pre-existing high-risk clones. [ABSTRACT FROM AUTHOR]

Abstract: Granulicatella and Abiotrophia spp. were known as nutritionally variant streptococci (NVS). Such strains have caused major diagnostic difficulties due to fastidious culturing and unspecific colony morphology. The present study is aimed at comparing the performance of laboratory available diagnostic methods for NVS isolates and determining the antimicrobial susceptibility of these isolates. Fourteen clinical invasive isolates, consisting of 10 Granulicatella adiacens, 1 Granulicatella elegans, and 3 Abiotrophia defectiva were in parallel analyzed by 2 matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) systems, i.e., Bruker MS and Vitek MS, as well as Vitek 2 for the species determination. 16S rRNA gene sequencing was applied as a reference method. The Vitek MS gave correct identification for all 14 isolates. The Bruker MS could correctly identify 8/10 G. adiacens, 0/1 G. elegans, and 3/3 A. defectiva isolates at the first analysis occasion, and all 14 isolates became identifiable after repeated tests. The Vitek 2 system could identify 6/10 G. adiacens, 1/1 G. elegans, and 2/3 A. defectiva isolates at the species level. Antimicrobial susceptibilities of 11 antibiotics were determined by Etest. Resistance against ciprofloxacin, ceftriaxone, rifampicin, and tetracycline were observed in 4, 10, 4, and 1 isolates, respectively. In conclusion, MALDI-TOF MS is a useful tool for the rapid diagnosis of NVS. Phenotypic testing by Vitek 2 is only partially effective for the accurate identification of such strains. The emergence of resistant NVS isolates indicates the necessity of monitoring antimicrobial susceptibilities of such uncommon pathogens. [Copyright &y& Elsevier]

Abstract: The purpose of this investigation was to evaluate the performance of 4 supplements: horse blood, fastidious organisms supplement (FOS), haemin isovitalex albumine (HIA), and brain heart infusion–haemin isovitalex albumine (BHI-HIA) and 5 blood culture bottles: Bactec Mycosis IC/F, Plus Aerobic/F, Peds Plus/F from the Bactec 9240 system, and BacT/Alert FA and BacT/Alert PF from the BacT/Alert 3D system, in detection of bacteria and Candida spp. in simulated sterile body fluids other than blood models. In total, 8 reference strains (Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae, Listeria monocytogenes, Candida albicans, and Candida parapsilosis) and 11 clinical bacteria and yeast isolates (6 isolates from cerebrospinal fluid and 5 isolates from blood) were included in this study. Horse blood, FOS, and HIA were significantly better than no supplements (P < 0.0001, P < 0.0002, and P = 0.05, respectively) in detection of bacteria. Interestingly, there was no significant difference between BHI-HIA and bottles without any supplements. Sixty bottles analyzed of which 59 (98.33%) bottles with horse blood, 53 (88.33%) with FOS, 45 (75.00%) with HIA, and 43 (71.67%) with BHI-HIA signaled positive. The positivity rates with horse blood were significantly higher than with HIA and BHI-HIA (P < 0.0005 and P < 0.0001, respectively). Similarly, the blood culture bottles with horse blood had shorter time to detection (TTD) compared to bottles with FOS and HIA (P < 0.05 and P < 0.0001, respectively). When yeasts were analyzed, almost all (124/125) blood culture bottles with Candida spp. signaled positive even in the absence of supplements. Bactec Mycosis IC/F had significantly shorter TTD compared to Bactec Peds Plus/F, Bactec Plus Aerobic/F, BacT/Alert FA, and BacT/Alert PF bottles in detection of Candida spp. (P < 0.005, P < 0.05, P < 0.001, and P < 0.001, respectively). The present study showed that horse blood was the most effective supplement in growth of bacteria in the blood culture bottles that were analyzed in the study. [Copyright &y& Elsevier]

Abstract: In the present study we investigated transport times for blood cultures from three tertiary-care hospitals to Karolinska University Laboratory and identified predictors of long transport times. Concomitantly, consequences of delayed incubation on total detection time (TDT) were analyzed by in vitro sepsis models. A total of 909 blood cultures were studied. The median (interquartile range) transport time was 9 (3–15) h. The hospital accommodating the microbiology laboratory had the shortest transport time compared to the other two hospitals (P < 0.0001). Samples taken between 16:00–24:00 had longer transport times compared to samples taken between 8:00–16:00 and 24:00–08:00 (P < 0.0001). In vitro experiments showed that TDT was longer for samples pre-incubated at room temperature (RT) for 19 h compared to the ones pre-incubated for 2 h or 9.5 h (P < 0.0001). In conclusion, off-site location, time of sampling and number of transports per day were related to, and predictors of transport time. [Copyright &y& Elsevier]

Abstract: The present study analyzed the performance of Bactec Mycosis IC/F, BacT/Alert FA, and BacT/Alert FN vials in detection and time to detection (TTD) of Candida spp. in 179 simultaneous blood cultures. The Mycosis IC/F, BacT/Alert FA, and BacT/Alert FN vials could detect Candida spp. in 144 (80.45%) of 179, 149 (83.24%) of 179, and 8 (4.47%) of 179 samples, respectively. With the presence of antifungal therapy, the numbers of positive vials were higher in BacT/Alert FA compared to Mycosis IC/F, 87/99 versus 73/99, respectively (P < 0.05). TTD (SD) for C. albicans was shorter in Mycosis IC/F than in BacT/Alert FA vials without antifungal therapy, 20.89 (9.33) versus 28.26 (9.77), respectively (P < 0.01). The detection of Candida spp., with concomitant bacteremia, was higher in Mycosis IC/F than in BacT/Alert FA vials, 28/30 and 19/30, respectively (P = 0.01). The present data show that the use of Bactec Mycosis IC/F together with BacT/Alert FA vials might improve the detection of Candida spp. [Copyright &y& Elsevier]

The T2Candida magnetic resonance assay is a direct-from-blood pathogen detection assay that delivers a result within 3–5 h, targeting the most clinically relevant Candida species. Between February 2019 and March 2021, the study included consecutive patients aged >18 years admitted to an intensive care unit or surgical high-dependency unit due to gastrointestinal surgery or necrotizing pancreatitis and from whom diagnostic blood cultures were obtained. Blood samples were tested in parallel with T2Candida and 1,3-β-D-glucan. Of 134 evaluable patients, 13 (10%) were classified as having proven intraabdominal candidiasis (IAC) according to the EORTC/MSG criteria. Two of the thirteen patients (15%) had concurrent candidemia. The sensitivity, specificity, positive predictive value, and negative predictive value, respectively, were 46%, 97%, 61%, and 94% for T2Candida and 85%, 83%, 36%, and 98% for 1,3-β-D-glucan. All positive T2Candida results were consistent with the culture results at the species level, except for one case of dual infection. The performance of T2Candida was comparable with that of 1,3-β-D-glucan for candidemic IAC but had a lower sensitivity for non-candidemic IAC (36% vs. 82%). In conclusion, T2Candida may be a valuable complement to 1,3-β-D-glucan in the clinical management of high-risk surgical patients because of its rapid results and ease of use. [ABSTRACT FROM AUTHOR]

Abstract: The aim of this study was to compare the performance of four methods that are widely used in the clinical microbiology laboratory for identification of Pasteurella species. The 4 methods evaluated were VITEK2, VITEK MS (BioMerieux), and Bruker Biotyper MS (Bruker) as well as traditional biochemical tests. Sequencing of the sodA gene was used as the reference method. Sixty-five isolates of Pasteurella spp. from 65 patients were analyzed. One Pasteurella multocida isolate from American Type Culture Collection (Manassas, VA, USA) was used as a reference. Traditional biochemical tests accurately identified 62/66 (94%) isolates. Both Bruker and Vitek matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) identified 59/66 (89%) strains, but VITEK2 could only identify 32/66 (48.5%) isolates correctly. The mean time to identification using biochemical tests was 20 hours; VITEK2 took 6 hours and MALDI-TOF approximately 10 minutes. In conclusion, MALDI-TOF is a quick method, which accurately identified most isolates of Pasteurella to the species level. Thus, MALDI-TOF constitutes a valuable diagnostic tool in the clinical laboratory. [Copyright &y& Elsevier]