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To support the clinical laboratory diagnosis of Pneumocystis jirovecii (PJ) pneumonia (PCP), an invasive fungal infection mainly occurring in HIV-negative patients, in-house or commercial PJ-specific real-time quantitative PCR (qPCR) assays are todays’ reliable options. The performance of these assays depends on the type of PJ gene (multi-copy mitochondrial versus single-copy nuclear) targeted by the assay. We described the development of a PJ-PCR assay targeting the dihydrofolate reductase (DHFR)-encoding gene. After delineating its analytical performance, the PJ-PCR assay was used to test bronchoalveolar lavage (BAL) fluid samples from 200 patients (only seven were HIV positive) with suspected PCP. Of 211 BAL fluid samples, 18 (8.5%) were positive and 193 (91.5%) were negative by PJ-PCR. Of 18 PJ-PCR-positive samples, 11 (61.1%) tested positive and seven (38.9%) tested negative with the immunofluorescence assay (IFA). All (100%) of the 193 PJ-PCR-negative samples were IFA negative. Based on IFA/PCR results, patients were, respectively, classified as having (n = 18) and not having (n = 182) proven (PJ-PCR+/IFA+) or probable (PJ-PCR+/IFA−) PCP. For 182 patients without PCP, alternative infectious or non-infectious etiologies were identified. Our PJ-PCR assay was at least equivalent to IFA, fostering studies aimed at defining a qPCR-based standard for PCP diagnosis in the future. [ABSTRACT FROM AUTHOR]

Background: Since December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged as a novel etiologic agent of viral pneumonia. We aimed to compare clinical features of 165 Italian patients with laboratory confirmed or unconfirmed 2019-nCoV pneumonia.Methods: On March 31, 2020, hospitalized patients who presented with fever and/or respiratory symptoms, exposures, and presence of lung imaging features consistent with 2019-nCoV pneumonia were included. Before admission to a hospital ward, patients underwent RT-PCR based SARS-CoV-2 RNA detection in their nasopharyngeal swab samples.Results: Of 165 patients studied, 119 had positive RT-PCR results and 46 were RT-PCR negative for 2 days or longer (i.e., when the last swab sample was obtained). The median age was 70 years (IQR, 58-78), and 123 (74.6%) of 165 patients had at least one comorbidity. The majority of patients (101/165, 61.2%) had a mild pneumonia, and the remaining patients (64/165, 38.8%) a severe/critical pneumonia. We did not find any substantial difference in symptoms, incubation periods, and radiographic/CT abnormalities as well as in many of the biological abnormalities recorded. However, at multivariable analysis, higher concentrations of hemoglobin (OR, 1.34; 95% CI, 1.11-1.65; P = 0.003) and lower counts of leukocytes (OR, 0.81; 95% CI, 0.72-0.90; P < 0.001) were statistically associated with confirmed COVID-19 diagnosis. While mortality rates were similar, patients with confirmed diagnosis were more likely to receive antivirals (95% vs 19.6%, P < 0.001) and to develop ARDS (63% vs 37%, P = 0.003) than those with unconfirmed COVID-19 diagnosis.Conclusions: Our findings suggest that unconfirmed 2019-nCoV pneumonia cases may be actually COVID-19 cases and that clinicians should be cautious when managing patients with presentations compatible with COVID-19. [ABSTRACT FROM AUTHOR]

Background: Candidaemia is an important infectious complication for haematological malignancy patients. Antifungal prophylaxis reduces the incidence of candidaemia but may be associated with breakthrough candidaemia. Objective: To analyse the Candida species' distribution and relative antifungal susceptibility profiles of candidaemia episodes in relation to the use of antifungal prophylaxis among Italian SEIFEM haematology centres. Methodology: This multicentre retrospective observational SEIFEM study included 133 single‐species candidaemia episodes of haematological malignancy patients for whom antifungal susceptibility testing results of blood Candida isolates were available between 2011 and 2015. Each participating centre provided both clinical and microbiological data. Results: Non‐Candida albicans Candida (NCAC) species were the mostly isolated species (89, 66.9%), which accounted for C parapsilosis (35, 26.3%), C glabrata (16, 12.0%), C krusei (14, 10.5%), C tropicalis (13, 9.8%) and uncommon species (11, 8.3%). C albicans caused the remaining 44 (33.1%) episodes. Excluding 2 C albicans isolates, 23 of 25 fluconazole‐resistant isolates were NCAC species (14 C krusei, 6 C glabrata, 2 C parapsilosis and 1 C tropicalis). Fifty‐six (42.1%) of 133 patients developed breakthrough candidaemia. Systemic antifungal prophylaxis consisted of azoles, especially fluconazole and posaconazole, in 50 (89.3%) of 56 patients in whom a breakthrough candidaemia occurred. Interestingly, all these patients tended to develop a C krusei infection (10/56, P =.02) or a fluconazole‐resistant isolate's infection (14/50, P =.04) compared to patients (4/77 and 10/77, respectively) who did not have a breakthrough candidaemia. Conclusions: Optimisation of prophylactic strategies is necessary to limit the occurrence of breakthrough candidaemia and, importantly, the emergence of fluconazole‐resistant NCAC isolates' infections in haematological malignancy patients. [ABSTRACT FROM AUTHOR]

Coinfections with bacteria or fungi may be a frequent complication of COVID-19, but coinfections with Candida species in COVID-19 patients remain rare. We report the 53-day clinical course of a complicated type-2 diabetes patient diagnosed with COVID-19, who developed bloodstream infections initially due to methicillin-resistant Staphylococcus aureus, secondly due to multidrug-resistant Gram-negative bacteria, and lastly due to a possibly fatal Candida glabrata. The development of FKS-associated pan-echinocandin resistance in the C. glabrata isolated from the patient after 13 days of caspofungin treatment aggravated the situation. The patient died of septic shock shortly before the prospect of receiving potentially effective antifungal therapy. This case emphasizes the importance of early diagnosis and monitoring for antimicrobial drug-resistant coinfections to reduce their unfavorable outcomes in COVID-19 patients. [ABSTRACT FROM AUTHOR]

We analyzed the bacterial communities of the nasopharynx in 40 SARS-CoV-2 infected and uninfected patients. All infected patients had a mild COVID-19 disease. We did not find statistically significant differences in either bacterial richness and diversity or composition. These findings suggest a nasopharyngeal microbiota at least early resilient to SARS-CoV-2 infection. [ABSTRACT FROM AUTHOR]

Improved standards of care depend on the development of new laboratory diagnostic and imaging procedures and the development of new antifungal compounds. Immunochromatography technologies have led to the development of lateral flow devices for the diagnosis of cryptococcal meningitis and invasive aspergillosis (IA). Similar devices are being developed for the detection of histoplasmosis that meet the requirements for speed (∼15 min assay time) and ease of use for point-of-care diagnostics. The evolution of molecular tools for the detection of fungal pathogens has been slow but the introduction of new nucleic acid amplification techniques appears to be helpful, for example T2Candida. An Aspergillus proximity ligation assay has been developed for a rapid near-patient bedside diagnosis of IA. CT remains the cornerstone for radiological diagnosis of invasive pulmonary fungal infections. MRI of the lungs may be performed to avoid radiation exposure. MRI with T2-weighted turbo-spin-echo sequences exhibits sensitivity and specificity approaching that of CT for the diagnosis of invasive pulmonary aspergillosis. The final part of this review looks at new approaches to drug discovery that have yielded new classes with novel mechanisms of action. There are currently two new classes of antifungal drugs in Phase 2 study for systemic invasive fungal disease and one in Phase 1. These new antifungal drugs show promise in meeting unmet needs with oral and intravenous formulations available and some with decreased potential for drug-drug interactions. Novel mechanisms of action mean these agents are not susceptible to the common resistance mechanisms seen in Candida or Aspergillus. Modification of existing antifungal susceptibility testing techniques may be required to incorporate these new compounds. [ABSTRACT FROM AUTHOR]

Objectives: To compare the performance of the Accelerate Pheno™ system with that of the conventional phenotypic VITEK® 2 system for rapid antimicrobial susceptibility testing (AST) of bacterial pathogens from positive blood culture (PBC) samples, based on the reference broth microdilution (BMD) method.Methods: Prospectively collected PBCs that represented patient-unique bloodstream infection episodes were included. For PBC samples showing monomicrobial growth (n = 86), AST was performed using both Accelerate Pheno™ and VITEK® 2 systems directly from PBC broth. Colony isolates derived from subculture of PBC broth were then used for BMD testing. AST results were interpreted according to 2017 EUCAST breakpoints.Results: The overall categorical agreement between Accelerate Pheno™ system and BMD was 92.7% (467/504) for Gram-negative organisms and 99.0% (95/96) for Gram-positive organisms, with rates for very major errors of 3.6% (6/166), major errors 2.2% (9/416) and minor errors 3.8% (23/600). The overall categorical agreement between the VITEK® 2 system and BMD was 91.7% (463/505) for Gram-negative organisms and 99.0% (97/98) for Gram-positive organisms, with rates of very major errors of 2.4% (4/169), major errors 1.0% (4/416) and minor errors 5.8% (35/603). Importantly, unlike the VITEK® 2 system, no false-susceptible results occurred with two colistin-resistant organism-growing PBCs tested using the Accelerate Pheno™ system.Conclusions: Based on these findings, the Accelerate Pheno™ system can be a valid alternative for the rapid AST of Gram-negative and Gram-positive bacteria in bloodstream infections. [ABSTRACT FROM AUTHOR]

Background: There is strong evidence that alcoholism leads to dysbiosis in both humans and animals. However, it is unclear how changes in the intestinal microbiota (IM) relate to ethanol (EtOH)‐induced disruption of gut–liver homeostasis. We investigated this issue using selectively bred Sardinian alcohol‐preferring (sP) rats, a validated animal model of excessive EtOH consumption. Methods: Independent groups of male adult sP rats were exposed to the standard, home‐cage 2‐bottle "EtOH (10% v/v) versus water" choice regimen with unlimited access for 24 h/d (Group Et) for 3 (T1), 6 (T2), and 12 (T3) consecutive months. Control groups (Group Ct) were composed of matched‐age EtOH‐naïve sP rats. We obtained samples from each rat at the end of each experimental time, and we used blood and colon tissues for intestinal barrier integrity and/or liver pathology assessments and used stool samples for IM analysis with 16S ribosomal RNA gene sequencing. Results: Rats in Group Et developed hepatic steatosis and elevated serum transaminases and endotoxin/lipopolysaccharide (LPS) levels but no other liver pathological changes (i.e., necrosis/inflammation) or systemic inflammation. While we did not find any apparent alteration of the intestinal colonic mucosa, we found that rats in Group Et exhibited significant changes in IM composition compared to the rats in Group Ct. These changes were sustained throughout T1, T2, and T3. In particular, Ruminococcus, Coprococcus, and Streptococcus were the differentially abundant microbial genera at T3. The KEGG Ortholog profile revealed that IM functional modules, such as biosynthesis, transport, and export of LPS, were also enriched in Group Et rats at T3. Conclusions: We showed that chronic, voluntary EtOH consumption induced liver injury and endotoxemia together with dysbiotic changes in sP rats. This work sets the stage for improving our knowledge of the prevention and treatment of EtOH‐related diseases. [ABSTRACT FROM AUTHOR]

Objectives: To evaluate the magnetic resonance-based T2Bacteria Panel assay for direct detection of ESKAPEc (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Escherichia coli) pathogens in blood samples of patients with suspected bloodstream infection (BSI). Patients and methods: Adult patients admitted to the Emergency Medicine Department, Infectious Diseases Unit and ICU of a large tertiary-care hospital were included if they had a blood culture (BC) ordered concomitantly with a whole-blood sample for T2Bacteria testing. Results were compared with those of BC and other clinically relevant information. Results: A total of 140 samples from 129 BSI patients were studied. Single bacteria were detected in 15.7% (22/140) and 12.1% (17/140), and multiple bacteria in 2.9% (4/140) and 1.4% (2/140), of samples tested by T2Bacteria and BC, respectively. With respect to the six target (ESKAPEc) species, overall sensitivity and specificity of T2Bacteria across all detection channels in comparison with BC were 83.3% and 97.6%, respectively; these values increased to 89.5% and 98.4%, respectively, when a true-infection criterion (i.e. the same microorganism detected only by T2Bacteria was cultured from another sample type reflecting the source of infection) was used as the comparator. There were 808 T2Bacteria detection results across 112 samples, with concordant negative results, yielding a negative predictive value of 99.8%. The mean time to negative result was 6.1±1.5 h, whereas the mean time to detection/species identification was 5.5±1.4 h. Conclusions: The T2Bacteria Panel assay has the potential to provide accurate and timely diagnosis of ESKAPEc bacteraemia, which might support the direct therapeutic management of BSI patients. [ABSTRACT FROM AUTHOR]

Objectives: To evaluate the magnetic resonance-based T2Bacteria Panel assay for direct detection of ESKAPEc (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Escherichia coli) pathogens in blood samples of patients with suspected bloodstream infection (BSI).Patients and methods: Adult patients admitted to the Emergency Medicine Department, Infectious Diseases Unit and ICU of a large tertiary-care hospital were included if they had a blood culture (BC) ordered concomitantly with a whole-blood sample for T2Bacteria testing. Results were compared with those of BC and other clinically relevant information.Results: A total of 140 samples from 129 BSI patients were studied. Single bacteria were detected in 15.7% (22/140) and 12.1% (17/140), and multiple bacteria in 2.9% (4/140) and 1.4% (2/140), of samples tested by T2Bacteria and BC, respectively. With respect to the six target (ESKAPEc) species, overall sensitivity and specificity of T2Bacteria across all detection channels in comparison with BC were 83.3% and 97.6%, respectively; these values increased to 89.5% and 98.4%, respectively, when a true-infection criterion (i.e. the same microorganism detected only by T2Bacteria was cultured from another sample type reflecting the source of infection) was used as the comparator. There were 808 T2Bacteria detection results across 112 samples, with concordant negative results, yielding a negative predictive value of 99.8%. The mean time to negative result was 6.1 ± 1.5 h, whereas the mean time to detection/species identification was 5.5 ± 1.4 h.Conclusions: The T2Bacteria Panel assay has the potential to provide accurate and timely diagnosis of ESKAPEc bacteraemia, which might support the direct therapeutic management of BSI patients. [ABSTRACT FROM AUTHOR]

Objectives: To determine the effects of a strategy that uses serum (1,3)-β-d-glucan (BDG) results for antifungal treatment of ICU patients at high risk of invasive candidiasis.Patients and Methods: Adult patients admitted to the ICU from January 2012 to June 2014 were included if they exhibited sepsis at the time of BDG testing and they met Candida score components ≥3. A retrospective analysis of collected data was performed.Results: In total, 198 patients were studied. Of 63 BDG-positive patients, 47 with candidaemia and 16 with probable Candida infection, all [31.8% (63/198)] received antifungal therapy. Of 135 BDG-negative patients, 110 [55.5% (110/198)] did not receive antifungal therapy, whereas 25 [12.6% (25/198)] were initially treated. Overall, antifungal therapy was started in 88 cases (44.4%), mostly with echinocandins. Antifungals were discontinued in 14 of 25 patients, as negative BDG results became available, and in 16 BDG-false-positive patients for whom subsequent findings allowed candidaemia (and other forms of invasive candidiasis) to be ruled out. Candidaemia was diagnosed only in one patient who did not receive prior antifungal therapy. The median antifungal therapy duration in candidaemic patients differed significantly from that in non-candidaemic patients [14 (IQR, 6-18) days versus 4 (IQR, 3-7) days; P < 0.001]. Using this approach, antifungal therapy was avoided in ∼73% of potentially treatable patients and it was shortened in another ∼20%.Conclusions: This study supports the use of serum BDG results in the management of systemic antifungal drug prescription in septic patients. These findings need to be confirmed in additional studies. [ABSTRACT FROM AUTHOR]

The epidemiology of Candida infections has changed in recent years. Although Candida albicans is still the main cause of invasive candidiasis in most clinical settings, a substantial proportion of patients is now infected with non- albicans Candida species. The various Candida species vary in their susceptibility to the most commonly used antifungal agents, and the intrinsic resistance to antifungal therapy seen in some species, along with the development of acquired resistance during treatment in others, is becoming a major problem in the management of Candida infection. A better understanding of the mechanisms and clinical impact of antifungal drug resistance is essential for the efficient treatment of patients with Candida infection and for improving treatment outcomes. Herein, we report resistance to the azoles and echinocandins among Candida species. [ABSTRACT FROM AUTHOR]

Background Mathematical or statistical tools are capable to provide a valid help to improve surveillance systems for healthcare and non-healthcare-associated bacterial infections. The aim of this work is to evaluate the time-varying auto-adaptive (TVA) algorithm-based use of clinical microbiology laboratory database to forecast medically important drug-resistant bacterial infections. Methods Using TVA algorithm, six distinct time series were modelled, each one representing the number of episodes per single „ESKAPE? (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species) infecting pathogen, that had occurred monthly between 2002 and 2011 calendar years at the Università Cattolica del Sacro Cuore general hospital. Results Monthly moving averaged numbers of observed and forecasted ESKAPE infectious episodes were found to show a complete overlapping of their respective smoothed time series curves. Overall good forecast accuracy was observed, with percentages ranging from 82.14% for E. faecium infections to 90.36% for S. aureus infections. Conclusions Our approach may regularly provide physicians with forecasted bacterial infection rates to alert them about the spread of antibiotic-resistant bacterial species, especially when clinical microbiological results of patients? specimens are delayed. [ABSTRACT FROM AUTHOR]

Highlights: [•] Our systematic review shows that several genetic variations were significantly associated with responsiveness to vaccines. [•] As most of the included studies investigated different polymorphisms, meta-analyses could be performed only for seven polymorphisms. [•] Future studies are required to further clarify the link between genetic variations and variability in immune responses to vaccines. [ABSTRACT FROM AUTHOR]

Abstract: Although there is evidence that liposomal amphotericin B (AmBisome) is non-inferior to amphotericin B (AmB) in terms of in vivo efficacy, in vitro data regarding the activity of AmBisome against clinical isolates of Aspergillus are rare. In this study, the susceptibilities to AmB and AmBisome of 103 Aspergillus complex isolates (48 Aspergillus flavus, 33 Aspergillus fumigatus, 13 Aspergillus terreus and 9 Aspergillus niger) recovered from haematological patients with invasive infection were compared. Minimum inhibitory concentrations (MICs) were determined by the broth microdilution (BMD) method according to the Clinical and Laboratory Standards Institute (CLSI), whilst AmB susceptibility was also determined by Etest. Using a susceptible/resistant MIC cut-off of 1mg/L, all A. fumigatus and A. niger complexes isolates were susceptible to both AmB and AmBisome. In contrast, 38.5% and 30.8% of the A. terreus complex isolates were resistant to AmB and AmBisome, respectively, with good agreement between BMD and Etest methods. With respect to A. flavus complex isolates, 43.7% and 16.7% were resistant by the BMD method to AmBisome and AmB, respectively. For isolates with discrepant results, AmB MICs obtained by Etest were higher than those obtained for AmB by the BMD method and they were closer to those obtained for AmBisome by BMD. Aspergillus flavus AmB MICs ranged from 0.5mg/L to 2mg/L by the BMD method and from 1mg/L to >16mg/L by the Etest method, and AmBisome MICs ranged from 0.06mg/L to >16mg/L by the BMD method. Etest appears to be superior to the CLSI BMD method using AmB in detecting AmB resistance of Aspergillus spp., although the CLSI BMD method might be a suitable procedure if AmBisome is used as the test drug. [Copyright &y& Elsevier]

Recent advances in the management of patients with haematological malignancies and transplant recipients have paralleled an increase in the incidence of fungal diseases due to pathogenic genera such as Candida and Aspergillus and the emergence of less common genera including Fusarium and Zygomycetes. Despite availability of new antifungal agents these opportunistic infections have high mortality. Rapid and reliable species identification is essential for antifungal treatment, but detection of the increasing diversity of fungal pathogens by conventional phenotypic methods remains difficult and time-consuming, and the results may sometimes be inconclusive, especially for unusual species. New diagnostic techniques (e.g., 1,3-beta-d-glucan detection) could improve this scenario, although further studies are necessary to confirm their usefulness in clinical practice. [ABSTRACT FROM AUTHOR]

The oligopeptide transport systems Opp belong to the nickel/peptide/opine PepT subfamily of ABC-transporters. The opportunist pathogen Staphylococcus aureus encodes four putative Opps and one orphean substrate binding protein Opp5A. Here, we report that the Opp2 permease complex (Opp2BCDF) and Opp5A are involved in nickel uptake and then renamed them NikBCDE and NikA respectively. S. aureus carries also a high-affinity nickel transporter NixA belonging to the NiCoT family of secondary transporters. The activity of these two nickel transporters determine that of urease, a multimeric nickel-dependent enzyme mainly involved in the neutralization of acidic environments. However, only the Nik system was responsible for the neutralization and deposit of pH-dependent crystals in human urine. Inactivation of the nik genes affected bacterial colonization of mouse urinary tract, as well as the 50% infective dose levels compared with the parental and nixA strains. Finally, complementation of the nik mutations restored bacterial colonization. Together, our results suggest a role for the Nik system in the urinary tract infection by S. aureus, probably due to the urease-mediated pH increase of the urine. [ABSTRACT FROM AUTHOR]

Our previous investigation on Candida glabrata azole-resistant isolates identified two isolates with unaltered expression of CgCDR1/ CgCDR2, but with upregulation of another ATP-binding cassette transporter, CgSNQ2, which is a gene highly similar to ScSNQ2 from Saccharomyces cerevisiae. One of the two isolates (BPY55) was used here to elucidate this phenomenon. Disruption of CgSNQ2 in BPY55 decreased azole resistance, whereas reintroduction of the gene in a CgSNQ2 deletion mutant fully reversed this effect. Expression of CgSNQ2 in a S. cerevisiae strain lacking PDR5 mediated not only resistance to azoles but also to 4-nitroquinoline N-oxide, which is a ScSNQ2-specific substrate. A putative gain-of-function mutation, P822L, was identified in CgPDR1 from BPY55. Disruption of CgPDR1 in BPY55 conferred enhanced azole susceptibility and eliminated CgSNQ2 expression, whereas introduction of the mutated allele in a susceptible strain where CgPDR1 had been disrupted conferred azole resistance and CgSNQ2 upregulation, indicating that CgSNQ2 was controlled by CgPDR1. Finally, CgSNQ2 was shown to be involved in the in vivo response to fluconazole. Together, our data first demonstrate that CgSNQ2 contributes to the development of CgPDR1-dependent azole resistance in C. glabrata. The overlapping in function and regulation between CgSNQ2 and ScSNQ2 further highlight the relationship between S. cerevisiae and C. glabrata. [ABSTRACT FROM AUTHOR]

Abstract: The subtype of the Saccharomyces cerevisiae yeast species known as S. cerevisiae Hansen CBS 5926 was formerly believed to be a separate species, Saccharomyces boulardii. It is widely considered non-pathogenic and is used as a probiotic agent for treatment and prevention of diarrhea. The biological properties of Saccharomyces spp. show considerable intraspecies variability and the beneficial properties of probiotic yeasts are considered strain-specific. Septicemia and fungemia caused by S. boulardii have recently been described in both immunocompromised and immunocompetent patients receiving biotherapy with this yeast. It cannot be distinguished from other S. cerevisiae strains by phenotypic criteria, so identification of these infections requires molecular typing. To identify the most effective approach for distinguishing S. boulardii, we typed 35 isolates of S. cerevisiae, of which 27 were from various clinical specimens and 8 were isolates of S. boulardii (6 obtained from probiotic preparations and 2 from clinical specimens) using four different molecular methods, two based on PCR-restriction enzyme analysis or sequencing of rDNA spacer regions, the third based on microsatellite polymorphism analysis of the S. cerevisiae genes YKL139w and YLR177w, and the last based on hybridization analysis with retrotransposon Ty917. Several clinical isolates appeared to be identical to one or more other isolates with the first three methods used, whereas with the Ty917 hybridization method all of the isolates tested appeared to be very heterogeneous. The eight S. boulardii isolates were clearly distinguishable from the clinical S. cerevisiae isolates only with Ty917 hybridization and microsatellite DNA analyses. In the latter method, the eight S. boulardii isolates exhibited an allelic variant at one of loci tested that was not shared with any other strain. Our results suggest that microsatellite polymorphism analysis of the YKL139w and YLR177w genes, as well as the analysis by Ty917 hybridization, are the most useful tools for a correct identification of S. boulardii strains. [Copyright &y& Elsevier]

Summary Resistance to fluconazole is a possible event during prolonged suppressive drug therapy for cryptococ-cal meningitis, the most frequently encountered life-threatening manifestation of cryptococcosis. The knowledge of this resistance at the molecular level is important for management of cryptococcosis. In order to identify genes involved in azole resistance in Cryptococcus neoformans , a cDNA subtraction library technique was chosen as a strategy. First, a fluconazole-resistant mutant BPY22.17 was obtained from a susceptible clinical isolate BPY22 by in vitro exposure to the drug. Then, a subtractive hybridization procedure was used to compare gene expression between the obtained strains. We identified a cDNA overexpressed in the fluconazole-resistant strain BPY22.17 that was used as a probe to isolate the entire gene in a C. neoformans genomic library. Sequence analysis of this gene identified an ATP Binding Cassette (ABC) transporter-encoding gene called C. neoformans AntiFungal Resistance 1 ( CnAFR1 ). Disruption of CnAFR1 gene in the resistant isolate (BPY22.17) resulted in an enhanced susceptibility of the knock-out mutant cnafr1 against fluconazole, whereas reintroduction of the gene in cnafr1 resulted in restoration of the resistance phenotype, thus confirming that CnAFR1 is involved in fluconazole resistance of C. neoformans . Our findings therefore reveal that an active drug efflux mechanism can be involved in the development of azole resistance in this important human pathogen. [ABSTRACT FROM AUTHOR]

The aim of this study was to characterize COVID-19 (SARS-CoV-2-infected) patients who develop bloodstream infection (BSI) and to assess risk factors associated with in-hospital mortality. We conducted a retrospective observational study of adult patients admitted for ≥48 h to a large Central Italy hospital for COVID-19 (1 March to 31 May 2020) who had or had not survived at discharge. We included only patients having blood cultures drawn or other inclusion criteria satisfied. Kaplan–Meier survival or Cox regression analyses were performed of 293 COVID-19 patients studied, 46 patients (15.7%) had a hospital-acquired clinically relevant BSI secondary to SARS-CoV-2 infection, accounting for 58 episodes (49 monomicrobial and 9 polymicrobial) in total. Twelve episodes (20.7%) occurred at day 3 of hospital admission. Sixty-nine species were isolated, including Staphylococcus aureus (32.8%), Enterobacterales (20.7%), Enterococcus faecalis (17.2%), Candida (13.8%) and Pseudomonas aeruginosa (10.3%). Of 69 isolates, 27 (39.1%) were multidrug-resistant organisms. Twelve (54.5%) of 22 patients for whom empirical antimicrobial therapy was inappropriate were infected by a multidrug-resistant organism. Of 46 patients, 26 (56.5%) survived and 20 (43.5%) died. Exploring variables for association with in-hospital mortality identified > 75-year age (HR 2.97, 95% CI 1.15–7.68, p = 0.02), septic shock (HR 6.55, 95% CI 2.36–18.23, p < 0.001) and BSI onset ≤ 3 days (HR 4.68, 95% CI 1.40–15.63, p = 0.01) as risk factors independently associated with death. In our hospital, mortality among COVID-19 patients with BSI was high. While continued vigilance against these infections is essential, identification of risk factors for mortality may help to reduce fatal outcomes in patients with COVID-19. [ABSTRACT FROM AUTHOR]

A young Down's syndrome patient developed tricuspid valve endocarditis several years after undergoing surgical closure of a congenital ventricular septal defect. Fungal etiology was established by PCR amplification of the Candida albicans ERG11 gene. Although antifungal therapy was administered, surgical replacement of the infected valve was required to eliminate the infection. [ABSTRACT FROM AUTHOR]

The aim of the study was to build a machine learning-based predictive model to discriminate between hospitalized patients at low risk and high risk of bloodstream infection (BSI). A Data Mart including all patients hospitalized between January 2016 and December 2019 with suspected BSI was built. Multivariate logistic regression was applied to develop a clinically interpretable machine learning predictive model. The model was trained on 2016–2018 data and tested on 2019 data. A feature selection based on a univariate logistic regression first selected candidate predictors of BSI. A multivariate logistic regression with stepwise feature selection in five-fold cross-validation was applied to express the risk of BSI. A total of 5660 hospitalizations (4026 and 1634 in the training and the validation subsets, respectively) were included. Eleven predictors of BSI were identified. The performance of the model in terms of AUROC was 0.74. Based on the interquartile predicted risk score, 508 (31.1%) patients were defined as being at low risk, 776 (47.5%) at medium risk, and 350 (21.4%) at high risk of BSI. Of them, 14.2% (72/508), 30.8% (239/776), and 64% (224/350) had a BSI, respectively. The performance of the predictive model of BSI is promising. Computational infrastructure and machine learning models can help clinicians identify people at low risk for BSI, ultimately supporting an antibiotic stewardship approach. [ABSTRACT FROM AUTHOR]

Endoscopic Retrograde Cholangio-Pancreatography (ERCP) with biliary stenting is a minimally invasive medical procedure employed to address both malignant and benign obstructions within the biliary tract. Benign biliary strictures (BBSs), typically arising from surgical interventions such as liver transplants and cholecystectomy, as well as chronic inflammatory conditions, present a common clinical challenge. The current gold standard for treating BBSs involves the periodic insertion of plastic stents at intervals of 3–4 months, spanning a course of approximately one year. Unfortunately, stent occlusion emerges as a prevalent issue within this treatment paradigm, leading to the recurrence of symptoms and necessitating repeated ERCPs. In response to this clinical concern, we initiated a pilot study, delving into the microbial composition present in bile and on the inner surfaces of plastic stents. This investigation encompassed 22 patients afflicted by BBSs who had previously undergone ERCP with plastic stent placement. Our preliminary findings offered promising insights into the microbial culprits behind stent occlusion, with Enterobacter and Lactobacillus spp. standing out as prominent bacterial species known for their biofilm-forming tendencies on stent surfaces. These revelations hold promise for potential interventions, including targeted antimicrobial therapies aimed at curtailing bacterial growth on stents and the development of advanced stent materials boasting anti-biofilm properties. [ABSTRACT FROM AUTHOR]

A letter to the editor is presented in response to the article which demonstrates a case-case-control study to examine the risk factors for fungemia caused by fluconazole-resistant Candida glabrata by Lee and colleagues.

The human bladder has been long thought to be sterile until that, only in the last decade, advances in molecular biology have shown that the human urinary tract is populated with microorganisms. The relationship between the urobiota and the development of urinary tract disorders is now of great interest. Patients with spina bifida (SB) can be born with (or develop over time) neurological deficits due to damaged nerves that originate in the lower part of the spinal cord, including the neurogenic bladder. This condition represents a predisposing factor for urinary tract infections so that the most frequently used approach to treat patients with neurogenic bladder is based on clean intermittent catheterization (CIC). In this study, we analyzed the urobiota composition in a pediatric cohort of patients with SB compared to healthy controls, as well as the urobiota characteristics based on whether patients received CIC or not. [ABSTRACT FROM AUTHOR]

Mannose-binding lectin (MBL) plays a key role in the human innate immune response. It has been shown that polymorphisms in the MBL2 gene, particularly at codon 54 (variant allele B; wild-type allele designated as A), impact upon host susceptibility to Candida infection. This systematic review and meta-analysis were performed to assess the association between MBL2 codon 54 genotype and vulvovaginal candidiasis (VVC) or recurrent VVC (RVVC). Studies were searched in MEDLINE, SCOPUS, and ISI Web of Science until April 2013. Five studies including 704 women (386 cases and 318 controls) were part of the meta-analysis, and pooled ORs were calculated using the random effects model. For subjects with RVVC, ORs of AB versus AA and of BB versus AA were 4.84 (95% CI 2.10-11.15; P for heterogeneity = 0.013; I(2) = 68.6%) and 12.68 (95% CI 3.74-42.92; P for heterogeneity = 0.932, I(2) = 0.0%), respectively. For subjects with VVC, OR of AB versus AA was 2.57 (95% CI 1.29-5.12; P for heterogeneity = 0.897; I (2) = 0.0%). This analysis indicates that heterozygosity for the MBL2 allele B increases significantly the risk for both diseases, suggesting that MBL may influence the women's innate immunity in response to Candida. [ABSTRACT FROM AUTHOR]

Candida parapsilosis is the major non-C. albicans species involved in the colonization of central venous catheters, causing bloodstream infections. Biofilm formation on medical devices is considered one of the main causes of healthcare-associated infections and represents a global public health problem. In this context, the development of new nanomaterials that exhibit anti-adhesive and anti-biofilm properties for the coating of medical devices is crucial. In this work, we aimed to characterize the antimicrobial activity of two different coated-surfaces, graphene oxide (GO) and curcumin-graphene oxide (GO/CU) for the first time, against C. parapsilosis. We report the capacity of GO to bind and stabilize CU molecules, realizing a homogenous coated surface. We tested the anti-planktonic activity of GO and GO/CU by growth curve analysis and quantification of Reactive Oxigen Species(ROS) production. Then, we tested the antibiofilm activity by adhesion assay, crystal violet assay, and live and dead assay; moreover, the inhibition of the formation of a mature biofilm was investigated by a viability test and the use of specific dyes for the visualization of the cells and the extra-polymeric substances. Our data report that GO/CU has anti-planktonic, anti-adhesive, and anti-biofilm properties, showing a 72% cell viability reduction and a decrease of 85% in the secretion of extra-cellular substances (EPS) after 72 h of incubation. In conclusion, we show that the GO/CU conjugate is a promising material for the development of medical devices that are refractory to microbial colonization, thus leading to a decrease in the impact of biofilm-related infections. [ABSTRACT FROM AUTHOR]

A correction to the article "A nickel ABC-transporter of Staphylococcus aureus is involved in urinary tract infection," by Aurelia Hiron, et al., published in the previous issue is presented.

We used nasopharyngeal swab samples of patients with a symptomatic (n = 82) or asymptomatic (n = 20) coronavirus disease 2019 (COVID-19) diagnosis to assess the ability of antigen detection tests to infer active (potentially transmissible) or inactive (potentially non-transmissible) infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Using the subgenomic RNA (sgRNA) as an active replication marker of SARS-CoV-2, 48 (76.2%), 56 (88.9%), and 63 (100%) of 63 samples with sgRNA positive results tested positive with the SD BIOSENSOR STANDARD Q COVID-19 Ag (Standard Q), the SD BIOSENSOR STANDARD F COVID-19 Ag FIA (Standard F), or the Fujirebio LUMIPULSE G SARS-CoV-2 Ag (Lumipulse) assay, respectively. Conversely, 37 (94.9%), 29 (74.4%), and 7 (17.9%) of 39 samples with sgRNA negative results tested negative with Standard Q, Standard F, or Lumipulse, respectively. Stratifying results by the number of days of symptoms before testing revealed that most antigen positive/sgRNA positive results were among samples tested at 2–7 days regardless of the assay used. Conversely, most antigen negative/sgRNA negative results were among samples tested at 16–30 days only when Standard Q or Standard F were used. In conclusion, based on our findings, a negative antigen test, especially with the Lumipulse assay, or a positive antigen test, especially with the Standard F assay, may suggest, respectively, the absence or presence of replication-competent SARS-CoV-2. [ABSTRACT FROM AUTHOR]

Background: The severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) has a tropism for the gastrointestinal tract and several studies have shown an alteration of the gut microbiota in hospitalized infected patients. However, long-term data on microbiota changes after recovery are lacking. Methods: We enrolled 30 patients hospitalized for SARS‑CoV‑2-related pneumonia. Their gut microbiota was analyzed within 48 h from the admission and compared with (1) that of other patients admitted for suspected bacterial pneumonia (control group) (2) that obtained from the same subject 6 months after nasopharyngeal swab negativization. Results: Gut microbiota alpha-diversity increased 6 months after the resolution of SARS-CoV-2 infection. Bacteroidetes relative abundance was higher (≈ 36.8%) in patients with SARS-CoV-2, and declined to 18.7% when SARS-CoV-2 infection resolved (p = 0.004). Conversely, Firmicutes were prevalent (≈ 75%) in controls and in samples collected after SARS-CoV-2 infection resolution (p = 0.001). Ruminococcaceae, Lachnospiraceae and Blautia increased after SARS-CoV-2 infection resolution, rebalancing the gut microbiota composition. Conclusion: SARS-CoV-2 infection is associated with changes in the gut microbiome, which tend to be reversed in long-term period. [ABSTRACT FROM AUTHOR]

Compared to RT-PCR, lower performance of antigen detection assays, including the Lumipulse G SARS-CoV-2 Ag assay, may depend on specific testing scenarios. We tested 594 nasopharyngeal swab samples from individuals with COVID-19 (RT-PCR cycle threshold [Ct] values ≤ 40) or non-COVID-19 (Ct values >40) diagnoses. RT-PCR positive samples were assigned to diagnostic, screening, or monitoring groups of testing. With a limit of detection of 1.2 × 104 SARS-CoV-2 RNA copies/mL, Lumipulse showed positive percent agreement (PPA) of 79.9% (155/194) and negative percent agreement of 99.3% (397/400), whereas PPAs were 100% for samples with Ct values of <18 or 18–<25 and 92.5% for samples with Ct values of 25–<30. By three groups, Lumipulse showed PPA of 87.0% (60/69), 81.1% (43/53), or 72.2% (52/72), respectively, whereas PPA was 100% for samples with Ct values of <18 or 18–<25, and was 94.4, 80.0, or 100% for samples with Ct values of 25–<30, respectively. Additional testing of RT-PCR positive samples for SARS-CoV-2 subgenomic RNA showed that, by three groups, PPA was 63.8% (44/69), 62.3% (33/53), or 33.3% (24/72), respectively. PPAs dropped to 55.6, 20.0, or 41.7% for samples with Ct values of 25–<30, respectively. All 101 samples with a subgenomic RNA positive result had a Lumipulse assay's antigen positive result, whereas only 54 (58.1%) of remaining 93 samples had a Lumipulse assay's antigen positive result. Lumipulse assay was highly sensitive in samples with low RT-PCR Ct values, implying repeated testing to reduce consequences of false-negative results. [ABSTRACT FROM AUTHOR]

Analyzes the patterns of azole susceptibility of oral Candida isolates in the highly active antiretroviral therapy. Identification of patients with relapsing oral pharyngeal candidiasis; Number of isolated bacterial strains; Determination of fluconazole resistance; Exhibition of different fingerprint profiles.

Background: Transmission of viral diseases (e.g., influenza A H1N1) via respiratory droplets takes place mainly in confined spaces, including in aircraft during commercial air travel. The adoption of hygiene measures may help to prevent disease spread aboard aircraft. This review summarizes the evidence on hand hygiene and the use of facemasks as viral disease prevention measures in aircraft.Methods: A literature search was performed in the PubMed, Scopus, and Web of Science databases up to 10 June 2020, according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses criteria. A population, intervention, comparison, outcomes, and study design (PICOS) approach was used to define the review question.Results: We included four studies published between 2007 and 2020, all targeting influenza virus disease, in the qualitative synthesis. Three studies used mathematical models to simulate single- or multiple-direction flights, and two of them showed that facemask (e.g., N95 respirator) use considerably reduced infection probability. In the third study, hand cleaning by 20 to 60% of people at any time in all airports (including on aircraft) reduced the measure of airports' power to spread the disease across the globe by ~ 24 to 69%. The fourth study was a case-control study designed to trace an influenza outbreak in two flights during the 2009 influenza A H1N1 pandemic. The study showed that none (0%) of nine infected passengers compared to 15 (47%) of 32 healthy control passengers in the aircraft cabin during one of these flights wore a facemask (odds ratio, 0.0; 95% confidence interval, 0.0-0.7). In contrast, both case and control passengers appeared to be equally compliant in self-assessed hand hygiene.Conclusions: Facemask use combined with hand hygiene may minimize the chance of droplet-transmitted virus spread by air travelers. Thus, it is necessary that hygiene measures become an integral part of standard procedures in commercial air travel. [ABSTRACT FROM AUTHOR]

• Mortality due to bloodstream infections is increased in geriatric patients. • Elderly and oldest old show different susceptibility to distinct pathogens. • MRSA and Enterococcus spp strongly affect survival in oldest old patients. Bloodstream infections (BSIs) are a major cause of mortality in elderly. Objective of the study is to identify factors predictive of mortality in old and oldest old patients. This is a single centre retrospective observational study, including all patients admitted to Fondazione Policlinico A. Gemelli university hospital and diagnosed with BSI. Patients were stratified into three groups according to age: adult (A), younger than 65; old (O), aged between 65 and 80; oldest old (OO), older than 80. Primary outcome was 30-day in-hospital mortality. Secondary outcomes were duration of antimicrobial therapy (DOT) and length of hospital stay (LOS). Of the 1034 patients included in the study, 346 were in group A, 447 in group O and 241 in group OO. The rate of 30-day mortality raised from 6.9% (24/346) in group A to 10.8% (84/447) in group O and 33.2% (80/241) in group OO (p<0.01), while DOT and LOS significantly decreased moving from adults to oldest old (p<0.01). Methicillin-resistant Staphylococcus aureus (MRSA) and Enterococcus spp were both independently correlated to an increased 30-day mortality risk selectively in patients older than 80 (MRSA: HR 2.37, p=0.03; Enterococcus spp: HR 2.44, p=0.01). BSIs have a high impact on survival in old and oldest old patients. BSIs by gram-positive pathogens, in particular MRSA and Enterococcus spp, should be a wake-up call for physicians, who should focus efforts on adequate and prompt antibiotic and support treatment. [ABSTRACT FROM AUTHOR]

The increasing COVID-19 widespread has created the necessity to assess the diagnostic accuracy of newly introduced (RT-PCR based) assays for SARS-CoV-2 RNA detection in respiratory tract samples. We compared the results of the Allplex™ 2019-nCoV assay with those of the Simplexa™ COVID-19 Direct assay and the Quanty COVID-19 assay, respectively, all performed on 125 nasal/oropharyngeal swab samples of patients with COVID-19 suspicion. Fifty-four samples were positive, and 71 were negative with the Allplex™ assay, whereas 47 of 54 samples were also positive with the Simplexa™ assay. The Quanty assay detected 55 positive samples, including the 54 positive samples with the Allplex™ assay and 1 sample that was Allplex™ negative but Simplexa™ positive. Using a consensus result criterion as the reference standard allowed to resolve the eight samples with discordant results (one Allplex™ negative and seven Simplexa™ negative) as truly false negative. Interestingly, a Spearman's negative association was found between the viral RNA loads quantified by the Quanty assay and the CT values of RT PCRs performed with either the Allplex™ assay or the Simplexa™ assay. However, the strength of this association was higher for the Allplex™ assay (N gene, ρ = − 0.92; RdRP gene, ρ = − 0.91) than for the Simplexa™ assay (ORF1ab gene, ρ = − 0.65; S gene, ρ = − 0.80). The Allplex™ 2019-nCoV, the Simplexa™ COVID-19 Direct, and the Quanty COVID-19 assays yielded comparable results. However, the role these assays might play in future clinical practice warrants larger comparison studies. [ABSTRACT FROM AUTHOR]

Aim of our study was to map the adenotonsillar lymphoid tissues' microbiome identifying its potential etiopathogenetic role in children affected by chronic tonsillitis or tonsillar hypertrophy with Obstructive Sleep Apnea Syndrome (OSAS). In our study, we examined tonsillar swabs from healthy children and children affected by chronic tonsillitis or by tonsillar hypertrophy with Obstructive Sleep Apnea Syndrome (OSAS). Microbiome's analysis was performed and bacterial 16Sr RNA gene was sequenced according to metagenomic principles. Variability was described according to the biodiversity concept, indicating species found in a certain environment and changes they undergo adapting to different environmental conditions. The most significant differences concern variation of microbes in a single sample (alpha diversity) of some phyla in children affected by chronic tonsillitis compared with alpha diversity in healthy children and in children affected by OSAS with tonsillar hyperplasia. Proteobacteria are prevalent in chronic tonsillitis group, Fusobacteria and Spirochete in OSAS and Firmicutes, Actinobacteria, and Bacteroidetes were found in healthy children. Finally, comparison between the groups showed that children with OSAS with tonsillar hypertrophy had a higher presence of the Fusobacterium genus. Recurrent upper airway inflammatory and/or infectious processes are polymicrobial; chronicity of such processes appear to be related to variations in microbiome's composition and interaction among various taxonomic units. Knowledge of the microbiomes' composition together with traditional clinical biomarkers can also determine relationships between oropharyngeal microbiome and systemic pathologies to determine preventive changes in lifestyle, eating habits, environmental exposure and use of probiotics. [ABSTRACT FROM AUTHOR]

Despite a widespread pertussis immunization in childhood, the I Bordetella pertussis i infection (BPI) - including pertussis (i.e. whooping cough) - has risen in many world regions [[1]], and factors contributing to resurgence (or emergence) of BPI include improved diagnostics [[2]]. This environment may hamper the thriving of I B. pertussis i in the upper respiratory tract [[3]], which is yet the preferred colonization site of I B. pertussis i and other I Bordetella i species, such as I Bordetella parapertussis i , I Bordetella bronchiseptica i and I Bordetella holmesii i . Thereafter, Bordet-Gengou agar cultures will be negative for I B. pertussis i , whereas the PCR assay - which works on multiple matrices - and, additionally, the BioFire® FilmArray® Respiratory Panel test - which detects three bacterial respiratory tract pathogens, including I B. pertussis i - yielded negative results for I B. pertussis i . [Extracted from the article]

We aimed to report a 32-month laboratory experience with the eazyplex® CSF direct panel assay for the rapid diagnosis of meningitis due to six most common bacterial species (Escherichia coli, Haemophilus influenzae, Listeria monocytogenes, Neisseria meningitidis, Streptococcus agalactiae, and Streptococcus pneumoniae). We included all cerebrospinal fluid (CSF) samples from patients admitted with a clinical suspicion of meningitis/encephalitis between May 2016 and December 2018 at our hospital. In addition to the eazyplex® assay, both Gram stain microscopy and culture were performed, and results were confirmed with 16S rRNA PCR/sequencing. Patients' demographics and relevant clinical information were collected. Of 135 studied patients, 44 (32.6%) had a microbiologically documented diagnosis of meningitis. Overall, we identified 21 S. pneumoniae, 10 N. meningitidis, 6 L. monocytogenes, 3 E. coli, 2 Streptococcus pyogenes, 1 S. agalactiae, and 1 Citrobacter koseri as aetiological agents. The eazyplex® assay allowed identification in 40 (90.9%) cases, with four not identified cases due to microorganisms not included in the panel at the time of testing. Thirty-two (72.7%) cases had positive culture results, whereas 28 (63.6%) cases had positive Gram stain results. Notably, combining Gram stain and eazyplex® assay allowed identification in 100% of cases. After notification of rapid results, physicians modified the empiric antibiotic therapy, which became appropriate in three patients (all with L. monocytogenes meningitis). The eazyplex® CSF panel assay worked better than culture in detecting the most common agents of bacterial meningitis and accelerated the diagnosis leading to timely initiation or continuation of appropriate antibiotic therapy. [ABSTRACT FROM AUTHOR]

Abstract: Infections are a major cause of morbidity and mortality in patients with myelodysplastic syndrome (MDS) due to quantitative and qualitative granulocytic defects. We evaluated the in vitro bactericidal and fungicidal activities of neutrophils isolated from MDS. With comparison to those from healthy individuals, MDS neutrophils following infection showed a significantly reduced killing activity against Escherichia coli at 8 (p =0.002), 24 (p <0.0001), 48 (p =0.0005), and 72h (p =0.0264), against Lactococcus lactis at 24 (p =0.0002), 48 (p <0.0001), and 72h (p <0.0001), and more against Candida albicans at 8 (p =0.0003), 24 (p <0.0001), 48 (p <0.0001), and 72h (p <0.0001). Our data show that MDS neutrophils have an impaired microbicidal function, which might account for the high susceptibility to infections of MDS patients. [Copyright &y& Elsevier]

Despite being members of gut microbiota, Enterobacteriaceae are associated with many severe infections such as bloodstream infections. The β-lactam drugs have been the cornerstone of antibiotic therapy for such infections. However, the overuse of these antibiotics has contributed to select β-lactam-resistant Enterobacteriaceae isolates, so that β-lactam resistance is nowadays a major concern worldwide. The production of enzymes that inactivate β-lactams, mainly extended-spectrum β-lactamases and carbapenemases, can confer multidrug resistance patterns that seriously compromise therapeutic options. Further, β-lactam resistance may result in increases in the drug toxicity, mortality, and healthcare costs associated with Enterobacteriaceae infections. Here, we summarize the updated evidence about the molecular mechanisms and epidemiology of β-lactamase-mediated β-lactam resistance in Enterobacteriaceae, and their potential impact on clinical outcomes of β-lactam-resistant Enterobacteriaceae infections. [ABSTRACT FROM AUTHOR]

The Fungitell assay (FA) and the Wako β-glucan test (GT) are employed to measure the serum/plasma 1,3-β-D-glucan (BDG), a well-known invasive fungal disease biomarker. Data to convincingly and/or sufficiently support the GT as a valuable alternative to the FA are yet limited. In this study, we evaluated the FA and the GT to diagnose invasive aspergillosis (IA), invasive candidiasis (IC), and Pneumocystis jirovecii pneumonia (PJP). The FA and GT performances were compared in sera of patients with IA (n = 40), IC (n = 78), and PJP (n = 17) with respect to sera of control patients (n = 187). Using the manufacturer's cutoff values of 80 pg/mL and 11 pg/mL, the sensitivity and specificity for IA diagnosis were 92.5% and 99.5% for the FA and 60.0% and 99.5% for the GT, respectively; for IC diagnosis were 100.0% and 97.3% for the FA and 91.0% and 99.5% for the GT, respectively; for PJP diagnosis were 100.0% and 97.3% for the FA and 88.2% and 99.5% for the GT, respectively. When an optimized cutoff value of 7.0 pg/mL for the GT was used, the sensitivity and specificity were 80.0% and 97.3% for IA diagnosis, 98.7% and 97.3% for IC diagnosis, and 94.1% and 97.3% for PJP diagnosis, respectively. At the 7.0-pg/mL GT cutoff, the agreement between the assays remained and/or became excellent for IA (95.1%), IC (97.3%), and PJP (96.5%), respectively. In conclusion, we show that the GT performed as well as the FA only with a lowered cutoff value for positivity. Further studies are expected to establish the equivalence of the two BDG assays. [ABSTRACT FROM AUTHOR]

Objective  To date, no information on late-onset infection in newborns to mother with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contracted in pregnancy are available. This study aimed to evaluate postdischarge SARS-CoV-2 status of newborns to mothers with COVID-19 in pregnancy that, at birth, were negative to SARS-CoV-2. Study Design  This is an observational study of neonates born to mothers with coronavirus disease 2019 (COVID-19). Results  Seven pregnant women with documented SARS-CoV-2 infection have been evaluated in our institution. One woman had a spontaneous abortion at 8 weeks of gestational age, four women recovered and are still in follow-up, and two women delivered. Two newborns were enrolled in the study. At birth and 3 days of life, newborns were negative to SARS-CoV-2. At 2-week follow-up, one newborn tested positive although asymptomatic. Conclusion  Our findings highlight the importance of follow-up of newborns to mothers with COVID-19 in pregnancy, since they remain at risk of contracting the infection in the early period of life and long-term consequences are still unknown. Key Points Newborns to mothers with coronavirus disease 2019 (COVID-19) in pregnancy can acquire the infection later after birth. Newborns to mothers with COVID-19 in pregnancy need a long-term follow-up, even if they tested negative at birth. Specific guidelines for the long-term follow-up of newborns to mothers with COVID-19 in pregnancy are needed. [ABSTRACT FROM AUTHOR]

Background & aims: Alcohol use disorder (AUD) represents the most common cause of liver disease. The gut microbiota plays a critical role in the progression of alcohol‐related liver damage. Aim of this study was to characterize the gut microbial composition and function in AUD patients with alcohol‐associated liver disease (AALD). Methods: This study included 36 AUD patients (14 with cirrhosis) who were active drinkers and an equal number of matched controls. Stool microbial composition, serum levels of lipopolysaccharide, cytokines/chemokines and gut microbiota functional profile were assessed. Results: AUD patients had a decreased microbial alpha diversity as compared to controls (0.092 vs 0.130, P =.047) and a specific gut microbial signature. The reduction of Akkermansia and the increase in Bacteroides were able to identify AUD patients with an accuracy of 93.4%. Serum levels of lipopolysaccharide (4.91 vs 2.43, P =.009) and pro‐inflammatory mediators (tumour necrosis factor alpha 60.85 vs 15.08, P =.001; interleukin [IL] 1beta 4.43 vs 1.72, P =.0001; monocyte chemoattractant protein 1 225.22 vs 16.43, P =.006; IL6 1.87 vs 1.23, P =.008) were significantly increased in AUD patients compared to controls and in cirrhotic patients compared to non‐cirrhotic ones (IL6 3.74 vs 1.39, P =.019; IL8 57.60 vs 6.53, P =.004). The AUD‐associated gut microbiota showed an increased expression of gamma‐aminobutyric acid (GABA) metabolic pathways and energy metabolism. Conclusions: AUD patients present a specific gut microbial fingerprint, associated with increased endotoxaemia, systemic inflammatory status and functional alterations that may be involved in the progression of the AALD and in the pathogenesis of AUD. [ABSTRACT FROM AUTHOR]

The aim of this study was to compare the Candida bromcresol green (BCG) medium with the chromogenic (CHROM) Brilliance Candida agar and Sabouraud dextrose agar (SDA) media in regard to their capability of detecting Candida isolates from mono- or dual-species cultures. We prepared Candida isolates' suspensions to obtain mono-species (n = 18) or dual-species (n = 153) culture plates per each medium, and three readers independently observed 513 plates at 24-h, 48-h and 72-h incubation time. We scored reading results as correct, over or under detection compared to the expected species number(s). BCG showed significantly higher correct-detection and lower under-detection rates for all Candida species when observed by at least one reader. At 24-h reading, 12 mono-species cultures had correct (or over) detections in all media, whereas 106, 60 and 78 dual-species cultures had correct (or over) detections in BCG, CHROM or SDA, respectively. BCG provides the basis for an accurate laboratory diagnosis of Candida infections. [ABSTRACT FROM AUTHOR]

We herein report on EUCAST RAST results for BCs consecutively collected between June 2019 and December 2019 that contained E. coli (n" 134) or K. pneumoniae (n" 66) isolates (Table S1, available as Supplementary data at JAC Online), of which 75 (37.5%) were phenotypically resistant to third-generation cephalosporins and/or carbapenems. In conclusion, we showed that the EUCAST RAST method affords an accurate and relatively easy means of testing antimicrobial susceptibility of E. coli and K. pneumoniae isolates directly in positive BC samples. Note that we tested only BC samples containing E. coli or K. pneumoniae, which are two species for which all DD plates could be read at the three timepoints. [Extracted from the article]

Objective: The early identification of gastric cancer (GC) represents a major clinical challenge. We conducted a systematic review of studies evaluating the miRNA expression profiling as a diagnostic tool in GC. Methods: We performed a search of PubMed, ISI Web of Science and SCOPUS databases for studies on diagnostic miRNAs and GC, published in English up to October 2017. Eligibility criteria included case-control studies evaluating blood or tissue-based miRNA expression profiles, and incorporating at least two detection phases (screening and validation). Results: We included 27 eligible studies, that reported on 97 deregulated miRNAs either in blood or tissue, out of which 30 were reported in at least two studies. Among 22 studies on tissue-diagnostic miRNAs, 13 consistently upregulated miRNAs (miR-214, miR-21, miR-103, miR-107, miR-196a, miR-196b, miR-7, miR-135b, miR-222, miR-23b, miR-25, miR-92 and miR-93), and six consistently downregulated miRNAs (miR-148a, miR-375, miR-133b, miR-30a, miR-193a and miR-204) were reported. Ten miRNAs with inconsistent direction of expression in tissues were identified. Among the five studies performed on blood samples, only one miRNA was consistently upregulated (miR-20a). Conclusions: This review shows that some tissue or blood miRNAs may be considered as potential biomarkers for GC diagnosis, that urgently needs to be confirmed from large prospective studies. [ABSTRACT FROM AUTHOR]

Desirability of outcome ranking (DOOR) has been developed for assessing desirability of outcome in interventional studies. However, its possible use in observational studies of the diagnosis and early treatment of infectious diseases has not been explored so far, and it might introduce interesting features in specific scenarios. This was a post hoc analysis of a prospective observational study in intensive care unit patients with sepsis and at risk of candidemia. The probabilities that a randomly selected patient would have a more, less, and equally cost-effective early therapeutic choice following a BDG-based diagnostic strategy rather than the empirical administration of antifungals to all patients were calculated using DOOR methods. The probability of a more cost-effective therapeutic choice following the BDG-based rather than the empirical strategy was 67.81% (95% CI 67.32-68.30), whereas the probabilities of a less and equally cost-effective early therapeutic choice were 19.68% (95% CI 19.27-20.10) and 12.50% (95% CI 12.16-12.85), respectively. The application of DOOR methods to observational studies focused on diagnosis and early treatment is a novel field that could merit further investigation. [ABSTRACT FROM AUTHOR]