Current characteristics of patients with hepatitis C virus: results from an automated alert system.

Alert systems are proving to be useful to increase hepatitis C virus (HCV) diagnoses and facilitating access to antiviral treatment. Since 2020, our health department has had a fully automated alert system set up at the Microbiology Department. In this study, we present the results of the 2022-2023 period to assess the current characteristics of HCV diagnosed patients. In addition, we analyzed, through a comparison, whether a limitation that we noticed during the 2020-2021 period (whose results were published) is still present. This limitation consists of that 24.2% (34/134) of those candidates for antiviral treatment were not treated because they could not be located or refused treatment. During the 2022-2023 period, 188 new cases were diagnosed, and 75% (141/188) were treated. The comparison of both periods showed that in 2022-2023, the rate of treatment rejection by the patient was significantly lower (1.4% vs 14.5%, p < 0.05) and, therefore, the rate of antiviral treatment increased (75% vs 58.9%, p < 0.05). These results suggest that our alert system is useful and efficient for the diagnosis and treatment of HCV.

Multidrug-Resistant Commensal and Infection-Causing Staphylococcus spp. Isolated from Companion Animals in the Valencia Region.

The emergence of antimicrobial resistance (AMR) and multidrug resistance (MDR) among microorganisms to commonly used antibiotics is a growing concern in both human and veterinary medicine. Companion animals play a significant role in the epidemiology of AMR, as their population is continuously increasing, posing a risk of disseminating AMR, particularly to strains of public health importance, such as methicillin-resistant Staphylococcus strains. Thus, this study aimed to investigate the prevalence of AMR and MDR in commensal and infection-causing Staphylococcus spp. in dogs and cats in Valencia region. For this purpose, 271 samples were taken from veterinary centers to assess antimicrobial susceptibility against 20 antibiotics, including some of the most important antibiotics for the treatment of Staphylococcus infections, including the five last resort antibiotics in this list. Of all the samples, 187 Staphylococcus spp. strains were recovered from asymptomatic and skin-diseased dogs and cats, of which S. pseudintermedius (≈60%) was more prevalent in dogs, while S. felis (≈50%) was more prevalent in cats. In the overall analysis of the isolates, AMR was observed for all antibiotics tested, including those crucial in human medicine. Furthermore, over 70% and 30% of the strains in dogs and cats, respectively, exhibited MDR. This study highlights the significance of monitoring the trends in AMR and MDR among companion animals. The potential contribution of these animals to the dissemination of AMR and its resistance genes to humans, other animals, and their shared environment underscores the necessity for adopting a One Health approach.

Evaluation of Eazyplex® LAMP test for fast Candida auris direct detection of colonized patients.

Candida auris is a multidrug-resistant pathogen yeast that produces nosocomial outbreaks, due to its ability in colonizing the skin, mucous membranes and surfaces. Rapid diagnosis is essential to control its spread. The aim of this study was to compare the Eazyplex® Candida auris kit (AmplexDiagnostics GmbH) for the rapid identification of patients colonized with C. auris, with the reference method used in our institution (culture and identification by MALDI-TOF). This easy-to-perform test allows obtaining a fast result, in ~30 min. First, we achieved a preliminary study from previously characterized Candida species colonies obtained from 51 clinical samples, with 100% agreement between culture isolation and the Eazyplex® Candida auris LAMP. Second, 152 epidemiological surveillance samples (pharyngeal and axillary-rectal swabs) were tested retrospectively. The sensitivity, specificity, positive and negative predictive values were 91.8%, 98.8%, 98.2% and 94.5%, respectively. Eazyplex® Candida auris showed acceptable results compared with culture in detecting C. auris from surveillance samples with the advantage of single-test and shorter time for handling and result than culture, in addition to its great specificity, positive and negative predictive values.

Candida auris from colonisation to candidemia: A four-year study.

BACKGROUND: Candida auris has become a worrisome multi-drug resistant healthcare-associated pathogen due to its capacity to colonise patients and surfaces and to cause outbreaks of invasive infections in critically ill patients. OBJECTIVES: This study evaluated the outbreak in our setting in a 4-year period, reporting the risk factors for developing candidemia in previously colonised patients, the therapeutic measures for candidemia and the outcome of candidemia and colonisation cases among all C. auris isolates and their susceptibility to antifungals. METHODS: Data were retrospectively collected from patients admitted to Consorcio Hospital General Universitario de Valencia (Spain) from September 2017 to September 2021. A retrospective case-control study was designed to identify risk factors for developing C. auris candidemia in previously colonised patients. RESULTS: C. auris affected 550 patients, of which 210 (38.2%) had some clinical sample positive. Isolates were uniformly resistant to fluconazole, 20 isolates were resistant to echinocandins (2.8%) and four isolates were resistant to ampfotericin B (0.6%). There were 86 candidemia cases. APACHE II, digestive disease and catheter isolate were proven to be independent risk factors for developing candidemia in previously colonised patients. Thirty-day mortality rate for C. auris candidemia cases was 32.6%, while for colonisation cases was 33.7%. CONCLUSIONS: Candidemia was one of the most frequent and severe infections caused by C. auris. The risk factors identified in this study should help to detect patients who are at more risk of developing candidemia, as long as an adequate surveillance of C. auris colonisation is performed.

On the Oral Microbiome of Oral Potentially Malignant and Malignant Disorders: Dysbiosis, Loss of Diversity, and Pathogens Enrichment.

The role of dysbiosis in the development and progression of oral potentially malignant disorders (OPMDs) remains largely unknown. Here, we aim to characterize and compare the oral microbiome of homogeneous leucoplakia (HL), proliferative verrucous leukoplakia (PVL), oral squamous cell carcinoma (OSCC), and OSCC preceded by PVL (PVL-OSCC). Fifty oral biopsies from HL (n = 9), PVL (n = 12), OSCC (n = 10), PVL-OSCC (n = 8), and healthy (n = 11) donors were obtained. The sequence of the V3-V4 region of the 16S rRNA gene was used to analyze the composition and diversity of bacterial populations. In the cancer patients, the number of observed amplicon sequence variants (ASVs) was lower and Fusobacteriota constituted more than 30% of the microbiome. PVL and PVL-OSCC patients had a higher abundance of Campilobacterota and lower Proteobacteria than any other group analyzed. A penalized regression was performed to determine which species were able to distinguish groups. HL is enriched in Streptococcus parasanguinis, Streptococcus salivarius, Fusobacterium periodonticum, Prevotella histicola, Porphyromonas pasteri, and Megasphaera micronuciformis; PVL is enriched in Prevotella salivae, Campylobacter concisus, Dialister pneumosintes, and Schaalia odontolytica; OSCC is enriched in Capnocytophaga leadbetteri, Capnocytophaga sputigena, Capnocytophaga gingivalis, Campylobacter showae, Metamycoplasma salivarium, and Prevotella nanceiensis; and PVL-OSCC is enriched in Lachnospiraceae bacterium, Selenomonas sputigena, and Prevotella shahii. There is differential dysbiosis in patients suffering from OPMDs and cancer. To the best of our knowledge, this is the first study comparing the oral microbiome alterations in these groups; thus, additional studies are needed.

Outcomes of an automated alert system from Microbiology to link diagnosis to treatment in patients with hepatitis C virus.

INTRODUCTION: simplification strategies for the care circuit of patients with hepatitis C virus (HCV) are key to achieve eradication. An electronic identification system was set up for HCV serology to link diagnosis to specialist management, aimed to reduce patient loss. MATERIAL AND METHODS: a retrospective, single-center study was performed in patients with HCV identified from 15/3/2020 to 15/12/2021, using an alert system from Microbiology that notified specialists of positive cases. The patient was contacted and appointed a Fibroscan® and viral load measurement, with antiviral therapy prescribed on the same day. Origin, public health data, patient location rate and antiviral therapy prescription were recorded. RESULTS: of 174 patients identified, 171 had positive viremia, with a mean age of 59.6 ± 15.9 years, 61.5 % were males and 81.2 % were Spanish nationals. Origin in the outpatient setting predominated (57.9 %, 99/171), particularly Primary Care (51/171), penitentiaries (21/171) and addiction units (14/171). Overall, 43.3 % (74/171) were aware of their diagnosis; 19.4 % (20/103) of patients had F3 fibrosis and 25.2 % (26/103) had F4 fibrosis. Also, 78.4 % (134/171) were deemed candidates for treatment. Of these, 74.6 % (100/134) were located and treatment was initiated, and all those who completed their treatment achieved a sustained viral response (96/96). This system managed 58.5 % (100/171) of the patients identified. The only association found between antiviral therapy and patient variables was comorbidities with being untreated (OR, 7.14; p ˂ 0.001). CONCLUSIONS: this alert system allows to minimize patient loss in the care circuit and provides high rates of treated patients.

Novel Chromogenic Medium CHROMagarTM Candida Plus for Detection of Candida auris and Other Candida Species from Surveillance and Environmental Samples: A Multicenter Study.

Epidemiological trends show a dramatic increase in the prevalence of fungal infections, and in the isolation of multidrug-resistant species, such as Candida auris. CHROMagarTM Candida (CC; CHROMagar, Paris, France) and other chromogenic media, which are widely used in the clinical laboratory because they allow a rapid identification of most Candida species. Recently, CHROMagarTM Candida Plus (CC-Plus; CHROMagar, Paris, France) was developed to detect and differentiate C. auris in addition to other major clinical Candida species, such as C. albicans, C. tropicalis, C. glabrata, or C. krusei. C. auris colonies display a differential light blue color with a blue halo. A multicentric study was designed to evaluate the performance of the CC-Plus medium in the detection of Candida species in patients' surveillance and environmental samples from three Spanish hospitals with active C. auris outbreaks. A total of 364 patients' surveillance samples and 212 environmental samples were tested. Samples were inoculated in CC and CC-Plus in parallel, and the plates were read at 24 and 48 h. All recovered colonies were presumptively identified according to colony color described by manufacturer, and the definitive identification was performed by mass spectrometry at 48 h. A total of 134 C. auris isolates were obtained (101 from patients' surveillance samples, and 33 from environmental samples). Sensitivity, specificity, and predictive positive and negative values were 99.5%, 100%, 100%, and 99.1%, respectively, for the main clinical Candida species, showing that CC-Plus is comparable to CC, with the advantage of being able to differentiate C. auris from C. parapsilosis. Furthermore, CC-Plus was able to detect one C. albicans, one C. glabrata, and eight C. auris that did not grow in CC. Additionally, the yeast colonies were generally larger, suggesting that this novel medium could be a richer medium, and suitable for surveillance and environmental cultures of C. auris and other clinically relevant Candida species.

The first wave of the COVID-19 epidemic in Spain was associated with early introductions and fast spread of a dominating genetic variant.

The coronavirus disease 2019 (COVID-19) pandemic has affected the world radically since 2020. Spain was one of the European countries with the highest incidence during the first wave. As a part of a consortium to monitor and study the evolution of the epidemic, we sequenced 2,170 samples, diagnosed mostly before lockdown measures. Here, we identified at least 500 introductions from multiple international sources and documented the early rise of two dominant Spanish epidemic clades (SECs), probably amplified by superspreading events. Both SECs were related closely to the initial Asian variants of SARS-CoV-2 and spread widely across Spain. We inferred a substantial reduction in the effective reproductive number of both SECs due to public-health interventions (Re < 1), also reflected in the replacement of SECs by a new variant over the summer of 2020. In summary, we reveal a notable difference in the initial genetic makeup of SARS-CoV-2 in Spain compared with other European countries and show evidence to support the effectiveness of lockdown measures in controlling virus spread, even for the most successful genetic variants.

Impact of the SARS-CoV-2 Pandemic in Candidaemia, Invasive Aspergillosis and Antifungal Consumption in a Tertiary Hospital.

In addition to the increase in fungal infections that has been observed in the last few decades, it has been reported that severe clinical COVID-19 can increase the risk of invasive fungal infections. The main objective of this study was to evaluate if there had been an increase in candidaemia and invasive pulmonary aspergillosis (IPA) cases since the onset of the SARS-CoV-2 pandemic. Data were retrospectively collected from April 2019 to March 2021, from patients admitted to Consorcio Hospital General Universitario de Valencia (Spain). A total of 152 candidaemia cases (56 of which were due to Candida auris) and 108 possible IPA cases were detected. A great increase in candidaemia cases was produced during the first and the third epidemic waves of the SARS-CoV-2 pandemic (June 2020, and January 2021, respectively), while an increase in IPA cases was produced during the third wave. The 28-day mortality rates in patients affected by candidaemia and IPA increased in 2020 and 2021. C. auris has displaced the other Candida species, becoming the most isolated Candida species in blood cultures since the onset of the SARS-CoV-2 pandemic. Antifungal consumption increased in 2020 when compared to 2019, especially echinocandins, voriconazole and isavuconazole.

Abnormal liver chemistry constitutes an independent prognostic factor of less favorable clinical course in patients with COVID-19.

INTRODUCTION: abnormal liver biochemistry (ALB) is correlated with increased clinical involvement or severity in COVID-19, but its prognostic implications have not been studied extensively. The aim of this study was to determine whether ALB is a risk factor for unfavorable clinical outcome and involvement. MATERIALS AND METHODS: a retrospective, single-center study in confirmed COVID-19 cases. Patients with pharmacological hepatotoxicity or liver diseases were excluded. ALB was defined as any elevation of total bilirubin, AST, ALT, alkaline phosphatase, and/or GGT above the upper limit of normal. First, an assessment was made of the correlation between ALB and need for hospitalization. This was followed by an assessment of the correlation of ALB in hospitalized patients with demographic variables, comorbidities, and treatment for COVID-19, and with clinical involvement and outcome. The statistical analysis was performed using an age-adjusted multiple logistic regression with a p-value < 0.05. RESULTS: of 1,277 confirmed cases, 346 required hospitalization and 302 were included. The prevalence of ALB was higher in hospitalized patients compared to non-hospitalized patients (60.9 % vs. 10.3 %, p ˂ 0.001). Among hospitalized patients, there was no correlation between ALB and demographic variables, comorbidities, or treatment for COVID-19, except for low molecular weight heparin. There was a significant correlation between ALB and moderate/severe COVID-19 involvement and between unfavorable clinical outcomes and elevated total bilirubin. The period of greatest clinical worsening and deterioration of liver biochemistry parameters occurred during the first seven days. There was a significant correlation of ALB with longer hospital stay and admission to the intensive care unit, but this did not imply increased mortality. CONCLUSIONS: ALB correlates with greater clinical involvement and worse clinical outcomes in hospitalized patients with COVID-19.

Artritis séptica por Sneathia sanguinegens en un varón. Primer caso descrito en la literatura científica / Septic Arthritis due to Sneathia Sanguinegens in a Male. First Case Described in the Scientific Literature

Varón de 88 años que ingresa por artritis séptica de hombro por un bacilo Gram negativo. Se identifica el microorganismo mediante secuenciación del gen 16 S ADNr como Sneathia sanguinegens. Se trata del primer caso descrito en la literatura en un varón, ya que hasta el momento solo se habían descrito infecciones en mujeres en edad fértil.(AU)

An 88-year-old male admitted with septic shoulder arthritis due to a gram-negative bacillus. The microorganism is identified by sequencing the 16 S rDNA gene as Sneathia sanguinegens. This is the first case described in the literature in a male, since so far only infections in women of childbearing age have been described.(AU)

Validation and implementation of a commercial real-time PCR assay for direct detection of Candida auris from surveillance samples.

BACKGROUND: Rapid and reliable laboratory methods are required for detecting the nosocomial yeast Candida auris. AurisID® (Olm Diagnostics) is a real-time PCR assay approved for detecting C. auris in fungal cultures and directly from blood samples, involving a nucleic acid extraction as a prior step. OBJECTIVES: The purpose of this study is to validate the AurisID® kit for direct detection of C. auris from surveillance samples without prior DNA extraction and to analyse the results of implementing this methodology to our daily laboratory routine protocol for C. auris surveillance studies. METHODS: Our PCR method using the AurisID® kit was compared with our routine protocol, consisting of culture in CHROMagar® Candida and identification by mass spectrometry. A total of 113 swabs were used for validation and 136 pair of surveillance samples were tested. Limit of detection (LOD) was determined by using swabs in Amies transport medium, which were spiked in a series of dilutions of a C. auris standardised suspension (0.5 McFarland). RESULTS: The PCR method showed high sensitivity, specificity, predictive positive value and predictive negative value (96.6%, 100%, 100% and 98.2%, respectively) when compared with the routine protocol. LOD was 500 CFU/ml, which corresponds to approximately 1 CFU/PCR. CONCLUSIONS: Our PCR method using the AurisID® kit allows a reduction in the turnaround time for surveillance of C. auris compared with other methods. These results are expected to contribute to control C. auris outbreaks, allowing isolation of patients and cleaning of environmental surfaces in advance.

Septic Arthritis due to Sneathia Sanguinegens in a Male. First Case Described in the Scientific Literature. / Artritis séptica por Sneathia sanguinegens en un varón. Primer caso descrito en la literatura científica.

An 88-year-old male admitted with septic shoulder arthritis due to a gram-negative bacillus. The microorganism is identified by sequencing the 16 S rDNA gene as Sneathia sanguinegens. This is the first case described in the literature in a male, since so far only infections in women of childbearing age have been described.

Characteristics and Management of Candidaemia Episodes in an Established Candida auris Outbreak.

The multi-resistant yeast Candida auris has become a global public health threat because of its ease to persist and spread in clinical environments, especially in intensive care units. One of the most severe manifestations of invasive candidiasis is candidaemia, whose epidemiology has evolved to more resistant non-albicansCandida species, such as C. auris. It is crucial to establish infection control policies in order to control an outbreak due to nosocomial pathogens, including the implementation of screening colonisation studies. We describe here our experience in managing a C. auris outbreak lasting more than two and a half years which, despite our efforts in establishing control measures and surveillance, is still ongoing. A total of 287 colonised patients and 47 blood stream infections (candidaemia) have been detected to date. The epidemiology of those patients with candidaemia and the susceptibility of C. auris isolates are also reported. Thirty-five patients with candidaemia (74.5%) were also previously colonised. Forty-three patients (91.5%) were hospitalised (61.7%) or had been hospitalised (29.8%) in the ICU before developing candidaemia. Antifungal therapy for candidaemia consisted of echinocandins in monotherapy or in combination with amphotericin B or isavuconazole. The most common underlying disease was abdominal surgery (29.8%). The thirty-day mortality rate was 23.4% and two cases of endophtalmitis due to C. auris were found. All isolates were resistant to fluconazole and susceptible to echinocandins and amphotericin B. One isolate became resistant to echinocandins two months after the first isolate. Although there are no established clinical breakpoints, minimum inhibitory concentrations for isavuconazole were low (≤ 1 µg/mL).

Evaluation of a novel chromogenic medium for Candida spp. identification and comparison with CHROMagar™ Candida for the detection of Candida auris in surveillance samples.

A shift to Candida non-albicans infections has been noted during the last years, and the emergence of multi-resistant Candida auris has complicated their management. The aim of this study was first to compare the performance of the novel chromogenic medium CHROMagar™ Candida Plus (CHROMagar, France) with CHROMagar™ Candida (Becton Dickinson, Germany) for the presumptive identification of Candida species; and then, to evaluate its utility in the detection of C. auris in surveillance samples. CHROMagar™ Candida Plus showed a good performance compared with the reference medium CHROMagar™ Candida. Sensitivity and specificity were 100% in both media for tested species at 48 h of incubation, except for Candida glabrata and Candida lusitaniae. Furthermore, the new medium allows a reliable presumptive identification of C. auris, as a new specific color for this species is assigned (light blue with a blue halo), obtaining a sensitivity and specificity of 100% at 36 h of incubation.