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.

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.

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.

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.

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.

Candida auris: descripción de un brote / Candida auris: report of an outbreak

Candida auris es una levadura multirresistente emergente que causa infecciones invasivas graves y brotes con una alta mortalidad. El control de C. auris es un reto. Laboratorios, clínicos e instituciones sanitarias deben trabajar conjuntamente para mejorar la identificación y el tratamiento de la infección, así como el control de la transmisión. Esta revisión describe los aspectos generales de la biología, diagnóstico y tratamiento de C. auris, al igual que las recomendaciones publicadas recientemente por un grupo de expertos. También se presenta la experiencia de un brote de C. auris en el Consorcio Hospital General Universitario de Valencia desde septiembre de 2017 hasta agosto de 2019. Se detectaron un total de 203 pacientes infectados y/o colonizados por C. auris. Se diagnosticaron 30 infecciones invasivas (29 candidemias y 1 meningitis). El 32% de las candidemias del año 2018 fueron por C. auris. Todas las cepas fueron resistentes a fluconazol

Candida auris is an emerging multidrug-resistant yeast that causes serious invasive infections and outbreaks with high mortality. Controlling C. auris is a challenge in which laboratories, clinicians and public health agencies are needed to identify and treat infections and prevent transmission. This review describes the general aspects of the biology, diagnosis and treatment of C. auris infection, as well as the main recommendations recently published by expert groups. We also present our experience of the C. auris outbreak at the Consorcio Hospital General Universitario de Valencia from September 2017 to August 2019. A total of 203 patients were colonised and/or infected by C. auris. Thirty invasive infections (29 blood cultures and one case of meningitis) were diagnosed. In all, 32% cases of candidemia were caused by C. auris in 2018. All strains were resistant to fluconazole

Evaluation of the DNA microarray "AMR Direct Flow Chip Kit" for detection of antimicrobial resistance genes from Gram-positive and Gram-negative bacterial isolated colonies / Evaluación de una micromatriz de ADN "AMR Direct Flow Chip Kit" para la detección de genes de resistencia antimicrobiana de bacterias grampositivas y gramnegativas a partir de colonias aisladas

INTRODUCTION: The AMR Direct Flow Chip assay allows the simultaneous detection of a large variety of antibiotic resistance genetic markers. To assess this kit's performance, we use isolated colonies as starting material. The assay has been approved by the European Economic Area as a suitable device for in vitro diagnosis (CE IVD) using clinical specimens. METHODS: A total of 210 bacterial isolates harbouring either one or more antimicrobial resistance genes including plasmid-encoded extended-spectrum β-lactamases (SHV, CTX-M) and carbapenemases (GES, SME, KPC, NMC/IMI, SIM, GIM, SPM, NDM, VIM, IMP, and OXA), mecA, vanA and vanB, and 30 controls were included. RESULTS: The assay displayed a sensitivity and specificity of 100% for all target genes included in the array. CONCLUSION: The AMR Direct Flow Chip Kit is an accurate assay for detecting genes which commonly confer resistance to β-lactams and vancomycin from isolated colonies in culture of Gram-positive and Gram-negative bacteria

INTRODUCCIÓN: El ensayo "AMR Direct Flow Chip Kit" permite detectar simultáneamente la presencia de una gran variedad de marcadores genotípicos de resistencia bacteriana. Evaluamos su rendimiento utilizando colonias aisladas como material de partida. El ensayo aludido ha sido aprobado por el Área Económica Europea como un dispositivo adecuado para el diagnóstico in vitro (CE IVD) utilizando muestras clínicas. MÉTODOS: El estudio ha incluido 210 aislados bacterianos con uno o más genes de resistencia a los antimicrobianos, incluidos genes plasmídicos que codifican β-lactamasas de espectro extendido (SHV y CTX-M) y carbapenemasas (GES, SME, KPC, NMC/IMI, SIM, GIM, SPM, NDM, VIM, IMP y OXA), mecA, vanA y vanB, y 30 controles. RESULTADOS: El ensayo mostró una sensibilidad y especificidad del 100% para todos los genes diana incluidos en la matriz. CONCLUSIÓN: El «AMR Direct Flow Chip Kit» es un ensayo fiable para la detección de genes que comúnmente confieren resistencia a β-lactámicos y vancomicina en bacterias grampositivas y gramnegativas a partir de colonias aisladas en cultivo

Evaluation of the DNA microarray "AMR Direct Flow Chip Kit" for detection of antimicrobial resistance genes from Gram-positive and Gram-negative bacterial isolated colonies.

INTRODUCTION: The AMR Direct Flow Chip assay allows the simultaneous detection of a large variety of antibiotic resistance genetic markers. To assess this kit's performance, we use isolated colonies as starting material. The assay has been approved by the European Economic Area as a suitable device for in vitro diagnosis (CE IVD) using clinical specimens. METHODS: A total of 210 bacterial isolates harbouring either one or more antimicrobial resistance genes including plasmid-encoded extended-spectrum ß-lactamases (SHV, CTX-M) and carbapenemases (GES, SME, KPC, NMC/IMI, SIM, GIM, SPM, NDM, VIM, IMP, and OXA), mecA, vanA and vanB, and 30 controls were included. RESULTS: The assay displayed a sensitivity and specificity of 100% for all target genes included in the array. CONCLUSION: The AMR Direct Flow Chip Kit is an accurate assay for detecting genes which commonly confer resistance to ß-lactams and vancomycin from isolated colonies in culture of Gram-positive and Gram-negative bacteria.

Susceptibility testing and detection of ß-lactam resistance mechanisms in Enterobacteriaceae: a multicentre national proficiency study.

A nationwide study was developed to evaluate the ability of 60 Spanish clinical microbiology laboratories to predict the underlying ß-lactam resistance mechanisms of 12 Enterobacteriaceae strains (CCS01-CCS12). Results obtained by two reference laboratories were compared with those reported by the participant laboratories that used their own routine susceptibility testing methodology. Clinical and Laboratory Standards Institute (CLSI) interpretive criteria were used in 53.3% of centres, whilst 46.7% used European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria. Overall categorical agreement (CA) was 85.5%. Rates of very major errors (VME), minor errors (MinE) and major errors (ME) were 5%, 9.7% and 5.5%, respectively. The lowest CA values were obtained for carbapenems (56.7-78.1%). ß-Lactam/ß-lactamase inhibitors were also problematic compounds: VME for amoxicillin/clavulanic acid were 8% (EUCAST criteria) and MinE for piperacillin/tazobactam were 45.7% (CLSI criteria). OXA-48 (CCS02, CCS10, CCS11), VIM-1 (CCS09) and KPC-3 (CCS05) were correctly identified by 75-87%, 65% and 71% of centres, respectively. Strains with an extended-spectrum ß-lactamase (ESBL) plus a carbapenemase (CCS03, CCS04, CCS06) were correctly detected in 32-68% of centres. Seven percent correct identifications were recorded for CCS08 (chromosomal K1 ß-lactamase hyperexpression plus IMP-8). Strains with permeability deficiencies [CCS07 (ACT-1 plus porin deficit) and CCS12 (TEM-24 plus porin deficit)] were correctly detected in 17% and 10% of centres, respectively. The TEM-1-producer (CCS01) was detected in 40% of centres. Microbiologists should be aware of new antibiotic resistance mechanisms, and these surveillance studies are particularly useful for this purpose and for the communication of such traits.

The potential role of 13-valent pneumococcal conjugate vaccine in preventing respiratory complications in bacteraemic pneumococcal community-acquired pneumonia.

INTRODUCTION: Pneumococcal 13-valent vaccine (PCV-13) has a potential role in preventing bacteraemic pneumococcal pneumonia and its complications, but little is known about its ability to specifically prevent respiratory complications. Our aim were to analyse the pneumococcal serotypes associated with the development of respiratory complications and the potential role of PCV-13 in preventing respiratory complications in bacteraemic pneumococcal pneumonia. MATERIAL AND METHODS: We analysed demographic characteristics, comorbidities, antibiotic resistances and the outcomes of a cohort of 65 vaccine-naïve bacteraemic pneumococcal pneumonias, stratified by the pneumococcal serotypes included in PCV13 vs. those not included. Complications were clustered as follows: respiratory complications (hypoxemic respiratory failure; mechanical ventilation), systemic complications (septic shock; multiorgan failure), suppurative complications (empyema; pleural effusion; lung abscess). RESULTS: From a population of 65 CAP-SP, 47.7% of the isolates belonged to PCV-13 serotypes group. No differences in comorbidities or clinical manifestations were found between groups. With regard to biochemical parameters, we found more profound hypoxemia levels in PCV-13 serotypes group comparing to non-vaccine group [PaO2/FiO2 209 (63) vs. 268 (57); p=0.007]. Global complications were identified in 69.2% (45 patients), and the most frequent were respiratory complications, found in 47.7%. Respiratory complications were detected more frequently in PCV-13 groups compared to non-vaccine groups (61.3% vs. 35.3%; p=0.036). Overall 30-day mortality was 30.8%. Mortality was similar between both groups (25.8% vs. 35.3%; p=0.408). CONCLUSIONS: Pneumococcal 13-valent conjugate vaccine includes the serotypes which cause more respiratory complications in our series; these serotypes were not associated with higher mortality in our series. PCV-13 may have a potential role in preventing respiratory complications due to bacteraemic pneumonoccal pneumonia.

[Microbiological diagnosis of urinary tract infections]. / Diagnóstico microbiológico de las infecciones urinarias.

Urinary tract infections (UTI) are the most common infectious diseases observed in primary care; up to one-third of women will have at least one symptomatic UTI by age 24, and more than one-half of women will be affected by the end of life. In addition, UTIs represent 40% of nosocomial infections, and being usually associated with urinary catheters. Although urine cultures would not be indicated in all cases, these samples are the most abundant in the laboratories of clinical microbiology. Thus, the working protocols applied to these samples have an important impact in the performance of the laboratory. The samples are collected by mid stream urine, and 60-70% of them are negative culture. At present, several commercial systems have been introduced in order to simplify and automate this process. A urine culture with ≥ 10(5) CFU/ml has classically been considered as positive, although lower counts are valued in certain clinical settings. Factors related to this count e.g. methods to obtain urine, conservation of the sample or use of chemical preservatives as well as low counts are critical points to be discussed in detail. The development of antimicrobial resistance logically affects uropathogens, mainly Escherichia coli, which remains the most frequently isolated in urine cultures. The aim of this paper is to review the most innovating aspects influencing the microbiological diagnosis of UTI.

Diagnóstico microbiológico de las infecciones urinarias / Microbiological diagnosis of urinary tract infections

La infección del tracto urinario es la infección bacteriana más frecuente observada en el ámbito ambulatorio: 1 de cada 3 mujeres desarrollará una infección urinaria que requerirá tratamiento con antibióticos antes de los 24 años y, al menos, el 50% una infección del tracto urinario durante su vida. Además, las infecciones del tracto urinario representan el 40% de las infecciones nosocomiales, usualmente asociadas a sondajes urinarios. Aunque el cultivo de orina no estaría indicado en todos los casos, estas muestras son las más abundantes en los laboratorios de microbiología clínica, y la carga de trabajo que conllevan tiene una repercusión importante en el funcionamiento del laboratorio. Se trata fundamentalmente de orinas ambulatorias de “micción media”, de las cuales el 60-70% son cultivo negativo. En la actualidad existen sistemas comerciales disponibles con objeto de automatizar y simplificar su procesamiento. Clásicamente se han considerado positivas orinas con recuento ≥ 105 UFC/ml, aunque se valoran recuentos más bajos en determinadas situaciones clínicas. Factores relacionados con este recuento, como el modo de obtención de la orina, su conservación y el uso de conservantes químicos, así como el significado de estos bajos recuentos son puntos críticos que se analizarán detalladamente. El desarrollo de resistencias antimicrobianas afecta, lógicamente, a los uropatógenos, fundamentalmente Escherichia coli, que sigue siendo el más frecuentemente aislado. El objetivo de este texto es hacer una revisión de los aspectos más relevantes que influyen en el diagnóstico microbiológico de las infecciones del tracto urinario

Urinary tract infections (UTI) are the most common infectious diseases observed in primary care; up to one-third of women will have at least one symptomatic UTI by age 24, and more than one-half of women will be affected by the end of life. In addition, UTIs represent 40% of nosocomial infections, and being usually associated with urinary catheters. Although urine cultures would not be indicated in all cases, these samples are the most abundant in the laboratories of clinical microbiology. Thus, the working protocols applied to these samples have an important impact in the performance of the laboratory. The samples are collected by mid stream urine, and 60-70% of them are negative culture. At present, several commercial systems have been introduced in order to simplify and automate this process. A urine culture with ≥ 105 CFU/ml has classically been considered as positive, although lower counts are valued in certain clinical settings. Factors related to this count e.g. methods to obtain urine, conservation of the sample or use of chemical preservatives as well as low counts are critical points to be discussed in detail. The development of antimicrobial resistance logically affects uropathogens, mainly Escherichia coli, which remains the most frequently isolated in urine cultures. The aim of this paper is to review the most innovating aspects influencing the microbiological diagnosis of UTI