Usefulness of inclusion of ertapenem and temocillin screening breakpoints in the EUCAST rapid antimicrobial susceptibility testing (RAST) for rapid detection of OXA-48-producing Klebsiella pneumoniae directly from positive blood cultures.

OBJECTIVES: The aims of this study were: (i) to assess the ability of the meropenem screening breakpoint as part of the screening rapid antimicrobial susceptibility testing (sRAST) of EUCAST for the detection of OXA-48 carbapenemase-producing Klebsiella pneumoniae directly from positive blood cultures (BCs); and (ii) to evaluate the inclusion of ertapenem and temocillin discs into the sRAST to enhance the detection of OXA-48-producing isolates. METHODS: BC bottles were spiked with a total of 117 K. pneumoniae isolates, including 77 previously characterized OXA-48 producers and 40 non-OXA-48 producers. Disc diffusion assays were directly performed from positive BCs with meropenem (10 µg), ertapenem (10 µg) and temocillin (30 µg) discs, and inhibition zones were manually measured after 4, 6 and 8 h of incubation. The screening cut-off values of sRAST were applied to evaluate their capability in detecting OXA-48-producing isolates. Receiver operating characteristic curves were constructed to illustrate the performance efficacy of the disc diffusion assays to detect OXA-48 producers. RESULTS: The meropenem cut-off values of sRAST only detected 90.91% of the OXA-48-producing isolates after 6 and 8 h of incubation. With the proposed cut-off points for ertapenem [<19 mm (4/6 h) and <20 mm (8 h)] and temocillin [<10 mm (4 h) and <11 mm (6/8 h)], all OXA-48-positive isolates were detected without any false-positive results at any reading time. CONCLUSIONS: In healthcare settings with a high prevalence of OXA-48 producers, the inclusion of ertapenem and temocillin discs in the sRAST procedure may improve the detection of OXA-48-producing K. pneumoniae isolates directly from positive BCs, providing reliable results after only a 4 h incubation period.

Whole Genome Sequencing for Studying Helicobacter pylori Antimicrobial Resistance.

Antibiotic resistance (AMR) is an alarming concern worldwide and Helicobacter pylori, one of the most prevalent bacteria, is not an exception. With antibiotics being its primary therapy, increasing resistance leads to a higher rate of treatment failure. Understanding the genomic mechanisms of resistance to clarithromycin, levofloxacin, metronidazole, amoxicillin, tetracycline, and rifampicin through next-generation sequencing-based molecular tools, such as whole genome sequencing (WGS), can be of great value, not only to direct a patient's treatment, but also to establish and optimize treatment guidelines according to the local epidemiology and to avoid the use of inappropriate antibiotics. WGS approaches allow us to gain insight into the genomic determinants involved in AMR. To this end, different pipelines and platforms are continuously being developed. In this study, we take a more detailed view of the use and progression of WGS for in-depth study of H. pylori's AMR.

Are molecular methods helpful for the diagnosis of Helicobacter pylori infection and for the prediction of its antimicrobial resistance?

Infections produced by Helicobacter pylori (H. pylori), a spiral Gram-negative bacterium, can cause chronic gastritis, peptic ulcer, and gastric cancer. Antibiotic therapy is the most effective treatment for H. pylori infection at present. However, owing to the increasing antibiotic resistance of H. pylori strains, it has become a serious threat to human health. Therefore, the accurate diagnosis of H. pylori infections and its antibiotic resistance markers is of great significance. Conventional microbiological diagnosis of H. pylori is based on culture; however, successful isolation of H. pylori from gastric biopsy specimens is a challenging task affected by several factors and has limitations in terms of the time of response. To improve conventional methods, some molecular techniques, such as PCR, have been recently used in both invasive and non-invasive H. pylori diagnosis, enabling simultaneous detection of H. pylori and point mutations responsible for frequent antibiotic resistance. The advantages and disadvantages of molecular methods, mainly PCR, versus conventional culture for the H. pylori identification and the detection of antibiotic resistance are discussed. As expected, the combination of both diagnostic methods will lead to the most efficient identification of the H. pylori strains and the resistance patterns.

Prevalencia e importancia de micobacterias no tuberculosas en pacientes adultos con fibrosis quística en un hospital de Madrid / Prevalence and importance of non-tuberculous mycobacteria in adult patients with cystic fibrosis in a hospital in Madrid

INTRODUCCIÓN: El papel de las micobacterias no tuberculosas (MNT) en los pacientes con fibrosis quística (FQ) está, en ocasiones, en controversia. El objetivo del trabajo es evaluar la prevalencia y las características clínicas/microbiológicas de pacientes adultos con FQ colonizados con MNT, destacando Mycobacterium abscessus (M. abscessus). MÉTODOS: Se ha realizado un estudio retrospectivo en 92 pacientes adultos con FQ en el que se diferenció: grupo control, 64 pacientes no colonizados por MNT, y grupo a estudio, 28 pacientes colonizados por MNT. Se han analizado variables como la edad, mutación F508del, función pulmonar, afectación pancreática, tinción de auramina y recolonizaciones entre ambos grupos. RESULTADOS: La prevalencia de MNT encontrada ha sido 30,4%. La MNT más prevalente fue Mycobacterium avium complex seguida por M. abscessus. Para M. abscessus, en el estudio comparativo con pacientes colonizados por otras MNT, se obtuvieron diferencias estadísticamente significativas en las variables de edad. DISCUSIÓN: Hemos encontrado alta prevalencia de MNT en pacientes adultos con FQ y relacionamos la aparición de M. asbcessus con edades inferiores a 30 años y F508del. Con el fin de conocer mejor el papel patógeno de las MNT, especialmente de M. asbcessus, se requieren estudios multicéntricos en población con FQ

INTRODUCTION: The role of non-tuberculous mycobacteria (NTM) among cystic fibrosis (CF) patients, on occasion, remains unknown. The aim of our study is to evaluate the prevalence and clinical/microbiological characteristics of CF adult patients colonized by NTM, highlighting Mycobacterium abscessus (M. abscessus). METHODS: A retrospective study was conducted with 92 CF adult patients: including a control group of 64 patients, not colonized by NTM, and a study group of 28 patients, colonized by NTM. We have analyzed variables such as age, F508del mutation, lung function, pancreatic involvement, auramine staining and co-colonizations between both groups. RESULTS: The prevalence of NTM found was 30.4%. The most prevalent was Mycobacterium avium complex followed by M. abscessus. For M. abscessus, in the comparative study with patients colonized by other NTM, significant results were obtained for variables age. DISCUSSION: We have found a high prevalence of NTM among adult patients with CF, and we associated the presence of M. asbcessus with ages less than 30 years and F508del. Due to the pathogenic role of NTM, especially M. asbcessus, multicenter studies are required within the population suffering from CF

Infección fúngica sinusal por Schizophyllum commune: a propósito de dos casos clínicos / Fungal sinus infection by Schizophyllum commune: report of two clinical cases

ANTECEDENTES: Schizophyllum commune es un hongo basidiomiceto ampliamente distribuido en la naturaleza. Su papel como responsable de enfermedad en el ser humano ha sido poco conocido, en parte debido a su difícil identificación. La incorporación a los laboratorios de técnicas de espectrometría de masas (MALDI-TOF) y biología molecular ha permitido la descripción de un mayor número de casos. CASO CLÍNICO: En este trabajo presentamos dos casos en los que se identificó S. commune como agente causal de enfermedad: un caso de rinosinusitis crónica en un paciente inmunocompetente y otro caso de infección del seno esfenoidal en un paciente inmunocomprometido. En ambos casos se aisló S. commune. Su identificación fue posible gracias al MALDI-TOF y esta se confirmó en ambos pacientes mediante la amplificación y secuenciación de la región ITS. CONCLUSIONES: Concluimos que S. commune debe ser considerado un posible agente causal de enfermedad micótica. Actualmente, las técnicas de MALDI-TOF y secuenciación son necesarias para su identificación

BACKGROUND: Schizophyllum commune is a basidiomycete fungus which is widely distributed in nature. Its role as responsible for disease in humans is not well known, partly due to its difficult identification. The incorporation of mass spectrometry techniques (MALDI-TOF) and molecular biology to the laboratories has allowed the description of a greater number of cases. CASE REPORT: In this paper, we present two cases in which S. commune was identified as the causative agent of disease: in the first case an immunocompetent patient suffered from chronic rhinosinusitis, and in the second one a sphenoid sinus infection was diagnosed in an immunocompromised patient. In both cases, S. commune was isolated. Its identification was possible by means of MALDI-TOF and this was confirmed in both patients by amplification and sequencing of the ITS region. CONCLUSIONS: In conclusion, S. commune should be considered a potential causative agent of fungal disease. Currently, MALDI-TOF and sequencing techniques are necessary for its identification

[Fungal sinus infection by Schizophyllum commune: Report of two clinical cases]. / Infección fúngica sinusal por Schizophyllum commune: a propósito de dos casos clínicos.

BACKGROUND: Schizophyllum commune is a basidiomycete fungus which is widely distributed in nature. Its role as responsible for disease in humans is not well known, partly due to its difficult identification. The incorporation of mass spectrometry techniques (MALDI-TOF) and molecular biology to the laboratories has allowed the description of a greater number of cases. CASE REPORT: In this paper, we present two cases in which S. commune was identified as the causative agent of disease: in the first case an immunocompetent patient suffered from chronic rhinosinusitis, and in the second one a sphenoid sinus infection was diagnosed in an immunocompromised patient. In both cases, S. commune was isolated. Its identification was possible by means of MALDI-TOF and this was confirmed in both patients by amplification and sequencing of the ITS region. CONCLUSIONS: In conclusion, S. commune should be considered a potential causative agent of fungal disease. Currently, MALDI-TOF and sequencing techniques are necessary for its identification.

Prevalence and importance of non-tuberculous mycobacteria in adult patients with cystic fibrosis in a hospital in Madrid. / Prevalencia e importancia de micobacterias no tuberculosas en pacientes adultos con fibrosis quística en un hospital de Madrid.

INTRODUCTION: The role of non-tuberculous mycobacteria (NTM) among cystic fibrosis (CF) patients, on occasion, remains unknown. The aim of our study is to evaluate the prevalence and clinical/microbiological characteristics of CF adult patients colonized by NTM, highlighting Mycobacterium abscessus (M. abscessus). METHODS: A retrospective study was conducted with 92 CF adult patients: including a control group of 64 patients, not colonized by NTM, and a study group of 28 patients, colonized by NTM. We have analyzed variables such as age, F508del mutation, lung function, pancreatic involvement, auramine staining and co-colonizations between both groups. RESULTS: The prevalence of NTM found was 30.4%. The most prevalent was Mycobacterium avium complex followed by M. abscessus. For M. abscessus, in the comparative study with patients colonized by other NTM, significant results were obtained for variables age. DISCUSSION: We have found a high prevalence of NTM among adult patients with CF, and we associated the presence of M. asbcessus with ages less than 30 years and F508del. Due to the pathogenic role of NTM, especially M. asbcessus, multicenter studies are required within the population suffering from CF.

Infection with multiple hepatitis C virus genotypes detected using commercial tests should be confirmed using next generation sequencing.

Current HCV genotyping methods may have some limitations in detecting mixed infections. We aimed to determine the accuracy of genotyping and the detection of mixed-genotype infections using the Abbott-RealTime HCV Genotype II assay (Abbott-RT-PCR) in comparison with a Roche-Next Generation Sequencing assay (Roche-NGS). Plasma samples collected from 139 HCV-infected patients tested with Abbott-RT-PCR, 114 with single genotype (GT) and 25 with mixed GTs were genotyped using Roche-NGS. Roche-NGS confirmed all single GTs obtained with Abbott-RT-PCR. One case of Abbott GT 4 was found as GT 1a using Roche-NGS. Genotype 5 was confirmed using Roche-NGS in 75% cases (3 out of 4 cases). Twenty-five patients were identified as having mixed HCVinfections using Abbott-RT-PCR. The concordance between Abbott-RT-PCR and Roche-NGS was 76% (19 out of 25 cases). Three mixed-GT infections identified with the Abbott assay (two (1b + 4); one (1a + 3)) were reported as pure 1b using Roche-NGS. Very divergent results were found for the other three samples. When compared to Roche-NGS, Abbott-RT-PCR has performed excellently for the determination of patients infected with single GTs. For patients that are categorized as having a mixed infection using Abbott-RT-PCR, we recommend an NGS assay as a confirmation test.

Ruminococcus gnavus infection of a metal-on-metal hip arthroplasty resembling a pseudo-tumour in a 72 year-old woman with no intestinal symptoms / Infección por Ruminococcus gnavus de prótesis de cadera metal-metal asemejando un pseudotumor, en una mujer de 72 años sin síntomas intestinales

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