RESUMO
BACKGROUND: Carbapenemase-producing Enterobacterales (CPE) are challenging in healthcare, with resistance to multiple classes of antibiotics. This study describes the emergence of imipenemase (IMP)-encoding CPE among diverse Enterobacterales species between 2016 and 2019 across a London regional network. METHODS: We performed a network analysis of patient pathways, using electronic health records, to identify contacts between IMP-encoding CPE-positive patients. Genomes of IMP-encoding CPE isolates were overlaid with patient contacts to imply potential transmission events. RESULTS: Genomic analysis of 84 Enterobacterales isolates revealed diverse species (predominantly Klebsiella spp, Enterobacter spp, and Escherichia coli); 86% (72 of 84) harbored an IncHI2 plasmid carrying blaIMP and colistin resistance gene mcr-9 (68 of 72). Phylogenetic analysis of IncHI2 plasmids identified 3 lineages showing significant association with patient contacts and movements between 4 hospital sites and across medical specialties, which was missed in initial investigations. CONCLUSIONS: Combined, our patient network and plasmid analyses demonstrate an interspecies, plasmid-mediated outbreak of blaIMPCPE, which remained unidentified during standard investigations. With DNA sequencing and multimodal data incorporation, the outbreak investigation approach proposed here provides a framework for real-time identification of key factors causing pathogen spread. Plasmid-level outbreak analysis reveals that resistance spread may be wider than suspected, allowing more interventions to stop transmission within hospital networks.SummaryThis was an investigation, using integrated pathway networks and genomics methods, of the emergence of imipenemase-encoding carbapenemase-producing Enterobacterales among diverse Enterobacterales species between 2016 and 2019 in patients across a London regional hospital network, which was missed on routine investigations.
Assuntos
Proteínas de Bactérias , Surtos de Doenças , Infecções por Enterobacteriaceae , Plasmídeos , beta-Lactamases , Humanos , Plasmídeos/genética , beta-Lactamases/genética , Infecções por Enterobacteriaceae/epidemiologia , Infecções por Enterobacteriaceae/microbiologia , Infecções por Enterobacteriaceae/transmissão , Proteínas de Bactérias/genética , Londres/epidemiologia , Antibacterianos/farmacologia , Filogenia , Genoma Bacteriano , Masculino , Feminino , Pessoa de Meia-Idade , Testes de Sensibilidade Microbiana , Adulto , Enterobacteriaceae/genética , Enterobacteriaceae/efeitos dos fármacos , Idoso , Enterobacteriáceas Resistentes a Carbapenêmicos/genética , Enterobacteriáceas Resistentes a Carbapenêmicos/isolamento & purificação , Colistina/farmacologiaRESUMO
BACKGROUND: We evaluated the recovery of fungal pathogens from clinical external ear samples from patients with otitis externa (OE) using the UK national Standard Microbiology Investigations of ear infection (SMI B1). METHOD: The UK SMI B1 protocol including a single Sabouraud dextrose agar with chloramphenicol (SABC) incubated at 37°C for 48 hours was compared with a standard fungal-specific culture method using two SABC agar plates incubated at 28 and 37°C for 2 weeks with an extra Candida chromogenic agar incubated at 37°C for 5 days. This real-life evaluation was undertaken on ear samples from patients with OE from January 2020 to December 2020. RESULTS: Altogether, 304 individual patient ear swabs were prospectively examined. The positivity rate of UK standard was 14% (42/304) versus 26% (79/304) for the fungal-specific protocol (p < .05). The standard protocol identified seven compared with 17 species using the fungal-specific protocol. A total of 93 fungal isolates were recovered; nine different yeasts and eight filamentous fungal species. Candida parapsilosis (38/304; 13%), C. albicans (10/304; 3%) and C. orthopsilosis (6/304; 2%) were common yeast species. Aspergillus niger complex (16/304; 5%) was the most common mould, followed by A. fumigatus complex (3/304; 1%). Many less common and emerging yeasts and moulds were only isolated from samples cultured using a fungal-specific protocol. CONCLUSION: Our results suggest that the UK SMI B1 media and procedures are inadequate to detect all fungal agents causing otomycosis. Fungal-specific culture protocols increase the recovery rate and diversity of fungal pathogens isolated from external ear samples.
Assuntos
Otite Externa , Otomicose , Candida albicans , Técnicas de Laboratório Clínico , Humanos , Otite Externa/diagnóstico , Otomicose/diagnóstico , Otomicose/microbiologia , Reino UnidoRESUMO
Respiratory specimens obtained from patients with chronic forms of aspergillosis contain phenotypic variants of azole-resistant Aspergillus fumigatus (ARAF) that co-exist in the airway. Here we aimed to study whether phenotypic variants of ARAF that co-exist in clinical specimens were genetically distinct. A panel of six phenotypic variants of ARAF cultured from two sputum samples collected from two patients with chronic aspergillosis were included. Preliminary identification of all isolates was obtained using MALDI-ToF mass spectrometry and confirmed by AsperGenius® real-time PCR assay. Antifungal susceptibility testing was determined using EUCAST E.Def 9.3 microbroth dilution. Genomic DNA libraries were constructed with the Illumina TruSeq Nano kit. Prepared whole-genome libraries were sequenced on an Illumina HiSeq 2500. Whole genome data were converted into presence/absence of a SNP with respect to the Af293 reference genome. Colonies of ARAF that co-existed in one respiratory sample demonstrated marked phenotypic diversity. Two cyp51A polymorphisms were found among azole-resistant isolates: TR34/L98H/T289A/I364V/G448S was consistently present in four variants with a pan-azole resistant phenotype and TR34/L98H was detected in two variants (itraconazole MIC > 16 mg/L). WGS typing showed that despite marked phenotypic variation, each sample contained a population of highly genetically related azole-resistant A. fumigatus variants. Our SNP analysis suggest that mechanisms additional to genetic-based variation are responsible for phenotypic diversity. Our data demonstrate that the phenotypic variants of ARAF that co-exist in clinical specimens are highly clonal and strongly suggest their origination from a single common ancestor.
Assuntos
Aspergilose , Aspergillus fumigatus , Humanos , Azóis/farmacologia , Farmacorresistência Fúngica/genética , Antifúngicos/farmacologia , Proteínas Fúngicas/genética , Testes de Sensibilidade Microbiana , Aspergilose/microbiologia , FenótipoRESUMO
Outbreaks of fungal infections due to emerging and rare species are increasingly reported in healthcare settings. We investigated a pseudo-outbreak of Rhinocladiella similis in a bronchoscopy unit of a tertiary care teaching hospital in London, UK. We aimed to determine route of healthcare-associated transmission and prevent additional infections. From July 2018 through February 2019, we detected a pseudo-outbreak of R. similis isolated from bronchoalveolar lavage (BAL) fluid samples collected from nine patients who had undergone bronchoscopy in a multispecialty teaching hospital, during a period of 8 months. Isolates were identified by MALDI-TOF mass spectrometry. Antifungal susceptibility testing was performed by EUCAST broth microdilution. To determine genetic relatedness among R. similis isolates, we undertook amplified fragment length polymorphism analysis. To determine the potential source of contamination, an epidemiological investigation was carried out. We reviewed patient records retrospectively and audited steps taken during bronchoscopy as well as the subsequent cleaning and decontamination procedures. Fungal cultures were performed on samples collected from bronchoscopes and automated endoscope washer-disinfector systems. No patient was found to have an infection due to R. similis either before or after bronchoscopy. One bronchoscope was identified to be used among all affected patients with positive fungal cultures. Physical damage was found in the index bronchoscope; however, no fungus was recovered after sampling of the affected scope or the rinse water of automated endoscope washer-disinfectors. Use of the scope was halted, and, during the following 12-month period, Rhinocladiella species were not isolated from any BAL specimen. All pseudo-outbreak isolates were identified as R. similis with high genetic relatedness (>90% similarity) on ALFP analysis. The study emphasises the emergence of a rare and uncommon black yeast R. similis, with reduced susceptibility to echinocandins, in a bronchoscope-related pseudo-outbreak with a potential water-related reservoir. Our findings highlight the importance of prolonged fungal culture and species-level identification of melanised yeasts isolated from bronchoscopy samples. Possibility of healthcare-associated transmission should be considered when R. similis is involved in clinical microbiology samples.
Assuntos
Ascomicetos/isolamento & purificação , Broncoscópios/microbiologia , Hospitais de Ensino/estatística & dados numéricos , Micoses/epidemiologia , Atenção Terciária à Saúde/estatística & dados numéricos , Idoso , Idoso de 80 Anos ou mais , Antifúngicos/farmacologia , Ascomicetos/química , Ascomicetos/efeitos dos fármacos , Líquido da Lavagem Broncoalveolar/microbiologia , Broncoscopia , Infecção Hospitalar/microbiologia , Surtos de Doenças , Contaminação de Equipamentos , Feminino , Humanos , Londres/epidemiologia , Masculino , Pessoa de Meia-Idade , Micoses/transmissão , Estudos RetrospectivosRESUMO
OBJECTIVES: Management of Candida auris infection is difficult as this yeast exhibits resistance to different classes of antifungals, necessitating the development of new antifungals. The aim of this study was to investigate the susceptibility of C. auris to a novel antifungal triazole, PC945, optimized for topical delivery. METHODS: A collection of 50 clinical isolates was obtained from a tertiary care hospital in North India. Nine isolates from the UK, 10 from a CDC panel (USA) and 3 from the CBS-KNAW culture collection (Japanese and South Korean isolates) were also obtained. MICs (azole endpoint) of PC945 and other triazoles were determined in accordance with CLSI M27 (third edition). Quality control strains were included [Candida parapsilosis (ATCC 22019) and Candida krusei (ATCC 6258)]. RESULTS: Seventy-four percent of isolates tested showed reduced susceptibility to fluconazole (≥64 mg/L). PC945 (geometric mean MICâ=â0.058 mg/L) was 7.4-fold and 1.5-fold more potent than voriconazole and posaconazole, respectively (both Pâ<â0.01). PC945 MIC values correlated with those of voriconazole or posaconazole, and only three isolates were found to be cross-resistant between PC945 and other azoles. ERG11 sequence analysis revealed several mutations, but no correlation could be established with the MIC of PC945. Tentative epidemiological cut-off values (ECOFFs) evaluated by CLSI's ECOFF Finder (at 99%) with 24 h reading of MICs were 1, 4 and 1 mg/L for PC945, voriconazole and posaconazole, respectively. MIC values for quality control strains of all triazoles were in the normal ranges. CONCLUSIONS: PC945 was found to be a more potent inhibitor than posaconazole, voriconazole and fluconazole of C. auris isolates collected globally, warranting further laboratory and clinical evaluations.
Assuntos
Antifúngicos/farmacologia , Benzamidas/farmacologia , Candida/efeitos dos fármacos , Triazóis/farmacologia , Ásia , Candida parapsilosis/efeitos dos fármacos , Candidíase/microbiologia , Humanos , Testes de Sensibilidade Microbiana , Centros de Atenção Terciária , Reino Unido , Estados UnidosRESUMO
Summary: The increase of antifungal drug resistance is a major global human health concern and threatens agriculture and food security; in order to tackle these concerns, it is important to understand the mechanisms that cause antifungal resistance. The curated Mycology Antifungal Resistance Database (MARDy) is a web-service of antifungal drug resistance mechanisms, including amino acid substitutions, tandem repeat sequences and genome ploidy. MARDy is implemented on a Linux, Apache, MySQL and PHP web development platform and includes a local installation of BLASTn of the database of curated genes. Availability and implementation: MARDy can be accessed at http://www.mardy.net and is free to use. The complete database can be retrieved, ordered by organism, gene and drug. Missing or new mycological antifungal resistance data can be relayed to the development team through a contribute entry form. Updates and news will be publicized via a dedicated Twitter feed: @MARDYfungi.
Assuntos
Bases de Dados Genéticas , Farmacorresistência Fúngica/genética , Genes Fúngicos , Antifúngicos/farmacologia , Humanos , Internet , Polimorfismo GenéticoAssuntos
Antifúngicos , Farmacorresistência Fúngica , Tinha , Trichophyton , Humanos , Antifúngicos/farmacologia , Tinha/transmissão , Tinha/tratamento farmacológico , Tinha/microbiologia , Trichophyton/isolamento & purificação , Trichophyton/efeitos dos fármacos , Masculino , Feminino , Pessoa de Meia-Idade , Adulto , Idoso , Doenças EndêmicasAssuntos
Antifúngicos , Farmacorresistência Fúngica , Terbinafina , Tinha , Trichophyton , Humanos , Terbinafina/uso terapêutico , Antifúngicos/uso terapêutico , Tinha/tratamento farmacológico , Tinha/microbiologia , Tinha/diagnóstico , Trichophyton/isolamento & purificação , Trichophyton/efeitos dos fármacos , Masculino , Londres , Viagem , Pessoa de Meia-Idade , FemininoAssuntos
Permetrina , Escabiose , Humanos , Permetrina/uso terapêutico , Escabiose/tratamento farmacológico , Londres , IvermectinaRESUMO
Infections caused by Rasamsonia argillacea complex have been reported in various clinical settings. Cystic fibrosis (CF) is one of the main underlying conditions. An observational cohort study of CF patients with Rasamsonia in respiratory samples was conducted. Eight isolates from 6 patients were identified as R. argillacea complex and tested for antifungal susceptibility. All isolates had high MICs to voriconazole and posaconazole and low MECs to echinocandins. Four patients experienced lung function decline in the year preceding first Rasamsonia isolation. This continued in the year following first isolation in 3 out of 4 cases. Antifungal therapy was initiated in 2 patients, to which only one exhibited a clinical response. Three out of 6 patients died within 3 years of isolating Rasamsonia. Genotyping suggests that similar genotypes of Rasamsonia can persist in CF airways. Consistent with other fungi in CF, the clinical impact of airway colonisation by Rasamsonia is variable. In certain patients, Rasamsonia may be able to drive clinical decline. In others, though a clear impact on lung function may be difficult to determine, the appearance of Rasamsonia acts as a marker of disease severity. In others it does not appear to have an obvious clinical impact on disease progression.
Assuntos
Antifúngicos/farmacologia , Azóis/farmacologia , Doenças Transmissíveis Emergentes/microbiologia , Fibrose Cística/complicações , Farmacorresistência Fúngica , Eurotiales/isolamento & purificação , Pneumopatias Fúngicas/microbiologia , Adulto , Criança , Estudos de Coortes , Equinocandinas/farmacologia , Eurotiales/classificação , Eurotiales/efeitos dos fármacos , Eurotiales/genética , Feminino , Genótipo , Técnicas de Genotipagem , Humanos , Masculino , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Técnicas de Tipagem Micológica , Adulto JovemRESUMO
Candida auris has caused nosocomial infections and transmissions within hospital settings. As little is known about the efficacy of skin and environmental decontamination products to kill C. auris, this study investigated the in vitro activity of chlorine, chlorhexidine, iodine povidone and vaporised hydrogen peroxide products against C. auris. H2 O2 vapour showed 96.6%-100% effective killing of C. auris. All isolates were inhibited by chlorhexidine gluconate concentrations at 0.125%-1.5% and for iodinated povidone at 0.07%-1.25%. Other species of Candida were also killed at 1000 ppm chlorine except C. parapsilosis which failed to be killed at 3 minutes contact time. We conclude that chlorhexidine gluconate, iodinated povidone, chlorine and H2 O2 vapour demonstrate effective killing activity against C. auris at concentrations used in clinical practice.
Assuntos
Candida/efeitos dos fármacos , Candidíase/prevenção & controle , Infecção Hospitalar/prevenção & controle , Desinfetantes/farmacologia , Candidíase/microbiologia , Clorexidina/análogos & derivados , Clorexidina/farmacologia , Cloro/farmacologia , Descontaminação/métodos , Surtos de Doenças , Hospitais , Humanos , Peróxido de Hidrogênio/farmacologia , Povidona-Iodo/farmacologia , VolatilizaçãoRESUMO
An 88-year-old man, receiving prednisolone for sarcoidosis, presented with a discrete keratotic lesion on the dorsum of his right hand following the placement of an intravenous cannula a month prior to its appearance. Medicopsis romeroi was isolated from the tissue and identified by sequencing the internal transcribed spacer region ITS-1 and the D1-2 fragment of the 28S rDNA gene. Histopathological examination showed fungal hyphae in the internal inflammatory cells layer and within the histocyte-macrophage layer, highly suggestive of deep mycosis. The patient was successfully treated with surgical excision of the cyst. M. romeroi exhibited high MIC values for echinocandin drugs in vitro, but appeared susceptible to newer triazole agents, amphotericin B and terbinafine. This is the first report of a subcutaneous phaeohyphomycotic cyst occurring following the placement of an intravenous cannula. This report highlights the potential role of M. romeroi as an emerging cause of deep, non-mycetomatous infection in immunocompromised patients.
Assuntos
Ascomicetos/isolamento & purificação , Cistos/etiologia , Cistos/patologia , Hospedeiro Imunocomprometido , Feoifomicose/diagnóstico , Feoifomicose/patologia , Idoso de 80 Anos ou mais , Antifúngicos/farmacologia , Antifúngicos/uso terapêutico , Cateterismo Periférico/efeitos adversos , Cistos/microbiologia , DNA Fúngico/química , DNA Fúngico/genética , DNA Ribossômico/química , DNA Ribossômico/genética , DNA Espaçador Ribossômico/química , DNA Espaçador Ribossômico/genética , Desbridamento , Mãos/microbiologia , Mãos/patologia , Histocitoquímica , Humanos , Imunossupressores/efeitos adversos , Imunossupressores/uso terapêutico , Masculino , Testes de Sensibilidade Microbiana , Microscopia , Prednisolona/efeitos adversos , Prednisolona/uso terapêutico , RNA Ribossômico 28S/genética , Sarcoidose/tratamento farmacológico , Análise de Sequência de DNARESUMO
BACKGROUND: Invasive aspergillosis (IA) is a life-threatening systemic fungal infection in immunocompromised individuals that is caused by Aspergillus fumigatus. The human serum opsonin, L-ficolin, has been observed to recognize A. fumigatus and could participate in fungal defense. METHODS: Using lung epithelial cells, primary human monocyte-derived macrophages (MDMs), and neutrophils from healthy donors, we assessed phagocytosis and killing of L-ficolin-opsonized live A. fumigatus conidia by flow cytometry and microscopy. Additionally, cytokines were measured by cytometric bead array, and L-ficolin was measured in bronchoalveolar lavage (BAL) fluid from lung transplant recipients by enzyme-linked immunosorbent assay. RESULTS: L-ficolin opsonization increased conidial uptake and enhanced killing of A. fumigatus by MDMs and neutrophils. Opsonization was also shown to manifest an increase in interleukin 8 release from A549 lung epithelial cells but decreased interleukin 1ß, interleukin 6, interleukin 8, interleukin 10, and tumor necrosis factor α release from MDMs and neutrophils 24 hours after infection. The concentration of L-ficolin in BAL fluid from patients with fungal infection was significantly higher than that for control subjects (P = .00087), and receiving operating characteristic curve analysis highlighted the diagnostic potential of L-ficolin for lung infection (area under the curve, 0.842; P < .0001). CONCLUSIONS: L-ficolin modulates the immune response to A. fumigatus. Additionally, for the first time, L-ficolin has been demonstrated to be present in human lungs.
Assuntos
Aspergilose/metabolismo , Aspergillus fumigatus/imunologia , Lectinas/metabolismo , Pulmão/metabolismo , Pneumonia/metabolismo , Aspergilose/imunologia , Aspergilose/microbiologia , Linhagem Celular Tumoral , Citocinas/metabolismo , Humanos , Imunidade Inata , Transplante de Pulmão , Macrófagos/imunologia , Macrófagos/microbiologia , Viabilidade Microbiana , Neutrófilos/imunologia , Neutrófilos/microbiologia , Fagocitose , Pneumonia/imunologia , Pneumonia/microbiologia , FicolinasRESUMO
Aspergillus fumigatus is an opportunistic fungal pathogen that typically infects the lungs of immunocompromised patients leading to a high mortality. H-Ficolin, an innate immune opsonin, is produced by type II alveolar epithelial cells and could participate in lung defences against infections. Here, we used the human type II alveolar epithelial cell line, A549, to determine the involvement of H-ficolin in fungal defence. Additionally, we investigated the presence of H-ficolin in bronchoalveolar lavage fluid from transplant patients during pneumonia. H-Ficolin exhibited demonstrable binding to A. fumigatus conidia via l-fucose, d-mannose and N-acetylglucosamine residues in a calcium- and pH-dependent manner. Moreover, recognition led to lectin complement pathway activation and enhanced fungal association with A549 cells. Following recognition, H-ficolin opsonization manifested an increase in interleukin-8 production from A549 cells, which involved activation of the intracellular signalling pathways mitogen-activated protein kinase MAPK kinase 1/2, p38 MAPK and c-Jun N-terminal kinase. Finally, H-ficolin concentrations were significantly higher in bronchoalveolar lavage fluid of patients with lung infections compared with control subjects (n = 16; P = 0·00726). Receiver operating characteristics curve analysis further highlighted the potential of H-ficolin as a diagnostic marker for lung infection (area under the curve = 0·77; P < 0·0001). Hence, H-ficolin participates in A. fumigatus defence through the activation of the lectin complement pathway, enhanced fungus-host interactions and modulated immune responses.
Assuntos
Células Epiteliais Alveolares/metabolismo , Aspergillus fumigatus/metabolismo , Ativação do Complemento , Lectina de Ligação a Manose da Via do Complemento , Glicoproteínas/metabolismo , Imunidade Inata , Lectinas/metabolismo , Pulmão/metabolismo , Pneumonia/metabolismo , Aspergilose Pulmonar/metabolismo , Células Epiteliais Alveolares/imunologia , Células Epiteliais Alveolares/microbiologia , Área Sob a Curva , Aspergillus fumigatus/imunologia , Aspergillus fumigatus/patogenicidade , Biomarcadores/metabolismo , Líquido da Lavagem Broncoalveolar/química , Estudos de Casos e Controles , Linhagem Celular Tumoral , Complemento C3b/imunologia , Complemento C3b/metabolismo , Glicoproteínas/imunologia , Interações Hospedeiro-Patógeno , Humanos , Interleucina-8/imunologia , Interleucina-8/metabolismo , Lectinas/imunologia , Pulmão/imunologia , Pulmão/microbiologia , Sistema de Sinalização das MAP Quinases , Pneumonia/imunologia , Pneumonia/microbiologia , Valor Preditivo dos Testes , Aspergilose Pulmonar/imunologia , Aspergilose Pulmonar/microbiologia , Curva ROC , Regulação para CimaAssuntos
Infecções por Coronavirus/epidemiologia , Pneumonia Viral/epidemiologia , Aspergilose Pulmonar/epidemiologia , Corticosteroides/uso terapêutico , Antifúngicos/uso terapêutico , Betacoronavirus , Líquido da Lavagem Broncoalveolar/microbiologia , Broncoscopia , COVID-19 , Coinfecção/diagnóstico , Coinfecção/tratamento farmacológico , Coinfecção/epidemiologia , Infecções por Coronavirus/tratamento farmacológico , Humanos , Fatores Imunológicos/uso terapêutico , Unidades de Terapia Intensiva , Aspergilose Pulmonar Invasiva/diagnóstico , Aspergilose Pulmonar Invasiva/tratamento farmacológico , Aspergilose Pulmonar Invasiva/epidemiologia , Pandemias , Pneumonia Viral/tratamento farmacológico , Aspergilose Pulmonar/diagnóstico , Aspergilose Pulmonar/tratamento farmacológico , Fatores de Risco , SARS-CoV-2 , Ventilação , Tratamento Farmacológico da COVID-19RESUMO
Rapid evaporative ionization mass spectrometry (REIMS) was investigated for its suitability as a general identification system for bacteria and fungi. Strains of 28 clinically relevant bacterial species were analyzed in negative ion mode, and corresponding data was subjected to unsupervised and supervised multivariate statistical analyses. The created supervised model yielded correct cross-validation results of 95.9%, 97.8%, and 100% on species, genus, and Gram-stain level, respectively. These results were not affected by the resolution of the mass spectral data. Blind identification tests were performed for strains cultured on different culture media and analyzed using different instrumental platforms which led to 97.8-100% correct identification. Seven different Escherichia coli strains were subjected to different culture conditions and were distinguishable with 88% accuracy. In addition, the technique proved suitable to distinguish five pathogenic Candida species with 98.8% accuracy without any further modification to the experimental workflow. These results prove that REIMS is sufficiently specific to serve as a culture condition-independent tool for the identification and characterization of microorganisms.