Microsatellite Typing of Aspergillus flavus Strains in a Tunisian Onco-hematology Unit

Gheith, Soukeina; Saghrouni, F.; Normand, Anne‐Cécile; Bannour, Wadiaa; Khélif, Abderrahim; Piarroux, Renaud; Saïd, M. Ben; Njah, Mansour; Ranque, Stéphane

doi:10.1007/s11046-015-9962-6

Cited by 4 publications

(2 citation statements)

References 18 publications

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“…MLP typing has also been applied to A. flavus (78). Using MLP typing to test A. flavus infections in hematology wards, investigators found identical genotypes in the environment, suggesting nosocomial transmission (79,80).…”

Section: Aspergillus Flavusmentioning

confidence: 99%

Investigating Clinical Issues by Genotyping of Medically Important Fungi: Why and How?

et al. 2017

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Genotyping studies of medically important fungi have addressed elucidation of outbreaks, nosocomial transmissions, infection routes, and genotype-phenotype correlations, of which secondary resistance has been most intensively investigated. Two methods have emerged because of their high discriminatory power and reproducibility: multilocus sequence typing (MLST) and microsatellite length polymorphism (MLP) using short tandem repeat (STR) markers. MLST relies on single-nucleotide polymorphisms within the coding regions of housekeeping genes. STR polymorphisms are based on the number of repeats of short DNA fragments, mostly outside coding regions, and thus are expected to be more polymorphic and more rapidly evolving than MLST markers. There is no consensus on a universal typing system. Either one or both of these approaches are now available for spp., spp., spp., spp., ,, and endemic mycoses. The choice of the method and the number of loci to be tested depend on the clinical question being addressed. Next-generation sequencing is becoming the most appropriate method for fungi with no MLP or MLST typing available. Whatever the molecular tool used, collection of clinical data (e.g., time of hospitalization and sharing of similar rooms) is mandatory for investigating outbreaks and nosocomial transmission.

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Section: Aspergillus Flavusmentioning

confidence: 99%

Investigating Clinical Issues by Genotyping of Medically Important Fungi: Why and How?

et al. 2017

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“…A study comparing the discriminatory power of these approaches among 52 clinical A. fumigatus isolates determined that STR typing was most suitable for use in outbreak investigation [239]. Several small cohort studies utilizing these various techniques, most commonly in a post hoc analysis, have demonstrated clonal spread with similar genotypes identified in a proportion of clinical and environmental isolates [240,[242][243][244]. Equally, other studies have shown no such pattern [245].…”

Section: Molecular Methods Employed In Aspergillus Outbreaksmentioning

confidence: 99%

Outbreaks of Fungal Infections in Hospitals: Epidemiology, Detection, and Management

Douglas,

Stewart,

Halliday

et al. 2023

JoF

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Nosocomial clusters of fungal infections, whilst uncommon, cannot be predicted and are associated with significant morbidity and mortality. Here, we review reports of nosocomial outbreaks of invasive fungal disease to glean insight into their epidemiology, risks for infection, methods employed in outbreak detection including genomic testing to confirm the outbreak, and approaches to clinical and infection control management. Both yeasts and filamentous fungi cause outbreaks, with each having general and specific risks. The early detection and confirmation of the outbreak are essential for diagnosis, treatment of affected patients, and termination of the outbreak. Environmental sampling, including the air in mould outbreaks, for the pathogen may be indicated. The genetic analysis of epidemiologically linked isolates is strongly recommended through a sufficiently discriminatory approach such as whole genome sequencing or a method that is acceptably discriminatory for that pathogen. An analysis of both linked isolates and epidemiologically unrelated strains is required to enable genetic similarity comparisons. The management of the outbreak encompasses input from a multi-disciplinary team with epidemiological investigation and infection control measures, including screening for additional cases, patient cohorting, and strict hygiene and cleaning procedures. Automated methods for fungal infection surveillance would greatly aid earlier outbreak detection and should be a focus of research.

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Identification of a clonal population of Aspergillus flavus by MALDI-TOF mass spectrometry using deep learning

Normand

Chaline

Mohammad

et al. 2022

Sci Rep

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The spread of fungal clones is hard to detect in the daily routines in clinical laboratories, and there is a need for new tools that can facilitate clone detection within a set of strains. Currently, Matrix Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry is extensively used to identify microbial isolates at the species level. Since most of clinical laboratories are equipped with this technology, there is a question of whether this equipment can sort a particular clone from a population of various isolates of the same species. We performed an experiment in which 19 clonal isolates of Aspergillus flavus initially collected on contaminated surgical masks were included in a set of 55 A. flavus isolates of various origins. A simple convolutional neural network (CNN) was trained to detect the isolates belonging to the clone. In this experiment, the training and testing sets were totally independent, and different MALDI-TOF devices (Microflex) were used for the training and testing phases. The CNN was used to correctly sort a large portion of the isolates, with excellent (> 93%) accuracy for two of the three devices used and with less accuracy for the third device (69%), which was older and needed to have the laser replaced.

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Microsatellite Typing of Aspergillus flavus Strains in a Tunisian Onco-hematology Unit

Cited by 4 publications

References 18 publications

Investigating Clinical Issues by Genotyping of Medically Important Fungi: Why and How?

Investigating Clinical Issues by Genotyping of Medically Important Fungi: Why and How?

Outbreaks of Fungal Infections in Hospitals: Epidemiology, Detection, and Management

Identification of a clonal population of Aspergillus flavus by MALDI-TOF mass spectrometry using deep learning

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