Molecular Markers of Antifungal Resistance: Potential Uses in Routine Practice and Future Perspectives

García‐Effrón, Guillermo

doi:10.3390/jof7030197

Cited by 13 publications

(12 citation statements)

References 151 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…[ 27 , 28 ] and CYP51A genotyping for azole resistance in Aspergillus spp. [ 29 ]). Further, our laboratory has already been routinely performing WGS for bacterial species identification, which is a batch test and requires more samples in one run to make it more cost effective.…”

Section: Discussionmentioning

confidence: 99%

Fungal Whole-Genome Sequencing for Species Identification: From Test Development to Clinical Utilization

Salem-Bango

Price

Chan

et al. 2023

JoF

View full text Add to dashboard Cite

Using next-generation sequencing (NGS), we developed and validated a whole-genome sequencing (WGS)-based clinical test for fungal species identification on clinical isolates. The identification is mainly based on the fungal ribosomal internal transcribed spacer (ITS) region as the primary marker, and additional marker and genomic analysis applied for species within the Mucorales family (using the 28S rRNA gene) and Aspergillus genus (using the beta-tubulin gene and k-mer tree-based phylogenetic clustering). The validation study involving 74 unique fungal isolates (22 yeasts, 51 molds, and 1 mushroom-forming fungus) showed high accuracy, with 100% (74/74) concordance on the genus-level identifications and 89.2% (66/74) concordance on the species level. The 8 discrepant results were due to either the limitation of conventional morphology-based methodology or taxonomic changes. After one year of implementation in our clinical laboratory, this fungal NGS test was utilized in 29 cases; the majority of them were transplant and cancer patients. We demonstrated the utility of this test by detailing five case studies, in which accurate fungal species identification led to correct diagnosis, treatment adjustment or was ruled out for hospital acquired infection. This study provides a model for validation and implementation of WGS for fungal identification in a complex health system that serves a large immunocompromised patient population.

show abstract

Section: Discussionmentioning

confidence: 99%

Fungal Whole-Genome Sequencing for Species Identification: From Test Development to Clinical Utilization

Salem-Bango

Price

Chan

et al. 2023

JoF

View full text Add to dashboard Cite

show abstract

“…Molecular methods to detect CYP51A mutations, e.g., TR 34 /L98H, TR 46 / Y1 2 1F, are established by using classic PCRs with sequencing, real-time PCRs, loopmediated isothermal amplification (LAMP), or whole-genome sequencing (WGS) [179]. These molecular methods have a high negative predictive value to rule out these resistant strains' infections [179]. However, they had narrow coverage and mutations at this point depending on association data between mutations and antifungal resistance property.…”

Section: Etiology and Clinical Significancementioning

confidence: 99%

“…However, they had narrow coverage and mutations at this point depending on association data between mutations and antifungal resistance property. Furthermore, commercial tools are still not approved by the US FDA [179].…”

Section: Etiology and Clinical Significancementioning

confidence: 99%

“…In areas with high rates of azole resistance, liposomal amphotericin B and a combination of voriconazole and echinocandin should be considered [2,127,128,156,180]. Therefore, the prevalence of azole-resistant Aspergillus strains using conventional culturing methods together with broth microdilution assays or using molecular biology (RT-PCR) is essential to decide the optimal treatment and to choose suitable antifungal agents to get rid of these infections [156,179].…”

Section: Management Of Azole-resistant Aspergillus and Novel Antifungal Candidatesmentioning

confidence: 99%

See 1 more Smart Citation

Aspergillus-Human Interactions: From the Environment to Clinical Significance

Thammahong¹

2022

The Genus Aspergillus - Pathogenicity, Mycotoxin Production and Industrial Applications

View full text Add to dashboard Cite

Aspergillus species are ubiquitous fungi found in the environment worldwide. The most common Aspergillus species causing diseases in humans are A. fumigatus, A. flavus, A. niger, and A. terreus. However, species causing human infections are also depending on human immune status. Host immune status and previous underlying diseases are important factors leading to different clinical manifestations and different disease spectra of Aspergillus infections. The most severe form of Aspergillus infections is invasive aspergillosis in human tissue, especially invasive pulmonary aspergillosis (IPA), which has high morbidity and mortality in immunocompromised patients. ICU patients with influenza infections and COVID-19 infections are recently risk factors of invasive pulmonary aspergillosis. New diagnostic criteria include galactomannan antigen assays, nucleic acid amplification assays, and lateral flow assays for early and accurate diagnosis. Voriconazole and the newest azole, isavuconazole, are antifungals of choice in IPA. Nevertheless, azole-resistant Aspergillus strains are increasing throughout the world. The etiology and spreading of azole-resistant Aspergillus strains may originate from the widespread use of fungicides in agriculture, leading to the selective pressure of azole-resistant strains. Therefore, there is a necessity to screen Aspergillus antifungal susceptibility patterns for choosing an appropriate antifungal agent to treat these invasive infections. In addition, mutations in an ergosterol-producing enzyme, i.e., lanosterol 14-α demethylase, could lead to azole-resistant strains. As a result, the detection of these mutations would predict the resistance to azole agents. Although many novel azole agents have been developed for invasive Aspergillus infections, the rate of novel antifungal discovery is still limited. Therefore, better diagnostic criteria and extensive antifungal resistant Aspergillus screening would guide us to better manage invasive Aspergillus infections with our existing limited resources.

show abstract

“…По данным отечественного исследования КРИТ (кандидоз в отделениях реанимации и интенсивной терапии) устойчивость к флуконазолу достигает 21% [2]. При этом природно-чувствительные к азолам C. albicans приобретают устойчивость за счет разнообразных механизмов приобретенной резистентности, таких как повышенная экспрессия генов эффлюксных переносчиков и амплификация гена белка-мишени [11,31].…”

Section: Introductionunclassified

CDR1, CDR2, MDR1 and ERG11 expression in azole resistant Сandida albicans isolated from HIV-infected patients in city of Moscow

Voropaev

Yekaterinchev

Urban

et al. 2022

Russian Journal of Infection and Immunity

View full text Add to dashboard Cite

Candida fungi are common opportunistic microorganisms capable of causing infections of various localization, as well as life-threatening conditions in immunocompromised patients, such as HIV-infected individuals, oncology patients, subjects undergoing HSCT, which number has been steadily increasing in recent years. In addition, resistance to anti-fungal drugs has been spreading as well. Naturally sensitive to azoles, C. albicans possess a variety of mechanisms of acquired resistance, including efflux transporters and target protein-encoding gene amplification. This study was conducted to assess a prevalence of such mechanisms in the isolates sample obtained from HIV-infected patients in the Moscow region of the Russian Federation, characterize a relationship between these mechanisms and patterns of developing drug resistance. 18 strains of C. albicans resistant to fluconazole and voriconazole were isolated from HIV-infected patients with recurrent oropharyngeal candidiasis in the Moscow region. The expression levels of the ERG11, MDR1, CDR1, CDR2 genes involved in the formation of acquired azole resistance were measured using quantitative PCR, the 2CT method with ACT and PMA genes as control genes and reference values of sensitive isolates. Expression levels exceeding the average values of sensitive isolates by more than 3 standard deviations were considered significantly elevated. In most of the isolates, elevated levels of CDR1 and CDR2 gene expression were found: 89% and 78%, respectively. The expression level of the MDR1 gene was increased only in 28% of cases. ERG11 expression levels were significantly elevated in 78% of the isolates. Expression levels of all resistance genes studied were significantly increased in 4 strains. In this sample of C. albicans isolates, acquired resistance is mainly associated with efflux vectors encoded by the CDR1 and CDR2 genes. Also, in most isolates, an increased expression level for the azole target protein gene ERG11 was detected. The expression level of the efflux transporter gene MDR1 was increased in the smallest number of samples. It is also impossible to exclude a potential role of other mechanisms in developing acquired resistance, such as mutations in the ERG11 gene. It can be assumed that the identified mechanisms of resistance result from long-term, widespread, and sometimes uncontrolled use of azoles, including those in treatment and prevention of candidiasis in HIV-infected patients.

show abstract

Molecular Markers of Antifungal Resistance: Potential Uses in Routine Practice and Future Perspectives

Cited by 13 publications

References 151 publications

Fungal Whole-Genome Sequencing for Species Identification: From Test Development to Clinical Utilization

Fungal Whole-Genome Sequencing for Species Identification: From Test Development to Clinical Utilization

Aspergillus-Human Interactions: From the Environment to Clinical Significance

<i>CDR1, CDR2, MDR1</i> and <i>ERG11</i> expression in azole resistant <i>Сandida albicans</i> isolated from HIV-infected patients in city of Moscow

Contact Info

Product

Resources

About