Machine learning to identify clinically relevant Candida yeast species

Fungal infections, especially due to Candida species, are on the rise. Multi-drug resistant organisms such as Candida auris are difficult and time consuming to identify accurately. Machine learning is increasingly being used in health care, especially in medical imaging. In this study, we evaluated the effectiveness of six convolutional neural networks (CNNs) to identify four clinically important Candida species. Wet-mounted images were captured using bright field live-cell microscopy followed by separating single-cells, budding-cells, and cell-group images which were then subjected to different machine learning algorithms (custom CNN, VGG16, ResNet50, InceptionV3, EfficientNetB0, and EfficientNetB7) to learn and predict Candida species. Among the six algorithms tested, the InceptionV3 model performed best in predicting Candida species from microscopy images. All models performed poorly on raw images obtained directly from the microscope. The performance of all models increased when trained on single and budding cell images. The InceptionV3 model identified budding cells of C. albicans, C. auris, C. glabrata (Nakaseomyces glabrata), and C. haemulonii in 97.0%, 74.0%, 68.0%, and 66.0% cases, respectively. For single cells of C. albicans, C. auris, C. glabrata, and C. haemulonii InceptionV3 identified 97.0%, 73.0%, 69.0%, and 73.0% cases, respectively. The sensitivity and specificity of InceptionV3 were 77.1% and 92.4%, respectively. Overall, this study provides proof of the concept that microscopy images from wet-mounted slides can be used to identify Candida yeast species using machine learning quickly and accurately.

Cladosporium halotolerans: Exploring an Unheeded Human Pathogen

BACKGROUND

Cladosporium halotolerans is a saprobic fungus, rarely implicated in human infections. The identification is challenging due to non-specific phenotypic features.

OBJECTIVE

To decipher clinical spectrum, microbiological and susceptibility profile of clinical and environmental isolates of Cladosporium halotolerans.

METHOD

All the isolates identified as Cladosporium halotolerans deposited in National Culture Collection for Pathogenic Fungi (NCCPF), Postgraduate Institute of Medical Education and Research, Chandigarh, India were revived. Phenotypic and molecular characterization targeting internal transcribed spacer (ITS) region of ribosomal DNA, large subunit of ribosomal DNA (LSU; NL1 and NL4), actin (ACT) and beta-tubulin (TUB) was done. Scanning electron microscopy (SEM) was performed to determine any phenotypic variations. Antifungal susceptibility testing (AFST) was carried out for eight antifungal agents as per CLSI M38 Ed3 guidelines. We also performed systematic literature review of all the cases of Cladosporium halotolerans reported till date.

RESULTS

A total of four isolates (clinical, n = 3; soil, n = 1) identified as Cladosporium halotolerans were included in the study. The clinical sites were skin, maxillary tissue and nail. All patients were apparently immunocompetent, and history of trauma was recorded in one patient. All patients improved on antifungal therapy. The cultures revealed growth of black mycelial fungus and microscopic examination demonstrated dematiaceous septate hyphae with erect conidiophores and conidia in branched acropetal chains. Based on molecular methods, all the four isolates were identified as C. halotolerans. SEM revealed no variation in length and width of the conidia, conidiophores, ramoconidium and hyphae among the isolates. All molecular targets, such as ITS region, LSU (partially sequenced), ACT and TUB were able to differentiate the isolates. Minimum inhibitory concentrations for antifungals were: triazoles (0.12-2 μg/ml), amphotericin B (4 μg/ml) and echinocandins (2-8 μg/ml).

CONCLUSION

We report role of the rarely isolated dematiaceous fungus, C. halotolerans, in causing human infections. The study emphasizes the role of molecular methods in precisely identifying these species. Triazoles are more active against these black fungi compared to polyenes or echinocandins.

Identification and Elimination of Antifungal Tolerance in Candida auris

Antimicrobial resistance is a global health crisis to which pathogenic fungi make a substantial contribution. The human fungal pathogen C. auris is of particular concern due to its rapid spread across the world and its evolution of multidrug resistance. Fluconazole failure in C. auris has been recently attributed to antifungal “tolerance”. Tolerance is a phenomenon whereby a slow-growing subpopulation of tolerant cells, which are genetically identical to susceptible cells, emerges during drug treatment. We use microbroth dilution and disk diffusion assays, together with image analysis, to investigate antifungal tolerance in C. auris to all three classes of antifungal drugs used to treat invasive candidiasis. We find that (1) C. auris is tolerant to several common fungistatic and fungicidal drugs, which in some cases can be detected after 24 h, as well as after 48 h, of antifungal drug exposure; (2) the tolerant phenotype reverts to the susceptible phenotype in C. auris; and (3) combining azole, polyene, and echinocandin antifungal drugs with the adjuvant chloroquine in some cases reduces or eliminates tolerance and resistance in patient-derived C. auris isolates. These results suggest that tolerance contributes to treatment failure in C. auris infections for a broad range of antifungal drugs, and that antifungal adjuvants may improve treatment outcomes for patients infected with antifungal-tolerant or antifungal-resistant fungal pathogens.

P096 Comprehensive analysis of Trichophyton mentagrophytes/interdigitale complex from human and animal origin

 

Poster session 1, September 21, 2022, 12:30 PM - 1:30 PM

Objectives

Taxonomic delineation of etiologic agents responsible for recalcitrant dermatophytosis causing epidemic in India is still debated. The organism responsible for this epidemic was previously designated as Trichophyton indotineae, a clonal offshoot of T. mentagrophytes.

To evaluate the accurate identity of the agent causing the epidemic, we performed multigene sequence analysis of Trichophyton species isolated from human and animal origin.

Methods

The clinical isolates of T. mentagrophytes/interdigitale complex (n = 213) from PGIMER, and six isolates of animal origin (canine) from IVRI were included in the study. Seven genomic loci including internal transcribed spacer (ITS) region (n = 219), translational elongation factor (TEF 1-α) (n = 40), partial beta tubulin (BT) (n = 40), large ribosomal subunit (LSU) (n = 34), calmodulin (CAL) (n = 29), high mobility group transcription factor (HMG) (n = 17), and α-box (n = 17) were amplified by polymerase chain reaction (PCR). Phylogenetic tree was constructed by neighbor-joining method using ours and sequences retrieved from NCBI database. Trichophyton quinckeanum was used as the outgroup due to its high divergence. The identity labeling was validated as per the phylogenetic analysis of ITS gene in the present study [ITS gene (n = 374), TEF1-α (n = 184), BT (n = 52), LSU (n = 50), CAL (n = 69) and HMG transcription factor (n = 102)].

Results

Phylogenetic analysis of ITS, TEF 1-α, LSU gene revealed that except for one isolate (PGI-IVRI B24-A) of animal origin belonged to ITS genotype III and rest all isolates [human (n = 213) and animal origin (n = 5)] belonged to the same cluster, i.e., T. mentagrophytes ITS genotype VIII. The phylogenetic tree constructed based on the BT gene (n = 39) also clustered all our isolates together and isolates belonging to T. mentagrophytes ITS genotype IV, VIII, and T. interdigitale and one isolate (PGI-IVRI B24-A) formed a separate cluster and did not coalesce with other genotypes. Whereas CAL gene clustered all our isolates (n = 28) together except PGI-IVRI B24-A isolate which grouped with T. mentagrophytes type VII. Further HMG analysis reveals that all the isolated Trichophyton species from humans (n = 11) and animals (n = 5) contained HMG transcription factors but lacked α-box genes. One animal isolate (PGI-IVRI B24-A) consisted of both HMG transcription factor and α-box genes. The accurate identity of the isolates was based on our phylogenetic analysis (ITS gene). Based on the analysis of the 374 ITS sequences deposited in the GenBank database, 107 sequences were mislabeled, ie, T. mentagrophytes was named T. interdigitale or vice versa. Similarly, 184, 52, 50, 69, and 102 sequences of TEF1-α, BT, LSU, CAL, and HMG transcription factor deposited in the GenBank have 6, 23, 25, 3, and 7 sequences were mislabeled, respectively. Further, for the identical isolates (n = 6), we found multiple accession numbers with different labels.

Conclusion

In this study, for the first time we isolated ‘Indian ITS genotype VIII’ from animal. Isolation of T. mentagrophytes type III from animal but none among humans indicates its niche among animals. Adding to the confusion, outdated/inaccurate naming for these dermatophytes in the public database has created confusion in using appropriate species designation.

Fatal cerebral phaeohyphomycosis caused by Cladophialophora bantiana mimicking tuberculous brain abscess

INTRODUCTION

Cladophialophora bantiana, a neurotropic phaeoid fungus, is the primary agent of cerebral phaeohyphomycosis. The disease more commonly affects immunocompetent males and is associated with a high mortality rate.

CASE REPORT

We report a case of brain abscess caused by Cladophialophora bantiana in a 50-year-old immunocompetent male who presented with headache for two months, weakness of both lower limbs for 15 days, and altered sensorium and aphasia for one day. Contrast-enhanced MRI of the brain showed multiple coalescent abscesses in the right basal ganglia and corpus callosum. Based on clinical and radiological suspicion of tuberculoma, treatment with antitubercular drugs was initiated. A month after discharge, the patient was re-admitted with history of loss of consciousness, altered sensorium, respiratory distress and aphasia. Brain CECT revealed multiple ring-enhancing lesions in the right basal ganglia with mass effect and a leftward midline shift. The patient underwent craniotomy and evacuation of abscess. Direct microscopy of pus aspirated from the lesions showed pigmented septate fungal hyphae, which was identified as C. bantiana in fungal culture. The patient was administered intravenous liposomal amphotericin B and voriconazole. However, he died due to multiple organ failure on day 19 after surgery.

CONCLUSIONS

Fungal etiology should be considered in the differential diagnosis of intracranial space occupying lesions, regardless of the host immune status. An early diagnosis, together with aggressive medical and neurosurgical interventions are imperative for improving the survival in such patients.

Phenotypic and molecular characterisation of Sporothrix globosa of diverse origin from India

Sporotrichosis is one of the neglected tropical diseases causing subcutaneous chronic granulomatous lesion by thermally dimorphic fungi belonging to Sporothrix species. Sporothrix brasiliensis, Sporothrix mexicana and Sporothrix globosa are the common pathogenic species. In Asian countries, S. globosa constitutes nearly 99.3% of all Sporothrix species. We studied 63 cases of sporotrichosis of geographically diverse origin from India and Sporothrix isolates were characterised for its growth in different media, temperatures, ability to assimilate sugars and antifungal susceptibility profile. Molecular characterization was performed by sequencing of the calmodulin (CAL), beta tubulin (BT) and translational elongation factor 1-alpha (TEF-1α) and typing by fluorescent amplified fragment length polymorphism (FAFLP). In patients who presented with fixed (49.2%), lymphocutaneous lesions (23.8%), in 26.9% the details were not known, none had systemic dissemination. All the isolates tested were Sporothrix globosa and that could grow up to 35 °C and unable to grow at and beyond 37 °C. The assimilation of sucrose, ribitol and raffinose helps in identifying S. globosa. Sequences of CAL or BT or TEF-1α can differentiate S. globosa from other species in the complex. FAFLP results exhibited low genetic diversity. No correlation was noted between genotypes and clinical presentation, or geographic distribution. Itraconazole, terbinafine and posaconazole showed good in vitro antifungal activity against S. globosa whereas fluconazole and micafungin had no activity. S. globosa of Indian origin is relatively less pathogenic than other pathogenic Sporothrix species as it does not cause systemic dissemination and in the diagnostic laboratory, incubation of the cultures below 37 °C is essential for effective isolation.

Rapid detection of terbinafine resistance in Trichophyton species by Amplified refractory mutation system-polymerase chain reaction

Dermatophytosis has gained interest in India due to rise in terbinafine resistance and difficulty in management of recalcitrant disease. The terbinafine resistance in dermatophytes is attributed to single nucleotide polymorphisms (SNPs) in squalene epoxidase (SE) gene. We evaluated the utility of amplified refractory mutation system polymerase chain reaction (ARMS PCR) for detection of previously reported point mutations, including a mutation C1191A in the SE gene in Trichophyton species. ARMS PCR was standardized using nine non-wild type isolates and two wild type isolates of Trichophyton species. Study included 214 patients with dermatophyte infection from March through December 2017. Antifungal susceptibility testing of isolated dermatophytes was performed according to CLSI-M38A2 guidelines. Among dermatophytes isolated in 68.2% (146/214) patients, Trichophyton species were predominant (66.4%). High (>2 mg/L, cut off) minimum inhibitory concentrations to terbinafine were noted in 15 (15.4%) Trichophyton mentagrophytes complex isolates. A complete agreement was noted between ARMS PCR assay and DNA sequencing. C to A transversion was responsible for amino acid substitution in 397th position of SE gene in terbinafine resistant isolates. Thus, the ARMS PCR assay is a simple and reliable method to detect terbinafine-resistant Trichophyton isolates.

Candida auris candidaemia in an intensive care unit - Prospective observational study to evaluate epidemiology, risk factors, and outcome

PURPOSE

To determine the prevalence of Candida auris candidaemia in our ICU patients and its molecular epidemiology.

METHODS

A prospective observational study was conducted on candidaemia in our ICU patients over 18 months during 2016-2017. Demographics, underlying disease, risk factors, antifungal therapy and outcome were studied. Risk factors of C. auris and non-auris candidaemia were compared.

RESULTS

During the study period, among 108 candidaemia cases recorded, the incidence was 6.75/1000 ICU bed days. C. auris topped the list (n = 42, 39.9%), followed by C. tropicalis (34.3%), and C. parapsilosis (15.7%). On bivariate analysis prior antibiotic therapy, long central line days, mechanical ventilation and length of ICU stay were significant risk factors for C. auris candidaemia compared to non-auris candidaemia. Multivariate analysis showed underlying respiratory and neurological diseases as significantly associated with risk of C. auris candidaemia. Fluconazole, amphotericin B, and caspofungin resistance were noted in 97.0%, 93.7% and 3% of C. auris isolates respectively.

CONCLUSION

Longer duration of central line days, prior antibiotic use, mechanical ventilation and prolonged ICU stay were important risk factors associated with C. auris candidaemia along with underlying respiratory or neurological disease. The isolates are non-clonal in origin, but they belong to a single clade.

Biofilm formation by Candida auris isolated from colonising sites and candidemia cases

BACKGROUND

Candida auris, an emerging nosocomial pathogen, exhibits phenotypic variation. Non-aggregating C. auris isolates display greater biofilm-forming capacity and virulence than aggregate-forming isolates. Most of the studies till date have focused on clinical isolates. The biofilm-forming capacity of colonising isolates remains uninvestigated.

OBJECTIVES

The present study aimed to elucidate the biofilm-forming capacity of the colonising isolates of C. auris, correlate it with their aggregation behaviour and antifungal susceptibility, and compare it with that of the isolates from blood-stream infection.

METHODS

Colonising and clinical (candidemia) isolates of C. auris were screened for aggregation behaviour, biofilm-forming capacity and antifungal susceptibility testing. Aggregation behaviour was assessed microscopically. Biofilm-forming capacity was determined on 96-well flat-bottomed microtitre plates. Antifungal susceptibility testing was performed by broth microdilution assay.

RESULTS

Aggregative and non-aggregative phenotypes were found to be predominantly associated with colonising and clinical isolates, respectively, with the former ones being stronger biofilm producers in the colonising group. Non-aggregative isolates in the colonising group showed lower susceptibility to amphotericin B and fluconazole than aggregative isolates. In contrast, no association was noted between biofilm formation, aggregation behaviour and antifungal susceptibility amongst the clinical isolates.

CONCLUSION

Biofilm formation is a strain-dependent trait in C. auris, strongly associated with the type and phenotypic behaviour of the isolates. Colonising isolates of this fungus were found to be predominantly aggregative in nature, with a higher biofilm-forming capacity than non-aggregative ones.

Molecular Typing and Antifungal Susceptibility of Candida viswanathii, India

We report invasive candidiasis caused by Candida viswanathii over 2 time periods during 2013–2015 in a tertiary care hospital in Chandigarh, India. Molecular typing revealed multiple clusters of the isolates. We detected high MICs for fluconazole in the second time period.

Identification of Malassezia species by MALDI-TOF MS after expansion of database

The taxonomy of Malassezia species is evolving with introduction of molecular techniques, and difficulty is faced to identify the species by phenotypic methods. Among 15 known Malassezia species, the present Bruker database could identify only 2 species. The present study was aimed to improve Matrix -assisted laser desorption ionization time-flight mass spectrometry (MALDI-TOF MS) based identification of Malassezia species. A total of 88 isolates (DNA sequencing confirmed) for database preparation and, for the validation of database, 190 isolates confirmed by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) were used. The main spectrum profile dendrogram showed the sufficient discrimination between all the species by MALDI-TOF MS. The updated Malassezia database could identify 94.7% and 5.3% strains to the species and genus level, respectively. MALDI-TOF MS is a significantly reliable technique, and results were comparable with PCR-RFLP with kappa value 0.9. In conclusion, MALDI-TOF MS could be a possible alternative tool to other molecular methods for rapid and accurate identification of Malassezia species.

Mutation in the Squalene Epoxidase Gene of Trichophyton interdigitale and Trichophyton rubrum Associated with Allylamine Resistance

Dermatophytosis, the commonest superficial fungal infection, has gained recent attention due to its change of epidemiology and treatment failures. Despite the availability of several agents effective against dermatophytes, the incidences of chronic infection, reinfection, and treatment failures are on the rise. Trichophyton rubrum and Trichophyton interdigitale are the two species most frequently identified among clinical isolates in India. Consecutive patients (n = 195) with suspected dermatophytosis during the second half of 2014 were included in this study. Patients were categorized into relapse and new cases according to standard definitions. Antifungal susceptibility testing of the isolated Trichophyton species (n = 127) was carried out with 12 antifungal agents: fluconazole, voriconazole, itraconazole, ketoconazole, sertaconazole, clotrimazole, terbinafine, naftifine, amorolfine, ciclopirox olamine, griseofulvin, and luliconazole. The squalene epoxidase gene was evaluated for mutation (if any) in 15 T. interdigitale and 5 T. rubrum isolates exhibiting high MICs for terbinafine. A T1189C mutation was observed in four T. interdigitale and two T. rubrum isolates. This transition leads to the change of phenylalanine to leucine in the 397th position of the squalene epoxidase enzyme. In homology modeling the mutant residue was smaller than the wild type and positioned in the dominant site of squalene epoxidase during drug interaction, which may lead to a failure to block the ergosterol biosynthesis pathway by the antifungal drug.