Development and Application of a Short Tandem Repeat Multiplex Typing Assay for Candida tropicalis

Genotyping of Candida tropicalis isolates uncovers nosocomial transmission of two lineages in Italian tertiary care hospital

OBJECTIVES

Candida tropicalis is a medically important yeast with increasing antifungal resistance, but nosocomial transmission is rarely reported. This study genotyped C. tropicalis isolates from Italian hospitals to uncover potential nosocomial transmission and assess resistance.

METHODS

In total, 197 C. tropicalis isolates from 161 patients were collected from five centres from 2013 to 2023. Short tandem repeat (STR) genotyping was conducted on all isolates, and a selection of 24 isolates were typed with whole-genome sequencing (WGS) and the novel Fourier-transform infrared (FTIR) spectroscopy method. Antifungal resistance was investigated with microbroth dilution and WGS.

RESULTS

STR genotyping revealed seven clusters with isolates from multiple patients. WGS single nucleotide polymorphism (SNP) analysis on five groups of isolates with related STR genotypes also separated these isolates into five groups, of which two groups contained a cluster of isolates from different patients distinguished by ≤59 SNPs. In comparison, sequential isolates within three patients were differentiated by ≤141 SNPs. The two C. tropicalis WGS clusters also clustered based on FTIR genotyping, although this method did not separate the isolates into five groups. None of the 24 isolates were resistant to common antifungals.

CONCLUSIONS

WGS SNP analysis indicated nosocomial transmission of two lineages within the same hospital, highlighting the need for enforced infection prevention measures and routine genotyping on this common yeast in clinical settings. While both STR and FTIR genotyping also clustered these lineages, WGS SNP analysis is required to determine whether isolates were transmitted clonally.

Clonal outbreak of Candida vulturna in a paediatric oncology ward in Maranhão, Brazil

OBJECTIVE

To describe an outbreak due to Candida vulturna, a newly emerging Candida species belonging to the Candida haemulonii species complex in the Metschnikowiaceae family.

METHODS

In this retrospective cohort study we genotyped 14 C. vulturna bloodstream isolates, occurring in a 4-month-period in paediatric cancer patients in a Brazilian hospital. To prove an outbreak, ITS sequence analysis and whole genome sequencing (WGS) was done. Antifungal susceptibility was performed with the reference CLSI method and the commercial Sensititre YeastOne (SYO) YO10 plates. A control C. vulturna isolate from another region in Brazil was included in all analyses.

RESULTS

MALDI-TOF-MS identified isolates as C. pseudohaemulonii and C. duobushaemulonii albeit with low scores and therefore molecular methods were required for accurate identification. ITS sequence analyses clearly differentiated C. vulturna from other species in the C. haemulonii species complex. WGS proved the presence of a clonal outbreak with C. vulturna involving 14 paediatric patients. Antifungal susceptibility testing (AFST) with two methods showed the isolates had low MICs of commonly available antifungals.

CONCLUSION

This study describes an outbreak due to the rare yeast C. vulturna, related to C. auris, during a four-month period in patients admitted to a paediatric oncology ward in a Brazilian hospital. In contrast to previous studies the yeast was susceptible to all antifungals and patient outcome was good.

Follow the Path: Unveiling an Azole Resistant Candida parapsilosis Outbreak by FTIR Spectroscopy and STR Analysis

Accurate identification and rapid genotyping of Candida parapsilosis, a significant opportunistic pathogen in healthcare settings, is crucial for managing outbreaks, timely intervention, and effective infection control measures. This study includes 24 clinical samples and 2 positive environmental surveillance swabs collected during a fluconazole-resistant Candida parapsilosis outbreak at the Tuscany Rehabilitation Clinic (Clinica di Riabilitazione Toscana, CRT), located in the province of Arezzo, Italy. Fourier-transform infrared (FTIR) spectroscopy, genetic sequencing of the ERG11 gene, and short tandem repeat (STR) analysis was applied to track the fluconazole-resistant C. parapsilosis outbreak at the CRT facility. FTIR analysis clustered the isolates into two major groups, correlating with resistance-associated ERG11 mutations (Y132F and R398I), azole resistance levels, and year of isolation. The combined use of FTIR spectroscopy and STR typing provided a comprehensive approach to identify and track fluconazole-resistant C. parapsilosis isolates, which identified specific clusters of genetically similar isolates. By comparison with feasible molecular techniques, we conclude that FTIR spectroscopy applied in real time can inform targeted infection control strategies and aid in the effective management of nosocomial infections.

Short Tandem Repeat Genotyping of Medically Important Fungi: A Comprehensive Review of a Powerful Tool with Extensive Future Potential

Fungal infections pose an increasing threat to public health. New pathogens and changing epidemiology are a pronounced risk for nosocomial outbreaks. To investigate clonal transmission between patients and trace the source, genotyping is required. In the last decades, various typing assays have been developed and applied to different medically important fungal species. While these different typing methods will be briefly discussed, this review will focus on the development and application of short tandem repeat (STR) genotyping. This method relies on the amplification and comparison of highly variable STR markers between isolates. For most common fungal pathogens, STR schemes were developed and compared to other methods, like multilocus sequence typing (MLST), amplified fragment length polymorphism (AFLP) and whole genome sequencing (WGS) single nucleotide polymorphism (SNP) analysis. The pros and cons of STR typing as compared to the other methods are discussed, as well as the requirements for the development of a solid STR typing assay. The resolution of STR typing, in general, is higher than MLST and AFLP, with WGS SNP analysis being the gold standard when it comes to resolution. Although most modern laboratories are capable to perform STR typing, little progress has been made to standardize typing schemes. Allelic ladders, as developed for Aspergillus fumigatus, facilitate the comparison of STR results between laboratories and develop global typing databases. Overall, STR genotyping is an extremely powerful tool, often complimentary to whole genome sequencing. Crucial details for STR assay development, its applications and merit are discussed in this review.

Multicenter Candida auris outbreak caused by azole-susceptible clade IV in Pernambuco, Brazil

BACKGROUND

Candida auris is an emerging multidrug-resistant yeast, frequently causing outbreaks in health care facilities. The pathogen persistently colonises human skin and inanimate surfaces such as catheters, aiding to its spread. Moreover, colonisation is a risk factor to develop invasive infection.

OBJECTIVES

We investigated 61 C. auris strains isolated from non-sterile human body sites (n = 53) and the hospital environment (n = 8), originating from four different centres in a single Brazilian state.

MATERIALS AND METHODS

Antifungal susceptibility testing (AFST) against common antifungals was performed, and resistance-associated genes were evaluated. Genetic relatedness was investigated with short tandem repeat (STR) genotyping and validated with whole-genome sequencing (WGS) single nucleotide polymorphism (SNP) analysis.

RESULTS

Antifungal susceptibility testing demonstrated that all isolates were susceptible to azoles, echinocandins and amphotericin B. No mutations were detected in ERG11 and FKS1 genes. With STR typing, isolates were allocated to clade IV and appeared closely related. This was confirmed by WGS SNP analysis of 6 isolates, which demonstrated a maximal difference of only 41 SNPs between these strains. Furthermore, the Brazilian isolates formed a distinct autochthonous branch within clade IV, excluding recent introductions from outside the country. A molecular clock analysis of clade IV isolates from various countries suggests that early in the previous century there was a unique event causing environmental spread of a C. auris ancestor throughout the Latin-American continent, followed by human introduction during the last decades.

CONCLUSION

We report the emergence of C. auris patient colonisation in multiple centres by fluconazole-susceptible clade IV close-related strains in Pernambuco State, Brazil.

Molecular typing and antifungal susceptibility profile of Candida krusei bloodstream isolates from Türkiye

Candida krusei also known as Pichia kudriavzevii is a potentially multidrug-resistant yeast because it is intrinsically resistant to fluconazole and develops acquired resistance to echinocandins and polyenes. Here, we aim to provide a better understanding of the epidemiology and transmission modes of C. krusei infections by comparing invasive bloodstream (n = 35) and non-invasive vaginal (n = 20) C. krusei isolates. The genetic relatedness of the isolates was assessed using a newly described short tandem repeat (STR) analysis and their sensitivity to eight antifungal compounds was evaluated by antifungal susceptibility testing using the CLSI microbroth dilution method. All C. krusei isolates revealed unique STR genotypes, indicating the absence of clonal transmission in the study group. Furthermore, no drug-resistant or non-wild-type isolates were identified. Our findings demonstrated high resolution of STR genotyping for the detection and simultaneous genetic analysis of multiple C. krusei strains in clinical samples and excellent in vitro activity of common antifungal agents against invasive strains.

The Gastrointestinal Tract Is Pinpointed as a Reservoir of Candida albicans, Candida parapsilosis, and Candida tropicalis Genotypes Found in Blood and Intra-Abdominal Samples

BACKGROUND

Candida spp., as part of the microbiota, can colonise the gastrointestinal tract. We hypothesised that genotyping Candida spp. isolates from the gastrointestinal tract could help spot genotypes able to cause invasive infections.

MATERIALS/METHODS

A total of 816 isolates of C. albicans (n = 595), C. parapsilosis (n = 118), and C. tropicalis (n = 103) from rectal swabs (n = 754 patients) were studied. Genotyping was conducted using species-specific microsatellite markers. Rectal swab genotypes were compared with previously studied blood (n = 814) and intra-abdominal (n = 202) genotypes.

RESULTS

A total of 36/754 patients had the same Candida spp. isolated from blood cultures, intra-abdominal samples, or both; these patients had candidemia (n = 18), intra-abdominal candidiasis (n = 11), both clinical forms (n = 1), and non-significant isolation (n = 6). Genotypes matching the rectal swab and their blood cultures (84.2%) or their intra-abdominal samples (92.3%) were found in most of the significant patients. We detected 656 genotypes from rectal swabs, 88.4% of which were singletons and 11.6% were clusters. Of these 656 rectal swab genotypes, 94 (14.3%) were also detected in blood cultures and 34 (5.2%) in intra-abdominal samples. Of the rectal swab clusters, 62.7% were previously defined as a widespread genotype.

CONCLUSIONS

Our study pinpoints the gastrointestinal tract as a potential reservoir of potentially invasive Candida spp. genotypes.

Application of Novel Short Tandem Repeat Typing for Wickerhamomyces anomalus Reveals Simultaneous Outbreaks within a Single Hospital

Wickerhamomyces anomalus, previously known as Candida pelliculosa, occasionally causes candidemia in humans, primarily infecting neonates, and infants. The mortality rate of these invasive infections is high, and isolates with a reduced susceptibility to fluconazole have been reported. W. anomalus outbreaks are regularly reported in healthcare facilities, especially in neonatal intensive care units (NICUs). In order to rapidly genotype isolates with a high-resolution, we developed and applied a short tandem repeat (STR) typing scheme for W. anomalus. Six STR markers were selected and amplified in two multiplex PCRs, M3 and M6, respectively. In total, 90 W. anomalus isolates were typed, leading to the identification of 38 different genotypes. Four large clusters were found, unveiling simultaneous outbreak events spread across multiple units within the same hospital. STR typing results of 11 isolates were compared to whole-genome sequencing (WGS) single nucleotide polymorphism (SNP) calling, and the identified genotypic relationships were highly concordant. We performed antifungal susceptibility testing of these isolates, and a reduced susceptibility to fluconazole was found for two (2.3%) isolates. ERG11 genes of these two isolates were examined using WGS data, which revealed a novel I469L substitution in one isolate. By constructing a homology model for W. anomalus ERG11p, the substitution was found in close proximity to the fluconazole binding site. In summary, we showed multiple W. anomalus outbreak events by applying a novel STR genotyping scheme.

Short Tandem Repeat Genotyping and Antifungal Susceptibility Testing of Latin American Candida tropicalis Isolates

Candida tropicalis is emerging as one of the most common Candida species causing opportunistic infections in Latin America. Outbreak events caused by C. tropicalis were reported, and antifungal resistant isolates are on the rise. In order to investigate population genomics and look into antifungal resistance, we applied a short tandem repeat (STR) genotyping scheme and antifungal susceptibility testing (AFST) to 230 clinical and environmental C. tropicalis isolates from Latin American countries. STR genotyping identified 164 genotypes, including 11 clusters comprised of three to seven isolates, indicating outbreak events. AFST identified one isolate as anidulafungin-resistant and harboring a FKS1 S659P substitution. Moreover, we identified 24 clinical and environmental isolates with intermediate susceptibility or resistance to one or more azoles. ERG11 sequencing revealed each of these isolates harboring a Y132F and/or Y257H/N substitution. All of these isolates, except one, were clustered together in two groups of closely related STR genotypes, with each group harboring distinct ERG11 substitutions. The ancestral C. tropicalis strain of these isolates likely acquired the azole resistance-associated substitutions and subsequently spread across vast distances within Brazil. Altogether, this STR genotyping scheme for C. tropicalis proved to be useful for identifying unrecognized outbreak events and better understanding population genomics, including the spread of antifungal-resistant isolates.