Multilocus sequence typing (MLST) analysis reveals many novel genotypes and a high level of genetic diversity in Candida tropicalis isolates from Italy and Africa

Investigation of multi-drug resistant Candida auris using species-specific molecular markers in immunocompromised patients from a tertiary care hospital in Quetta, Pakistan

INTRODUCTION

Candida auris is an emerging multidrug-resistant pathogen responsible for nosocomial infections worldwide, characterized by high mortality rates and significant challenges in detection due to frequent misidentification. Classified by the WHO as a pathogen of critical importance since it exhibits resistance to multiple antifungal agents, particularly fluconazole, and is highly transmissible in healthcare settings. Conventional detection methods often lack the accuracy required for effective infection control. This study aimed to conduct inferential and molecular analyses of C. auris and other yeast species infecting immunocompromised patients in the Special and Intensive Care Units (SCU and ICU) of a tertiary care hospital in Quetta, Pakistan. In this region, C. auris remains rarely studied and is frequently misdiagnosed by clinical staff due to limited awareness and diagnostic challenges. Notably, no prior research has been conducted on C. auris in Quetta. The study also sought to develop reliable diagnostic methods suitable for resource-limited settings, addressing a critical gap in healthcare infrastructure.

MATERIALS AND METHODS

Samples (150 each) from the ear, axilla, groin, and saliva of SCU/ICU patients were collected and processed on yeast malt agar, with preliminary identification using Brilliance Candida Agar (BCA) and CHROMagar Candida Plus (CCP). Advanced techniques, including PCR amplification of ITS regions, DNA sequencing, RFLP with Msp1, MALDI-TOF, Vitek 2, and species-specific primers, were used for identification. Antifungal susceptibility to fluconazole, amphotericin B, and voriconazole were also assessed.

RESULTS

The culture test revealed that 42.6% samples were positive for yeast infections. In addition to detecting Candida auris in 4 cultures, chromogenic media identified 6 other Candida species: C. albicans, C. dubliniensis, C. glabrata, C. krusei, C. parapsilosis, and C. tropicalis. Further validation through advanced techniques, including molecular diagnostics and MALDI-TOF, enabled the identification of additional species: C. famata, C. kefyr, C. lusitaniae, and Meyerozyma (Candida) guilliermondii. Out of all identified yeast species C. dubliniensis was the most common, followed by C. albicans and C. tropicalis, with the highest infection rates observed in saliva samples. Antifungal Susceptibility Tests (AST) revealed that C. auris isolates were resistant to Fluconazole, Amphotericin B, and Voriconazole, highlighting multidrug resistance. This study represents the first report of novel multidrug-resistant C. auris from Quetta, Pakistan, indicating that C. auris is prevalent among ICU and SCU patients. Novel species specific primers targeting phospholipase B, topoisomerase II, CDR and 18s genes were designed in our laboratory and not previously reported in earlier studies, proved highly effective for the rapid identification of Candida species. The established protocol using these primers is recommended for implementation in resource-limited laboratory settings. The statistical analysis demonstrated significant correlations between Candida species infection (dependent variable) and several independent factors (variables) emphasizing the importance of targeted diagnostics and intervention strategies.

Trichosporon asahii: emerging challenges in pathogenesis and drug resistance

Trichosporon asahii (T. asahii) is an opportunistic pathogenic fungus that often causes severe infections in immunosuppressed patients. Among Trichosporon species, T. asahii is the most pathogenic and lethal species. Current research faces challenges related to unknown pathogenic mechanisms, complex resistance mechanisms, insufficiently rapid and accurate diagnostic methods, and insufficient research on susceptibility to infection. These issues need to be explored in depth. This review summarizes research progress on the origin and classification of T. asahii, its virulence factors and pathogenic mechanisms, epidemiological characteristics, infection modes, diagnostic methods, drug treatment options, and drug resistance mechanisms. Traditional culture combined with molecular biology techniques, such as polymerase chain reaction and gene sequencing, has improved the accuracy and speed of detection. Treatment relies mainly on azole antifungal drugs and amphotericin B; however, patients are facing the problem of drug resistance. New techniques, such as gene knockout and gene sequencing, have identified resistance mechanisms, thus supporting the development of novel antifungal drugs. In summary, an in-depth study of T. asahii will aid in developing more effective diagnostic and therapeutic methods and improve patient prognosis.

Multi-locus sequence typing of Candida tropicalis among Candiduria shows an outbreak in azole-susceptible isolates and clonal cluster enriched in azole-resistant isolates

BACKGROUND

The increasing detection rate of C. tropicalis and its azole resistance have made clinical treatment difficult. The presence of candiduria seems to correlate with invasive candida infection, especially for patients admitted to ICUs. However, the prevalence and antifungal resistance of C. tropicalis isolates in urine samples has not been well studied.

AIM

To retrospectively investigate the clinical features, antifungal resistance, and genetic relatedness of C. tropicalis isolates from urine samples.

METHODS

A total of 107 clinical C. tropicalis isolates were retrospectively studied, including phenotypes of isolates and characteristics of patients. The genetic profiles of 107 isolates were genotyped using multi-locus sequence typing (MLST). Phylogenetic analysis was inferred using unweighted pair group method with arithmetic averages. MLST clonal clusters (CCs) were analysed by goeBURST.

FINDINGS

Of the 107 isolates, 27.1% were resistant to fluconazole, and there was a notable increasing trend of fluconazole resistance from 16.1% in 2019 to 40.0% in 2021. Forty-seven diploid sequence types (DSTs) were assigned to ten major CCs. CC1 was the predominant fluconazole-susceptible group; 24 isolates from CC1 belonged to DST333, an outbreak clone in NICU ward. The azole-resistant CC4 contained 19 isolates, accounting for 65.5% of the azole-resistant isolates in this study. CC4 belongs to a prevalent FNS CC1 globally, of which the putative founder genotype was DST225.

CONCLUSION

This study revealed an outbreak of azole-susceptible C. tropicalis isolates in urine specimens and a high azole resistance rate of C. tropicalis in candiduria, and the MLST type showed clonal aggregation in azole-resistant isolates from urine samples.

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.

Bioprotective yeasts: Potential to limit postharvest spoilage and to extend shelf life or improve microbial safety of processed foods

Yeasts are a widespread group of microorganisms that are receiving increasing attention from scientists and industry. Their diverse biological activities and broad-spectrum antifungal activity make them promising candidates for application, especially in postharvest biocontrol of fruits and vegetables and food biopreservation. The present review focuses on recent knowledge of the mechanisms by which yeasts inhibit pathogenic fungi and/or spoilage fungi and bacteria. The main mechanisms of action of bioprotective yeasts include competition for nutrients and space, synthesis and secretion of antibacterial compounds, mycoparasitism and the secretion of lytic enzymes, biofilm formation, quorum sensing, induced systemic resistance of fruit host, as well as the production of reactive oxygen species. Preadaptation of yeasts to abiotic stresses such as cold acclimatization and sublethal oxidative stress can improve the effectiveness of antagonistic yeasts and thus more effectively play biocontrol roles under a wider range of environmental conditions, thereby reducing economic losses. Combined application with other antimicrobial substances can effectively improve the efficacy of yeasts as biocontrol agents. Yeasts show great potential as substitute for chemical additives in various food fields, but their commercialization is still limited. Hence, additional investigation is required to explore the prospective advancements of yeasts in the field of biopreservation for food.

Rapid identification of the predominant azole-resistant genotype in Candida tropicalis

Candida tropicalis is a leading cause of nonalbicans candidemia in tropical/subtropical areas and a predominant genotype of azole-resistant C. tropicalis clinical isolates belongs to clade 4. The aim of this study was to reveal markers for rapidly identifying the predominant azole-resistant C. tropicalis genotype. We analysed XYR1, one of the six genes used in the multilocus sequence typing analysis, and SNQ2, an ATP-binding cassette transporter in 281 C. tropicalis, including 120 and 161 from Taiwan and global areas, respectively. Intriguingly, the first 4-mer of codon sequences ATRA of CTRG_05978 (96/119 versus 21/162, P < .001, at phi = 0. 679) and the SNQ2 A2977G resulting in amino acid I993V alternation (105/118 versus 12/163, P < .001, at phi = 0.81) was significantly associated with the clade 4 genotype. The sensitivity and specificity of the clade 4 genotype detection with a combination of SNPs of CTRG_05978 and SNQ2 were 0.812 and 0.994, respectively, at phi = 0.838. Furthermore, we successfully established a TaqMan SNP genotyping assay to identify the clade 4 genotype. Our findings suggest that to improve the management of C. tropicalis infections, rapidly identifying azole-resistant C. tropicalis by detecting SNPs of CTRG_05978 and SNQ2 is promising.

Environmental monitoring for filamentous fungal pathogens in hematopoietic cell transplant units

The incidence of invasive fungal disease (IFD) is on the rise due to increasing numbers of highly immunocompromized patients. Nosocomial IFD remains common despite our better understanding of its risk factors and pathophysiology. High-efficiency particulate air filtration with or without laminar air flow, frequent air exchanges, a positive pressure care environment, and environmental hygiene, amongst other measures, have been shown to reduce the mould burden in the patient environment. Environmental monitoring for moulds in areas where high-risk patients are cared for, such as hematopoietic cell transplant units, has been considered an adjunct to other routine environmental precautions. As a collaborative effort between authors affiliated to the Infection Prevention and Control Working Group and the Fungal Infection Working Group of the International Society of Antimicrobial Chemotherapy (ISAC), we reviewed the English language literature and international guidance to describe the evidence behind the need for environmental monitoring for filamentous fungi as a quality assurance approach with an emphasis on required additional precautions during periods of construction. Many different clinical sampling approaches have been described for air, water, and surface sampling with significant variation in laboratory methodologies between reports. Importantly, there are no agreed-upon thresholds that correlate with an increase in the clinical risk of mould infections. We highlight important areas for future research to assure a safe environment for highly immunocompromized patients.

Clonal aggregation of fluconazole-resistant Candida tropicalis isolated from sterile body fluid specimens from patients in Hefei, China

Candida tropicalis, a human conditionally pathogenic yeast, is distributed globally, especially in Asia-Pacific. The increasing morbidity and azole resistance of C. tropicalis have made clinical treatment difficult. The correlation between clonality and antifungal susceptibility of clinical C. tropicalis isolates has been reported. To study the putative correlation in C. tropicalis isolated from normally sterile body fluid specimens and explore the distinct clonal complex (CC) in Hefei, 256 clinical C. tropicalis isolates were collected from four teaching hospitals during 2016-2019, of which 30 were fluconazole-resistant (FR). Genetic profiles of 63 isolates, including 30 FR isolates and 33 fluconazole-susceptible (FS) isolates, were characterized using multilocus sequence typing (MLST). Phylogenetic analysis of the data was conducted using UPGMA (unweighted pair group method with arithmetic averages) and the minimum spanning tree algorithm. MLST clonal complexes (CCs) were analyzed using the goeBURST package. Among 35 differentiated diploid sequence types (DSTs), 16 DSTs and 1 genotype were identified as novel. A total of 35 DSTs were assigned to five major CCs based on goeBURST analysis. CC1 (containing DST376, 505, 507, 1221, 1222, 1223, 1226, and 1229) accounted for 86.7% (26/30) of the FR isolates. However, the genetic relationships among the FS isolates were relatively decentralized. The local FR CC1 belongs to a large fluconazole non-susceptible CC8 in global isolates, of which the putative founder genotype was DST225. The putative correlation between MLST types and antifungal susceptibility of clinical C. tropicalis isolates in Hefei showed that DSTs are closely related to FR clones.

Genotyping and susceptibility testing uncovers large azole-resistant Candida tropicalis clade in Alexandria, Egypt

OBJECTIVES

Candida tropicalis is an emerging medically relevant Candida species. The yeast primarily causes opportunistic infections in intensive care units and is highly prevalent in tropical countries. The genetic diversity within this species is high, and nosocomial transmission has been reported. C. tropicalis genotyping of isolates from low- and middle-income countries is underrepresented when compared with that from high-income countries. Also, in Egypt, only limited genotyping has been conducted for C. tropicalis isolates, while antifungal resistance seems to increase, especially against azoles.

METHODS

Antifungal susceptibility testing was performed on 64 C. tropicalis isolates from ICU patients collected from multiple hospitals in Alexandria, Egypt. Genotyping by means of short tandem repeat (STR) and whole genome sequencing (WGS) single nucleotide polymorphism (SNP) analysis was performed.

RESULTS

Using antifungal susceptibility testing, fluconazole resistance was observed in 24 isolates (38%), of which 23 harboured an ERG11 G464S substitution, previously shown to cause resistance in Candida albicans. STR genotyping showed that these 23 isolates were related, forming a distinct resistant clade. WGS SNP analysis subsequently confirmed this genetic relationship, although isolates within this clade differed in at least 429 SNPs, suggesting that these were independently introduced.

CONCLUSION

Overall, STR and WGS SNP analysis of this collection indicates limited C. tropicalis nosocomial transmission in Alexandria, while the presence of this large azole-resistant C. tropicalis clade within this city hampers the treatment of intensive care unit patients.

Prevalence and Characterization of Salmonella Isolated from Chickens in Anhui, China

Salmonella is one of the most important zoonotic pathogens that can cause both acute and chronic illnesses in poultry flocks, and can also be transmitted to humans from infected poultry. The purpose of this study was to investigate the prevalence, antimicrobial resistance, and molecular characteristics of Salmonella isolated from diseased and clinically healthy chickens in Anhui, China. In total, 108 Salmonella isolates (5.66%) were successfully recovered from chicken samples (n = 1908), including pathological tissue (57/408, 13.97%) and cloacal swabs (51/1500, 3.40%), and S. Enteritidis (43.52%), S. Typhimurium (23.15%), and S. Pullorum (10.19%) were the three most prevalent isolates. Salmonella isolates showed high rates of resistance to penicillin (61.11%), tetracyclines (47.22% to tetracycline and 45.37% to doxycycline), and sulfonamides (48.89%), and all isolates were susceptible to imipenem and polymyxin B. In total, 43.52% isolates were multidrug-resistant and had complex antimicrobial resistance patterns. The majority of isolates harbored cat1 (77.78%), blaTEM (61.11%), and blaCMY-2 (63.89%) genes, and the antimicrobial resistance genes in the isolates were significantly positively correlated with their corresponding resistance phenotype. Salmonella isolates carry high rates of virulence genes, with some of these reaching 100% (invA, mgtC, and stn). Fifty-seven isolates (52.78%) were biofilm-producing. The 108 isolates were classified into 12 sequence types (STs), whereby ST11 (43.51%) was the most prevalent, followed by ST19 (20.37%) and ST92 (13.89%). In conclusion, Salmonella infection in chicken flocks is still serious in Anhui Province, and not only causes disease in chickens but might also pose a threat to public health security.

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

Candida tropicalis is a clinically important yeast that causes candidemia in humans with a high mortality rate. The yeast primarily infects immunocompromised patients, and causes outbreaks in health care facilities. Antifungal resistant isolates have been reported. We developed a short tandem repeat (STR) typing scheme for C. tropicalis to enable fast, cost-effective, and high-resolution genotyping. For the development of the typing scheme, 6 novel STR markers were selected, combined into 2 multiplex PCRs. In total, 117 C. tropicalis isolates were typed, resulting in the identification of 104 different genotypes. Subsequently, the outcome of STR typing of 10 isolates was compared to single nucleotide polymorphism (SNP) calling from whole-genome sequencing (WGS). Isolates with more than 111 SNPs were differentiated by the typing assay. Two isolates, which were identical according to SNP analysis, were separated by STR typing in 1 marker. To test specificity, the STR typing was applied to 15 related yeast species, and we found no amplification of these targets. For reproducibility testing, 2 isolates were independently typed five times, which showed identical results in each experiment. In summary, we developed a reliable and multiplex STR genotyping for C. tropicalis, which was found to correlate well to SNP calling by WGS. WGS analysis from and extensive collection of isolates is required to establish the precise resolution of this STR assay. IMPORTANCE Candida tropicalis frequently causes candidemia in immunocompromised patients. C. tropicalis infections have a high mortality rate, and the yeast is able to cause outbreaks in health care facilities. Further, antifungal resistant isolates are on the rise. Genotyping is necessary to investigate potential outbreaks. Here, we developed and applied a STR genotyping scheme in order to rapidly genotype isolates with a high-resolution. WGS SNP outcomes were highly comparable with STR typing results. Altogether, we developed a rapid, high-resolution, and specific STR genotyping scheme for C. tropicalis.