Draft Genome Sequences of 19 Clinical Isolates of Candida auris from Hong Kong

Candida auris-associated hospitalizations and outbreaks, China, 2018-2023

The emerging human fungal pathogen Candida auris has become a serious threat to public health. This pathogen has spread to 10 provinces in China as of December 2023. Here we describe 312 C. auris-associated hospitalizations and 4 outbreaks in healthcare settings in China from 2018 to 2023. Three genetic clades of C. auris have been identified during this period. Molecular epidemiological analyses indicate that C. auris has been introduced and local transmission has occurred in multiple instances in China. Most C. auris isolated from China (98.7%) exhibited resistance to fluconazole, while only a small subset of strains were resistant to amphotericin B (4.2%) and caspofungin (2.2%).

Two outbreaks and sporadic occurrences of Candida auris from one hospital in China: an epidemiological, genomic retrospective study

OBJECTIVES

To investigate the clinical relevance, origin, transmission, and resistance of Candida auris (C. auris) isolates from two outbreaks and sporadic occurrences from one hospital in China.

METHODS

A total of 135 C. auris isolates were collected. Clinical characteristics were obtained and antifungal susceptibility testing (AFST) was performed using the method of broth microdilution. Phylogenetic tree, WGS analysis, and single nucleotide polymorphisms (SNPs) were used to determine the origin, transmission, and resistance mechanisms.

RESULTS

A total of 31 patients (91.2%, 31/34) received invasive medical procedures and 13 patients (38.2%, 13/34) had antifungal agents before C. auris infection/colonization, except one patient whose clinical information was missing. Only 4 cases of C. auris candidemia were observed. 18 patients died, 13 patients recovered, and the outcomes of 3 patients were not available. A total of 35 C. auris isolates, which were successfully cultivated and the first isolated or harbored specific drug-resistant phenotype from each patient, were selected to be sequenced and further analyzed. C. auris isolates presented low genetic variability and belonged to clade I, possibly originating from BJ004-H7 in Beijing. All 35 isolates were resistant to Fluconazole (FCZ) and amphotericin B (AMB), and 3 isolates were resistant to caspofungin (CAS). Mutations in ERG11 and FKS1 were linked to reduced azole and echinocandin susceptibility, respectively.

CONCLUSIONS

Two outbreaks of highly clonal, multidrug-resistant C. auris isolates within the medical facility were reported. The intensive performance of disinfection measures helped block in-hospital transmission. Understanding the epidemiology, drug resistance and management of C. auris will be helpful for implementing effective infection control and treatment strategies.

Antifungal efficacy of natural antiseptic products against Candida auris

Candida auris is an emerging fungal pathogen responsible for healthcare-associated infections and outbreaks with high mortality around the world. It readily colonizes the skin, nares, respiratory and urinary tract of hospitalized patients, and such colonization may lead to invasive Candida infection in susceptible patients. However, there is no recommended decolonization protocol for C. auris by international health authorities. The aim of this study is to evaluate the susceptibility of C. auris to commonly used synthetic and natural antiseptic products using an in vitro, broth microdilution assay. Synthetic antiseptics including chlorhexidine, povidone-iodine, and nystatin were shown to be fungicidal against C. auris. Among the natural antiseptics tested, tea tree oil and manuka oil were both fungicidal against C. auris at concentrations less than or equal to 1.25% (v/v). Manuka honey inhibited C. auris at 25% (v/v) concentrations. Among the commercial products tested, manuka body wash and mouthwash were fungicidal against C. auris at concentrations less than or equal to 0.39% (w/v) and 6.25% (v/v) of products as supplied for use, respectively, while tea tree body wash and MedihoneyTM wound gel demonstrated fungistatic properties. In conclusion, this study demonstrated good in vitro antifungal efficacy of tea tree oil, manuka oil, manuka honey, and commercially available antiseptic products containing these active ingredients. Future studies are warranted to evaluate the effectiveness of these antiseptic products in clinical settings.

Long-range air dispersion of Candida auris in a cardiothoracic unit outbreak in Hong Kong

BACKGROUND

Nosocomial outbreaks of Candida auris, a multidrug-resistant fungus, are increasingly reported worldwide; the mode of transmission has usually been reported to be via direct contact. Some studies previously suggested potential short-distance air dispersal during high-turbulence activities, but evidence on long-range air dispersal remains scarce.

AIM

To describe a C. auris nosocomial outbreak involving two wards (H7, 5E) in two local hospitals.

METHODS

Samples were taken from patients, ward surfaces (frequently touched items and non-reachable surfaces) while settle plates were used for passive air sampling to investigate possible contributions by direct contact and air dispersal. Epidemiological and phylogenetic analyses were also performed on the C. auris isolates from this outbreak.

FINDINGS

Eighteen patients were confirmed to have asymptomatic C. auris skin colonization. C. auris was expectedly identified in samplings from frequently touched ward items but was also isolated in two samples from ceiling supply air grilles which were 2.4 m high and inaccessible by patients. Moreover, one sample from a corridor return air grille as far as 9.8 m away from the C. auris cohort area was also positive. Two passive air samplings were positive, including one from a cubicle with no confirmed cases for four days, suggesting possible air dispersal of C. auris. Whole-genome sequencing confirmed clonality of air, environment, and patients' isolates.

CONCLUSION

This is the first study to demonstrate potential long-range air dispersal of C. auris in an open-cubicle ward setting. Ventilation precautions and decontamination of out-of-reach high-level surfaces should be considered in C. auris outbreak management.

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

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.

Candida auris: A Mini Review on Epidemiology in Healthcare Facilities in Asia

Candida auris, a newly emerging healthcare-associated yeast pathogen from the Metschnikowiaceae family, was first described in the ear canal of an elderly Japanese patient in 2009. The yeast is one of the causative agents of candidemia, which has been linked with nosocomial outbreaks and high mortality rates in healthcare facilities worldwide. Since its first isolation, the occurrence of C. auris in six continents has becomes a grave concern for the healthcare professionals and scientific community. Recent reports showed the identification of five geographically distinct clades and high rates of antifungal resistance associated with C. auris. Till date, there are no effective treatment options, and standardized measures for prevention and control of C. auris infection in healthcare facilities. This leads to frequent therapeutic failures and complicates the eradication of C. auris infection in healthcare facilities. Thus, this review focuses on the recent understanding of the epidemiology, risk factors, diagnosis, transmission and prevention and control strategies of C. auris infection in healthcare facilities in Asia.

The First Invasive Candida auris Infection in Taiwan

Candida auris, a multidrug resistant pathogenic yeast, has spread worldwide and caused several outbreaks in healthcare settings. Here, we report the first case of C. auris candidemia in Taiwan in a patient with a two-month history of hospitalization in Vietnam. We performed further investigation on the isolate from the present case as well as the previously reported C. auris isolate identified from a wound in 2018 in Taiwan, which was the first case reported in Taiwan. Both C. auris isolates were found to be susceptible to fluconazole, amphotericin B, and echinocandins. Additionally, mutations in ERG11 or FKS1 were not detected in either isolate. Microsatellite genotyping revealed that both isolates belonged to the South Asian clade. In recent years, C. auris has emerged as a global concern, and differences in clades and susceptibility patterns mandate further awareness and systematic surveillance.

Population genomic analyses reveal evidence for limited recombination in the superbug Candida auris in nature

Candida auris is a recently emerged, multidrug-resistant pathogenic yeast capable of causing a diversity of human infections worldwide. Genetic analyses based on whole-genome sequences have clustered strains in this species into five divergent clades, with each clade containing limited genetic variation and one of two mating types, MTLa or MTLα. The patterns of genetic variations suggest simultaneous emergence and clonal expansion of multiple clades of this pathogen across the world. At present, it is unclear whether recombination has played any role during the evolution of C. auris. In this study, we analyzed patterns of associations among single nucleotide polymorphisms in both the nuclear and the mitochondrial genomes of 1,285 strains to investigate potential signatures of recombination in natural C. auris populations. Overall, we found that polymorphisms in the nuclear and mitochondrial genomes clustered the strains similarly into the five clades, consistent with a lack of evidence for recombination among the clades after their divergence. However, variable percentages of SNP pairs showed evidence of phylogenetic incompatibility and linkage equilibrium among samples in both the nuclear and the mitochondrial genomes, with the percentages higher in the total population than those within individual clades. Our results are consistent with limited but greater frequency of recombination before the divergence of the clades than afterwards. SNPs at loci related to antifungal resistance showed frequencies of recombination similar to or lower than those observed for SNPs in other parts of the genome. Together, though very limited, evidence for the observed recombination for both before and after the divergence of the clades suggests the possibility for continuous genetic exchange in natural populations of this important yeast pathogen.

A case of Candida auris candidemia in Xiamen, China, and a comparative analysis of clinical isolates in China

The recently emerged fungal pathogen Candida auris often displays resistance to one or more antifungal drugs. Its infections have been identified in at least 40 countries on six continents to date. Here we report a case of C. auris candidemia in a patient in Xiamen, a city in south China. We also review currently reported cases of C. auris infection in China and compare the genetic and biological features of C. auris strains isolated from this country. Our phylogenetic analysis indicates that there are at least two C. auris genetic clades present in China (the South African clade and the south Asian clade) that display opposite mating type loci (one is MTL a and the other is MTLα). We also found that there are several distinct features among the clinical isolates studied, including the expression of virulence factors, antifungal susceptibilities, and cellular morphologies, and that these features could be associated with the mating-type of the isolate. For example, C. auris MTL a isolates generally secreted higher levels of secreted aspartyl proteases (Saps) at ambient environmental temperatures. Taken together, this study demonstrates that C. auris clinical isolates from China exhibit diversity in both biological and genetic features.

Genomic epidemiology of Candida auris in a general hospital in Shenyang, China: a three-year surveillance study

Candida auris is an emerging pathogenic fungal species found worldwide. Since April 2016, C. auris colonization/infection cases have been found in a general hospital in Shenyang, China. The genome-based phylogenetic studies of these isolates remain undefined. In the current study, the microbiological characteristics and antifungal susceptibility of these C. auris isolates, which were collected in Shenyang during the three-year period (2016–2018), were investigated. Whole-genome sequencing was applied to investigate the genetic variation and molecular epidemiological characteristics. A total of 93 C. auris isolates, including 92 clinical isolates and 1 environmental screening isolate were identified. Among the investigated wards, the C. auris cases were the most prevalent (97.4%, 37/38) in four intensive care units (ICUs). The Shenyang isolates carrying the VF125AL mutation in the key drug-resistance gene ERG11 were mainly fluconazole resistant and formed a distinct subclade under the South African clade according to the phylogenetic and population structural analyses. In addition, the Shenyang subclade was found to be closely related to the British subclade in the aspect of genetic distance. As a conclusion, this study provides an important clue for revealing the origin of C. auris found in Shenyang and could also contribute to improve the understanding of the epidemiological characteristics of C. auris worldwide.