Draft Genome Sequence of Candida auris Strain LOM, a Human Clinical Isolate from Greater Metropolitan Houston, Texas

Intra-host genomic variation of serologically nontypeable Haemophilus influenzae isolates from otitis media

Serologically nontypeable Haemophilus influenzae is a human pathogen that causes infections ranging in severity from mild otitis media and sinusitis to life-threatening pneumonia, bacteremia, and meningitis. Although intra-host genomic variation in infected humans has been studied, many important questions remain unanswered. To address this knowledge deficit, we sequenced the genomes of 500 isolates recovered from ear drainage fluid collected from 11 Icelandic children with otorrhea. We discovered substantial genomic diversity among the H. influenzae strains infecting each patient. In total, we identified 88 genes that acquired nonsynonymous (amino acid-changing) or nonsense (protein-truncating) single-nucleotide polymorphisms, insertions, or deletions in at least one isolate. Of these, 13 genes were recurrently polymorphic. The polymorphic genes encoded proteins with varied inferred functions, including carbohydrate metabolism, cell wall biosynthesis, environmental stress response, glycolipid metabolism, iron metabolism, recombination, small molecule transport, and transcription and translation. No amino acid substitutions or protein truncations were identified in proven H. influenzae virulence factors or major transcription regulators. However, many of the polymorphic genes likely contribute to fitness, virulence, or host-pathogen molecular interactions. Our study of intra-host variation in otitis media provides a framework for understanding the genomic adaptability of H. influenzae during human infections.IMPORTANCESerologically nontypeable H. influenzae is a human pathogen responsible for a range of diseases, including mild otitis media (middle ear infection) and sinusitis, and severe pneumonia, bacteremia, and meningitis. While research has begun advancing our understanding of the population genomic structure of H. influenza strains infecting humans, little is known about intra-host genomic variation. To address this knowledge gap, we sequenced the genomes of 500 H. influenzae isolates recovered from ear drainage fluid of Icelandic children diagnosed with otitis media. Our findings revealed that intra-host genomic variation involves many different genes encoding proteins with diverse functions. The data provide novel information bearing on the complexity of intra-host diversity and improve our understanding of H. influenzae strain fitness and molecular pathogenesis. This information could generate new hypotheses bearing on host-pathogen interactions and identify new therapeutic and vaccine targets.

A cluster investigation of Candida auris among hospitalized incarcerated patients

Objective

Investigate and mitigate a cluster of Candida auris cases among incarcerated patients in a maximum-security prison hospital utilizing contact tracing, screening, whole genome sequencing, and environmental sampling and decontamination.

Design

Outbreak investigation.

Setting

Inpatient prison hospital affiliated with an academic tertiary referral center.

Patients

Inmates of the Texas Department of Criminal Justice.

Methods

Epidemiologic and environmental investigations were conducted including contact tracing, point prevalence surveys, and environmental sampling. Whole genome sequencing was performed on positive patient isolates.

Results

Following a clinical case of C. auris fungemia, 344 patients underwent C. auris surveillance screening. Eight (2.3%) patients were identified with C. auris colonization. All patients were male. Our index patient was the only clinical case and death. Whole genome sequencing was performed on the nine patient isolates. All isolates were clade III (Africa) and clustered together with the largest SNP difference being 21. Environmental cultures from 7 of 61 rooms (11.5%) were positive following terminal disinfection with bleach. Sites nearest to the patient were most often positive including the hospital bed rails and bedside table. The transmission cluster was successfully mitigated within 60 days of identification.

Conclusions

Implementation of an aggressive surveillance and decontamination program resulted in mitigation of a C. auris transmission cluster among our incarcerated patients. This investigation provides valuable insight into C. auris transmission in the incarcerated population, which is not considered a classic high-risk population as well as the challenges faced to stop transmission in a facility that requires the use of shared patient environments.

Development of a Novel Method for the Clinical Visualization and Rapid Identification of Multidrug-Resistant Candida auris

Outbreaks of multidrug-resistant Candida auris infections, associated with a mortality rate of 30% to 60%, are of serious global concern. Candida auris demonstrates high transmission rates in hospital settings; however, its rapid and accurate identification using currently available clinical identification techniques is challenging. In this study, we developed a rapid and effective method for detecting C. auris based on recombinase-aided amplification combined with lateral flow strips (RAA-LFS). We also screened the appropriate reaction conditions. Furthermore, we investigated the specificity and sensitivity of the detection system and its ability to distinguish other fungal strains. Candida auris was accurately identified and differentiated from related species at 37°C within 15 min. The minimum detection limit was 1 CFU (or 10 fg/reaction) and was not affected by high concentrations of related species or host DNA. The simple and cost-efficient detection method established in this study exhibited high specificity and sensitivity and successfully detected C. auris in simulated clinical samples. Compared with other traditional detection methods, this method greatly reduces the time and cost of testing and is thus suitable for hospitals or clinics in remote underfunded areas for screening C. auris infection and colonization. IMPORTANCE Candida auris is a highly lethal, multidrug-resistant, invasive fungus. However, conventional methods of C. auris identification are time-consuming and laborious and have low sensitivity and high error rates. In this study, a new molecular diagnostic method based on recombinase-aided amplification combined with lateral flow strips (RAA-LFS) was developed, and accurate results could be obtained by catalyzing the reaction at body temperature for 15 min. This method can be used for rapid clinical detection of C. auris, consequently saving valuable treatment time for patients.

Genomic Characterizations of Clade III Lineage of Candida auris, California, USA

Candida auris is an emerging multidrug-resistant yeast. We describe an ongoing C. auris outbreak that began in October 2019 in Los Angeles, California, USA. We used genomic analysis to determine that isolates from 5 of 6 patients belonged to clade III; 4 isolates were closely related.

Human Infections Caused by Clonally Related African Clade (Clade III) Strains of Candida auris in the Greater Houston Region

Candida auris is a pathogen of considerable public health importance. It was first reported in 2009. Five clades, determined by genomic analysis and named by the distinct regions where they were initially identified, have been defined. We previously completed a draft genome sequence of an African clade (clade III) strain cultured from the urine of a patient hospitalized in the greater Houston metropolitan region (strain LOM). Although initially uncommon, reports of the African clade in the United States have grown to include a recent cluster in California. Here, we describe a second human C. auris infection in the Houston area. Whole-genome sequence analysis demonstrated the Houston patient isolates to be clonally related to one another but distantly related to other African clade organisms recovered in the United States or elsewhere. Infections in these patients were present on admission to the hospital and occurred several months apart. Taken together, the data demonstrate the emergence and persistence of a clonal C. auris population and highlights the importance of routine high-resolution genomic surveillance of emerging human pathogens in the clinical laboratory.