Notes from the Field: Probable Mucormycosis Among Adult Solid Organ Transplant Recipients at an Acute Care Hospital - Pennsylvania, 2014-2015

Epidemiology of COVID-19-Associated Mucormycosis

Purpose of the Review

To describe the epidemiology and risk factors for Coronavirus disease-19 (COVID-19)-associated mucormycosis (CAM) based on current published literature.

Recent Findings

COVID-19 is associated with an increased risk of secondary infections. Mucormycosis is an uncommon invasive fungal infection that typically affects people with immunocompromising conditions and uncontrolled diabetes. Treatment of mucormycosis is challenging and is associated with high mortality even with standard care. During the second wave of the COVID 19 pandemic, an abnormally high number of CAM cases were seen particularly in India. Several case series have attempted to describe the risk factors for CAM.

Summary

A common risk profile identified for CAM includes uncontrolled diabetes and treatment with steroids. COVID-19-induced immune dysregulation as well as some unique pandemic specific risk factors may have played a role.

Perceptions, knowledge, and communication preferences about indoor mold and its health implications among persons affected by Hurricane Harvey: a focus group analysis

Background

Among people affected by Hurricane Harvey, we assessed experiences and perceptions (e.g., knowledge, attitudes, and practices) regarding mold and its impact on health and elicited participants’ opinions about how to improve public health messaging about indoor mold after a large flooding event.

Methods

Houston Health Department conducted four focus groups with 31 Houston metropolitan area residents during January to March 2020, using a semi-structured discussion guide and federal communication materials about indoor mold. Drawing from a theoretical framework analysis, transcripts were grouped into relevant themes using inductive and deductive coding.

Results

Hurricane Harvey had a large impact on participants’ living standards, and widespread financial barriers to remediation led to long-term mold exposure for many participants. Knowledge about mold’s impact on health and proper mold clean-up practices varied, and clean-up behaviors did not commonly align with federal guidance. Participants generally preferred traditional forms of outreach, such as in-person, radio, and television announcements, to communicate public health messaging.

Conclusions

More strategic dissemination of expanded public health educational materials about proper mold clean-up practices and the health risks of mold exposure following flooding events is needed.

Nosocomial Fungal Infections: Epidemiology, Infection Control, and Prevention

Invasive fungal infections are an important cause of morbidity and mortality in hospitalized patients and in the immunocompromised population. This article reviews the current epidemiology of nosocomial fungal infections in adult patients, with an emphasis on invasive candidiasis (IC) and invasive aspergillosis (IA). Included are descriptions of nosocomial infections caused by Candida auris, an emerging pathogen, and IC- and IA-associated with coronavirus disease 2019. The characteristics and availability of newer nonculture-based tests for identification of nosocomial fungal pathogens are discussed. Recently published recommendations and guidelines for the control and prevention of these nosocomial fungal infections are summarized.

COVID-19 associated Mucormycosis (CAM): risk factors and mechanisms of disease

The severe surge of COVID-19 cases in the Indian subcontinent in early 2021 was marked by an unusually high number of cases of COVID-19 associated mucormycosis (CAM) reported during this period. This is significantly higher than predicted based on available data about prevalence or risk factors for this condition. This may be from an unusual alignment of multiple risk factors for this condition. There is high background prevalence of mucormycosis in India probably from high prevalence of risk factors, including undiagnosed or poorly controlled diabetes. COVID-19 induced immune dysregulation, and immune suppression from steroid therapy increase the risk. The role of environmental exposure is unclear. System factors like lack of access to healthcare during a pandemic may result in delayed diagnosis or suboptimal management with potentially poor outcomes. This is a review of currently identified risk factors and pathogenesis of CAM in a pandemic surge.

Surveillance practices and air-sampling strategies to address healthcare-associated invasive mold infections in Society for Healthcare Epidemiology of America (SHEA) Research Network hospitals-United States, 2020

With this survey, we investigated healthcare-associated invasive mold infection (HA-IMI) surveillance and air sampling practices in US acute-care hospitals. More than half of surveyed facilities performed HA-IMI surveillance and air sampling. HA-IMI surveillance was more commonly performed in academic versus nonacademic facilities. HA-IMI case definitions and sampling strategies varied widely among respondents.

Patient notification about suspected hospital-associated outbreaks of invasive mold infections: Considerations for public health and hospital personnel

A common type of fungal disease investigation involves hospital-associated clusters of invasive mold infections (IMIs), which typically occur among immunocompromised patients. Responding to IMI clusters can be challenging for public health and hospital personnel for several reasons such as difficulty of confirming the existence of an outbreak, difficulty of determining source. Although many resources exist to guide patient notification about healthcare incidents (eg, bloodborne exposures, disease outbreaks), IMI clusters involve special considerations related to the complex diseases, uncertain exposures, and differential benefits and risks of notification. Early, nuanced communication about hospital-associated IMI clusters is almost always the best course of action to help reduce risks to patients' health and foster trust between patients and hospitals.

Genetic diversity of clinical and environmental Mucorales isolates obtained from an investigation of mucormycosis cases among solid organ transplant recipients

Mucormycoses are invasive infections by Rhizopus species and other Mucorales. Over 10 months, four solid organ transplant (SOT) recipients at our centre developed mucormycosis due to Rhizopus microsporus (n=2), R. arrhizus (n=1) or Lichtheimia corymbifera (n=1), at a median 31.5 days (range: 13-34) post-admission. We performed whole genome sequencing (WGS) on 72 Mucorales isolates (45 R. arrhizus, 19 R. delemar, six R. microsporus, two Lichtheimia species) from these patients, from five patients with community-acquired mucormycosis, and from hospital and regional environments. Isolates were compared by core protein phylogeny and global genomic features, including genome size, guanine-cytosine percentages, shared protein families and paralogue expansions. Patient isolates fell into six core phylogenetic lineages (clades). Phylogenetic and genomic similarities of R. microsporus isolates recovered 7 months apart from two SOT recipients in adjoining hospitals suggested a potential common source exposure. However, isolates from other patients and environmental sites had unique genomes. Many isolates that were indistinguishable by core phylogeny were distinct by one or more global genomic comparisons. Certain clades were recovered throughout the study period, whereas others were found at particular time points. In conclusion, mucormycosis cases could not be genetically linked to a definitive environmental source. Comprehensive genomic analyses eliminated false associations between Mucorales isolates that would have been assigned using core phylogenetic or less extensive genomic comparisons. The genomic diversity of Mucorales mandates that multiple isolates from individual patients and environmental sites undergo WGS during epidemiological investigations. However, exhaustive surveillance of fungal populations in a hospital and surrounding community is probably infeasible.

A Guide to Investigating Suspected Outbreaks of Mucormycosis in Healthcare

This report serves as a guide for investigating mucormycosis infections in healthcare. We describe lessons learned from previous outbreaks and offer methods and tools that can aid in these investigations. We also offer suggestions for conducting environmental assessments, implementing infection control measures, and initiating surveillance to ensure that interventions were effective. While not all investigations of mucormycosis infections will identify a single source, all can potentially lead to improvements in infection control.

CRISPR-Cas9 induces point mutation in the mucormycosis fungus Rhizopus delemar

Rhizopus delemar causes devastating mucormycosis in immunodeficient individuals. Despite its medical importance, R. delemar remains understudied largely due to the lack of available genetic markers, the presence of multiple gene copies due to genome duplication, and mitotically unstable transformants resulting from conventional and limited genetic approaches. The clustered regularly interspaced short palindromic repeat (CRISPR)-associated nuclease 9 (Cas9) system induces efficient homologous and non-homologous break points and generates individual and multiple mutant alleles without requiring selective marker genes in a wide variety of organisms including fungi. Here, we have successfully adapted this technology for inducing gene-specific single nucleotide (nt) deletions in two clinical strains of R. delemar: FGSC-9543 and CDC-8219. For comparative reasons, we first screened for spontaneous uracil auxotrophic mutants resistant to 5-fluoroorotic acid (5-FOA) and obtained one substitution (f1) mutationin the FGSC-9543 strain and one deletion (f2) mutation in the CDC-8219 strain. The f2 mutant was then successfully complemented with a pyrF-dpl200 marker gene. We then introduced a vector pmCas9:tRNA-gRNA that expresses both Cas9 endonuclease and pyrF-specific gRNA into FGSC-9543 and CDC-8219 strains and obtained 34 and 42 5-FOA resistant isolates, respectively. Candidate transformants were successively transferred eight times by propagating hyphal tips prior to genotype characterization. Sequencing of the amplified pyrF allele in all transformants tested revealed a single nucleotide (nt) deletion at the 4th nucleotide before the protospacer adjacent motif (PAM) sequence, which is consistent with CRISPR-Cas9 induced gene mutation through non-homologous end joining (NHEJ). Our study provides a new research tool for investigating molecular pathogenesis mechanisms of R. delemar while also highlighting the utilization of CRISPR-Cas9 technology for generating specific mutants of Mucorales fungi.

Comparative genome-wide analysis of extracellular small RNAs from the mucormycosis pathogen Rhizopus delemar

Rhizopus delemar is an emerging fungal pathogen causing devastating mucormycosis in immunocompromised individuals. The organism remains understudied and there are urgent needs for new methods of rapid disease diagnosis for timely therapy. Extracellular vesicles with encapsulated RNAs have recently been discovered to have great potential applications for disease diagnoses and treatments. To explore the utilization of ex-RNA in studies of mucormycosis, we have performed RNA-Seq of ex-sRNAs from two clinical strains of R. delemar. Approximately 3.3 and 3.2 million clean reads were obtained from FGSC-9543 and CDC-8219 strains, respectively. The median sequence length of the sRNAs was 22 nts, with a minimum of 18 and a maximum of 30 nts. Further annotation identified 560 and 526 miRNAs from FGSC-9543 and CDC-8219 strains, respectively. miRNA target prediction and analysis of GO and KEGG pathways have revealed that the regulation of metabolism, secondary metabolite biosynthesis, and two-component system signaling are important during growth. We have also validated RNA-Seq by qRT-PCR and Northern blotting analysis of randomly selected miRNAs. Our results show that R. delemar has a rich reservoir of secreted ex-sRNAs and our studies could facilitate the development of improved diagnostic methods as well as elucidating virulence mechanisms for R. delemar infection.

Emerging issues, challenges, and changing epidemiology of fungal disease outbreaks

Several high-profile outbreaks have drawn attention to invasive fungal infections (IFIs) as an increasingly important public health problem. IFI outbreaks are caused by many different fungal pathogens and are associated with numerous settings and sources. In the community, IFI outbreaks often occur among people without predisposing medical conditions and are frequently precipitated by environmental disruption. Health-care-associated IFI outbreaks have been linked to suboptimal hospital environmental conditions, transmission via health-care workers' hands, contaminated medical products, and transplantation of infected organs. Outbreak investigations provide important insights into the epidemiology of IFIs, uncover risk factors for infection, and identify opportunities for preventing similar events in the future. Well recognised challenges with IFI outbreak recognition, response, and prevention include the need for improved rapid diagnostic methods, the absence of routine surveillance for most IFIs, adherence to infection control practices, and health-care provider awareness. Additionally, IFI outbreak investigations have revealed several emerging issues, including new populations at risk because of travel or relocation, occupation, or immunosuppression; fungal pathogens appearing in geographical areas in which they have not been previously recognised; and contaminated compounded medications. This report highlights notable IFI outbreaks in the past decade, with an emphasis on these emerging challenges in the USA.

Trends in Hospitalizations Related to Invasive Aspergillosis and Mucormycosis in the United States, 2000-2013

BACKGROUND

Invasive aspergillosis (IA) and mucormycosis contribute to substantial mortality, especially among immunocompromised persons, including those with hematopoietic stem cell transplant (HSCT), hematologic malignancy (HM), and solid organ transplant (SOT).

METHODS

Using International Classification of Diseases, Ninth Revision codes available in the National Inpatient Sample, a hospital discharge database, we estimated IA-related hospitalizations (IA-RH), mucormycosis-RH (M-RH), HSCT-RH, HM-RH, and SOT-RH during 2000-2013. United States census data were used to calculate overall M-RH and IA-RH rates and present trends; estimated annual numbers of HSCT-RH, HM-RH, and SOT-RH served as denominators to calculate M-RH and IA-RH rates occurring with these conditions. Weighted least-squares technique was used to test for linear trends and calculate average annual percentage change (APC).

RESULTS

There were an estimated 169 110 IA-RH and 9966 M-RH during 2000-2013. Overall, IA-RH and M-RH rates per million persons rose from 32.8 to 46.0 (APC = +2.9; P < .001) and 1.7 to 3.4 (APC = +5.2%; P < .001), respectively, from 2000 to 2013. Among HSCT-RH, there was no significant change in M-RH rate, but a significant decline occurred in IA-RH rate (APC = -4.6%; P = .004). Among HM-RH, the rate of M-RH increased (APC = +7.0%; P < .001), but the IA-RH rate did not change significantly (APC = +1.2%; P = .073). Among SOT-RH, M-RH (APC = +6.3%; P = .038) and IA-RH rates (APC = +4.1%; P < .001) both increased.

CONCLUSIONS

Overall IA-RH and M-RH rates increased during 2000-2013, with a doubling of M-RH. Mucormycosis-related hospitalization occurring in conjunction with certain comorbidities increased, whereas IA-RH rates among patients with the comorbidities, decreased, remained stable, or increased to a lesser extent than M-RH.