The use of genome sequencing to investigate an outbreak of hospital‐acquired mucormycosis in transplant patients

Abstract

Mucorales are environmental fungi, often found in soil and decaying matter. 1,2 Most infections are sporadic-and community-acquired, although there are reported cases of hospital acquisition. Healthcareassociated outbreaks have been linked to adhesive bandages, ostomy bags, wooden tongue depressors, environmental contamination, and invasive medical devices. 3 During a 6-month period, three cases of mucormycosis were identified in recipients of solid organ transplantation. The cases occurred within 3 weeks of the transplant surgery suggesting hospital acquisition. Following this cluster of cases, Infection Prevention and Control (IPC) conducted an outbreak investigation, which included the use of genome sequencing. Herein, we report these cases and demonstrate how genome sequencing can complement traditional IPC outbreak investigations of mucormycosis. Case patients were defined as solid organ transplant recipients from July to December 2017 who had phenotypically identified Rhizomucor species from clinical samples ≥14 days after hospital admission. 3-5 No case patients were discharged from hospital between the time of transplant to diagnosis of mucormycosis. Case-patient 1 is a 70-year-old male who underwent double lung transplantation for idiopathic pulmonary fibrosis. Bronchoscopies post-transplant day (PTD) 1 and 6 were negative for fungal growth. A bronchoalveolar lavage specimen from PTD 11 grew Rhizomucor species in fungal culture. He was started on intravenous liposomal and inhaled amphotericin B on PTD 14. Repeat bronchoscopy samples collected on PTD 26 showed fungal elements but fungal cultures were negative. On PTD 47, treatment was changed to isavuconazole because of kidney injury. His hypoxia improved, and he was repatriated to a community hospital for convalescence and ultimate discharge. Fourteen months after his transplant, he has not had a relapse. Case-patient 2 is a 64-year-old male who underwent double lung transplantation 5 months after case-patient 1 for chronic obstructive pulmonary disease. Following an episode of acute hypoxia, a bronchoscopy was done on PTD 13. Samples collected grew a fungus microscopically identified as Rhizomucor species, although this result was not noted immediately by clinicians. On PTD 33, the patient underwent gastroscopy for an upper gastrointestinal bleed which revealed a gastric ulcer. Biopsies from a repeat gastroscopy showed fungal elements consistent with mucormycosis. Repeat bronchoscopies on PTD 41 and 49 again isolated a fungus microscopically identified as Rhizomucor species. Cranial imaging, to assess altered AbstractWe report three cases of hospital-acquired mucormycosis in heart and lung transplant patients over a 6-month period. Traditional epidemiological investigation tools were used to look for a common link between patients to explain the outbreak.

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

“…In the French study mentioned above, burns patients were infected with strains that clustered within four phylogenomic clades; besides the two patients who shared a common strain (defined by percentage nucleotide differences), patients were infected with genetically diverse isolates. In a study from Edmonton, Rhizomucor pusillus that infected a lung transplant and a heart transplant recipient over 6 months were found to be phylogenomically distinct by core genome SNP analysis [26]. A third study included Apophysomyces trapeziformis isolates from patients with community-acquired mucormycosis following a tornado in Joplin, MO [24, 27].…”

“…Emerging data suggest that these approaches do not provide necessary resolution for discriminating between strains of a particular species, or adequately reflect genome-scale differences in phylogeny [23, 24]. Phylogenetic analysis of whole genome sequence (WGS) data has been applied infrequently in studies of mucormycosis [24–26]. A major challenge for genomic epidemiological studies is that Mucorales phylogeny is poorly understood.…”

Epidemiology, Modern Diagnostics, and the Management of Mucorales Infections

“…Investigations should involve robust hypothesis-testing, the detection of potential healthcare sources, and consideration of environmental testing [ 125 , 126 ]. Molecular methods, including WGS, have emerged to characterise the genomic epidemiology of these outbreaks (see Section 4.8 ) [ 128 , 129 , 130 , 131 ]. “Pseudo-outbreaks” of Mucorales have also been described, and it is important to differentiate true noscomial clusters from environmental contamination or issues resulting from changes in surveillance or testing.…”

“…Earlier investigations of mucormycosis case clusters have detailed epidemiological linkages without data on the genetic relatedness between strains, partly as there are no established genotyping makers for Mucorales [ 105 , 132 ]. The advent of WGS approaches for phylogenetic analyses has yielded new information, as well as challenges in delineating genetic diversity within different species [ 128 , 129 , 130 , 131 , 141 , 223 ]. Firstly, a WGS analysis of Mucorales is problematic due to the large size of their genomes (45.3 Mbp for R. arrhizus ), as well as the presence of whole-genome duplication events [ 221 ].…”

The Canadian Fungal Research Network: current challenges and future opportunities

“…Currently, provincial and federal public health labs are not resourced as repositories; however, they accommodate requests from researchers as much as possible. With respect to fungi, the National Microbiology Laboratory (NML), run by the Public Health Agency of Canada, interfaces with provincial health authorities and has recently increased its capacity for identification and analysis of clinical fungal isolates (Marek et al 2019). However, since it is not a repository, there may be impediments to access strains, which slows or even halts important research taking place outside of government labs.…”