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Sa'diyah W, Zhao YJ, Chiba Y, Kondo H, Suzuki N, Ban S, Yaguchi T, Urayama SI, Hagiwara D. New lineages of RNA viruses from clinical isolates of Rhizopus microsporus revealed by fragmented and primer-ligated dsRNA sequencing (FLDS) analysis. mSphere 2024; 9:e0034524. [PMID: 39072615 PMCID: PMC11351042 DOI: 10.1128/msphere.00345-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 06/27/2024] [Indexed: 07/30/2024] Open
Abstract
Rhizopus microsporus is a species in the order Mucorales that is known to cause mucormycosis, but it is poorly understood as a host of viruses. Here, we examined 25 clinical strains of R. microsporus for viral infection with a conventional double-stranded RNA (dsRNA) assay using agarose gel electrophoresis (AGE) and the recently established fragmented and primer-ligated dsRNA sequencing (FLDS) protocol. By AGE, five virus-infected strains were detected. Then, full-length genomic sequences of 12 novel RNA viruses were revealed by FLDS, which were related to the families Mitoviridae, Narnaviridae, and Endornaviridae, ill-defined groups of single-stranded RNA (ssRNA) viruses with similarity to the established families Virgaviridae and Phasmaviridae, and the proposed family "Ambiguiviridae." All the characterized viruses, except a potential phasmavirid with a negative-sense RNA genome, had positive-sense RNA genomes. One virus belonged to a previously established species within the family Mitoviridae, whereas the other 11 viruses represented new species or even new genera. These results show that the fungal pathogen R. microsporus harbors diverse RNA viruses and extend our understanding of the diversity of RNA viruses in the fungal order Mucorales, division Mucoromycota. Identifying RNA viruses from clinical isolates of R. microsporus may expand the repertoire of natural therapeutic agents for mucormycosis in the future.IMPORTANCEThe diversity of mycoviruses in fungal hosts in the division Mucoromycota has been underestimated, mainly within the species Rhizopus microsporus. Only five positive-sense RNA genomes had previously been discovered in this species. Because current sequencing methods poorly complete the termini of genomes, we used fragmented and primer-ligated double-stranded RNA sequencing to acquire the full-length genomes. Eleven novel mycoviruses were detected in this study, including the first negative-sense RNA genome reported in R. microsporus. Our findings extend the understanding of the viral diversity in clinical strains of Mucoromycota, may provide insights into the pathogenesis and ecology of this fungus, and may offer therapeutic options.
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Grants
- Institute for Fermentation, Osaka (IFO)
- 22KJ0440 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 22H04879 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 21K18217 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
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Affiliation(s)
- Wasiatus Sa'diyah
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), University of Tsukuba, Ibaraki, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Yan-Jie Zhao
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), University of Tsukuba, Ibaraki, Japan
| | - Yuto Chiba
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), University of Tsukuba, Ibaraki, Japan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Sayaka Ban
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Takashi Yaguchi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Syun-ichi Urayama
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), University of Tsukuba, Ibaraki, Japan
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan
| | - Daisuke Hagiwara
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), University of Tsukuba, Ibaraki, Japan
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan
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Lax C, Nicolás FE, Navarro E, Garre V. Molecular mechanisms that govern infection and antifungal resistance in Mucorales. Microbiol Mol Biol Rev 2024; 88:e0018822. [PMID: 38445820 PMCID: PMC10966947 DOI: 10.1128/mmbr.00188-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Abstract
SUMMARYThe World Health Organization has established a fungal priority pathogens list that includes species critical or highly important to human health. Among them is the order Mucorales, a fungal group comprising at least 39 species responsible for the life-threatening infection known as mucormycosis. Despite the continuous rise in cases and the poor prognosis due to innate resistance to most antifungal drugs used in the clinic, Mucorales has received limited attention, partly because of the difficulties in performing genetic manipulations. The COVID-19 pandemic has further escalated cases, with some patients experiencing the COVID-19-associated mucormycosis, highlighting the urgent need to increase knowledge about these fungi. This review addresses significant challenges in treating the disease, including delayed and poor diagnosis, the lack of accurate global incidence estimation, and the limited treatment options. Furthermore, it focuses on the most recent discoveries regarding the mechanisms and genes involved in the development of the disease, antifungal resistance, and the host defense response. Substantial advancements have been made in identifying key fungal genes responsible for invasion and tissue damage, host receptors exploited by the fungus to invade tissues, and mechanisms of antifungal resistance. This knowledge is expected to pave the way for the development of new antifungals to combat mucormycosis. In addition, we anticipate significant progress in characterizing Mucorales biology, particularly the mechanisms involved in pathogenesis and antifungal resistance, with the possibilities offered by CRISPR-Cas9 technology for genetic manipulation of the previously intractable Mucorales species.
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Affiliation(s)
- Carlos Lax
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Francisco E. Nicolás
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Eusebio Navarro
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Victoriano Garre
- Departamento de Genética y Microbiología, Facultad de Biología, Universidad de Murcia, Murcia, Spain
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Michael JS, Venkatesan M, Ninan MM, Solaimalai D, Sumanth LJ, Varghese L, Kurien R, Varghese RP, C GPD. Whole genome analysis of Rhizopus species causing rhino-cerebral mucormycosis during the COVID-19 pandemic. Front Cell Infect Microbiol 2023; 13:1251456. [PMID: 38029246 PMCID: PMC10644343 DOI: 10.3389/fcimb.2023.1251456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/11/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Mucormycosis is an acute invasive fungal disease (IFD) seen mainly in immunocompromised hosts and in patients with uncontrolled diabetes. The incidence of mucormycosis increased exponentially in India during the SARS-CoV-2 (henceforth COVID-19) pandemic. Since there was a lack of data on molecular epidemiology of Mucorales causing IFD during and after the COVID-19 pandemic, whole genome analysis of the Rhizopus spp. isolated during this period was studied along with the detection of mutations that are associated with antifungal drug resistance. Materials and methods A total of 50 isolates of Rhizopus spp. were included in this prospective study, which included 28 from patients with active COVID-19 disease, 9 from patients during the recovery phase, and 13 isolates from COVID-19-negative patients. Whole genome sequencing (WGS) was performed for the isolates, and the de novo assembly was done with the Spades assembler. Species identification was done by extracting the ITS gene sequence from each isolate followed by searching Nucleotide BLAST. The phylogenetic trees were made with extracted ITS gene sequences and 12 eukaryotic core marker gene sequences, respectively, to assess the genetic distance between our isolates. Mutations associated with intrinsic drug resistance to fluconazole and voriconazole were analyzed. Results All 50 patients presented to the hospital with acute fungal rhinosinusitis. These patients had a mean HbA1c of 11.2%, and a serum ferritin of 546.8 ng/mL. Twenty-five patients had received steroids. By WGS analysis, 62% of the Rhizopus species were identified as R. delemar. Bayesian analysis of population structure (BAPS) clustering categorized these isolates into five different groups, of which 28 belong to group 3, 9 to group 5, and 8 to group 1. Mutational analysis revealed that in the CYP51A gene, 50% of our isolates had frameshift mutations along with 7 synonymous mutations and 46% had only synonymous mutations, whereas in the CYP51B gene, 68% had only synonymous mutations and 26% did not have any mutations. Conclusion WGS analysis of Mucorales identified during and after the COVID-19 pandemic gives insight into the molecular epidemiology of these isolates in our community and establishes newer mechanisms for intrinsic azole resistance.
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Affiliation(s)
- Joy Sarojini Michael
- Department of Clinical Microbiology, Christian Medical College, Vellore, Vellore, Tamil Nadu, India
| | - Manigandan Venkatesan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Vellore, Tamil Nadu, India
| | - Marilyn Mary Ninan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Vellore, Tamil Nadu, India
| | - Dhanalakshmi Solaimalai
- Department of Clinical Microbiology, Christian Medical College, Vellore, Vellore, Tamil Nadu, India
| | - Lydia Jennifer Sumanth
- Department of Clinical Microbiology, Christian Medical College, Vellore, Vellore, Tamil Nadu, India
| | - Lalee Varghese
- Department of Otorhinolaryngology, Christian Medical College, Vellore, Vellore, India
| | - Regi Kurien
- Department of Otorhinolaryngology, Christian Medical College, Vellore, Vellore, India
| | - Rinku Polachirakkal Varghese
- Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology (VIT) University, Vellore, Tamil Nadu, India
| | - George Priya Doss C
- Department of Integrative Biology, School of Biosciences and Technology, Vellore Institute of Technology (VIT) University, Vellore, Tamil Nadu, India
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Li Z, Shi CH, Huang Y, Wang HC, Li WH, Cai LT. Phenotypic analysis and genome sequence of Rhizopus oryzae strain Y5, the causal agent of tobacco pole rot. Front Microbiol 2023; 13:1031023. [PMID: 36687611 PMCID: PMC9846616 DOI: 10.3389/fmicb.2022.1031023] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/07/2022] [Indexed: 01/06/2023] Open
Abstract
Rhizopus oryzae is a destructive pathogen that frequently causes tobacco pole rot in curing chambers. Phenotypic characterization of the pathogen was conducted to provide basic biological and pathological information using Biolog Phenotype MicroArray (PM). In addition, the Y5 strain of R. oryzae was sequenced using Illumina HiSeq and Pacific Biosciences (PacBio) technologies. Using PM plates 1-8, 758 growth conditions were tested. Results indicated that R. oryzae could metabolize 54.21% of tested carbon sources, 86.84% of nitrogen sources, 100% of sulfur sources, and 98.31% of phosphorus sources. About 37 carbon compounds, including D-xylose, N-acetyl-D-glucosamine, D-sorbitol, β-methyl-D-glucoside, D-galactose, L-arabinose, and D-cellobiose, significantly supported the growth of the pathogen. PM 3 indicated the active nitrogen sources, including Gly-Asn, Ala-Asp., Ala-Gln, and uric acid. PM 6-8 showed 285 different nitrogen pathways, indicating that different combinations of different amino acids support the growth of the pathogen. Genome sequencing results showed that the R. oryzae Y5 strain had raw data assembled into 2,271 Mbp with an N50 value of 10,563 bp. A genome sequence of 50.3 Mb was polished and assembled into 53 contigs with an N50 length of 1,785,794 bp, maximum contig length of 3,223,184 bp, and a sum of contig lengths of 51,182,778 bp. A total of 12,680 protein-coding genes were predicted using the Nonredundant, Gene Ontology, Clusters of Orthologous Groups, Kyoto Encyclopedia of Genes and Genomes, and SWISS-PROT databases. The genome sequence and annotation resources of R. oryzae provided a reference for studying its biological characteristics, trait-specific genes, pathogen-host interaction, pathogen evolution, and population genetic diversity. The phenomics and genome of R. oryzae will provide insights into microfungal biology, pathogen evolution, and the genetic diversity of epidemics.
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Affiliation(s)
- Zhen Li
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, China,Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, Guizhou, China
| | - Cai-hua Shi
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, China,School of Food Science and Technology & School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang, China,*Correspondence: Cai-hua Shi,
| | - Yang Huang
- China Tobacco Sichuan Industrial Corporation Technical Centre, Chengdu, China
| | - Han-cheng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, Guizhou, China,Han-cheng Wang,
| | - Wen-hong Li
- Guizhou Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Liu-ti Cai
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, Guizhou, China
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Cheng S, Fleres G, Chen L, Liu G, Hao B, Newbrough A, Driscoll E, Shields RK, Squires KM, Chu TY, Kreiswirth BN, Nguyen MH, Clancy CJ. Within-Host Genotypic and Phenotypic Diversity of Contemporaneous Carbapenem-Resistant Klebsiella pneumoniae from Blood Cultures of Patients with Bacteremia. mBio 2022; 13:e0290622. [PMID: 36445082 PMCID: PMC9765435 DOI: 10.1128/mbio.02906-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 12/02/2022] Open
Abstract
It is unknown whether bacterial bloodstream infections (BSIs) are commonly caused by single organisms or mixed microbial populations. We hypothesized that contemporaneous carbapenem-resistant Klebsiella pneumoniae (CRKP) strains from blood cultures of individual patients are genetically and phenotypically distinct. We determined short-read whole-genome sequences of 10 sequence type 258 (ST258) CRKP strains from blood cultures in each of 6 patients (Illumina HiSeq). Strains clustered by patient by core genome and pan-genome phylogeny. In 5 patients, there was within-host strain diversity by gene mutations, presence/absence of antibiotic resistance or virulence genes, and/or plasmid content. Accessory gene phylogeny revealed strain diversity in all 6 patients. Strains from 3 patients underwent long-read sequencing for genome completion (Oxford Nanopore) and phenotypic testing. Genetically distinct strains within individuals exhibited significant differences in carbapenem and other antibiotic responses, capsular polysaccharide (CPS) production, mucoviscosity, and/or serum killing. In 2 patients, strains differed significantly in virulence during mouse BSIs. Genetic or phenotypic diversity was not observed among strains recovered from blood culture bottles seeded with index strains from the 3 patients and incubated in vitro at 37°C. In conclusion, we identified genotypic and phenotypic variant ST258 CRKP strains from blood cultures of individual patients with BSIs, which were not detected by the clinical laboratory or in seeded blood cultures. The data suggest a new paradigm of CRKP population diversity during BSIs, at least in some patients. If validated for BSIs caused by other bacteria, within-host microbial diversity may have implications for medical, microbiology, and infection prevention practices and for understanding antibiotic resistance and pathogenesis. IMPORTANCE The long-standing paradigm for pathogenesis of bacteremia is that, in most cases, a single organism passes through a bottleneck and establishes itself in the bloodstream (single-organism hypothesis). In keeping with this paradigm, standard practice in processing positive microbiologic cultures is to test single bacterial strains from morphologically distinct colonies. This study is the first genome-wide analysis of within-host diversity of Klebsiella pneumoniae strains recovered from individual patients with bloodstream infections (BSIs). Our finding that positive blood cultures comprised genetically and phenotypically heterogeneous carbapenem-resistant K. pneumoniae strains challenges the single-organism hypothesis and suggests that at least some BSIs are caused by mixed bacterial populations that are unrecognized by the clinical laboratory. The data support a model of pathogenesis in which pressures in vivo select for strain variants with particular antibiotic resistance or virulence attributes and raise questions about laboratory protocols and treatment decisions directed against single strains.
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Affiliation(s)
- Shaoji Cheng
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - Guojun Liu
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Binghua Hao
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | | | | | - Ryan K. Shields
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | | | - Ting-yu Chu
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - Barry N. Kreiswirth
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, New Jersey, USA
| | - M. Hong Nguyen
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Cornelius J. Clancy
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
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6
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Jordan A, James AE, Gold JAW, Wu K, Glowicz J, Wolfe F, Vyas K, Litvintseva A, Gade L, Liverett H, Alverson M, Burgess M, Wilson A, Li R, Benowitz I, Gulley T, Patil N, Chakravorty R, Chu W, Kothari A, Jackson BR, Garner K, Toda M. Investigation of a Prolonged and Large Outbreak of Healthcare-Associated Mucormycosis Cases in an Acute Care Hospital-Arkansas, June 2019-May 2021. Open Forum Infect Dis 2022; 9:ofac510. [PMID: 36320193 PMCID: PMC9605704 DOI: 10.1093/ofid/ofac510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022] Open
Abstract
Background Outbreaks of healthcare-associated mucormycosis (HCM), a life-threatening fungal infection, have been attributed to multiple sources, including contaminated healthcare linens. In 2020, staff at Hospital A in Arkansas alerted public health officials of a potential HCM outbreak. Methods We collected data on patients at Hospital A who had invasive mucormycosis during January 2017-June 2021 and calculated annual incidence of HCM (defined as mucormycosis diagnosed within ≥7 days after hospital admission). We performed targeted environmental assessments, including linen sampling at the hospital, to identify potential sources of infection. Results During the outbreak period (June 2019-June 2021), 16 patients had HCM; clinical features were similar between HCM patients and non-HCM patients. Hospital-wide HCM incidence (per 100 000 patient-days) increased from 0 in 2018 to 3 in 2019 and 6 in 2020. For the 16 HCM patients, the most common underlying medical conditions were hematologic malignancy (56%) and recent traumatic injury (38%); 38% of HCM patients died in-hospital. Healthcare-associated mucormycosis cases were not epidemiologically linked by common procedures, products, units, or rooms. At Hospital A and its contracted offsite laundry provider, suboptimal handling of laundered linens and inadequate environmental controls to prevent mucormycete contamination were observed. We detected Rhizopus on 9 (9%) of 98 linens sampled at the hospital, including on linens that had just arrived from the laundry facility. Conclusions We describe the largest, single-center, HCM outbreak reported to date. Our findings underscore the importance of hospital-based monitoring for HCM and increased attention to the safe handling of laundered linens.
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Affiliation(s)
- Alexander Jordan
- Correspondence: Alexander Jordan, MPH, 1600 Clifton Road NE, Atlanta, GA 30329, USA ()
| | - Allison E James
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA,Arkansas Department of Health, Little Rock, Arkansas, USA
| | - Jeremy A W Gold
- Mycotic Diseases Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Karen Wu
- Mycotic Diseases Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Janet Glowicz
- Prevention and Response Branch, Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Frankie Wolfe
- Medical Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Keyur Vyas
- Medical Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Anastasia Litvintseva
- Mycotic Diseases Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lalitha Gade
- Mycotic Diseases Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Hazel Liverett
- Medical Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Mary Alverson
- Medical Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Mary Burgess
- Medical Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Amy Wilson
- Medical Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Ruoran Li
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA,Prevention and Response Branch, Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Isaac Benowitz
- Prevention and Response Branch, Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Trent Gulley
- Arkansas Department of Health, Little Rock, Arkansas, USA
| | - Naveen Patil
- Arkansas Department of Health, Little Rock, Arkansas, USA
| | | | - Winston Chu
- Arkansas Department of Health, Little Rock, Arkansas, USA
| | - Atul Kothari
- Arkansas Department of Health, Little Rock, Arkansas, USA
| | - Brendan R Jackson
- Mycotic Diseases Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kelley Garner
- Arkansas Department of Health, Little Rock, Arkansas, USA
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7
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Zhao H, Nie Y, Jiang Y, Wang S, Zhang TY, Liu XY. Comparative Genomics of Mortierellaceae Provides Insights into Lipid Metabolism: Two Novel Types of Fatty Acid Synthase. J Fungi (Basel) 2022; 8:jof8090891. [PMID: 36135616 PMCID: PMC9503022 DOI: 10.3390/jof8090891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/16/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Fungal species in the family Mortierellaceae are important for their remarkable capability to synthesize large amounts of polyunsaturated fatty acids, especially arachidonic acid (ARA). Although many genomes have been published, the quality of these data is not satisfactory, resulting in an incomplete understanding of the lipid pathway in Mortierellaceae. We provide herein two novel and high-quality genomes with 55.32% of syntenic gene pairs for Mortierella alpina CGMCC 20262 and M. schmuckeri CGMCC 20261, spanning 28 scaffolds of 40.22 Mb and 25 scaffolds of 49.24 Mb, respectively. The relative smaller genome for the former is due to fewer protein-coding gene models (11,761 vs. 13,051). The former yields 45.57% of ARA in total fatty acids, while the latter 6.95%. The accumulation of ARA is speculated to be associated with delta-5 desaturase (Delta5) and elongation of very long chain fatty acids protein 3 (ELOVL3). A further genomic comparison of 19 strains in 10 species in three genera in the Mortierellaceae reveals three types of fatty acid synthase (FAS), two of which are new to science. The most common type I exists in 16 strains of eight species of three genera, and was discovered previously and consists of a single unit with eight active sites. The newly revealed type II exists only in M. antarctica KOD 1030 where the unit is separated into two subunits α and β comprised of three and five active sites, respectively. Another newly revealed type III exists in M. alpina AD071 and Dissophora globulifera REB-010B, similar to type II but different in having one more acyl carrier protein domain in the α subunit. This study provides novel insights into the enzymes related to the lipid metabolism, especially the ARA-related Delta5, ELOVL3, and FAS, laying a foundation for genetic engineering of Mortierellaceae to modulate yield in polyunsaturated fatty acids.
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Affiliation(s)
- Heng Zhao
- College of Life Sciences, Shandong Normal University, Jinan 250358, China
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Yong Nie
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma’anshan 243002, China
| | - Yang Jiang
- College of Life Sciences, Shandong Normal University, Jinan 250358, China
| | - Shi Wang
- College of Life Sciences, Shandong Normal University, Jinan 250358, China
| | - Tian-Yu Zhang
- College of Life Sciences, Shandong Normal University, Jinan 250358, China
| | - Xiao-Yong Liu
- College of Life Sciences, Shandong Normal University, Jinan 250358, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence:
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8
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Garre V. Recent Advances and Future Directions in the Understanding of Mucormycosis. Front Cell Infect Microbiol 2022; 12:850581. [PMID: 35281441 PMCID: PMC8907824 DOI: 10.3389/fcimb.2022.850581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
Mucormycosis is an emerging infection caused by fungi of the order Mucorales that has recently gained public relevance due to the high incidence among COVID-19 patients in some countries. The reduced knowledge about Mucorales pathogenesis is due, in large part, to the historically low interest for these fungi fostered by their reluctance to be genetically manipulated. The recent introduction of more tractable genetic models together with an increasing number of available whole genome sequences and genomic analyses have improved our understanding of Mucorales biology and mucormycosis in the last ten years. This review summarizes the most significant advances in diagnosis, understanding of the innate and acquired resistance to antifungals, identification of new virulence factors and molecular mechanisms involved in the infection. The increased awareness about the disease and the recent successful genetic manipulation of previous intractable fungal models using CRISPR-Cas9 technology are expected to fuel the characterization of Mucorales pathogenesis, facilitating the development of effective treatments to fight this deadly infection.
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Affiliation(s)
- Victoriano Garre
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia, Spain
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9
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Sundermann AJ, Clancy CJ, Pasculle AW, Liu G, Cheng S, Cumbie RB, Driscoll E, Ayres A, Donahue L, Buck M, Streifel A, Muto CA, Nguyen MH. Remediation of Mucorales-contaminated Healthcare Linens at a Laundry Facility Following an Investigation of a Case Cluster of Hospital-acquired Mucormycosis. Clin Infect Dis 2021; 74:1401-1407. [PMID: 34282829 DOI: 10.1093/cid/ciab638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND In an investigation of hospital-acquired mucormycosis cases among transplant recipients, healthcare linens (HCLs) delivered to our center were found to be contaminated with Mucorales. We describe an investigation and remediation of Mucorales contamination at the laundry supplying our center. METHODS We performed monthly RODAC cultures of HCLs upon hospital arrival, and conducted site inspections and surveillance cultures at the laundry facility. Remediation was designed and implemented by infection prevention and facility leadership teams. RESULTS Prior to remediation, 20% of HCLs were culture-positive for Mucorales upon hospital arrival. Laundry facility layout and processes were consistent with industry standards. Significant step-ups in Mucorales and mould culture-positivity of HCLs were detected at the post-dryer step (0% to 12% (p=0.04) and 5% to 29% (p=0.01), respectively). Further increases to 17% and 40% culture-positivity, respectively, were noted during pre-transport holding. Site inspection revealed heavy Mucorales-positive lint accumulation in rooftop air intake and exhaust vents that cooled driers; intake and exhaust vents that were facing each other; rooftop and plant-wide lint accumulation, including in the pre-transport clean room; uncovered carts with freshly-laundered HCLs. Following environmental remediation, quality assurance measures and education directed toward these sources, Mucorales culture-positivity of newly-delivered HCLs was reduced to 0.3% (p=0.0001); area of lint-contaminated rooftop decreased from 918 m 2 to 0 m 2 on satellite images. CONCLUSIONS Targeted laundry facility interventions guided by site inspections and step-wise culturing significantly reduced Mucorales-contaminated HCLs delivered to our hospital. Collaboration between infection prevention and laundry facility teams was crucial to successful remediation.
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Affiliation(s)
- Alexander J Sundermann
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,University of Pittsburgh Graduate School of Public Health, PA, USA.,Contributed equally
| | - Cornelius J Clancy
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,University of Pittsburgh Medical Center, Pittsburgh, PA, USA.,Contributed equally
| | | | - Guojun Liu
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Shaoji Cheng
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Eileen Driscoll
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Ashley Ayres
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Lisa Donahue
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Michael Buck
- University of Minnesota Department of Environmental Health and Safety, MN, USA
| | - Andrew Streifel
- University of Minnesota Department of Environmental Health and Safety, MN, USA
| | - Carlene A Muto
- University of Virginia Division of Infectious Diseases and International Health, VA, USA
| | - M Hong Nguyen
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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