Publications
61 results found
Simmons BC, Rhodes J, Rogers TR, et al., 2023, Genomic Epidemiology Identifies Azole Resistance Due to TR34/L98H in European Aspergillus fumigatus Causing COVID-19-Associated Pulmonary Aspergillosis, Journal of Fungi, Vol: 9, Pages: 1104-1104
<jats:p>Aspergillus fumigatus has been found to coinfect patients with severe SARS-CoV-2 virus infection, leading to COVID-19-associated pulmonary aspergillosis (CAPA). The CAPA all-cause mortality rate is approximately 50% and may be complicated by azole resistance. Genomic epidemiology can help shed light on the genetics of A. fumigatus causing CAPA, including the prevalence of resistance-associated alleles. We present a population genomic analysis of 21 CAPA isolates from four European countries with these isolates compared against 240 non-CAPA A. fumigatus isolates from a wider population. Bioinformatic analysis and antifungal susceptibility testing were performed to quantify resistance and identify possible genetically encoded azole-resistant mechanisms. The phylogenetic analysis of the 21 CAPA isolates showed that they were representative of the wider A. fumigatus population with no obvious clustering. The prevalence of phenotypic azole resistance in CAPA was 14.3% (n = 3/21); all three CAPA isolates contained a known resistance-associated cyp51A polymorphism. The relatively high prevalence of azole resistance alleles that we document poses a probable threat to treatment success rates, warranting the enhanced surveillance of A. fumigatus genotypes in these patients. Furthermore, potential changes to antifungal first-line treatment guidelines may be needed to improve patient outcomes when CAPA is suspected.</jats:p>
Gangneux J-P, Rhodes JL, Papon N, 2023, Airway microbiome: environmental exposure-respiratory health nexus., Trends Mol Med, Vol: 29, Pages: 875-877
Toxicants such as smoke, biofuel, and pollutants constantly challenge our respiratory health, but little is known about the pathophysiological processes involved. In a new report, Lin et al. provide evidence that our bacterial and fungal lung populations orchestrate the interplay between environmental exposure and lung functions, thereby conditioning health outcomes.
Auxier B, Debets AJM, Stanford FA, et al., 2023, The human fungal pathogen Aspergillus fumigatus can produce the highest known number of meiotic crossovers, PLoS Biology, Vol: 21, Pages: 1-17, ISSN: 1544-9173
Sexual reproduction involving meiosis is essential in most eukaryotes. This produces offspring with novel genotypes, both by segregation of parental chromosomes as well as crossovers between homologous chromosomes. A sexual cycle for the opportunistic human pathogenic fungus Aspergillus fumigatus is known, but the genetic consequences of meiosis have remained unknown. Among other Aspergilli, it is known that A. flavus has a moderately high recombination rate with an average of 4.2 crossovers per chromosome pair, whereas A. nidulans has in contrast a higher rate with 9.3 crossovers per chromosome pair. Here, we show in a cross between A. fumigatus strains that they produce an average of 29.9 crossovers per chromosome pair and large variation in total map length across additional strain crosses. This rate of crossovers per chromosome is more than twice that seen for any known organism, which we discuss in relation to other genetic model systems. We validate this high rate of crossovers through mapping of resistance to the laboratory antifungal acriflavine by using standing variation in an undescribed ABC efflux transporter. We then demonstrate that this rate of crossovers is sufficient to produce one of the common multidrug resistant haplotypes found in the cyp51A gene (TR34/L98H) in crosses among parents harboring either of 2 nearby genetic variants, possibly explaining the early spread of such haplotypes. Our results suggest that genomic studies in this species should reassess common assumptions about linkage between genetic regions. The finding of an unparalleled crossover rate in A. fumigatus provides opportunities to understand why these rates are not generally higher in other eukaryotes.
Hemmings SJ, Rhodes JL, Fisher MC, 2023, Long-read Sequencing and de novo Genome Assembly of Three <i>Aspergillus fumigatus</i> Genomes, MYCOPATHOLOGIA, Vol: 188, Pages: 409-412, ISSN: 0301-486X
Shelton JMG, Rhodes J, Uzzell CB, et al., 2023, Citizen science reveals landscape-scale exposures to multiazole-resistant Aspergillus fumigatus bioaerosols., Science Advances, Vol: 9, Pages: 1-9, ISSN: 2375-2548
Using a citizen science approach, we identify a country-wide exposure to aerosolized spores of a human fungal pathogen, Aspergillus fumigatus, that has acquired resistance to the agricultural fungicide tebuconazole and first-line azole clinical antifungal drugs. Genomic analysis shows no distinction between resistant genotypes found in the environment and in patients, indicating that at least 40% of azole-resistant A. fumigatus infections are acquired from environmental exposures. Hotspots and coldspots of aerosolized azole-resistant spores were not stable between seasonal sampling periods. This suggests a high degree of atmospheric mixing resulting in an estimated per capita cumulative annual exposure of 21 days (±2.6). Because of the ubiquity of this measured exposure, it is imperative that we determine sources of azole-resistant A. fumigatus to reduce treatment failure in patients with aspergillosis.
Rhodes J, 2023, Genomic surveillance urgently needed to control wheat blast pandemic spreading across continents, PLOS BIOLOGY, Vol: 21, ISSN: 1544-9173
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Winter DJ, Weir BS, Glare T, et al., 2022, A single fungal strain was the unexpected cause of a mass aspergillosis outbreak in the world's largest and only flightless parrot., iScience, Vol: 25, Pages: 105470-105470, ISSN: 2589-0042
Kākāpō are a critically endangered species of parrots restricted to a few islands off the coast of New Zealand. Kākāpō are very closely monitored, especially during nesting seasons. In 2019, during a highly successful nesting season, an outbreak of aspergillosis affected 21 individuals and led to the deaths of 9, leaving a population of only 211 kākāpō. In monitoring this outbreak, cultures of aspergillus were grown, and genome sequenced. These sequences demonstrate that, very unusually for an aspergillus outbreak, a single strain of aspergillus caused the outbreak. This strain was found on two islands, but only one had an outbreak of aspergillosis; indicating that the strain was necessary, but not sufficient, to cause disease. Our analysis provides an understanding of the 2019 outbreak and provides potential ways to manage such events in the future.
Abdolrasouli A, Rhodes JL, 2022, Phenotypic Variants of Azole-Resistant <i>Aspergillus Fumigatus</i> that Co-exist in Human Respiratory Samples are Genetically Highly Related, MYCOPATHOLOGIA, Vol: 187, Pages: 497-508, ISSN: 0301-486X
Rhodes J, Abdolrasouli A, Dunne K, et al., 2022, Population genomics confirms acquisition of drug-resistant <i>Aspergillus fumigatus</i> infection by humans from the environment (vol 7, pg 663, 2022), NATURE MICROBIOLOGY, Vol: 7, Pages: 1944-1944, ISSN: 2058-5276
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- Citations: 2
West AG, Digby A, Lear G, et al., 2022, Influence of management practice on the microbiota of a critically endangered species: a longitudinal study of kākāpō chick faeces and associated nest litter, Animal Microbiome, Vol: 4, Pages: 1-15, ISSN: 2524-4671
BACKGROUND: The critically endangered kākāpō is a flightless, nocturnal parrot endemic to Aotearoa New Zealand. Recent efforts to describe the gastrointestinal microbial community of this threatened herbivore revealed a low-diversity microbiota that is often dominated by Escherichia-Shigella bacteria. Given the importance of associated microbial communities to animal health, and increasing appreciation of their potential relevance to threatened species conservation, we sought to better understand the development of this unusual gut microbiota profile. To this end, we conducted a longitudinal analysis of faecal material collected from kākāpō chicks during the 2019 breeding season, in addition to associated nest litter material. RESULTS: Using an experimental approach rarely seen in studies of threatened species microbiota, we evaluated the impact of a regular conservation practice on the developing kākāpō microbiota, namely the removal of faecal material from nests. Artificially removing chick faeces from nests had negligible impact on bacterial community diversity for either chicks or nests (p > 0.05). However, the gut microbiota did change significantly over time as chick age increased (p < 0.01), with an increasing relative abundance of Escherichia-Shigella coli over the study period and similar observations for the associated nest litter microbiota (p < 0.01). Supplementary feeding substantially altered gut bacterial diversity of kākāpō chicks (p < 0.01), characterised by a significant increase in Lactobacillus bacteria. CONCLUSIONS: Overall, chick age and hand rearing conditions had the most marked impact on faecal bacterial communities. Similarly, the surrounding nest litter microbiota changed significantly over time since a kākāpō chick was first placed in the nest, though we found no evidence that removal of faecal material influenced the bacterial communities of either litter or faecal sampl
Fisher MC, Alastruey-Izquierdo A, Berman J, et al., 2022, Tackling the emerging threat of antifungal resistance to human health, NATURE REVIEWS MICROBIOLOGY, Vol: 20, Pages: 557-571, ISSN: 1740-1526
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- Citations: 153
Taori S, Rhodes J, Khonyongwa K, et al., 2022, First experience of implementing Candida auris Real Time PCR for surveillance in the UK: detection of multiple introductions with two international clades and improved patient outcomes, Journal of Hospital Infection, Vol: 127, Pages: 111-120, ISSN: 0195-6701
Background: Candida auris has been associated with rapid transmission and high mortality. A novelPCR based surveillance programme was initiated at a London teaching hospital from January 2018.The results of this implementation until March 2019 are presented along with the clinical,transmission and phylogenetic characteristics encountered in that setting.Methods: A real time-PCR assay for C auris was developed, validated, and implemented for directuse on skin swabs and urine. Environmental swabs were also tested by PCR as an emergencyoutbreak control measure. Clinical risk factors and outcomes of patients were determined.Environmental dispersal was assessed using 24 h settle plate cultures around 9 colonised patientsfollowed by air sampling around one colonised patient during high and low turbulence activities.Sequencing was performed using Illumina HiSeq and maximum likelihood phylogenies wereconstructed using rapid bootstrap analysis.Results 21 C. auris colonised patients were identified. Median turnaround time of colonisationdetection reduced from 141 h (5.8 d) to approximately 24 h enabling rapid infection controlprecautions. Settle plates detected 70 to 600 CFU/m2 around colonised patients over 24 h and airsampling suggested dispersal during turbulent activities. C. auris DNA was detected from 35.7%environmental swabs. Despite being in a high-risk setting, no patients developed invasive infection.Sequencing analysis of isolates from this centre identified two introductions of the South Asian(Clade I) and one of the South African (Clade III) strain.Conclusion: The PCR offers a rapid, scalable method of screening and supports clinical risk reductionin settings likely to encounter multiple introductions.
Furukawa T, van Rhijn N, Chown H, et al., 2022, Exploring a novel genomic safe-haven site in the human pathogenic mould br <i>Aspergillus fumigatus</i>, FUNGAL GENETICS AND BIOLOGY, Vol: 161, ISSN: 1087-1845
Rhodes J, 2022, Population genomics confirms acquisition of drug resistant Aspergillus fumigatus infection by humans from the environment, Nature Microbiology, Vol: 7, ISSN: 2058-5276
Infections caused by the fungal pathogen Aspergillus fumigatus are increasingly resistant to first-line azole antifungal drugs. However, despite its clinical importance, little is known about how susceptible patients acquire infection from drug resistant genotypes in the environment. Here, we present a population genomic analysis of 218 A. fumigatus from across the United Kingdom and Ireland (comprising 153 clinical isolates from 143 patients, and 65 environmental isolates). First, phylogenomic analysis shows strong genetic structuring into two clades (‘A’ and ‘B’) with little interclade recombination and the majority of environmental azole resistance found within Clade A. Secondly, we show occurrences where azole resistant isolates of near identical genotypes were obtained from both environmental and clinical sources, indicating with high confidence the infection of patients with resistant isolates transmitted from the environment. Third, genome-scans identified selective sweeps across multiple regions indicating a polygenic basis to the trait in some genetic backgrounds. These signatures of positive selection are seen for loci containing the canonical genes encoding fungicide resistance in the ergosterol biosynthetic pathway, whilst other regions under selection have no defined function. Lastly, pangenome analysis identified genes linked to azole resistance and novel resistance mechanisms. Understanding the environmental drivers and genetic basis of evolving fungal drug resistance needs urgent attention, especially in light of increasing numbers of patients with severe viral respiratory tract infections who are susceptible to opportunistic fungal superinfections.
Rhodes J, 2022, Microbial Genetics in Mycology, Encyclopedia of Infection and Immunity, Pages: 462-473, ISBN: 9780128187319
Fungi are a diverse kingdom, containing at least 140,000 species, and estimated to contain between 2.2 and 3.8 million species. The advancement of genomics and typing methods in the later half of the 20th century and into the 21st century have amassed a wealth of knowledge about this kingdom, including species identification and taxonomy, as well as surveillance of outbreaks and life histories of fungal pathogens. In this article, we review how genomics, including whole genome sequencing and other “omics” technologies, has shaped the field of mycology to increase our understanding of the fungal kingdom. Yet with these advancements, challenges also arise. Fungal genomes are complex, and software to analyze these data are typically not written specifically for fungi. We also discuss these challenges, and discuss approaches and further research that is needed in order to overcome these hurdles. Ultimately, this article summarizes how genomics and genetics-based approaches are revolutionizing this important field of biology.
Duong T-MN, Le T-V, Tran K-LH, et al., 2021, Azole-resistant Aspergillus fumigatus is highly prevalent in the environment of Vietnam, with marked variability by land use type, Environmental Microbiology, Vol: 23, Pages: 7632-7642, ISSN: 1462-2912
Azole-resistant environmental Aspergillus fumigatus presents a threat to public health but the extent of this threat in Southeast Asia is poorly described. We conducted environmental surveillance in the Mekong Delta region of Vietnam, collecting air and ground samples across key land-use types, and determined antifungal susceptibilities of Aspergillus section Fumigati (ASF) isolates and azole concentrations in soils. Of 119 ASF isolates, 55% were resistant (or non-wild type) to itraconazole, 65% to posaconazole and 50% to voriconazole. Azole resistance was more frequent in A. fumigatus sensu stricto isolates (95%) than other ASF species (32%). Resistant isolates and agricultural azole residues were overrepresented in samples from cultivated land. cyp51A gene sequence analysis showed 38/56 resistant A. fumigatus sensu stricto isolates carried known resistance mutations, with TR34/L98H most frequent (34/38).
McMillan M, Rhodes J, Winder P, et al., 2021, Comparing evaluation responses of an interprofessional education initiative with students in undergraduate nursing and medical programmes, NURSE EDUCATION TODAY, Vol: 105, ISSN: 0260-6917
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- Citations: 2
Brackin A, Hemmings S, Fisher M, et al., 2021, Fungal genomics in respiratory medicine: what, how and when?, Mycopathologia, Vol: 186, Pages: 589-608, ISSN: 0301-486X
Respiratory infections caused by fungal pathogens present a growing global healthconcern and are a major cause of death in immunocompromised patients. Worryingly,coronavirus disease-19 (COVID-19) resulting in acute respiratory distress syndrome,has been shown to predispose some patients to fungal co-infection and secondarypulmonary aspergillosis. Aspergillosis is most commonly caused by the fungalpathogen Aspergillus fumigatus and primarily treated using the triazole drug group,however in recent years, this fungus has been rapidly gaining resistance against theseantifungals. This is of serious clinical concern as multi-azole resistant forms ofaspergillosis have a higher risk of mortality when compared against azole-susceptibleinfections. With the increasing numbers of COVID-19 and other classes ofimmunocompromised patients, early diagnosis of fungal infections is critical to ensuringpatient survival. However, time-limited diagnosis is difficult to achieve with currentculture-based methods. Advances within fungal genomics have enabled moleculardiagnostic methods to become a fast, reproducible, and cost-effective alternative fordiagnosis of respiratory fungal pathogens and detection of antifungal resistance. Herewe describe what techniques are currently available within molecular diagnostics, howthey work and when they have been used.
Edwards H, Rhodes J, 2021, Accounting for the biological complexity of pathogenic fungi in phylogenetic dating, Journal of Fungi, Vol: 7, ISSN: 2309-608X
In the study of pathogen evolution, temporal dating of phylogenies provides information on when species and lineages may have diverged in the past. When combined with spatial and epidemiological data in phylodynamic models, these dated phylogenies can also help infer where and when outbreaks occurred, how pathogens may have spread to new geographic locations and/or niches, and how virulence or drug resistance has developed over time. Although widely applied to viruses and, increasingly, to bacterial pathogen outbreaks, phylogenetic dating is yet to be widely used in the study of pathogenic fungi. Fungi are complex organisms with several biological processes that could present issues with appropriate inference of phylogenies, clock rates, and divergence times, including high levels of recombination and slower mutation rates although with potentially high levels of mutation rate variation. Here, we discuss some of the key methodological challenges in accurate phylogeny reconstruction for fungi in the context of the temporal analyses conducted to date and make recommendations for future dating studies to aid development of a best practices roadmap in light of the increasing threat of fungal outbreaks and antifungal drug resistance worldwide.
Soraggi S, Rhodes J, Altinkaya I, et al., 2021, HMMploidy: inference of ploidy levels from short-read sequencing data
<jats:title>Abstract</jats:title><jats:p>The inference of ploidy levels from genomic data is important to understand molecular mechanisms underpinning genome evolution. However, current methods based on allele frequency and sequencing depth variation do not have power to infer ploidy levels at low-and mid-depth sequencing data, as they do not account for data uncertainty. Here we introduce <jats:monospace>HMMploidy</jats:monospace>, a novel tool that leverages the information from multiple samples and combines the information from sequencing depth and genotype likelihoods. We demonstrate that <jats:monospace>HMMploidy</jats:monospace> outperforms existing methods in most tested scenarios, especially at low-depth with large sample size. We apply <jats:monospace>HMMploidy</jats:monospace> to sequencing data from the pathogenic fungus <jats:italic>Cryptococcus neoformans</jats:italic> and retrieve pervasive patterns of aneuploidy, even when artificially downsampling the sequencing data. We envisage that <jats:monospace>HMMploidy</jats:monospace> will have wide applicability to low-depth sequencing data from polyploid and aneuploid species.</jats:p>
Verweij PE, Lucas JA, Arendrup MC, et al., 2020, The one health problem of azole resistance in <i>Aspergillus fumigatus</i>: current insights and future research agenda, FUNGAL BIOLOGY REVIEWS, Vol: 34, Pages: 202-214, ISSN: 1749-4613
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- Citations: 47
Ghosh P, Brookes L, Edwards H, et al., 2020, Cross-Disciplinary Genomics Approaches to Studying Emerging Fungal Infections, Life, Vol: 10, ISSN: 2075-1729
Emerging fungal pathogens pose a serious, global and growing threat to food supply systems, wild ecosystems, and human health. However, historic chronic underinvestment in their research has resulted in a limited understanding of their epidemiology relative to bacterial and viral pathogens. Therefore, the untargeted nature of genomics and, more widely, -omics approaches is particularly attractive in addressing the threats posed by and illuminating the biology of these pathogens. Typically, research into plant, human and wildlife mycoses have been largely separated, with limited dialogue between disciplines. However, many serious mycoses facing the world today have common traits irrespective of host species, such as plastic genomes; wide host ranges; large population sizes and an ability to persist outside the host. These commonalities mean that -omics approaches that have been productively applied in one sphere and may also provide important insights in others, where these approaches may have historically been underutilised. In this review, we consider the advances made with genomics approaches in the fields of plant pathology, human medicine and wildlife health and the progress made in linking genomes to other -omics datatypes and sets; we identify the current barriers to linking -omics approaches and how these are being underutilised in each field; and we consider how and which -omics methodologies it is most crucial to build capacity for in the near future.
Yu L-S, Rodriguez-Manzano J, Moser N, et al., 2020, Rapid detection of azole-resistant Aspergillus fumigatus in clinical and environmental isolates using lab-on-a-chip diagnostic system, Journal of Clinical Microbiology, Vol: 58, Pages: 1-11, ISSN: 0095-1137
Aspergillus fumigatus has widely evolved resistance to the most commonly used class of antifungal chemicals, the azoles. Current methods for identifying azole resistance are time-consuming and depend on specialized laboratories. There is an urgent need for rapid detection of these emerging pathogens at point-of-care to provide the appropriate treatment in the clinic and to improve management of environmental reservoirs to mitigate the spread of antifungal resistance. Our study demonstrates the rapid and portable detection of the two most relevant genetic markers linked to azole resistance, the mutations TR34 and TR46, found in the promoter region of the gene encoding the azole target, cyp51A. We developed a lab-on-a-chip platform consisting of: (1) tandem-repeat loop-mediated isothermal amplification, (2) state-of-the-art complementary metal-oxide-semiconductor microchip technology for nucleic-acid amplification detection and, (3) and a smartphone application for data acquisition, visualization and cloud connectivity. Specific and sensitive detection was validated with isolates from clinical and environmental samples from 6 countries across 5 continents, showing a lower limit-of-detection of 10 genomic copies per reaction in less than 30 minutes. When fully integrated with a sample preparation module, this diagnostic system will enable the detection of this ubiquitous fungus at the point-of-care, and could help to improve clinical decision making, infection control and epidemiological surveillance.
Armstrong-James D, Youngs J, Bicanic T, et al., 2020, Confronting and mitigating the risk of COVID-19 Associated Pulmonary Aspergillosis (CAPA), European Respiratory Journal, Vol: 56, Pages: 1-10, ISSN: 0903-1936
Cases of COVID-19 associated pulmonary aspergillosis (CAPA) are being increasingly reported and physicians treating patients with COVID-19-related lung disease need to actively consider these fungal co-infections.The SARS-CoV-2 (COVID-19) virus causes a wide spectrum of disease in healthy individuals as well as those with common comorbidities [1]. Severe COVID-19 is characterised acute respiratory distress syndrome (ARDS) secondary to viral pneumonitis, treatment of which may require mechanical ventilation or extracorporeal membrane oxygenation (ECMO) [2]. Clinicians are alert to the possibility of bacterial co-infection as a complication of lower respiratory tract viral infection; for example a recent review found that 72% of patients with COVID-19 received antimicrobial therapy [3]. However, the risk of fungal co-infection, in particular COVID-19 associated pulmonary aspergillosis (CAPA), remains underappreciated.Fungal disease consistent with invasive aspergillosis (IA) has been observed with other severe Coronaviruses such as Severe Acute Respiratory Syndrome (SARS-CoV-2003) [4, 5] and Middle East Respiratory Syndrome (MERS-CoV) [6]. From the outset of the COVID-19 pandemic, there were warning signs of secondary invasive fungal infection; Aspergillus flavus was isolated from the respiratory tract from one of 99 patients in the first COVID-19 cohort from Wuhan to be reported in any detail [2] and Aspergillus spp. were isolated from 2/52 (3.8%) of a subsequent cohort of critically unwell patients from this region [7]. More recently, retrospective case series from Belgium [8], France [9], The Netherlands [10] and Germany [11] have reported evidence of CAPA in an alarming 20–35% of mechanically ventilated patients.
Rhodes J, Fisher MC, 2019, Global epidemiology of emerging Candida auris, Current Opinion in Microbiology, Vol: 52, Pages: 84-89, ISSN: 1369-5274
The discovery in 2009 of a new species of yeast, Candida auris, heralded the arrival of a novel emerging human infectious disease. This review highlights the unique characteristics of C. auris that have lled to it being of public health concern worldwide, namely public health concern, namely its global emergence, its ability to cause nosocomial outbreaks in healthcare settings, its innate and emerging resistance to multiple antifungal drugs and its resilience in the face of hygiene and infection control measures. Genomic epidemiology has identified four emergences of C. auris marked by four clades of the pathogen. These clades of C. auris are genetically dissimilar and are associated with differential resistance to antifungal drugs, suggesting that they will continue to phenotypically diverge into the future. The global emergence of C. auris testifies to the unmapped nature of Kingdom Fungi, and represents a new nosocomial threat that will require enhanced infection control across diverse healthcare and community settings.
Rhodes J, 2019, Rapid worldwide emergence of pathogenic fungi, Cell Host & Microbe, Vol: 26, Pages: 12-14, ISSN: 1931-3128
The recent coverage in the mainstream media of global Candida auris outbreaks has provided the general public with an awareness of the unprecedented emergence rate of pathogenic fungi. Scientific communities need to collaboratively address this threat to public health.
Sewell TR, Zhang Y, Brackin AP, et al., 2019, Elevated prevalence of azole resistant Aspergillus fumigatus in urban versus rural environments in the United Kingdom., Antimicrob Agents Chemother
Azole resistance in the opportunistic pathogen Aspergillus fumigatus is increasing, dominated primarily by two environmentally-associated resistance alleles: TR34/L98H and TR46/Y121F/T289A. By sampling soils across the South of England we assess the prevalence of azole resistant A. fumigatus (ARAf) in samples collected in both urban and rural locations. We characterise the susceptibility profiles of the resistant isolates to three medical azoles, identify the underlying genetic basis of resistance and investigate their genetic relationships. ARAf was detected in 6.7% of the soil samples, with a higher prevalence in urban (13.8%) compared to rural (1.1%) locations. Twenty isolates were confirmed to exhibit clinical breakpoints for resistance to at least one of three medical azoles, with 18 isolates exhibiting resistance to itraconazole, six to voriconazole and two showing elevated minimum inhibitory concentration to posaconazole. Thirteen of the resistant isolates harboured the TR34/L98H resistance allele and six isolates carried the TR46/Y121F/T289A allele. The 20 azole-resistant isolates were spread across five csp1 genetic subtypes, t01, t02, t04B, t09 and t18 with t02 the predominant subtype. Our study demonstrates that ARAf can be easily isolated in the South of England, especially in urban city centres, which appear to play an important role in the epidemiology of environmentally-linked drug resistant A. fumigatus.
Sewell T, Zhu J, Rhodes J, et al., 2019, Non-random distribution of azole resistance across the global population of Aspergillus fumigatus, mBio, Vol: 10, ISSN: 2150-7511
The emergence of azole resistance in the pathogenic fungus Aspergillus fumigatus has continued to increase, with the dominant resistance mechanisms, consisting of a 34-nucleotide tandem repeat (TR34)/L98H and TR46/Y121F/T289A, now showing a structured global distribution. Using hierarchical clustering and multivariate analysis of 4,049 A. fumigatus isolates collected worldwide and genotyped at nine microsatellite loci using analysis of short tandem repeats of A. fumigatus (STRAf), we show that A. fumigatus can be subdivided into two broad clades and that cyp51A alleles TR34/L98H and TR46/Y121F/T289A are unevenly distributed across these two populations. Diversity indices show that azole-resistant isolates are genetically depauperate compared to their wild-type counterparts, compatible with selective sweeps accompanying the selection of beneficial mutations. Strikingly, we found that azole-resistant clones with identical microsatellite profiles were globally distributed and sourced from both clinical and environmental locations, confirming that azole resistance is an international public health concern. Our work provides a framework for the analysis of A. fumigatus isolates based on their microsatellite profile, which we have incorporated into a freely available, user-friendly R Shiny application (AfumID) that provides clinicians and researchers with a method for the fast, automated characterization of A. fumigatus genetic relatedness. Our study highlights the effect that azole drug resistance is having on the genetic diversity of A. fumigatus and emphasizes its global importance upon this medically important pathogenic fungus.IMPORTANCE Azole drug resistance in the human-pathogenic fungus Aspergillus fumigatus continues to emerge, potentially leading to untreatable aspergillosis in immunosuppressed hosts. Two dominant, environmentally associated resistance mechanisms, which are thought to have evolved through selection by the agricultural application of azole fungic
Sewell TR, Zhang Y, Brackin AP, et al., 2019, Elevated prevalence of azole resistant <i>Aspergillus fumigatus</i> in urban versus rural environments in the United Kingdom
<jats:title>Abstract</jats:title><jats:p>Azole resistance in the opportunistic pathogen <jats:italic>Aspergillus fumigatus</jats:italic> is increasing, dominated primarily by two environmentally-associated resistance alleles: TR<jats:sub>34</jats:sub>/L98H and TR<jats:sub>46</jats:sub>/Y121F/T289A. Using an environmental sampling strategy across the South of England we assess the prevalence of azole resistant <jats:italic>A. fumigatus</jats:italic> (AR<jats:italic>Af</jats:italic>) in soil samples collected in both urban and rural locations. We characterise the susceptibility profiles of the resistant isolates to three medical azoles, identify the underlying genetic basis of resistance and investigate their genetic relationships. AR<jats:italic>Af</jats:italic> was detected in 6.7% of the soil samples, with a higher prevalence in urban (13.8%) compared to rural (1.1%) locations. Nineteen isolates were confirmed to exhibit clinical breakpoints for resistance to at least one of three medical azoles, with 18 isolates exhibiting resistance to itraconazole, four to voriconazole, with two also showing additional elevated minimum inhibitory concentration to posaconazole. Thirteen of the resistant isolates harboured the TR<jats:sub>34</jats:sub>/L98H resistance allele and six isolates carried TR<jats:sub>46</jats:sub>/Y121F/T289A allele. The 19 azole-resistant isolates were spread across five <jats:italic>csp1</jats:italic> genetic subtypes, t01, t02, t04B, t09 and t18 with t02 the predominant subtype. Our study demonstrates that AR<jats:italic>Af</jats:italic> can be easily isolated in the South of England, especially in urban city centres, which appear to play an important role in the epidemiology of environmentally-linked drug resistant <jats:italic>A. fumigatus</jats:italic>.</jats:p>
Stone NRH, Rhodes J, Fisher MC, et al., 2019, Dynamic ploidy changes drive fluconazole resistance in human cryptococcal meningitis, Journal of Clinical Investigation, Vol: 129, Pages: 999-1014, ISSN: 0021-9738
Background: Cryptococcal meningitis (CM) causes an estimated 180,000 deaths annually, predominantly in sub-Saharan Africa, where most patients receive fluconazole (FLC) monotherapy. While relapse after FLC monotherapy with resistant strains is frequently observed, the mechanisms and impact of emergence of FLC resistance in human CM are poorly understood. Heteroresistance (HetR) — a resistant subpopulation within a susceptible strain — is a recently described phenomenon in Cryptococcus neoformans (Cn) and Cryptococcus gattii (Cg), the significance of which has not previously been studied in humans.Methods: A cohort of 20 patients with HIV-associated CM in Tanzania was prospectively observed during therapy with either FLC monotherapy or in combination with flucytosine (5FC). Total and resistant subpopulations of Cryptococcus spp. were quantified directly from patient cerebrospinal fluid (CSF). Stored isolates underwent whole genome sequencing and phenotypic characterization.Results: Heteroresistance was detectable in Cryptococcus spp. in the CSF of all patients at baseline (i.e., prior to initiation of therapy). During FLC monotherapy, the proportion of resistant colonies in the CSF increased during the first 2 weeks of treatment. In contrast, no resistant subpopulation was detectable in CSF by day 14 in those receiving a combination of FLC and 5FC. Genomic analysis revealed high rates of aneuploidy in heteroresistant colonies as well as in relapse isolates, with chromosome 1 (Chr1) disomy predominating. This is apparently due to the presence on Chr1 of ERG11, which is the FLC drug target, and AFR1, which encodes a drug efflux pump. In vitro efflux levels positively correlated with the level of heteroresistance.Conclusion: Our findings demonstrate for what we believe is the first time the presence and emergence of aneuploidy-driven FLC heteroresistance in human CM, association of efflux levels with heteroresistance, and the successful suppression of hetero
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