Are we flooded by emerging pathogens?
- Numerous publication titles contain the word ‘emerging’. According to Oxford Dictionary, this means ‘becoming apparent or prominent’. That suggests that the new fungus is spotted at increasing frequency after its first discovery. This is, however, not so common. Candida auris is one of the few really emerging pathogens. Discovered in 2009 from a single ear infection in Japan (Satoh et al. 2009), it now is a causing hospital epidemics globally with six geographic genotypes (Welsh et al. 2019; Szekely et al. 2019). Another example is Emergomyces africanus, causing an epidemic with severe disseminated infections in HIV-positive patients in South Africa (Schwartz et al. 2015), and the cat-transmitted Sporothrix brasiliensis (Ortiz Sanchotene et al. 2015). Trichophyton indotineae, a high-virulent clone in the T. mentagrophytes complex and expanding from India is emerging (Singh et al. 2018). In animals, the American white-nose disease caused by Pseudogymnoascus destructans has emerged in an epidemic fashion killing thousands of hibernating bats (Verant et al. 2014). Sometimes an entire group is emerging. Human infections by species of the genus Emergomyces (named after their emergence) were not known prior to the year 2000 – even though they are not difficult to recognize – while during the last decades we observe several human-associated species rather regularly (Jiang et al. 2018). A recent, dramatic example is the increase of severe rhinocerebral infection by members of the order Mucorales (Sen et al. 2021). In lay language, this infection is known as ‘black fungus’. This name does not refer to the fungus (black fungi are melanized ascomycetes), but to the necrotic tissue in the face of patients suffering from this very acute infection. Probably mostly Rhizopus species are concerned, although in many reports no detailed identification is performed.
- Thus, indeed: emerging fungi do exist. But single cases by species which are rarely seen afterwards are much more common. Most extant fungi, now recognized by sequencing and comparison with GenBank data, are opportunists from the environment. They have a habitat outside the human or animal host and cause infections only reluctantly, when they are introduced into tissue by unfortunate coincidence. They just try to survive. Mycocentrospora acerina was reported once: in 1957, and it took 100 years before a second infection by Wallemia sebi was reported. Each year, large amounts of pathogens and opportunists are added to the list of clinically relevant fungi. See the table below: these are new names, introduced since we started to produce the book-version of the Atlas of Clinical Fungi; we are working on their inclusion. Many of them will remain very rare in clinical settings.
- Another part of the new names you encounter in recent literature are for fungi that actually had already been observed before, but were not recognized as separate species. A major trend in mycology is the splitting of large, variable species into smaller entities, together forming a species complex. Many ubiquitous fungi such as Aspergillus fumigatus, Alternaria alternata, Histoplasma capsulatum or Cryptococcus neoformans comprise groups of lineages which can be separated by molecular methods and show reduced interbreeding. It is quite likely that most species that thus far have not been described to comprise a complex of lineages are simply too rare; when we have more material, strains form different origins will probably appear to be genetically heterogeneous.
- Another type of novelties concern fungi that could not be distinguished with classical microscopy, due to absence of sporulation providing the necessary characters for morphological identification. Some remain rare, with less than a handful of described species, such as the exclusively hyphal genera Emarellia (Borman et al. 2016) or Hongkongmyces (Tsang et al. 2014). Others appear important but were overlooked or unrecognized previously, such as the pulmonary occurrence of shelf fungi (Chowdhary et al. 2013), or the pycnidium-forming genus Tintelnotia (Ahmed et al. 2017) which has been encountered repeatedly during the last few years (Roels et al. 2020).
- Another addition to the Atlas are veterinary fungi. The enormous diversity of vertebrates has only fragmentarily been investigated for the presence of infectious fungi. Several fungi show a pronounced specialization on particular hosts. We know this for example from the dermatophytes on cattle (Trichophyton verrucosum), hedghogs (T. erinacei) or guinea pigs (T. benhamiae). A family Nannizziopsidaceae has been proposed for species almost exclusively infecting reptiles (Stchigel et al. 2014). Also Pneumocystis species show remarkable host-specificity (Danesi et al. 2019). This area is largely unexplored.
- Ahmed SA, Hofmüller W, Seibold M, et al. 2017. Tintelnotia, a new genus in Phaeosphaeriaceae harbouring agents of cornea and nail infections in humans. Mycoses 60, 244-253.
- Borman AM, Desnos-Ollivier M, Campbell CK, et al. (2016) Novel taxa associated with human fungal black-grain mycetomas: Emarellia grisea gen. nov., sp. nov., and Emarellia paragrisea sp. nov. J. Clin. Microbiol. 54: 1738-1745.
- Chowdhary A, Agarwal K, Kathuria S, et al. (2013) Clinical significance of filamentous basidiomycetes illustrated by isolates of the novel opportunist Ceriporia lacerata from the human respiratory tract. J. Clin. Microbiol. 51: 585-590.
- Danesi P, da Rold G, Rizzoli A, et al. (2016) Barcoding markers for Pneumocystis species in wildlife. Fung. Biol. 120: 191-206.
- Jiang Y, Dukik K, Muñoz JF, et al. (2018) Phylogeny, ecology and taxonomy of systemic pathogens and their relatives in Ajellomycetaceae (Onygenales): Blastomyces, Emergomyces, Emmonsia, Emmonsiellopsis. Fung. Div. 90: 245-291.
- Luo Y, Zeng F, Huang X, et al. (2014) Successful treatment of a necrotizing fasciitis patient caused by Mucor indicus with amphotericin B and skin grafting. Mycopathologia 177: 187-192.
- Ortiz Sanchotene K, Martins Madrid I, Baracy Klafke G, et al. (2015) Sporothrix brasiliensis outbreaks and the rapid emergence of feline sporotrichosis. Mycoses 58: 652-658.
- Roels D, Coorevits L, Lagrou K. (2020) Tintelnotia destructans as an emerging opportunistic pathogen: First case of T. destructans superinfection in herpetic keratitis. Am. J. Ophthalm. Case Rep. 19: doi 10.1016/j.ajoc.2020.100791.
- Satoh K, Makimura K, Hasumi Y, et al. (2009) Candida auris sp. nov., a novel ascomycetous yeast isolated from the external ear canal of an inpatient in a Japanese hospital. Med. Immunol. 53: 41-44.
- Schwartz IS, Govender NP, Corcoran C, et al. (2015) Clinical characteristics, diagnosis, management, and outcomes of disseminated emmonsiosis: a retrospective case series. Clin. Infect. Dis. 61: 1004-1012.
- Sen M, Honavar SG, Bansal R, et al. (2021) Epidemiology, clinical profile, management, and outcome of COVID-19-associated rhino-orbital-cerebral mucormycosis in 2826 patients in India – Collaborative OPAI-IJO study on mucormycosis in COVID-19 (COSMIC), Report 1. Indian J. Ophthalmol. 69: 1670-1692.
- Singh A, Masih A, Khurana A, et al. (2018) High terbinafine resistance in Trichophyton interdigitale isolates in Delhi, India harbouring mutations in the squalene epoxidase gene. Mycoses 61: 477-484.
- Stchigel AM, Sutton DA, Cano-Lira JF, et al. (2014) Phylogeny of chrysosporia infecting reptiles: proposal of the new family Nannizziopsiaceae and five new species. Persoonia 31: 86-100.
- Szekely A, Borman AM, Johnson EM (2019) Candida auris isolates of the southern Asian and South African lineages exhibit different phenotypic and antifungal susceptibility profiles in vitro. J. Clin. Microbiol. 57: doi 0.1128/JCM.02055-18.
- Tsang CC, Chan JF, Ip PP, et al. (2014) Subcutaneous phaeohyphomycotic nodule due to Phialemoniopsis hongkongensis sp. nov. J. Clin. Microbiol. 52: 3280-3289.
- Verant ML, Meteyer CU, Speakman JR, et al. (2014) White-nose syndrome initiates a cascade of physiologic disturbances in the hibernating bat host. BMC Physiol. 14: 10.
- Welsh RM, Sexton DJ, Forsberg K, et al. (2019) Insights into the unique nature of the East Asian clade of the emerging pathogenic yeast Candida auris. J. Clin. Microbiol. 57: doi 10.1128/JCM.00007-19.
|Aspergillus parafelis (A viridinutans complex)||3|
|Aspergillus pseudoviridinutans (A viridinutans complex)||3|
|Trichophyton africanum (T benhamiae complex)||3|
|Trichophyton europaeum (T benhamiae complex)||3|
|Trichophyton japonicum (T benhamiae complex)||3|