Coinfections in COVID-19

Fungi in COVID-19

Aspergillus flavus noted in one of the early Chinese demographic studies, as well as Candida glabrata and Candida albicans. Aspergillus subsequently noted in these two studies:

https://onlinelibrary.wiley.com/doi/abs/10.1111/myc.13096

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We’re slowly working our way through samples we collected (biofilm on endotracheal tubes) from Covid-19 +ve patients the last 4 weeks. First 4: 4/4 + for Candida (likely albicans), 1/4 + for something that looks like Aspergillus. Very early day and much more work needed, but fungi are there.

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Thanks for sharing, Tom. Are these mixed fungal/bacterial biofilms? Also any chance the candida are glabrata (I don’t know how obviously different those two are)? Have heard from a clinical microbiologist locally that they’d been seeing nonstandard candida a bit more and piqued my curiosity given C.glabrata being spotted before.

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A nice article in Lancet Infectious Diseases on underestimation of fungal diagnosis in COVID (more so than in flu)

https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(20)30027-6/fulltext

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And another couple of special issues. Diagnostic problems significant here https://twitter.com/GermHunterMD/status/1258971212908081162?s=19

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COVID-19 associated pulmonary aspergillosis here from the Netherlands. High incidence in a small cohort of ICU patients. Aspergillus fumigatus identified in 5.

https://www.atsjournals.org/doi/abs/10.1164/rccm.202004-1038LE#.XrsVmhMqK2C.twitter

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Aspergillus, Mucor, Candida and Cryptococcus identified in the paper being discussed in the journal club thread Co-infections Journal Club

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More invasive aspergillosis, from France this time. Publication pending in Lancet Respiratory Medicine https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3575581

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Disclaimer to start with: n=6. We see C. albicans in 4 patients (4) and non-albicans Candida species also in 4. Two patients (2) seem to have both. We haven’t identified the non-albicans to the species level, but actually doubt they are C. glabrata based on phenotype.
We have 4 additional patients that likely had Candida, but haven’t ID to species level yet. In conclusion, so far 10/11 Candida +ve.
All of these mixed with a lot of different bacteria.

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Our numbers for Aspergillus are in line with the study from The Netherlands, approx. 20% (2/11) - so far.

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Interesting results, Tom
How are you ID to the species level? May be we could help with long ribosomal amplicons

Hi Olga, so far by growth on Candida ChromAgar only and I do realise we will need more accurate methods and/or confirmatory tests to be able to say something more final about this. Let me get back to you once we have an idea about how many isolates we’re talking about. I’m not an expert in fungal ID, so any advice or help would be greatly appreciated!

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Hi Tom, neither am I!
We work on microbiome and mycobiome profiles with long fragments though, and may be that could be useful for your isolates. Here is the link, let me know if we can help wheneer you need it

Pneumocystis jirovecii case study https://www.atsjournals.org/doi/abs/10.1164/rccm.202003-0766LE

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Update - 21 patients (reminder: biofilms recovered from endotracheal tube) - 20/21 have fungi (besides a lot of different bacteria)
8/20: C. albicans only
5/20: C. albicans + other Candida
3/20: other Candida only
2/20: C. albicans + Aspergillus
1/20: C. albicans + other Candida + Aspergillus
1/20: other Candida + Aspergillus

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That’s pretty extensive candida! Out of interest was there anything different about the one who didn’t?

No, not really. Did seem to have low overall diversity (only Micrococcus and CoNS on culture). Maybe related to duration of intubation but we don’t have these data (yet).

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Triazole resistant Aspergillus and COVID

https://onlinelibrary.wiley.com/doi/abs/10.1111/myc.13185?af=R

Invasive aspergillosis in Covid - 7 cases