Coinfections in COVID-19

Co-infections Journal Club

A thread for sharing and discussing publications around secondary infections or coinfections in COVID-19.

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Chen et al in Lancet was one of the first I came across. Characterisation of 99 patients from Wuhan, China.

  • Sputum or endotrachaeal aspirate for culture on admission
  • 71% received antibiotics, 15% antifungals
  • 25% antibiotic monotherapy, 45% combination
  • One patient with VAP
  • No other viruses detected (viral panel)
  • Acinetobacter baumannii, Klebsiella pneumoniae, and Aspergillus flavus were all cultured in one patient.
  • One case of fungal infection was diagnosed as Candida glabrata and three cases of fungal infection were diagnosed as Candida albicans
  • Antibiotics used included “cephalosporins, quinolones, carbapenems, tigecycline against methicillin-resistant Staphylococcus aureus , linezolid, and antifungal drugs.” Suggests MRSA also detected?
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From Goyal et al. in NEJM last week:

I thought the relatively higher rate of bacteraemia on mechanical ventilation compared to unventilated patients was interesting.

Viral co-infection rates (in supplementary) were low:

Sadly I could not see what bugs were causing the bacteraemias.

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Think viral panels are pretty variable in numbers of things they test for in addition to sensitivity and specificity?

These tables are my nemesis, a nice summary, but unlinked from individuals. Were the patients with COPD also those that got bacteraemia? Think raw anonymised data should be deposited for clinical cohort descriptions.

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Yes, it’s not very helpful unless you know how many people were actually tested as well (i.e. are ventilated patients more likely to have blood cultures sent?). And I agree, the case data should be provided.

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Great stuff. I’ve got an Msc student starting who will be doing a literature review of this so this would be super helpful. I will add him later this week once we’ve had a chance to chat


Publication here from Etienne Ruppé and seems they are doing similar amongst COVID-19 patients. Extended spectrum beta-lactamase detection in oral and rectal swabs during VAP. Readcube link in the tweet below.

Monitoring the gut and oropharyngeal microbiota in #ICU patients is simple and useful. Very important publication by @IAME_Center @Laurence_Armand @romsonnevil @demontmol @yourICM Currently leading a wider study on #COVID19 #ICU patients

— Etienne Ruppé (@RuppeEtienne) April 21, 2020

Cross posting from the AMR thread, collated set of publications here with an AMR and secondary infection theme


Also Wang et al for other respiratory viruses

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Metatranscriptomics of nasal swabs here from the Mason group

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Blood cultures were negative in all six hospitalized patients tested, including those obtained from four patients treated empirically for bacterial pneumonia. Molecular testing for influenza A and B on respiratory specimens was negative and multipathogen respiratory PCR panels were negative for all targets in all hospitalized patients (Table 2).


That’s interesting, particularly the antibiotic treatment without indication for bacterial infection. They note that these are likely milder end of the disease spectrum so perhaps wouldn’t expect secondary infection amongst these 12? Also, this is a lot of authors for 12 patients :wink: though I suspect there’ll be more to come from this group!

I’ve been doing a rapid literature search/summary to identify organisms reported in the emerging literature as co-infections/secondary infections. The challenge I’m finding is that these are usually not the main focus of papers so difficult to search for, very limited detail, and finding a lot of papers that mention co-infections/secondary infections but don’t specify organisms.
Organisms of identified:

  • Mycoplasma pneumoniae
  • Influenza A
  • Influenza B
  • RSV
  • Legionella pneumophila
  • Cytomegalovirus
  • Other coronavridae
  • Parainfluenza
  • Rhinovirus
  • Enterovirus
  • Panton-Valentine leukocidin–secreting Staphylococcus aureus
    I’m happy to share what I have gathered so far if it would be useful to anyone.

Hi Laura,

I’ve done a brief scan too, finding the same thing, not a lot of detail and often poor recording of methods too. @freyaharrison is starting a more formal meta analysis but collating those reported in publications seems really useful to me.

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Yep, often no/limited microbiology and no idea of timing. @LauraMac do you want to compare lists of papers we’ve each found?

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Self-referential link warning! Our letter, which I will summarise as “don’t forget other bugs!”


Congrats Mike! And quite a record for the fastest acceptance into Lancet! :slight_smile:

A study on nosocomial infections in Wuhan by He et al.

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Has anyone read Sixty‐eight consecutive patients assessed for COVID‐19 infection: Experience from a UK Regional infectious diseases Unit by Easom et al? It is unclear if these were just the first 68 patient’s assessed for COVID-19 or if it was the first 68 to test positive. Abstract says microbiological diagnosis included SARS-CoV-2 and a list of other pathogens, but I’m not seeing any numbers in the paper. Any clarification is appreciated!

I found the following article interesting.

I also found it to be very interesting the possible coinfection not only with the bacillus bacteria such as pertussis and tuberculosis, but even more notable with measles. Keep in mind that the following symptoms include diarrhea, encephalitis, blood clotting and skin rash. Check out the following article titled

What Are ‘COVID Toes’? Dermatologists Say Foot Lesions May Be New Coronavirus Symptom (

How many people have not had their vaccinations updated (booster vaccine for pertussis, measles, streptococcus pneumoniae or tests for tuberculosis) The majority of these people (adults) are candidates for coinfection. According to my research, the population with the best immunization due to the vaccine protocols include the military (Roosevelt Ship), inmates (Ohio Prison), refugees (5.6 million Syrians into Turkey), health care providers (HCP exposed to COVID-19) and younger people that have their immunization/vaccinations current all show asymptomatic symptoms and low death rate. Upon doing further research, another piece of information that caught my attention includes medication that was assumed to have been a good candidate to treat COVID-19 such as Remdesivir (which was used to treat Ebola and that alone was known to have had a common infection rate with tuberculosis) They treated a significant number of health care providers in the U.S. and Australia with the BCG vaccine to prevent getting COVID-19. I will upload other articles that I found interesting.