THE MICROBIAL CO-INFECTION IN COVID-19

Kelompok Mikrobiologi dan Penyakit Infeksi :

Tatat Novianti
Amadea Risanggita Kinanthi
Dedeh Yuniarti
Nancy Pakpahan
Stephanie Triseptya H

MIP VIII – 11 DESEMBER 2021

OUTLINE
 Background
 SARS-CoV-2
 Viral Co-infection in COVID-19
 Bacterial Co-infection in COVID-19
 Fungal Co-infection in COVID-19
 Diagnosis of Co-infection in COVID-19
 Summary
 Update- Dec, 8 2021

Cases Death
Worldwide 268M 5.28M
Indonesia 4.26M 144K
Background
• During this COVID-19 attack, besides the primary infection of SARS-
CoV-2, many other complications are emerging, contributing greatly
to mortality. Among these, co-infections plays a crucial role,
threating many COVID-19 patient’s lives.
• As were reported by researchers, the prevalence of co-infections
was variable, being found occurred in half of the non survivors.
• The pathogens of respiratory co-infections could be many, either
common or rare, including bacteria, virus, fungus etc.

He et al. 2021
Background
• Beyond the pathogenesis of SARS-CoV-2, microbial coinfection plays
an important role in the occurrence and development of SARS-CoV-
2 infection by raising the difficulties of diagnosis, treatment,
prognosis of COVID-19 and even increasing the disease symptoms
and mortality
• Netea et al (2020) found that in most individuals, SARS-CoV-2
infection is mild, while coinfection can increase the susceptibility of
patients to severe disease by affecting the body’s immune function

Chen et al. 2020

Background
• Cawcutt and Kalil (2017) found that viral coinfection is usually
connected with the need for :
- Higher level of care
- Increased length of stay (LOS)
- Development of acute respiratory distress syndrome (ARDS)

Chen et al. 2020

SARS - COV- 2
SARS-CoV-2
• The virus was first reported to the WHO Country Office in China, on
December 31, 2019.
• On February 11, 2020, the WHO Director-General, Dr. Tedros
Adhanom Ghebreyesus, announced that the disease caused by this
new CoV was a "COVID-19," which is the acronym of "coronavirus
disease 2019“
• Initially, the new virus was called 2019-nCoV. Subsequently, the
task of experts of the International Committee on Taxonomy of
Viruses (ICTV) termed it the SARS-CoV-2 virus as it is very similar to
the one that caused the SARS outbreak (SARS-CoVs). 

Cascella et al. 2020

SARS-CoV-2
• Novel betacorona virus. It has round or elliptic and often
pleomorphic form, and a diameter of approximately 60–140 nm
• Positive sense ssRNA virus, its genome contains 29891 nucleotides,
encoding for 9860 amino acids.
• Phylogenetic diversity studies have highlighted that SARS-CoV-2
shares 79% nucleotide sequence identity with another virus of the
same family SARS-CoV which caused major epidemic in 2002-2003
that resulted in 8000 cases in 26 countries.
• SARS-CoV-2 also displays sequence identities of 96% and 89.6% for
the envelope and nucleocapsid proteins respectively with SARS-CoV
Dhar & Mohanty, 2020
Cascella et al. 2020
SARS-CoV-2
• The clinical spectrum of COVID-19 varies from asymptomatic or
paucisymptomatic forms to clinical conditions characterized by
respiratory failure that necessitates mechanical ventilation and
support in an ICU, to multiorgan and systemic manifestations in
terms of sepsis, septic shock, and multiple organ dysfunction
syndromes (MODS)

Cascella et al. 2020

Viral Co-infection in COVID-19
Prevalence of Viral Co-infection in Covid-19 Patient

• Musuuza et al. 2021: pooled estimated prevalence

of virus co-infection in COVID-19 is 10%. (the
study mostly conducted in China and US)

• Malekifar et al. 2021: pooled estimated

prevalence of virus co-infection in COVID-19 is
12,58% --> from every 1000 COVID-19 patients, 73
to 190 individuals had viral coinfections (study
from Western Pacific Region and Eastern
Mediterranean).
Viral Co-infection Type

Musuuza et al. 2021 Chen et al. 2020

Co- Viruses SARS-CoV-2 & other Viral
Viruses infection Chlamydia pneumoniae Respiratory
(%)
Coronavirus (nonCOVID-19) 1. SARS-CoV-2 & Influenza
Non SARS-CoV2 coronavirus strains 2 Virus
Coronavirus HKU1 (HKU1)
2. SARS-CoV-2 & Adenovirus
Human Influenza A 22.3 Entero/rhinovirus (hRV)
3. SARS-CoV-2 & human CoV
Human Influenza B 3.8 H1N1
H3N2
Respiratory Syncytial virus 3.8 SARS-CoV-2 & Systemic
Human metapneumovirus Disease causing Virus
Parainfluenza 0.9 (hMPV)
1. SARS-CoV-2 & HIV
Human metapneumovirus 1 Influenza A 2. SARS-CoV-2 & HBV
Metapneumovirus 3. SARS-CoV-2 & CMV
Rhinovirus 3.6
Mycoplasma pneumoniae 4. SARS-CoV-2 & EBV
Adenovira 1.8
Parainfluenza 1/2/3/4
Respiratory syncytial virus Journal of Medical Virology, Volume: 93, Issue: 9, Pages:
(RSV) 5310-5322, First published: 25 May 2021, DOI:
(10.1002/jmv.27102)
Mechanism of Viral Co-infection
Reduced
Viral Airway Immune system Promote the posibility
mucociliary
infection damage damage of infection by other
clearance
viruses

Epithelial damage
• Epithelial create impermeable barrier for
C-Reactive
pathogen. Primary virus infection caused Protein (CRP)
epithelial damage (dysfunction of tight
junctions and cytoskeleton) leads to
higher susceptibility of another Procalcitonin
pathogen (including virus). (PCT)

https://doi.org/10.1007/s00253-020-10814-6
 Mechanism of Viral Co-infection

Journal of Medical Virology, Volume: 93, Issue: 9, Pages: 5310-5322, First published: 25 May 2021, DOI: (10.1002/jmv.27102)
Viral Co-infection in Covid-19 Outcomes
Co-Infection

Development of Higher level of

acute respiratory Increased care
distress LOS

SARS-CoV-2 + Influenza SARS-CoV-2 + Adenovirus SARS-CoV-2 + HIV

potentially disrupt the instigate a cascade of inhibition of the immune system
patient response to detrimental sequelae --> contribute to the severity of
therapeutic agents for rendering the patient dependent disease, resulting in adverse
either infection on mechanical ventilation consequences and persistence of
viral infection
SARS-CoV-2 + CMV
exacerbate the underlying
disease and induce cytokine
storms
Journal of Medical Virology, Volume: 93, Issue: 9, Pages: 5310-5322, First published: 25 May 2021, DOI: (10.1002/jmv.27102)
Bacterial co-infection with SARS-
CoV-2
Prevalence
• Through a single center, retrospective case series study including 55
severe patients and 166 nonsevere patients with laboratory-
confirmed SARS-CoV-2 pneumonia, Zhang et al. (2020) found that in
all 221 patients the bacterial coinfection rate is 7.7%, and the fungal
coinfection rate is 3.2%
• In Guqin Zhang’s study, the severely affected patients suffered a
significantly higher rate of coinfection with bacteria (25.5%) and
fungus (10.9%), while the bacterial and the fungal coinfection rates
from the patients who were not severely affected are 1.8% and 0.6%
respectively

Zhang et al. 2020

Zhang et al. 2020
Mirzae at al, 2020
Mirzae at al, 2020
Potential Mechanism Responsible for Bacterial co-infection with Viral
Respiratory Infections

Mirzae at al, 2020

Potential Mechanism Responsible for Bacterial co-infection with Viral
Respiratory Infections

Mirzae at al, 2020

Postulated Schematic of Bacterial Co-infection

• It has been proposed when SARS-COV-2

infects lung cells can damage the cells and
the lung infrastructure.
• This situation attracts neutrophil and
macrophages to the site of infection and
promoting the inflammation.
• Finally, the changed situation and ephitelial
damage can cause bacteria to adhere and
invasion of the cells and proliferation.
• MQ : Macrophage

Mirzae at al, 2020

 The Interplay between
SARS-COV-2, bacteria and
the host in co-infection
A. SARS-COV-2 virulence factors interact
with the lungs and evoke an immune
response. These interactions may
compromise innate immunity at
several levels resulting in increased
bacterial attachment, growth and
dissemination. Viral infection may
uncover bacterial receptors mediating
bacterial attachment. Co-infection
may result in an exuberant
inflammatory response. It also
plausible that the type of immune
response induced by SARS-COV-2 may
enable bacteria to flourish in the
lungs. On the other hand, bacterial
colonization may predispose to SARS-
COV-2 infection because the innate
host defences may be down-regulated
enabling virus survival, growth and
pathology.
B. Co-infection may exacerbate the
tissue damage, and the exuberant
inflammatory response may further Bengoechea and Bamford 2020
amplify the lung damage triggered by
Bacterial co-infection
Outcome
• Coinfection can increase the degree of systemic inflammation in the patient, thereby
increasing the severity of the disease and delaying the cure time. In patients with
COVID-19, the number of proinflammatory cytokines associated with severe lung
injury, especially IL-6, has increased significantly (Tan et al. 2020).
• Moreover, the bacterial and fungal coinfection was associated with a 2.5-fold increase
in the risk of death in SARS-CoV-2 (Martins-Filho et al. 2020) indicating that there is a
certain interaction between bacteria or fungi and SARS-CoV-2.
• SARS-CoV-2 infection can damage lymphocytes, especially B cells, T cells, and NK cells,
which will lead to the immune system’s impairment during the period of disease
(Wang et al. 2020a).
• The decrease of lymphocytes and host immune function may be the main reason for
the coinfection (Luo et al. 2019). The mortality is more significant in severe cases
compared with the nonsevere group (Qin et al. 2020) due to the higher coinfection
rate in severe patients.
Bacterial co-infection
Outcome
• Moreover, we found a large effect size for procalcitonin in nonsurvivor patients of
COVID-19 which may be associated with the release of some cytokines, especially
IL-6.
• It is well known that procalcitonin is a better marker to estimate the severity,
prognosis, or further course of the sepsis and is helpful to guide antibiotic
management.
• The increased levels of procalcitonin in critical ill patients with COVID-19 can
represent a bacterial coinfection and collected blood cultures for bacteria are
needed to a prompt response.
• In the study by Wang et al., 81.7% of patients who died with COVID-19 had
associated bacterial infection. We found that sepsis was associated with a 2.5-
fold increase in the risk of death in COVID.
Martins-Filho et al. 2020
Fungal co-infection with SARS-CoV-2
Fungal Diseases and COVID-19 - Overview
• Symptoms of some fungal diseases can be similar to those of COVID-19, including
fever, cough, and shortness of breath
• Laboratory testing is necessary to determine if a person has a fungal infection or
COVID-19. Some patients can have COVID-19 and a fungal infection at the same
time
• People with severe COVID-19, such as those in an intensive care unit (ICU), are
particularly vulnerable to bacterial and fungal infections.
• The main fungal pathogens for fungal coinfections in severe COVID-19 patients are
Aspergillus and Candida. Other infrequent opportunistic pathogenic fungus caused
lung infections also need to be considered, such as Mucor and Cryptococcus.
• Awareness of the possibility of fungal co-infection is essential to reduce delays in
diagnosis and treatment in order to help prevent severe illness and death from
these infections.
J. Pemán et al, 2020
Fungal Diseases and COVID-19 - Prevalence
• In China, Chen et al. performed fungal culture on all 99 COVID-19 patients at
admission and found five (5%, 5/99) cases of fungal infection, including one case
of Aspergillus flavus, one case of Candida glabrata and three cases of C. albicans
Yang et al. found there (3/52, 5.8%) patients had fungal co-infection in 52
critically ill patients, including A. flavus, A. fumigatus and C. albicans
• A German study found COVID-19 associated invasive pulmonary aspergillosis
(IPA) was found in five (26.3%) of 19 consecutive critically ill patients with
moderate to severe ARDS
• In Netherlands, there were six patients (19.4%) presumed IPA in 31 ICU patients,
of which five were identified A. fumigatus. Besides, among the 5 first well
described French COVID-19 patients, an old severely ill man was co-infected
with A. flavus by tracheal aspirates culture

Song et al, 2020

Proportion of all identified SARS-CoV-2 fungal co-infections

Alhumaid, 2021

Ezeokoli, 2021
Fungal Diseases and COVID-19

• COVID-19-Associated Pulmonary Aspergillosis (CAPA)

• Invasive Candidiasis
• Mucormycosis
• Invasive Cryptococcosis
 1. COVID-19-Associated Pulmonary Aspergillosis (CAPA)

• Scientists are still learning about aspergillosis (infections caused by

the fungus Aspergillus) in people with severe COVID-19.
• In the past, scientists thought aspergillosis occurred almost entirely
in people with severely weakened immune systems.
• However, aspergillosis has been increasingly reported in patients
without weakened immune systems but who have severe
respiratory infections caused by viruses, including influenza.
Several recent reports describe COVID-19-associated pulmonary
aspergillosis (CAPA)

J. Pemán et al, 2020

1. COVID-19-Associated Pulmonary Aspergillosis (CAPA)

Available information indicates that CAPA:

• Usually occurs in patients with severe COVID-19 (e.g., patients on
ventilators in ICUs)
• Can be difficult to diagnose because patients often have non-specific
symptoms and testing typically requires a specimen from deep in the
lungs
• Can cause severe illness and death

J. Pemán et al, 2020

1. COVID-19-Associated Pulmonary Aspergillosis (CAPA)

Diagnosing a CAPA episode is a real challenge for clinicians.

The symptoms are non-specific and imaging techniques, including
computed tomography scan, so useful in immunocompromised
patients, are not helpful as the findings are similar to those seen
in patients with COVID-19 and ARDS. In addition, detection of IFI
biomarkers, such as GM and 1,3-B-d-glucan (BDG), and fungal DNA
in serum or in respiratory secretions have been shown of limited
value in the reported CAPA episodes

J. Pemán et al. / Rev Iberoam Micol. 2020

2. Invasive Candidiasis in Patients with COVID-19
• For the severe COVID-19 patients who have more opportunities to be treat
with broad-spectrum antibacterial drugs, parenteral nutrition and invasive
examinations, or the patients accompanied with prolonged neutropenia
and other immune impairment factors, the risk of infection with Candida
species may significantly increase
• Diagnosis of IC depends on culture methods including culture of blood or
other samples collected under sterile conditions which are usually
considered as gold standards for IC, and nonculture diagnostic tests
including mannan and antimannan IgG tests, C. albicans germ tube
antibody (CAGTA), BDG and PCR-based assays, which are now entering
clinical practice as adjuncts to cultures
Song, 2020
3. COVID-19-associated Mucormycosis
• COVID-19–associated mucormycosis is less common than other COVID-19–
associated fungal infections. COVID-19 patients with trauma, diabetes mellitus, GC
use, HM, prolonged neutropenia, allo-HSCT, SOT are more likely to develop
mucormycosis
• Some medications used to treat severe COVID-19, including high-dose
corticosteroids and tocilizumab, might predispose patients with COVID-19 to
mucormycosis.
• The use of corticosteroids can also increase blood glucose levels to hyperglycemia
even though the individual is healthy, causing the condition called corticosteroid-
induced diabetes. This corticosteroid and the diabetogenic state later can cause
immunosuppression and hyperglycemia, increasing the growth of fungal infections,
including mucormycosis
J. Pemán et al, 2020
Pathophysiological
of
Mucormycosis

Muthu, 2021
4. Invasive Cryptococcosis

• COVID-19 patients with human immunodeficiency virus (HIV) infection

accompanied by CD4 + T lymphocyte count<200 cells/lL, allo-HSCT,
SOT, or other immune impaired are susceptible to cryptococcosis
which predominantly present as meningoencephalitis
• The diagnosis of cryptococcosis is usually based on a combination of
clinical and laboratory confirmation. The methods used to confirm the
infection are culture, direct microscopy, histopathology, serology, and
molecular detection

Song, 2020
The Fungal co-Infections
• we surmise that the fungal co-infections associated with global COVID-19
might be missed or misdiagnosed. Further, as a life-threatening infectious
disease, COVID-19 patients showed overexpression of inflammatory
cytokines, and impaired cell-mediated immune response with decreased
CD4 + T and CD8 + T cell counts, indicating its susceptibility to fungal
coinfection.
• Moreover, COVID-19 patients accompanied with immunocompromised
state, such as prolonged neutropenia, HSCT, GC use, SOT, inherited or
acquired immunodeficiencies, and tumor are more likely to develop fungal
co-infection.

Song et al, 2020

Diagnostic and
therapeutic pathway
for invasive fungal
co-infection
Diagnosis of co-infection in COVID-19
COVID 19 and Antimicrobial Resistance
• COVID 19 still treated with
Antibiotic broad spectrum
• COVID 19 is caused by virus
• Excessive use or inappropriate
use of antibiotic can cause
antimicrobial resistance

Langford BJ, So M, Raybardhan S, Leung V, Westwood D, MacFadden DR, et

al. Bacterial co-infection and secondary infection in patients with COVID-19:
a living rapid review and meta-analysis. Clinical Microbiology and Infection.
Prodia.co.i 2020 26(12):1622–9.
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The Need of Diagnosis
• Early diagnosis of co-infections
• Using methods capable of detecting broad range of potential
pathogens and antimicrobial resistance
• Diagnosis could start with symptoms and type of pathogen
• Bacterial pneumonia, seasonal respiratory virus, fungal pneumonia
have same clinical and radiological features with COVID19
• Difficulties in giving the right treatment without additional test
• Increased risk of mortality and morbidity if missed

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Prodia.co.i
Chen et al. 2020
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Diagnosis using PCT
• Procalcitonin (PCT)
• More accurate predictor than CRP in patients with community
acquired pneumonia (CAP) and Influenza

• Based on the research, PCT is superior to the other

biomarker in identifying COVID19 patients with bacterial
co-infection
• Based on this results, American thoracic society and
infectious disease society of America endorse
withholding of antibiotics in patients with non severe
COVID19 with low PCT levels
• The diagnosis should be made also with physician’s
judgment on the symptoms and the result to rule out all
possible result

Prodia.co.i Kaal A et al. 2021

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Diagnosis using Conventional Culture
• Conventional method
• Culture based method
• Long turnover time
• Samples : bronchial aspirates
• Semiquantitative methode
• Culture using Horse blood agar, salt-mannitol
agar, Herellea agar, Hamophilus chocolate
agar.
• Bacterial identification at species level MALDI
TOF MS
• Antimicrobial susceptibility testing : broth
microdilution method

Foschi C et al.2021
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Diagnosis using Film Array
• Molecular test provide rapid TAT, together
with identifications and semi quantitative
results for many pathogens responsive to
antibiotic therapy
• BioFire FilmArray Pneumonia Plus Panel
• Method : Multiplex PCR assay (1h)
• Check wide range of clinically relevant
pathogens and limited number of
antimicrobial resistance markers
• Film Array sensitivity 89.6% Specificity 98.3%
• Limitation : Missed several pathogens
(Stenotrophomonas matophillia, Citrobacter
koseri)

Foschi C et al.2021
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Diagnosis using Film Array

Prodia.co.i Video of Film Array Tech

d nology
Prodia.co.i Zhu X et al. 2020

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Diagnosis using Nanopore Technologies
• Nanopore sequencing
• Direct, real-time analysis of long DNA or RNA fragments
• Works by monitoring changes to an electrical current as
nucleic acids are passed through a protein nanopore. The
resulting signal is decoded to provide the specific DNA or
RNA sequence
Video of Nanopore seque
ncing

Prodia.co.i Zhu X et al. 2020

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Summary
• The co-infection between different microorganism and SARS-COV-2 is a serious problem. Co-
infections plays a crucial role, threating many COVID-19 patient’s lives.
• The pathogens of respiratory co-infections including bacteria, virus, fungus.
• Coinfection can increase the susceptibility of patients to severe disease by affecting the
body’s immune function
• Inappropriate use and excessive use of antibiotics could lead to AMR
• The clinical data of those will be a great value for guiding evidence-based treatment of
COVID19.
• Need a fast and accurate method to detect coinfection
• Physicians need to consider the use of antibiotics and not to apply it to all patients
COVID19.Prodia.co.i
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References
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