The Use of PCR for Respiratory Virus Detection on the Diagnosis and Treatment Decision of Respiratory Tract Infections in Iraq

Abstract

Diseases of the respiratory system are a common cause of antibiotic prescription in Iraq and worldwide. Technology has been recently used for its diagnosis, such as the Film Array Respiratory Panel. This study aims to identify the correlation between the diagnosis and treatment of respiratory tract infections with the result of polymerase chain reaction (PCR) for respiratory viruses. A descriptive, cross-sectional, retrospective study included 134 patients treated at Alkharama Hospital and the Private Hospital in Baghdad, Iraq, in the period from January 2020 to March 2020 For all cases, the results of the panel and the treatment received by the patients were analysed. 58% received antibiotic treatment upon admission, 13% combined treatment (antibiotic + antiviral), 27% received symptomatic treatment, and 2% were treated with the first-instance antiviral. After the result, 38% continued with antibiotics, 30% with antibiotics and antivirals, 13.8% with antivirals and 18.2% with symptomatic treatment. Despite the worldwide alarm over antimicrobial resistance, patients continue to be treated with antibiotics due to a situation that is influenced by several factors.

Full text

*Correspondence: hany_akeel2000@yahoo.com
(Received: October 12, 2021; accepted: November 29, 2021)
 Al-hussaniy HA, Altalebi RR, Albu-Rghaif AH, Abdul-Amir AGA. The Use of PCR for Respiratory Virus Detecon on the
Diagnosis and Treatment Decision of Respiratory Tract Infecons in Iraq. J Pure Appl Microbiol. Published online January 7,
2022. doi: 10.22207/JPAM.16.1.10
© The Author(s) 2022. Open Access. This arcle is distributed under the terms of the Creave Commons Aribuon 4.0 Internaonal License which
permits unrestricted use, sharing, distribuon, and reproducon in any medium, provided you give appropriate credit to the original author(s) and
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Al-hussaniy et al. | J Pure Appl Microbiol
Arcle 7368 | hps://doi.org/10.22207/JPAM.16.1.10
Print ISSN: 0973-7510; E-ISSN: 2581-690X
RESEARCH ARTICLE OPEN ACCESS
www.microbiologyjournal.org1Journal of Pure and Applied Microbiology

Diagnosis and Treatment Decision of Respiratory Tract

Hany Akeel Al-hussaniy1*, Raghid R. Altalebi2, Ali H. Albu-Rghaif3 
4
1Department of Clinical Pharmacy, Al-Karama Hospital, Baghdad, Iraq.
2College of Family Physicians of Canada, College of Physicians and Surgeons of Alberta, Canada.
3Department of Pharmacy, Ashur University Collage, Baghdad, Iraq.
4Department of Pharmacology, College of Pharmacy, University of Baghdad, Iraq.
Abstract

Technology has been recently used for its diagnosis, such as the Film Array Respiratory Panel. This study
 







  

Respiratory viral infecons, PR FilmArray, anbiocs, anmicrobial resistance

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Al-hussaniy et al. | J Pure Appl Microbiol | hps://doi.org/10.22207/JPAM.16.1.10
INTRODUCTION
Diseases of the respiratory system
represent one of the leading causes of medical
care in the world. They are common ailments
of all ages, whose aetiology varies according
to age, environmental circumstances, climate,
healthcare setting, and underlying diseases.1,2
Most respiratory infections only affect the
upper respiratory tract and can be considered
mild, benign, and self-limited (common cold,
rhinis, and pharyngotonsillis). In Iraq, acute
upper respiratory infection is considered the
leading cause of illness and a primary reason
for seeking medical attention. Respiratory
viruses are the main cause in up to 70–90%
of cases. Rhinovirus has been documented in
adulthood, followed by inuenza A and B viruses,
coronavirus, and adenovirus; the most common
in children are respiratory syncyal virus (RSV),
parainuenza virus 1,2,3, inuenza A and B virus,
adenovirus and rhinovirus. In a smaller proporon,
between 15 and 30% of cases in children and
between 5 and 20% in adults, the aeology is
bacterial: Streptococcus pyogenes, Streptococcus
pneumoniae, Mycoplasma pneumoniae, Neisseria
meningides, and Neisseria gonorrhoeae.3,4
However, only 5% Of respiratory diseases
it is esmated that may involve the lower and
middle respiratory tract (bronchis, bronchiolis,
and pneumonia); they are potenally more severe
and, most mes, require hospital admission.5 The
complications of these diseases in adulthood
are related to comorbidies in the paent and
senescence.2,6,7 Acute lower respiratory tract
infecons and other chronic lung diseases are
considered among the most common causes of
severe illness and death worldwide.8
In previous years, idenfying the aeology
of the virus was methodologically dicult, which
is why few hospitals followed this approach. In
recent years, techniques for diagnosing respiratory
tract infecons have advanced, currently using the
detecon of nucleic acids of the virus, with tests
such as polymerase chain reacon (PCR), with a
sensivity of 95–100% and 99–100% specicity.9
Because it is common for more than one virus to
be involved in these infecons, it was necessary to
design mulplex PCR methods in which dierent
viruses can be simultaneously idened.10 Other
options are PCR coupled to optical enzyme
immunoassay, which are systems for detecng
amplicaon products using probes immobilised
on a dierent chemical nature surface.1
The current use of anbiocs, anvirals,
and other anmicrobials are increasingly alarming.
However, it is known that anmicrobial resistance
is a phenomenon that appears naturally over me.
This process is accelerated by the inappropriate
use of anmicrobials, as well as their excessive
prescripon. The use of anbiocs is considered
unnecessary or inappropriate in up to half of the
paents.11-13
It is hoped that when the doctors have
studies to idenfy the possible aeology of the
respiratory infection being treated, they will
make more raonal use of anbiocs. This study
evaluated therapeutic behaviour in a private
hospital when a positive result was given in
idenfying respiratory viruses. The most frequent
viral agents and the respiratory pathologies in
those who underwent the test are described.

A descriptive, cross-sectional, and
retrospecve study was conducted. Paents of all
ages who had had posive respiratory virus results
in a mulplex PCR reacon test carried out in the
period from January 2020 to March 2020 were
selected from Al-karama hospital - Baghdad, Iraq.
All paents included in the study underwent a
respiratory virus PCR test during their hospital
stay. The Film Array Respiratory Panel® was used
(RP), a qualitative test for the simultaneous
detecon and idencaon of mulple nucleic
acids of viruses and bacteria in the nasopharyngeal
aspirate. A minimum sample volume of 0.3
ml (300 ml) was taken from each patient’s
respiratory tract. It is a test that simultaneously
identifies the following viruses and bacteria:
adenovirus, coronavirus 229E, coronavirus
HKU1, coronavirus NL63, coronavirus OC43,
inuenza A virus (with subtyping for hemagglunin
genes H1, H1-2009 and H3) and influenza B,
human metapneumovirus, parainuenza virus 1,
parainuenza 2, parainuenza 3, and parainuenza
4, respiratory syncytial virus, rhinovirus or
enterovirus, Bordetella pertussis, Chlamydophila
pneumoniae and Mycoplasma pneumoniae.
The sample was introduced into the
FilmArray RP cartridge, which was then placed

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in the FilmArray Module; a test report was
automacally generated at the end of the analysis.
The enre process takes about an hour. The test
has a sensivity and specicity of 95 and 99%,
respecvely.14
In each positive case, the following
were analysed: the clinical, radiological diagnosis
established by the treating physician, the
prescribed treatment, the behaviour regarding
the treatment that was followed when the test
result was obtained, the anmicrobial prescripon
me and the condions at the paent's discharge.
RESULTS
The initial sample consisted of 172
paents of all ages, of which 38 were excluded
due to not having complete medical records.
The nal sample was 134 paents, of
which 49.2% were men and 50.8% were women.
Patients of all ages were included: 56% were
infants, 16% preschool, 2% schoolchildren, 4%
adolescents, and 22% adults.
From the results of the viral panel, RSV
was idened in 25% of the samples, followed
by inuenza A (18%), rhinovirus or enterovirus
(10%), metapneumovirus (10%), inuenza B (9%),
parainuenza (5%), coronavirus (4%), B. pertussis
(2%), M. pneumoniae (1%) and in 16% of the
samples more than one virus was isolated (Fig. 1).
Radiological clinical diagnoses in all
patients were pneumonia in 42%, 10% with
bronchiolitis, 17% with influenza, 8% with
bronchis, asthmac aacks in 2%, rhinopharyngis
in 2%, 19% with other diagnoses.
Of all the paents, 58% received only
anbioc treatment upon admission, 13% received
combined treatment (antibiotic + antiviral),
27% received symptomac treatment, and 2%
were treated rst with an anviral as shown in
( Table 1).
Of the patients who initially received
anbiocs (71%), on obtaining the result of the
posive viral panel, only 10% disconnued this
Fig. 1. Percentage distribuon of viruses idened by a polymerase chain reacon in nasopharyngeal samples.
Table 1. Illustrate medicine received by the paent
upon admission to the hospital
Medicaon Number of Percentage
paents
received only anbioc 78 58%
anbioc + anviral 17 13%
symptomac treatment 37 27%
Anviral 3 2%
Total number of paents 134

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treatment; 2.3% connued only with the anviral
that was administered after their admission.
In 1.5%, the anbioc was suspended and an
anviral was added, and in 6.2%, the anbioc was
suspended, and they were treated symptomacally.
A total of 22% added anviral to the anbioc
treatment they already had and 8% connued
with combined treatment; 31% connued with
anbiocs only. 12% of the paents connued
only with symptomac treatment, 7% added an
anbioc to their symptomac treatment aer
the respiratory panel's posive result, and 10%
added anviral to the symptomac treatment.
Aer the posive result, 38% received
antibiotics as definitive treatment, 30% were
treated with combined therapy (antibiotic +
anviral), 13.8% were treated with anviral alone,
and 18.2% symptomacally (Fig. 2).
Of the 68% of patients who received
anbiocs empirically or as denive treatment,
41% received more than one anbioc during their
hospital stay. As monotherapy or associated with
another anbioc, 45% received a cephalosporin,
17% macrolides, 11% quinolones, and 5% others
as shown in (table 2). In 39% of the paents,
diagnoses or laboratory studies (such as a culture
of bronchial secreon) were found that jused
the use of anbiocs.
The days of hospital stay in paents who
received anbioc treatment despite obtaining
a positive viral panel (38%) were reported
between 5 to 6 days and 30% who were treated
with anbiocs and anvirals. In the 13.8% who
received anviral treatment, the stay ranged from
3 to 4 days. In those who received symptomac
treatment, their hospital stays ranged from 4 to 5
days. There were two deaths (1.5%), one paent
required transfer to a high speciality unit, and 131
did not present complicaons and were discharged
due to improvement.
DISCUSSION
Several studies show a high prevalence
of viral agents as the cause of acute respiratory
processes in adult and paediatric paents, leading
to hospitalisaon.15,16
Knowing the aeology and clinical picture
of respiratory diseases, supported by current
Table 2. Illustrate the anbioc category prescribed
to the paent
Type of Paent (percentage Mostly used
anbioc to total paent) anbioc
Cephalosporin 60(45%) Ceriaxone
Macrolides 23(17%) azithromycin
Quinolones 15(11%) Levooxacin
Other anbioc 7(5%) Metronidazole
Fig. 2. Final treatment received by paents despite having a posive virus report.

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methods for their diagnosis, should facilitate
decision-making on the appropriate treatment for
each paent. When the clinical picture adequately
correlates with the laboratory ndings, the doctor
has the elements to support his therapeutic
decision.6
This study evaluated how much a posive
result of the respiratory panel by PCR inuences
the treatment that the paents received.
At a global level, reducing the use of
anbiocs by having a posive result in a viral
panel is variable. In a study in Sweden of paents
identified with a virus, 21% were definitively
treated with anbiocs.10 In the present study,
71% of the paents received an anbioc upon
admission, and 68% received it as definitive
treatment, even though they subsequently had a
posive result for the virus. The result is similar to
the experience of outpaents in Sri Lanka.17 During
the endemic inuenza season, detecng the virus
made it possible to reduce the use of anbiocs by
20%, from 83.7 to 62.3%, despite a posive test for
inuenza. The high volume of paents and the fear
of bacterial superinfecon were important factors
in the excessive use of anbiocs in that study.
The design in our study does not allow us
to know the factors that inuenced the treang
physicians to connue prescribing anbiocs. In
39% of the les, some juscaon for its use was
found due to bacterial superinfecon, but no data
of greater severity were found. Perhaps the most
inuencing factor was the hospitalisaon of the
paents. The anbiocs that were used the most
as denive treatment were cephalosporins (45%)
and macrolides (17%).
In the analysed samples, we had a
predominance of RSV in 25%, followed by
inuenza A with 18% and B with 9%; in 16% of the
samples, more than one virus was detected. In a
study conducted in our country on paents with
inuenza-like illness, the proporon of viruses
idened was predominantly rhinovirus (36.5%),
followed by influenza (22.6%), coronavirus
(17.9%) and RSV (14.2%). Although the samples
appear to correspond to this inuenza, 47% were
hospitalized.17 This reects the wide circulaon
of respiratory viruses, which can condition
moderate-to-severe symptoms that require
hospital management. In particular, RSV and
the inuenza virus tend to cause more serious
conditions. In the winter season, rhinoviruses
predominate. However, in cases with community
pneumonia or a respiratory infecon requiring
hospitalisation, the influenza virus, RSV, and
metapneumovirus predominate.18,19 There is a
discrepancy as to whether viral coinfecons can
cause a more serious course of infecon. 18,19
Although antimicrobial resistance
is currently one of the leading public health
problems in the world,12 its prescripon connues
without reason. It is necessary to give the correct
weight to the associaon of laboratory studies
that detect viruses in patients with moderate
to severe respiratory infections and to accept
that in the highest percentage of these cases,
the use of anmicrobials is not required. Some
studies nd respiratory viruses in paents with
community pneumonia and paents with severe
respiratory infections requiring intensive care
management in which no bacterial associaon
was demonstrated.20,21 The medical behaviour
regarding their therapeuc decision in a private
hospital shows that despite having carried out a
study to search for viruses as the cause of acute
respiratory infecon, the results obtained were not
used to generate a modicaon regarding the use
of anbiocs.
It will be necessary to know the reasons
that lead to the continuation of antimicrobial
management, even in the presence of viral
aetiology. Probably there is no confidence in
laboratory studies because their sensivity and
specicity are unknown. There is also a fear of not
oering a treatment ‘that can cure the infecon’,
primarily because few anviral alternaves exist.
There is intense family pressure because, in private
hospitals, the doctor is the caregiver and assumes
the decisions and responsibilies for their paent.
Greater disseminaon of informaon is required
on the participation of viruses in respiratory
infecons of moderate-to-severe evoluon that
does not require antimicrobial treatment. It
probably takes me to accept the usefulness of
the new diagnosc laboratory techniques that
have recently been incorporated into hospitals.

The authors would like to thank
Dr. Al-kuraishy Haidar for his support during the
study.

www.microbiologyjournal.org6Journal of Pure and Applied Microbiology
Al-hussaniy et al. | J Pure Appl Microbiol | hps://doi.org/10.22207/JPAM.16.1.10
CONFLICT OF INTEREST
The authors declare that there is no
conict of interest.
AUTHORS’ CONTRIBUTION
All authors listed have made a substanal,
direct and intellectual contribuon to the work and
approved it for publicaon.
FUNDING
None.
DATA AVAILABILITY
All datasets generated or analysed during
this study are included in the manuscript.

The study was approved by the
Institutional Ethics Committee of Alkarama
hospital and the University of Baghdad, School of
Medicine (approval number; 11942, 21/2/2019).
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