Indian Journal of Medical Microbiology 48 (2024) 100548
Contents lists available at ScienceDirect
Indian Journal of Medical Microbiology
journal homepage: www.journals.elsevier.com/indian-journal-of-medical-microbiology
Special Article
Approach towards surveillance-based diagnosis of acute respiratory illness
in India: Expert recommendations
Vikas Manchanda a, *, 1, Jayshree Muralidharan b, **, 1, Neeraj Nischal c, 1, Kshitij Aggarwal d, 1,
Swati Gupta e, Nivedita Gupta f, Anoop Velayudhan f, Harmanmeet Kaur f, Megha Brijwal g,
Mala Chhabra h, Rajlakshmi Vishwanathan i, Rahul Dhodapkar j, Sanjay K. Mahajan k,
Saumya Deol f, Jerin C. Sekhar l, Srestha Mitra a, Sonal Saxena a, Jyoti Kumar e, Anju Garg e,
Rakesh Lodha m, V. Ravi n, Manish Soneja c, Valsan Philip Verghese o, Camilla Rodrigues p
a
Department of Microbiology, Maulana Azad Medical College, Delhi, India
b
Department of Pediatric Medicine (Advanced Pediatric Centre), PGIMER, Chandigarh, India
c
Department of Medicine, All India Institute of Medical Sciences (AIIMS), Delhi, India
d
Department of Pulmonary and Critical Care Medicine, Institute of Heart and Lung Diseases, Bahadurgarh, Haryana, India
e
Department of Radiodiagnosis, Maulana Azad Medical College, Delhi, India
f
Division of Epidemiology & Communicable Diseases, ICMR Headquarters, New Delhi, India
g
Department of Microbiology, All India Institute of Medical Sciences (AIIMS), Delhi, India
h
Department of Microbiology, Atal Bihari Vajpayee Institute of Medical Sciences (ABVIMS) and Dr. Ram Manohar Lohia Hospital (RML), Delhi, India
i
Bacteriology Group, National Institute of Virology (ICMR-NIV), Pune, India
j
Department of Microbiology, JIPMER, Puducherry, India
k
Department of Medicine, Indira Gandhi Medical College & Hospital (IGMC), Shimla, India
l
Pediatric Critical Care, PGIMER, Chandigarh, India
m
Department of Pediatrics, All India Institute of Medical Sciences (AIIMS), Delhi, India
n
Department of Neurovirology, NIMHANS, Bengaluru, India
o
Pediatric Infectious Diseases, Christian Medical College (CMC), Vellore, India
p
PD Hinduja Hospital, Mahim, Mumbai, India
A R T I C L E I N F O A B S T R A C T
Keywords: Background: Emerging infectious diseases, often zoonotic, demand a collaborative “One-Health” surveillance
Acute respiratory illness approach due to human activities. The need for standardized diagnostic and surveillance algorithms is empha
One health sized to address the difficulty in clinical differentiation and curb antimicrobial resistance.
Outbreaks
Objective: The present recommendations are comprehensive diagnostic and surveillance algorithm for ARIs,
Diagnostic algorithm
ICMR
developed by the Indian Council of Medical Research (ICMR), which aims to enhance early detection and
treatment with improved surveillance. This algorithm shall be serving as a blueprint for respiratory infections
landscape in the country and early detection of surge of respiratory infections in the country.
Content: The ICMR has risen up to the threat of emerging and re-emerging infections. Here, we seek to recom
mend a structured approach for diagnosing respiratory illnesses. The recommendations emphasize the signifi
cance of prioritizing respiratory pathogens based on factors such as the frequency of occurrence (seasonal or
geographical), disease severity, ease of diagnosis and public health importance. The proposed surveillance-based
diagnostic algorithm for ARI relies on a combination of gold-standard conventional methods, innovative sero
logical and molecular techniques, as well as radiological approaches, which collectively contribute to the
detection of various causative agents.
Abbreviations: ARI, Acute Respiratory Infections; SARI, Severe acute respiratory infection; LMIC, low-middle income countries; ICMR, Indian Council of Medical
Research; WHO, World Health organization; ILI, Influenza-like Illness; URTI, Upper respiratory tract infection; LRTI, Lower respiratory tract infection; PCP, Pneu
mocystis jirovecii pneumonia; CRP, C-reactive protein; PCT, procalcitonin; CT, Computed Tomography; TLC, Total Leucocyte Count.
* Corresponding author. Department of Microbiology, Maulana Azad Medical College, Delhi, India.
** Corresponding author. Chief Pediatric Emergency and Intensive Care Units, Advanced Pediatric Centre, PGIMER, Chandigarh, India.
E-mail addresses: (V. Manchanda), , (J. Muralidharan).
1
Shared First Authors.
https://doi.org/10.1016/j.ijmmb.2024.100548
Received 22 December 2023; Received in revised form 15 February 2024; Accepted 19 February 2024
Available online 3 March 2024
0255-0857/© 2024 Indian Association of Medical Microbiologists. Published by Elsevier B.V. All rights reserved.
Downloaded for Anonymous User (n/a) at All India Institute of Medical Sciences - Jodhpur from ClinicalKey.com by Elsevier on
April 30, 2024. For personal use only. No other uses without permission. Copyright ©2024. Elsevier Inc. All rights reserved.
, V. Manchanda et al. Indian Journal of Medical Microbiology 48 (2024) 100548
The diagnostic part of the integrated algorithm can be dealt at the local microbiology laboratory of the
healthcare facility with the few positive and negative specimens shipped to linked viral disease research labo
ratories (VRDLs) and other ICMR designated laboratories for genome characterisation, cluster identification and
identification of novel agents.
1. Introduction consisting of frontline clinical microbiologists, infectious disease spe
cialists of adult and pediatric age group specialty and experienced ra
Acute Respiratory Infections (ARI) constitute a silent but ever- diologists to develop the diagnostic algorithm (Fig. 1.)
prevalent global epidemic with profound health, economic, and socie Regularly scheduled meetings were held between the groups, from
tal consequences, being a major cause of mortality among children August 2022 to February 2023, with detailed discussions to ensure the
worldwide with an estimated 740,000 deaths in children under five development of a comprehensive algorithm for the early detection of
years of age [1]. In India, pneumonia is the single largest contributor to cases. The practical guidelines for the diagnosis and management of
under-five mortality (17.1%) [2]. Severe acute respiratory infection acute respiratory infections in adults [8–11] and children [11–14] were
(SARI) has been considered an important contributor to preventable reviewed from various sources.
morbidity and mortality in all age groups, particularly in children under
5 years, the elderly, and individuals with compromised immunity and 3. Priority pathogens
underlying cardiac, respiratory and renal co-morbidities. It is estimated
that SARI causes approximately 4.2 million deaths annually; of which Various viral and bacterial pathogens are associated with severe
90% occur in low-middle income countries (LMIC) [3]. acute respiratory infections (SARI). Due to their extremely high poten
Many newly emerging infectious diseases are zoonotic, the driving tial for human-to-human transmission, these pathogens pose a sub
force of which can be linked to human activities such as urbanization, stantial risk to human health. The potential viral pathogens of ARIs
alterations in ecosystems, and intensification of international travel and include seasonal A and B influenza viruses, human metapneumovirus
trade. To effectively tackle this issue, a collaborative and interdisci (HMPV), human rhinovirus (HRV), human adenovirus (HAdV), human
plinary One Health surveillance program is essential [4]. The emergence parainfluenza viruses (HPIV), respiratory syncytial virus (RSV), human
of outbreaks and pandemics caused by respiratory viruses has brought to bocavirus (HBoV), human coronaviruses (HCoVs) and enterovirus (EV).
the fore the need for building capacities (both for healthcare settings and ARIs can also result from infection with bacteria such as Streptococcus
providers) to establish and sustain a response system. Diagnostic and pneumoniae, Staphylococcus aureus and Haemophilus influenzae [3].
surveillance algorithms for acute respiratory illnesses will ensure uni Recent evidence from Delhi shows Chlamydia pneumoniae, Escherichia
formity in approach across healthcare settings [5]. coli, and Mycoplasma pneumoniae cause more than 10% of pneumonia
Acute respiratory infections are usually caused by either viral or individually, whereas these were described as rare pathogens in the past
bacterial pathogens or both, and rarely by fungi and parasites. Clinical [15,16]. Among adults, acute respiratory illness is primarily attributed
differentiation is difficult given the frequently overlapping and non- to the Influenza B virus, human rhinovirus and human parainfluenza
specific clinical presentations, leading to the overuse of antibiotics virus (1–3). For individuals with chronic pulmonary diseases, atypical
that further contribute to the development of antimicrobial resistance bacteria like Mycoplasma pneumoniae emerge as a significant causative
[6]. The current understanding of acute respiratory infections (ARIs) factor, as illustrated in the Supplementary Table 1. The introduction of
may have some gaps that could benefit from the development of a molecular diagnostic techniques has led to the increasing identification
diagnostic algorithm that incorporates uncommon and atypical clinical of Cytomegalovirus, respiratory illnesses caused by endemic mycoses
presentations of both common and uncommon pathogens will guide and Pneumocystis jirovecii. These agents, once predominantly found in
clinicians to consider a broad range of possibilities and improve diag immunocompromised individuals, are now frequently detected in
nostic accuracy. Risk stratification by an algorithm based on severity of immunocompetent adults (unpublished data).
disease, comorbidities of patients and identification of emerging path The data reviewed from existing published studies (Supplementary
ogens would prompt immediate containment and appropriate manage Table 1) and recent studies done by one of the ICMR centers on the
ment measures. There is also an urgent need for rapid and accurate virological profile of pathogens causing acute respiratory illness in
diagnostic tests that are both cost-effective and applicable across various children [17] and adults (unpublished data) were reviewed for priori
healthcare settings, especially in LMIC [7]. tization of pathogens causing infections. The aetiology of pneumonia
The Indian Council of Medical Research (ICMR) has risen up to the and its association with adverse outcomes in patients were discussed,
threat of emerging and re-emerging infections by addressing the gaps keeping in mind the rapid urbanization and change in the topography of
and proposing a well-designed diagnostic algorithm for acute respira the most populous country - India. There was a consensus about the need
tory illnesses which could enhance early detection and appropriate to prioritize respiratory pathogens based on the frequency of occur
treatment, ultimately leading to improved patient outcomes. The pro rence, disease severity, ease of diagnosis and their public health
posed algorithm will also serve as a blueprint for defining the landscape importance (Table 1).
of respiratory infections in the country and will help early identification
of future outbreaks. As a part of this effort, ICMR has proposed to un 4. Diagnosis of acute respiratory illness
dertake systematic One Health surveillance at interfaces with increased
animal-human-bird interaction. This review aims to provide a structured 4.1. Establishment of clinical diagnosis and severity of illness
approach for the diagnosis of patients suffering from acute respiratory
infections to rapidly and adequately manage the disease. The committees also recognized the need for the establishment of a
network of laboratories for detection of respiratory pathogens with the
2. Developing the algorithm extension of existing influenza surveillance or the establishment of a
new network altogether for detection of extended pathogens in patients
A syndromic diagnostic algorithm for the detection of priority presenting with Influenza-like illness (ILI) and severe acute respiratory
pathogens, both novel and re-emerging, causing acute respiratory in infection (SARI) based on the surveillance definitions given by WHO, in
fections for both children and adults was developed. The ICMR secre adults [8]. Similarly, the development of a surveillance network in
tariat formulated the Core Committee and the Expert Committee children for acute respiratory illnesses was considered which would
2
Downloaded for Anonymous User (n/a) at All India Institute of Medical Sciences - Jodhpur from ClinicalKey.com by Elsevier on
April 30, 2024. For personal use only. No other uses without permission. Copyright ©2024. Elsevier Inc. All rights reserved.
Contents lists available at ScienceDirect
Indian Journal of Medical Microbiology
journal homepage: www.journals.elsevier.com/indian-journal-of-medical-microbiology
Special Article
Approach towards surveillance-based diagnosis of acute respiratory illness
in India: Expert recommendations
Vikas Manchanda a, *, 1, Jayshree Muralidharan b, **, 1, Neeraj Nischal c, 1, Kshitij Aggarwal d, 1,
Swati Gupta e, Nivedita Gupta f, Anoop Velayudhan f, Harmanmeet Kaur f, Megha Brijwal g,
Mala Chhabra h, Rajlakshmi Vishwanathan i, Rahul Dhodapkar j, Sanjay K. Mahajan k,
Saumya Deol f, Jerin C. Sekhar l, Srestha Mitra a, Sonal Saxena a, Jyoti Kumar e, Anju Garg e,
Rakesh Lodha m, V. Ravi n, Manish Soneja c, Valsan Philip Verghese o, Camilla Rodrigues p
a
Department of Microbiology, Maulana Azad Medical College, Delhi, India
b
Department of Pediatric Medicine (Advanced Pediatric Centre), PGIMER, Chandigarh, India
c
Department of Medicine, All India Institute of Medical Sciences (AIIMS), Delhi, India
d
Department of Pulmonary and Critical Care Medicine, Institute of Heart and Lung Diseases, Bahadurgarh, Haryana, India
e
Department of Radiodiagnosis, Maulana Azad Medical College, Delhi, India
f
Division of Epidemiology & Communicable Diseases, ICMR Headquarters, New Delhi, India
g
Department of Microbiology, All India Institute of Medical Sciences (AIIMS), Delhi, India
h
Department of Microbiology, Atal Bihari Vajpayee Institute of Medical Sciences (ABVIMS) and Dr. Ram Manohar Lohia Hospital (RML), Delhi, India
i
Bacteriology Group, National Institute of Virology (ICMR-NIV), Pune, India
j
Department of Microbiology, JIPMER, Puducherry, India
k
Department of Medicine, Indira Gandhi Medical College & Hospital (IGMC), Shimla, India
l
Pediatric Critical Care, PGIMER, Chandigarh, India
m
Department of Pediatrics, All India Institute of Medical Sciences (AIIMS), Delhi, India
n
Department of Neurovirology, NIMHANS, Bengaluru, India
o
Pediatric Infectious Diseases, Christian Medical College (CMC), Vellore, India
p
PD Hinduja Hospital, Mahim, Mumbai, India
A R T I C L E I N F O A B S T R A C T
Keywords: Background: Emerging infectious diseases, often zoonotic, demand a collaborative “One-Health” surveillance
Acute respiratory illness approach due to human activities. The need for standardized diagnostic and surveillance algorithms is empha
One health sized to address the difficulty in clinical differentiation and curb antimicrobial resistance.
Outbreaks
Objective: The present recommendations are comprehensive diagnostic and surveillance algorithm for ARIs,
Diagnostic algorithm
ICMR
developed by the Indian Council of Medical Research (ICMR), which aims to enhance early detection and
treatment with improved surveillance. This algorithm shall be serving as a blueprint for respiratory infections
landscape in the country and early detection of surge of respiratory infections in the country.
Content: The ICMR has risen up to the threat of emerging and re-emerging infections. Here, we seek to recom
mend a structured approach for diagnosing respiratory illnesses. The recommendations emphasize the signifi
cance of prioritizing respiratory pathogens based on factors such as the frequency of occurrence (seasonal or
geographical), disease severity, ease of diagnosis and public health importance. The proposed surveillance-based
diagnostic algorithm for ARI relies on a combination of gold-standard conventional methods, innovative sero
logical and molecular techniques, as well as radiological approaches, which collectively contribute to the
detection of various causative agents.
Abbreviations: ARI, Acute Respiratory Infections; SARI, Severe acute respiratory infection; LMIC, low-middle income countries; ICMR, Indian Council of Medical
Research; WHO, World Health organization; ILI, Influenza-like Illness; URTI, Upper respiratory tract infection; LRTI, Lower respiratory tract infection; PCP, Pneu
mocystis jirovecii pneumonia; CRP, C-reactive protein; PCT, procalcitonin; CT, Computed Tomography; TLC, Total Leucocyte Count.
* Corresponding author. Department of Microbiology, Maulana Azad Medical College, Delhi, India.
** Corresponding author. Chief Pediatric Emergency and Intensive Care Units, Advanced Pediatric Centre, PGIMER, Chandigarh, India.
E-mail addresses: (V. Manchanda), , (J. Muralidharan).
1
Shared First Authors.
https://doi.org/10.1016/j.ijmmb.2024.100548
Received 22 December 2023; Received in revised form 15 February 2024; Accepted 19 February 2024
Available online 3 March 2024
0255-0857/© 2024 Indian Association of Medical Microbiologists. Published by Elsevier B.V. All rights reserved.
Downloaded for Anonymous User (n/a) at All India Institute of Medical Sciences - Jodhpur from ClinicalKey.com by Elsevier on
April 30, 2024. For personal use only. No other uses without permission. Copyright ©2024. Elsevier Inc. All rights reserved.
, V. Manchanda et al. Indian Journal of Medical Microbiology 48 (2024) 100548
The diagnostic part of the integrated algorithm can be dealt at the local microbiology laboratory of the
healthcare facility with the few positive and negative specimens shipped to linked viral disease research labo
ratories (VRDLs) and other ICMR designated laboratories for genome characterisation, cluster identification and
identification of novel agents.
1. Introduction consisting of frontline clinical microbiologists, infectious disease spe
cialists of adult and pediatric age group specialty and experienced ra
Acute Respiratory Infections (ARI) constitute a silent but ever- diologists to develop the diagnostic algorithm (Fig. 1.)
prevalent global epidemic with profound health, economic, and socie Regularly scheduled meetings were held between the groups, from
tal consequences, being a major cause of mortality among children August 2022 to February 2023, with detailed discussions to ensure the
worldwide with an estimated 740,000 deaths in children under five development of a comprehensive algorithm for the early detection of
years of age [1]. In India, pneumonia is the single largest contributor to cases. The practical guidelines for the diagnosis and management of
under-five mortality (17.1%) [2]. Severe acute respiratory infection acute respiratory infections in adults [8–11] and children [11–14] were
(SARI) has been considered an important contributor to preventable reviewed from various sources.
morbidity and mortality in all age groups, particularly in children under
5 years, the elderly, and individuals with compromised immunity and 3. Priority pathogens
underlying cardiac, respiratory and renal co-morbidities. It is estimated
that SARI causes approximately 4.2 million deaths annually; of which Various viral and bacterial pathogens are associated with severe
90% occur in low-middle income countries (LMIC) [3]. acute respiratory infections (SARI). Due to their extremely high poten
Many newly emerging infectious diseases are zoonotic, the driving tial for human-to-human transmission, these pathogens pose a sub
force of which can be linked to human activities such as urbanization, stantial risk to human health. The potential viral pathogens of ARIs
alterations in ecosystems, and intensification of international travel and include seasonal A and B influenza viruses, human metapneumovirus
trade. To effectively tackle this issue, a collaborative and interdisci (HMPV), human rhinovirus (HRV), human adenovirus (HAdV), human
plinary One Health surveillance program is essential [4]. The emergence parainfluenza viruses (HPIV), respiratory syncytial virus (RSV), human
of outbreaks and pandemics caused by respiratory viruses has brought to bocavirus (HBoV), human coronaviruses (HCoVs) and enterovirus (EV).
the fore the need for building capacities (both for healthcare settings and ARIs can also result from infection with bacteria such as Streptococcus
providers) to establish and sustain a response system. Diagnostic and pneumoniae, Staphylococcus aureus and Haemophilus influenzae [3].
surveillance algorithms for acute respiratory illnesses will ensure uni Recent evidence from Delhi shows Chlamydia pneumoniae, Escherichia
formity in approach across healthcare settings [5]. coli, and Mycoplasma pneumoniae cause more than 10% of pneumonia
Acute respiratory infections are usually caused by either viral or individually, whereas these were described as rare pathogens in the past
bacterial pathogens or both, and rarely by fungi and parasites. Clinical [15,16]. Among adults, acute respiratory illness is primarily attributed
differentiation is difficult given the frequently overlapping and non- to the Influenza B virus, human rhinovirus and human parainfluenza
specific clinical presentations, leading to the overuse of antibiotics virus (1–3). For individuals with chronic pulmonary diseases, atypical
that further contribute to the development of antimicrobial resistance bacteria like Mycoplasma pneumoniae emerge as a significant causative
[6]. The current understanding of acute respiratory infections (ARIs) factor, as illustrated in the Supplementary Table 1. The introduction of
may have some gaps that could benefit from the development of a molecular diagnostic techniques has led to the increasing identification
diagnostic algorithm that incorporates uncommon and atypical clinical of Cytomegalovirus, respiratory illnesses caused by endemic mycoses
presentations of both common and uncommon pathogens will guide and Pneumocystis jirovecii. These agents, once predominantly found in
clinicians to consider a broad range of possibilities and improve diag immunocompromised individuals, are now frequently detected in
nostic accuracy. Risk stratification by an algorithm based on severity of immunocompetent adults (unpublished data).
disease, comorbidities of patients and identification of emerging path The data reviewed from existing published studies (Supplementary
ogens would prompt immediate containment and appropriate manage Table 1) and recent studies done by one of the ICMR centers on the
ment measures. There is also an urgent need for rapid and accurate virological profile of pathogens causing acute respiratory illness in
diagnostic tests that are both cost-effective and applicable across various children [17] and adults (unpublished data) were reviewed for priori
healthcare settings, especially in LMIC [7]. tization of pathogens causing infections. The aetiology of pneumonia
The Indian Council of Medical Research (ICMR) has risen up to the and its association with adverse outcomes in patients were discussed,
threat of emerging and re-emerging infections by addressing the gaps keeping in mind the rapid urbanization and change in the topography of
and proposing a well-designed diagnostic algorithm for acute respira the most populous country - India. There was a consensus about the need
tory illnesses which could enhance early detection and appropriate to prioritize respiratory pathogens based on the frequency of occur
treatment, ultimately leading to improved patient outcomes. The pro rence, disease severity, ease of diagnosis and their public health
posed algorithm will also serve as a blueprint for defining the landscape importance (Table 1).
of respiratory infections in the country and will help early identification
of future outbreaks. As a part of this effort, ICMR has proposed to un 4. Diagnosis of acute respiratory illness
dertake systematic One Health surveillance at interfaces with increased
animal-human-bird interaction. This review aims to provide a structured 4.1. Establishment of clinical diagnosis and severity of illness
approach for the diagnosis of patients suffering from acute respiratory
infections to rapidly and adequately manage the disease. The committees also recognized the need for the establishment of a
network of laboratories for detection of respiratory pathogens with the
2. Developing the algorithm extension of existing influenza surveillance or the establishment of a
new network altogether for detection of extended pathogens in patients
A syndromic diagnostic algorithm for the detection of priority presenting with Influenza-like illness (ILI) and severe acute respiratory
pathogens, both novel and re-emerging, causing acute respiratory in infection (SARI) based on the surveillance definitions given by WHO, in
fections for both children and adults was developed. The ICMR secre adults [8]. Similarly, the development of a surveillance network in
tariat formulated the Core Committee and the Expert Committee children for acute respiratory illnesses was considered which would
2
Downloaded for Anonymous User (n/a) at All India Institute of Medical Sciences - Jodhpur from ClinicalKey.com by Elsevier on
April 30, 2024. For personal use only. No other uses without permission. Copyright ©2024. Elsevier Inc. All rights reserved.
