Journal of Clinical and Diagnostic Research, ISSN - 0973 - 709X

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Dr Mohan Z Mani

"Thank you very much for having published my article in record time.I would like to compliment you and your entire staff for your promptness, courtesy, and willingness to be customer friendly, which is quite unusual.I was given your reference by a colleague in pathology,and was able to directly phone your editorial office for clarifications.I would particularly like to thank the publication managers and the Assistant Editor who were following up my article. I would also like to thank you for adjusting the money I paid initially into payment for my modified article,and refunding the balance.
I wish all success to your journal and look forward to sending you any suitable similar article in future"



Dr Mohan Z Mani,
Professor & Head,
Department of Dermatolgy,
Believers Church Medical College,
Thiruvalla, Kerala
On Sep 2018




Prof. Somashekhar Nimbalkar

"Over the last few years, we have published our research regularly in Journal of Clinical and Diagnostic Research. Having published in more than 20 high impact journals over the last five years including several high impact ones and reviewing articles for even more journals across my fields of interest, we value our published work in JCDR for their high standards in publishing scientific articles. The ease of submission, the rapid reviews in under a month, the high quality of their reviewers and keen attention to the final process of proofs and publication, ensure that there are no mistakes in the final article. We have been asked clarifications on several occasions and have been happy to provide them and it exemplifies the commitment to quality of the team at JCDR."



Prof. Somashekhar Nimbalkar
Head, Department of Pediatrics, Pramukhswami Medical College, Karamsad
Chairman, Research Group, Charutar Arogya Mandal, Karamsad
National Joint Coordinator - Advanced IAP NNF NRP Program
Ex-Member, Governing Body, National Neonatology Forum, New Delhi
Ex-President - National Neonatology Forum Gujarat State Chapter
Department of Pediatrics, Pramukhswami Medical College, Karamsad, Anand, Gujarat.
On Sep 2018




Dr. Kalyani R

"Journal of Clinical and Diagnostic Research is at present a well-known Indian originated scientific journal which started with a humble beginning. I have been associated with this journal since many years. I appreciate the Editor, Dr. Hemant Jain, for his constant effort in bringing up this journal to the present status right from the scratch. The journal is multidisciplinary. It encourages in publishing the scientific articles from postgraduates and also the beginners who start their career. At the same time the journal also caters for the high quality articles from specialty and super-specialty researchers. Hence it provides a platform for the scientist and researchers to publish. The other aspect of it is, the readers get the information regarding the most recent developments in science which can be used for teaching, research, treating patients and to some extent take preventive measures against certain diseases. The journal is contributing immensely to the society at national and international level."



Dr Kalyani R
Professor and Head
Department of Pathology
Sri Devaraj Urs Medical College
Sri Devaraj Urs Academy of Higher Education and Research , Kolar, Karnataka
On Sep 2018




Dr. Saumya Navit

"As a peer-reviewed journal, the Journal of Clinical and Diagnostic Research provides an opportunity to researchers, scientists and budding professionals to explore the developments in the field of medicine and dentistry and their varied specialities, thus extending our view on biological diversities of living species in relation to medicine.
‘Knowledge is treasure of a wise man.’ The free access of this journal provides an immense scope of learning for the both the old and the young in field of medicine and dentistry as well. The multidisciplinary nature of the journal makes it a better platform to absorb all that is being researched and developed. The publication process is systematic and professional. Online submission, publication and peer reviewing makes it a user-friendly journal.
As an experienced dentist and an academician, I proudly recommend this journal to the dental fraternity as a good quality open access platform for rapid communication of their cutting-edge research progress and discovery.
I wish JCDR a great success and I hope that journal will soar higher with the passing time."



Dr Saumya Navit
Professor and Head
Department of Pediatric Dentistry
Saraswati Dental College
Lucknow
On Sep 2018




Dr. Arunava Biswas

"My sincere attachment with JCDR as an author as well as reviewer is a learning experience . Their systematic approach in publication of article in various categories is really praiseworthy.
Their prompt and timely response to review's query and the manner in which they have set the reviewing process helps in extracting the best possible scientific writings for publication.
It's a honour and pride to be a part of the JCDR team. My very best wishes to JCDR and hope it will sparkle up above the sky as a high indexed journal in near future."



Dr. Arunava Biswas
MD, DM (Clinical Pharmacology)
Assistant Professor
Department of Pharmacology
Calcutta National Medical College & Hospital , Kolkata




Dr. C.S. Ramesh Babu
" Journal of Clinical and Diagnostic Research (JCDR) is a multi-specialty medical and dental journal publishing high quality research articles in almost all branches of medicine. The quality of printing of figures and tables is excellent and comparable to any International journal. An added advantage is nominal publication charges and monthly issue of the journal and more chances of an article being accepted for publication. Moreover being a multi-specialty journal an article concerning a particular specialty has a wider reach of readers of other related specialties also. As an author and reviewer for several years I find this Journal most suitable and highly recommend this Journal."
Best regards,
C.S. Ramesh Babu,
Associate Professor of Anatomy,
Muzaffarnagar Medical College,
Muzaffarnagar.
On Aug 2018




Dr. Arundhathi. S
"Journal of Clinical and Diagnostic Research (JCDR) is a reputed peer reviewed journal and is constantly involved in publishing high quality research articles related to medicine. Its been a great pleasure to be associated with this esteemed journal as a reviewer and as an author for a couple of years. The editorial board consists of many dedicated and reputed experts as its members and they are doing an appreciable work in guiding budding researchers. JCDR is doing a commendable job in scientific research by promoting excellent quality research & review articles and case reports & series. The reviewers provide appropriate suggestions that improve the quality of articles. I strongly recommend my fraternity to encourage JCDR by contributing their valuable research work in this widely accepted, user friendly journal. I hope my collaboration with JCDR will continue for a long time".



Dr. Arundhathi. S
MBBS, MD (Pathology),
Sanjay Gandhi institute of trauma and orthopedics,
Bengaluru.
On Aug 2018




Dr. Mamta Gupta,
"It gives me great pleasure to be associated with JCDR, since last 2-3 years. Since then I have authored, co-authored and reviewed about 25 articles in JCDR. I thank JCDR for giving me an opportunity to improve my own skills as an author and a reviewer.
It 's a multispecialty journal, publishing high quality articles. It gives a platform to the authors to publish their research work which can be available for everyone across the globe to read. The best thing about JCDR is that the full articles of all medical specialties are available as pdf/html for reading free of cost or without institutional subscription, which is not there for other journals. For those who have problem in writing manuscript or do statistical work, JCDR comes for their rescue.
The journal has a monthly publication and the articles are published quite fast. In time compared to other journals. The on-line first publication is also a great advantage and facility to review one's own articles before going to print. The response to any query and permission if required, is quite fast; this is quite commendable. I have a very good experience about seeking quick permission for quoting a photograph (Fig.) from a JCDR article for my chapter authored in an E book. I never thought it would be so easy. No hassles.
Reviewing articles is no less a pain staking process and requires in depth perception, knowledge about the topic for review. It requires time and concentration, yet I enjoy doing it. The JCDR website especially for the reviewers is quite user friendly. My suggestions for improving the journal is, more strict review process, so that only high quality articles are published. I find a a good number of articles in Obst. Gynae, hence, a new journal for this specialty titled JCDR-OG can be started. May be a bimonthly or quarterly publication to begin with. Only selected articles should find a place in it.
An yearly reward for the best article authored can also incentivize the authors. Though the process of finding the best article will be not be very easy. I do not know how reviewing process can be improved. If an article is being reviewed by two reviewers, then opinion of one can be communicated to the other or the final opinion of the editor can be communicated to the reviewer if requested for. This will help one’s reviewing skills.
My best wishes to Dr. Hemant Jain and all the editorial staff of JCDR for their untiring efforts to bring out this journal. I strongly recommend medical fraternity to publish their valuable research work in this esteemed journal, JCDR".



Dr. Mamta Gupta
Consultant
(Ex HOD Obs &Gynae, Hindu Rao Hospital and associated NDMC Medical College, Delhi)
Aug 2018




Dr. Rajendra Kumar Ghritlaharey

"I wish to thank Dr. Hemant Jain, Editor-in-Chief Journal of Clinical and Diagnostic Research (JCDR), for asking me to write up few words.
Writing is the representation of language in a textual medium i e; into the words and sentences on paper. Quality medical manuscript writing in particular, demands not only a high-quality research, but also requires accurate and concise communication of findings and conclusions, with adherence to particular journal guidelines. In medical field whether working in teaching, private, or in corporate institution, everyone wants to excel in his / her own field and get recognised by making manuscripts publication.


Authors are the souls of any journal, and deserve much respect. To publish a journal manuscripts are needed from authors. Authors have a great responsibility for producing facts of their work in terms of number and results truthfully and an individual honesty is expected from authors in this regards. Both ways its true "No authors-No manuscripts-No journals" and "No journals–No manuscripts–No authors". Reviewing a manuscript is also a very responsible and important task of any peer-reviewed journal and to be taken seriously. It needs knowledge on the subject, sincerity, honesty and determination. Although the process of reviewing a manuscript is a time consuming task butit is expected to give one's best remarks within the time frame of the journal.
Salient features of the JCDR: It is a biomedical, multidisciplinary (including all medical and dental specialities), e-journal, with wide scope and extensive author support. At the same time, a free text of manuscript is available in HTML and PDF format. There is fast growing authorship and readership with JCDR as this can be judged by the number of articles published in it i e; in Feb 2007 of its first issue, it contained 5 articles only, and now in its recent volume published in April 2011, it contained 67 manuscripts. This e-journal is fulfilling the commitments and objectives sincerely, (as stated by Editor-in-chief in his preface to first edition) i e; to encourage physicians through the internet, especially from the developing countries who witness a spectrum of disease and acquire a wealth of knowledge to publish their experiences to benefit the medical community in patients care. I also feel that many of us have work of substance, newer ideas, adequate clinical materials but poor in medical writing and hesitation to submit the work and need help. JCDR provides authors help in this regards.
Timely publication of journal: Publication of manuscripts and bringing out the issue in time is one of the positive aspects of JCDR and is possible with strong support team in terms of peer reviewers, proof reading, language check, computer operators, etc. This is one of the great reasons for authors to submit their work with JCDR. Another best part of JCDR is "Online first Publications" facilities available for the authors. This facility not only provides the prompt publications of the manuscripts but at the same time also early availability of the manuscripts for the readers.
Indexation and online availability: Indexation transforms the journal in some sense from its local ownership to the worldwide professional community and to the public.JCDR is indexed with Embase & EMbiology, Google Scholar, Index Copernicus, Chemical Abstracts Service, Journal seek Database, Indian Science Abstracts, to name few of them. Manuscriptspublished in JCDR are available on major search engines ie; google, yahoo, msn.
In the era of fast growing newer technologies, and in computer and internet friendly environment the manuscripts preparation, submission, review, revision, etc and all can be done and checked with a click from all corer of the world, at any time. Of course there is always a scope for improvement in every field and none is perfect. To progress, one needs to identify the areas of one's weakness and to strengthen them.
It is well said that "happy beginning is half done" and it fits perfectly with JCDR. It has grown considerably and I feel it has already grown up from its infancy to adolescence, achieving the status of standard online e-journal form Indian continent since its inception in Feb 2007. This had been made possible due to the efforts and the hard work put in it. The way the JCDR is improving with every new volume, with good quality original manuscripts, makes it a quality journal for readers. I must thank and congratulate Dr Hemant Jain, Editor-in-Chief JCDR and his team for their sincere efforts, dedication, and determination for making JCDR a fast growing journal.
Every one of us: authors, reviewers, editors, and publisher are responsible for enhancing the stature of the journal. I wish for a great success for JCDR."



Thanking you
With sincere regards
Dr. Rajendra Kumar Ghritlaharey, M.S., M. Ch., FAIS
Associate Professor,
Department of Paediatric Surgery, Gandhi Medical College & Associated
Kamla Nehru & Hamidia Hospitals Bhopal, Madhya Pradesh 462 001 (India)
E-mail: drrajendrak1@rediffmail.com
On May 11,2011




Dr. Shankar P.R.

"On looking back through my Gmail archives after being requested by the journal to write a short editorial about my experiences of publishing with the Journal of Clinical and Diagnostic Research (JCDR), I came across an e-mail from Dr. Hemant Jain, Editor, in March 2007, which introduced the new electronic journal. The main features of the journal which were outlined in the e-mail were extensive author support, cash rewards, the peer review process, and other salient features of the journal.
Over a span of over four years, we (I and my colleagues) have published around 25 articles in the journal. In this editorial, I plan to briefly discuss my experiences of publishing with JCDR and the strengths of the journal and to finally address the areas for improvement.
My experiences of publishing with JCDR: Overall, my experiences of publishing withJCDR have been positive. The best point about the journal is that it responds to queries from the author. This may seem to be simple and not too much to ask for, but unfortunately, many journals in the subcontinent and from many developing countries do not respond or they respond with a long delay to the queries from the authors 1. The reasons could be many, including lack of optimal secretarial and other support. Another problem with many journals is the slowness of the review process. Editorial processing and peer review can take anywhere between a year to two years with some journals. Also, some journals do not keep the contributors informed about the progress of the review process. Due to the long review process, the articles can lose their relevance and topicality. A major benefit with JCDR is the timeliness and promptness of its response. In Dr Jain's e-mail which was sent to me in 2007, before the introduction of the Pre-publishing system, he had stated that he had received my submission and that he would get back to me within seven days and he did!
Most of the manuscripts are published within 3 to 4 months of their submission if they are found to be suitable after the review process. JCDR is published bimonthly and the accepted articles were usually published in the next issue. Recently, due to the increased volume of the submissions, the review process has become slower and it ?? Section can take from 4 to 6 months for the articles to be reviewed. The journal has an extensive author support system and it has recently introduced a paid expedited review process. The journal also mentions the average time for processing the manuscript under different submission systems - regular submission and expedited review.
Strengths of the journal: The journal has an online first facility in which the accepted manuscripts may be published on the website before being included in a regular issue of the journal. This cuts down the time between their acceptance and the publication. The journal is indexed in many databases, though not in PubMed. The editorial board should now take steps to index the journal in PubMed. The journal has a system of notifying readers through e-mail when a new issue is released. Also, the articles are available in both the HTML and the PDF formats. I especially like the new and colorful page format of the journal. Also, the access statistics of the articles are available. The prepublication and the manuscript tracking system are also helpful for the authors.
Areas for improvement: In certain cases, I felt that the peer review process of the manuscripts was not up to international standards and that it should be strengthened. Also, the number of manuscripts in an issue is high and it may be difficult for readers to go through all of them. The journal can consider tightening of the peer review process and increasing the quality standards for the acceptance of the manuscripts. I faced occasional problems with the online manuscript submission (Pre-publishing) system, which have to be addressed.
Overall, the publishing process with JCDR has been smooth, quick and relatively hassle free and I can recommend other authors to consider the journal as an outlet for their work."



Dr. P. Ravi Shankar
KIST Medical College, P.O. Box 14142, Kathmandu, Nepal.
E-mail: ravi.dr.shankar@gmail.com
On April 2011
Anuradha

Dear team JCDR, I would like to thank you for the very professional and polite service provided by everyone at JCDR. While i have been in the field of writing and editing for sometime, this has been my first attempt in publishing a scientific paper.Thank you for hand-holding me through the process.


Dr. Anuradha
E-mail: anuradha2nittur@gmail.com
On Jan 2020

Important Notice

Original article / research
Year : 2022 | Month : March | Volume : 16 | Issue : 3 | Page : DC01 - DC05 Full Version

Microbiological Evaluation of Patients Admitted with Acute Respiratory Illness during First Wave of COVID-19 Pandemic in New Delhi, India


Published: March 1, 2022 | DOI: https://doi.org/10.7860/JCDR/2022/51598.16057
Gitali Bhagawati, Sania Paul, Sarita Rani Jaiswal, Ashutosh Bhardwaj, Rekha Saji Kumar, Mansi, Anita Bhatia, Suparno Chakrabarti

1. Consultant and Head, Department of Microbiology and Infection Control, Dharamshila Narayana Superspeciality Hospital, Narayana Health, New Delhi, India. 2. Senior Resident, Department of Microbiology, Dharamshila Narayana Superspeciality Hospital, New Delhi, India. 3. Program Director- Haploidentical BMT and Consultant- BMT and Haematology, Department of BMT, Dharamshila Narayana Superspeciality Hospital, Narayana Health, New Delhi, India. 4. Clinical Lead and Senior Consultant, Department of Critical Care Medicine, Dharamshila Narayana Superspeciality Hospital, Narayana Health, New Delhi, India. 5. Laboratory Technologist, Department of Microbiology, Dharamshila Narayana Superspeciality Hospital, Narayana Health, New Delhi, India. 6. Laboratory Technician, Department of Microbiology, Dharamshila Narayana Superspeciality Hospital, Narayana Health, New Delhi, India. 7. Infection Control Nurse, Department of Infection Control, Dharamshila Narayana Superspeciality Hospital, Nara

Correspondence Address :
Dr. Gitali Bhagawati,
Consultant and Head, Department of Microbiology and Infection Control,
Dharamshila Narayana Superspeciality Hospital, Narayana Health, Vasundhara Enclave,
Near Ashok Nagar Metro Station, New Delhi, India.
E-mail: gitali.bhagawati.dr@narayanahealth.org

Abstract

Introduction: The Coronavirus Disease-2019 (COVID-19) is associated with damage of cells of both innate and adaptive immunity, which results in immune system’s impairment leading to secondary infections. Microbiological evaluation helps in diagnostic as well as antimicrobial stewardship leading to accurate treatment of COVID-19 infected patients.

Aim: To evaluate superadded bacterial and fungal infections in COVID-19 infected patients and to evaluate bacterial and fungal infections in COVID-19 non infected patients admitted with Acute Respiratory Illness (ARI).

Materials and Methods: This retrospective study was carried out in a tertiary care hospital in Delhi, India, over a period of eight months (May to December 2020). Respiratory samples, received from indoor patients with history of ARI, were processed for COVID-19 (TrueNat based real time polymerase chain reaction) as well as for bacterial and fungal cultures following Standard Operating Procedures (SOP). Identification and susceptibility pattern was evaluated by Vitek2 compact system (bioMérieux, Inc. Durham, North Carolina/USA). Quality control strains used were American Type Culture Collection (ATCC) Staphylococcus aureus 29213, Escherichia coli 25922 and Candida parapsilosis ATCC 22019. Minimum Inhibitory Concentration (MIC) levels were standardised as per Clinical and Laboratory Standards Institute (CLSI) guideline 2020. All statistical analysis was done by Chi-square test using Software Statistical Package for the Social Sciences (SPSS) version 22.0.

Results: Total patients admitted with the history of ARI were 542; COVID-19 Positive Group (CPG) included 115 (21.22%) while COVID-19 Negative Group (CNG) included 427 (78.78%). Growth in bacterial and fungal cultures in CPG was 59.13% (68/115) while in CNG; it was 47.78% (204/427). Among the bacterial isolates, most common isolate was Klebsiella pneumoniae {CPG: 41.93% (26/62); CNG: 36.72% (76/207)}, followed by Pseudomonas aeruginosa {CPG: 33.87% (21/62); CNG: 31.88% (66/207)}. Fungal isolates in CPG was 19.48% (15/77) (p-value 0.0445). On comparing Antimicrobial Susceptibility (AST) pattern of Enterobacterales in both CPG (n=36) and CNG (n=102), no statistically significant difference was observed. Co-morbid conditions were found mostly in CNG 89% (140/158) with ARI while only 11% (18/158) was found in CPG.

Conclusion: Secondary respiratory infections are quite common amongst COVID-19 positive patients. However, growth in culture, type of isolates, Antimicrobial Resistance (AMR) was almost similar with COVID-19 non infected patients admitted with ARI. Co-morbidity had the similar impact as COVID-19 infection with respect to co-infections.

Keywords

Co-infection, Coronavirus disease-2019 infection, Respiratory tract infection, Superinfection, TrueNat real time polymerase chain reaction

The coronavirus pandemic is a biggest global health threat that we have faced after the Second World War with 42,32,949 confirmed cases and 1,02,896 deaths till date (1). The COVID-19 illness has demonstrated variability in severity, from asymptomatic or mildly symptomatic to Acute Respiratory Distress Syndrome (ARDS) and Multi-Organ Failure (MOF) (2). This disease is associated with damage of B cells, T cells and Natural Killer (NK) cells, which leads to the immune system’s impairment leading to secondary infections (3). Secondary infections can be superinfections or co-infections. Superinfection is defined as an infection following a previous infection especially when caused by microorganisms that are resistant or have become resistant to the antibiotics used earlier, while a co-infection is one occurring concurrently with the initial infection, the difference being purely temporal [4-6].

These secondary infections can raise the difficulties of diagnosis, treatment, prognosis of COVID-19 and even increase the morbidity and mortality (7). Therefore, simultaneous evaluation of co-infections in COVID-19 infected patients is necessary so that one can provide a better patient treatment (8). There are many published reports of respiratory co-infections and superinfections in COVID-19 patients especially in the hospitalised patients (3),(8),(9),(10).

As the world continues to respond to COVID-19, there is a larger hidden threat of AMR lurking behind, one that is already killing hundreds of thousands of people globally (about 700000 deaths annually) (11). Moreover, AMR amongst the pathogens causing secondary infections is also a hidden threat lurking behind COVID-19 (11). However, this should be noted that in the pre-COVID era, the rise in Multidrug-Resistant Organisms (MDROs), related to AMR, were undetected, undiagnosed, and increasingly untreatable threatening the health of people globally projecting death of 10 million people per year by 2050. During COVID-19 pandemic, antibiotics were rampantly used which again exacerbated the prevailing AMR as shown by United States (US) multicentre study reporting 72% of COVID-19 patients received antibiotics without indication (12).

This study was to analyse superadded bacterial and Yeast and Yeast Like Fungus (YYLF) infections apart from COVID-19 infection in patients admitted with ARI. Here, authors also compared the microbiological isolates and their AST of two groups of patients: COVID-19 infected patients and COVID-19 non infected patients.

Material and Methods

The retrospective study was carried out amongst hospitalised patients at a tertiary care hospital in Delhi, India, over a period of eight months (May to December 2020), during the 1st wave of COVID-19 in India. Data was retrieved from the Microbiology and Molecular Department of the hospital from the sample request forms, Laboratory Information Management System (LIS) and WHONET 5.6 software. Analysis of the study was done from the collected data during the declined phase of 1st wave of COVID-19 infection in India over a period of three months (January to March 2021).

To rule out secondary infections, non duplicate respiratory samples were subjected to culture in microbiology laboratory. Respiratory samples comprised of sputum, Bronchoalveolar Lavage (BAL) and Endotracheal Aspirate (ET). Sample size was based on duration of study period including 1st wave of COVID-19 in India, from May to December 2020. Microbiological isolates were reviewed along with their susceptibility pattern.

Inclusion criteria:

a. Sputum: Samples showing Bartlett’s score more than 1 (13).
b. BAL: Colony count ≥104 CFU/mL in quantitative culture (14),(15).
c. ET: Colony count ≥105 CFU/mL in quantitative ET culture (15).

Exclusion criteria:

a. Salivary sample with Bartlett’s score less than 1 (13).
b. >1% bronchial cells in BAL fluid smears (15).
c. >10 squamous cells in the lower field magnification in ET smears (15).

Identification and Susceptibility Testing

All the samples were inoculated on routine culture media like Blood Agar (BA), Macconkey Agar (MA) and Chocolate Agar (CA). YYLF easily grows in routine culture media used for bacterial culture. However, for pure growth to check further identification and antifungal susceptibility pattern colonies were inoculated on two Sabouraud’s Dextrose Agar (SDA) slants; one was incubated at room temperature and other at 37°C for 24-48 hours. Identification of bacteria was done by gram stain, motility test and other biochemical tests as per standard protocol (16). For identification YYLFs, gram stain, Lactophenol Cotton Blue (LPCB) test, germ tube test were performed (17). The final identification and antifungal susceptibility tests were performed by Identification cards and AST cards respectively using Vitek 2 Compact System 8.01 (bioMérieux, Inc. Durham, North Carolina/USA). Control strains used were: Staphylococcus aureus ATCC 29213, Escherichia coli ATCC 25922, Candida parapsilosis ATCC 22019.

The TrueNat based RT-Rt PCR for Detection of COVID-19 (18),(19)

All COVID-19 tests were done by Truenat Rt RT-PCR test. Samples taken were oropharyngeal or nasopharyngeal swab collected using standard nylon flocked swab. Swab is inserted into the Viral Transport Medium (VTM) were provided from the same company (Molbio diagnostics Pvt., Ltd., Goa, India). Samples were transported immediately to the molecular laboratory maintaining proper temperature and processed as per manufacturer’s guideline. (Truenat Beta CoV Chip-based RT-PCR test for Beta Coronavirus, Molbio diagnostics Pvt., Ltd., Goa, India).

The target sequence for this assay is I#IEI?I gene of Sarbecovirus and human RNaseP (serves as internal positive control). Confirmatory gene used was RdRP gene or ORF1a gene.

Statistical Analysis

All statistical analysis was done by Chi-square test using Software Statistical Package for the Social Sciences (SPSS) version 22.0. The outcome was determined to be significantly different if the observed p-value was <0.05.

Results

Total patients suspected of ARI were 542; out of which 115 (21.22%) were found to be positive for COVID-19 by TrueNat based RT-PCR CPG, while rest 427 (78.78%) were found to be CNG. Being a known cancer care hospital, cancer treatment was also going on simultaneously irrespective of COVID-19 status of the patients. Since, COVID-19 infects irrespective of immunocompromised status, control group was taken from the cancer patients.

In both CPG and CNG, males predominated over females, 88 (76.52%) and 317 (74.24%) respectively. Overall, age group of the study varied from 4-91 years with a mean±Standard Deviation (SD) age of 59.70±14.73 years, median age was 62. However, age group range of CPG was 20-91 years with a mean±SD age of 61.30±14.75 years, median age 63 and that of CNG ranged from 4-88 years with a mean±SD age of 59.24±14.74 years, median age 61. No statistically significant variation was found on comparing both the groups with respect to age.

Respiratory culture results were divided into three categories:

a. Significant Growth (SG)
b. Insignificant Growth (IG)
c. No growth (NG)

In case of culture with SG, the growth was further processed for final identification and antimicrobial/antifungal susceptibility testing. No further processing was done in case of IG or NG.

In CPG, SG in sputum and ET cultures was 43/79 (54.43%) and 25/34 (73.53%) respectively. No SG was seen in BAL. In CPG, the number of cultures with SG in overall respiratory samples (Sputum, BAL and ET) was found to found to be 68/115 (59.13%). This depicts rate of secondary infection in SARS-Cov-2 patients was 59.13% (Table/Fig 1), (Table/Fig 2).

On comparing significant growth (SG) in sputum, BAL and ET cultures in both CPG and CNG, no statistically significant difference (p-value >0.05) was observed (Table/Fig 1), (Table/Fig 2). Number of respiratory cultures with SG in CPG was 68. The SG in culture was either of single isolate or of double isolates.

Number of total isolates (bacterial and or fungal) in CPG was 77 while that in CNG it was 232. Cultures with single isolate in CPG were 59/68 (86.76%) while the rest showed growth of double isolates 9/68 (13.23%). Cultures with double isolates in CNG were 34/204 (16.67%). No statistically significant difference was observed in both CPG and CNG with respect to number of isolates in cultures (Table/Fig 3).

When CPG and CNG groups were compared as per Gram Negative (GN), Gram Positive (GP) and YYLF isolates, no such statistically significant difference was observed with respect to GN and GP. However, as per YYLF infection, CPG group isolation rate 15/77 (19.48) which was found to be statistically significant with p-value 0.0445 (Table/Fig 4).

Overall bacterial isolate (Gram positive and gram negative) in CPG was 62 (80.52%) and in CNG it was 207 (89.22%) (Table/Fig 4). Among the bacterial isolates, most common isolate in CPG was Klebsiella pneumoniae 26/62 (41.93%), followed by Pseudomonas aeruginosa 21/62 (33.87%) and Escherichia coli 9/62 (14.52%). Similarly, in CNG also, Klebsiella pneumoniae 76/207 (36.72%) was the predominant isolate followed by Pseudomonas aeruginosa 66/207 (31.88%) and Escherichia coli 20/207 (9.66%) (Table/Fig 5).

Out of YYLFs, C. albicans was the predominating isolate in both CPG and CNG, 8/15 (53.33%) and 14/25 (56%), respectively. This was followed by C. tropicalis, 6/15 (40%) in CPG and 5/25 (20%) in CNG (Table/Fig 6). On comparing AST pattern of Enterobacterales in both CPG (n=36) and CNG (n=102), no statistically significant difference was observed (Table/Fig 7).

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infects people irrespective of the immune status of the host. In present study, co-morbidity was mostly associated with CNG 140/158 (89%)with ARI while only 18/158 (11%) was found in CPG. Type of cancer was not found to be statistically significant with respect to COVID-19 infection, except the lung cancer (p-value=0.003) (Table/Fig 8).

Among expired patients of COVID-19, 10/16 (62.5%) had SG in respiratory culture. However, on comparing mortality, no statistically significant variation was observed in CPG and CNG with SG in respiratory samples (Table/Fig 9).

Discussion

During the 1st wave of SARS-Cov-2 pandemic in India, a total 542 patients were admitted with ARI in our hospital that underwent COVID-19 test by TrueNat based RT-PCR. Out of these patients, 115/542 (21.22%) were laboratory confirmed COVID-19 positive patients. In present study, median age of SARS-Cov-2 infected patients was 63 (20-91 year) which was almost similar to the finding of Zhang JJ et al., 57 years and Contou D et al., 61 years (20),(21). Present study found 76.52% males in CPG which was similar the finding of Contou D et al., 73% but dissimilar to the finding of Zhang JJ et al., 56% (20),(21). However, when CPG and CNG groups were compared with respect to age and sex, no statistically significant difference was observed. Significant growth in respiratory samples in CPG, 68/115 (59.13%) was considered as the secondary infection rate in that group. Secondary infection rate in SARS-Cov-2 positive patients varied in literature; range varied from, 28% by Contou D et al., 34.8% by Hughes S et al., and 11% by Huttner B et al., (21),(22),(23). Low rate of isolation of secondary infections in previous literatures were because of many reasons. First, the scare associated with the pandemic at its onset along with the high workload, high levels of stress amongst healthcare workers for which secondary infections might not get the importance. Secondly, the guidelines were particularly made for COVID-19 sample collections but not for respiratory sample collection for microbiological evaluation under proper safety precaution to avoid droplet infection. Third, adequate microbiological set ups were not available in most of the hospitals worldwide for proper evaluation. Forth, shortage of Personal Protective Equipment (PPEs) at the onset of the pandemic made it difficult for biosample collection for better diagnostic evaluation. As time passed with the pandemic, acceptance level of COVID-19 had increased, availability of PPEs were increased and patients were properly evaluated for rest of the superadded infections in those hospitals where adequate facilities were available. The same reasons were applicable to the mortality rate amongst CPG; out of 16 deaths, 10 had co-infections (62.5%) [Table/Fig 9]. On contrary, Huttner B et al., mentioned that in Italy 16,654 patients who died of COVID-19 had superadded infections in only 11% (23).

In present study, gram negative isolates predominated (77.92%) over YYLFs (19.48%) and gram positives (2.60%) isolates in CPG. Enterobacterales isolated among CPG in present study was 36/77 (46.75%) which was similar to finding of Hughes S et al., 32% while dissimilar to finding of Contou D et al., 16% (21),(22). Amongst Enterobacterales, Klebsiella pneumoniae 26/77 (33.77%) was the most common respiratory tract isolate in COVID positive patients which was in concordance with Chen X et al., Pseudomonas aeruginosa was also second most common isolate, 21/77 (27.27%) in Covid positive patients which is in concordance to other findings of Hughes S et al., 36% but dissimilar to the finding of Contou D et al., 6%. No S. aureus was isolated from respiratory samples in present study which was in contrast to other findings; Hughes S et al., 31% and Sharifipour E et al., 10% (22),(24). Isolation rate of Acinetobacter baumannii, one of the most common hospital acquired respiratory isolate was 2/77 (2.6%) in present study. This was in contrast to some literatures; Sharifipour E et al., 90%, Wang Z et al., 20% (24),(25) while similar to other literatures; Contou D et al., 3% and Lansbury L et al., 7.40% (21),(26). Bacterial isolates and related AMR in both the groups had no statistically significant difference (p-value >0.05). This implies that AMR was a global crisis which was prevailing before the onset of COVID-19 pandemic. Antibiotic use in inappropriate dose and duration at inappropriate indication with inadequate infection control practices increased the burden of AMR in pre-COVID era itself. That is why, in September 2016 (years prior to the emergence of the COVID-19 pandemic), the World Health Organisation (WHO) committed itself to fighting AMR, which had become a problem of global public health importance (27). Various COVID-19 management protocols itself had heightened the concern of AMR over the prevailing crisis.

In CPG, YYLF was the second most common respiratory isolate (19.48%) which was almost similar to the finding of other literature; Hughes S et al., 21.81% (22). On comparing with CNG, YYLFs were found to be statistically significant amongst CPG with p-value 0.0445. C. albicans predominated amongst all YYLF (53%, 8/15) which was in concordance with one study, Salehi M et al., 70% (28). COVID-19 infection is associated with over-expression of inflammatory cytokines, and impaired cell-mediated immune response with decreased CD4 + T and CD8 + T cell counts, indicating its susceptibility to fungal co-infection (29). Other reasons for YYLF infection include use of steroid, monoclonal antibodies, anti-virals, anti-malarials and use of broad spectrum antibiotics amongst moderate to severe forms of COVID-19 infected patients in the hospitalised group. In present study, co-morbidity in CPG was less (11%) as compared to CNG (89%) as because majority of our patients in CNG were immunocompromised patients with cancer or chronic kidney diseases. In CPG, present study finding was in contrast to the findings various literatures (20),(30).

Limitation(s)

Since, the study was done retrospectively, samples processed for YYLFs were only included in this study. Other fungal isolates were excluded.

Conclusion

Secondary respiratory infections are common in SARS-Cov-2 infected patients. Bacterial flora of COVID-19 infected patients is not different than that of rest of the patients with respiratory illness. However, YYLF infections in COVID-19 infected patients were found to be more because of the association of the viral strain itself and its management with steroid, broad spectrum antibiotics, monoclonal antibodies etc. AMR is a raising global concern in pre-COVID-19 era; which was exacerbated by the COVID-19 pandemic. This novel virus seems to stay with human being infecting in the form outbreak, endemic or epidemic in future. Therefore, microbiological evaluation with AST of the isolates with respect to antimicrobial stewardship is the utmost need of the hour to preserve some antibiotics as well as anti-fungals for near future.

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DOI and Others

DOI: 10.7860/JCDR/2022/51598.16057

Date of Submission: Jul 27, 2021
Date of Peer Review: Sep 02, 2021
Date of Acceptance: Jan 17, 2022
Date of Publishing: Mar 01, 2022

AUTHOR DECLARATION:
• Financial or Other Competing Interests: None
• Was Ethics Committee Approval obtained for this study? NA
• Was informed consent obtained from the subjects involved in the study? NA
• For any images presented appropriate consent has been obtained from the subjects. NA

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