Changes in Respiratory Microorganism Distribution and Antimicrobial Resistance Patterns in Intensive Care Units: A Comparative Analysis Before and During the COVID-19 Pandemic

Gülsüm Kaya; Burcu Gürer Giray; Didem Özgür; Elmas Pınar Kahraman Kılbaş; Sinem Solmaz; Mehtap Oskay; Ece Yilmaz Erbay; Hülya İncirkuş Küçük; Şeyma Trabzon; Hasan Ergenç; Sebahat Aksaray

doi:10.32708/uutfd.1972680

EN TR

Changes in Respiratory Microorganism Distribution and Antimicrobial Resistance Patterns in Intensive Care Units: A Comparative Analysis Before and During the COVID-19 Pandemic

Abstract

This study aimed to evaluate changes in the distribution of microorganisms isolated from respiratory tract specimens and antimicrobial resistance patterns in intensive care units (ICUs) before and during the COVID-19 pandemic. Microbiological data from respiratory tract specimens obtained from patients admitted to the ICUs of a state hospital between January 1, 2019, and April 30, 2021, were retrospectively reviewed. The study period was divided into the pre-pandemic period (January 1, 2019–February 29, 2020) and the pandemic period (March 1, 2020–April 30, 2021). A total of 634 patients and 757 respiratory tract isolates were included. The median age was 79 years (IQR: 66–85), and 55.2% of the patients were male. Acinetobacter spp. was the most frequently isolated microorganism overall, followed by Klebsiella spp., Pseudomonas spp., Escherichia coli, and Staphylococcus aureus. Overall microorganism distribution differed significantly between the pre-pandemic and pandemic periods (p<0.001). Antimicrobial resistance analyses were performed for the most frequently isolated bacterial pathogens. No significant changes were observed in resistance rates among Pseudomonas spp. isolates. Among Acinetobacter spp. isolates, trimethoprim-sulfamethoxazole resistance increased significantly during the pandemic period. Among Klebsiella spp. isolates, trimethoprim-sulfamethoxazole resistance increased significantly. These findings indicate that the COVID-19 pandemic period was associated with changes in respiratory microorganism distribution and selected antimicrobial resistance patterns in ICUs.

Keywords

Supporting Institution

no

Project Number

no

Ethical Statement

Approving Committee: Non-Interventional Clinical Research Ethics Committee of Sakarya University Faculty of Medicine Approval Date: 30.01.2024 Decision No: E-71522473/050.01.04-330358-25

Thanks

none

Yoğun Bakım Ünitelerinde Solunum Yolu Mikroorganizma Dağılımı ve Antimikrobiyal Direnç Paternlerindeki Değişimler: COVID-19 Pandemisi Öncesi ve Pandemi Döneminin Karşılaştırmalı Analizi

Abstract

Bu çalışmada, COVID-19 pandemisi öncesi ve pandemi döneminde yoğun bakım ünitelerinde (YBÜ) solunum yolu örneklerinden izole edilen mikroorganizmaların dağılımı ve antimikrobiyal direnç paternlerindeki değişimlerin değerlendirilmesi amaçlandı. Bir devlet hastanesinin YBÜ’lerinde 1 Ocak 2019–30 Nisan 2021 tarihleri arasında yatan hastalardan alınan solunum yolu örneklerine ait mikrobiyolojik veriler retrospektif olarak incelendi. Çalışma dönemi pandemi öncesi dönem (1 Ocak 2019–29 Şubat 2020) ve pandemi dönemi (1 Mart 2020–30 Nisan 2021) olarak ikiye ayrıldı. Toplam 634 hasta ve 757 solunum yolu izolatı çalışmaya dahil edildi. Hastaların medyan yaşı 79 yıl (IQR: 66–85) olup, %55,2’si erkekti. Genel olarak en sık izole edilen mikroorganizma Acinetobacter spp. olup, bunu Klebsiella spp., Pseudomonas spp., Escherichia coli ve Staphylococcus aureus izledi. Mikroorganizma dağılımı pandemi öncesi ve pandemi dönemleri arasında anlamlı farklılık gösterdi (p<0,001). Antimikrobiyal direnç analizleri en sık izole edilen bakteriyel etkenler için gerçekleştirildi. Pseudomonas spp. izolatlarında direnç oranlarında anlamlı bir değişiklik saptanmadı. Acinetobacter spp. izolatlarında trimetoprim-sülfametoksazol direnci pandemi döneminde anlamlı olarak arttı. Klebsiella spp. izolatlarında trimetoprim-sülfametoksazol G. Kaya et al. Journal of Uludağ University Medical Faculty 52, 1972680, 2026 2 direnci anlamlı olarak arttı. Bu bulgular, COVID-19 pandemi döneminin YBÜ’lerde solunum yolu mikroorganizma dağılımı ve seçilmiş antimikrobiyal direnç paternlerinde değişikliklerle ilişkili olduğunu göstermektedir.

Keywords

Supporting Institution

Yoktur

Project Number

no

Ethical Statement

Onay Kurulu: Sakarya Üniversitesi Tıp Fakültesi Girişimsel Olmayan Klinik Araştırma Etik Kurulu Onay Tarihi: 30.01.2024 Karar No: E-71522473/050.01.04-330358-25

Thanks

yoktur

References

1. World Health Organization. Coronavirus disease (COVID-19) pandemic. Available from: https://www.who.int/europe/ emergencies/situations/covid-19. Accessed June 1, 2026.
2. Centers for Disease Control and Prevention. COVID-19 overview and infection prevention and control priorities in non- U.S. healthcare settings. Available from: https://archive.cdc.gov/www_cdc_gov/coronavirus/2019- ncov/hcp/non-us-settings/overview/index.html. Accessed June 1, 2026.
3. 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. Clin Microbiol Infect. 2020;26(12):1622-1629. doi:10.1016/j.cmi.2020.07.016.
4. Torres A, Niederman MS, Chastre J, Ewig S, Fernandez- Vandellos P, Hanberger H, et al. International ERS/ESICM/ESCMID/ALAT guidelines for the management of hospital-acquired pneumonia and ventilator associated pneumonia. Eur Respir J. 2017;50(3):1700582. doi:10.1183/13993003.00582-2017.
5. Zuglian G, Ripamonti D, Tebaldi A, Cuntrò M, Riva I, Farina C, et al. The changing pattern of bacterial and fungal respiratory isolates in patients with and without COVID-19 admitted to intensive care unit. BMC Infect Dis. 2022;22(1):185. doi:10.1186/s12879-022-07176-x.
6. Patel A, Emerick M, Cabunoc MK, Williams MH, Preas MA, Schrank G, et al. Rapid spread and control of multidrugresistant Gram-negative bacteria in COVID-19 patient care units. Emerg Infect Dis. 2021;27(4):1234-1237. doi:10.3201/eid2704.204036.
7. World Health Organization. Global antimicrobial resistance and use surveillance system (GLASS) report: 2022. Available from: https://www.who.int/publications/i/item/9789240062702. Accessed June 2, 2026.
8. World Health Organization. Antimicrobial resistance. Fact sheet. Available from: https://www.who.int/news room/factsheets/ detail/antimicrobial-resistance. Accessed June 2, 2026.

Details

Primary Language

English

Subjects

Clinical Sciences (Other)

Journal Section

Research Article

Authors

Gülsüm Kaya ^*
0000-0003-2517-5512
Türkiye

Burcu Gürer Giray
0000-0003-3165-8924
Türkiye

Didem Özgür
0000-0002-8320-9453
Türkiye

Elmas Pınar Kahraman Kılbaş
0000-0003-1348-625X
Türkiye

Sinem Solmaz
0009-0006-9367-4566
Türkiye

Mehtap Oskay
0000-0002-7287-3631
Türkiye

Ece Yilmaz Erbay
0009-0007-8047-7587
Türkiye

Hülya İncirkuş Küçük
0000-0002-6739-6463
Türkiye

Şeyma Trabzon
0000-0001-9030-7804
Türkiye

Hasan Ergenç
0000-0003-0519-0264
Türkiye

Sebahat Aksaray
0000-0002-0552-1337
Türkiye

Publication Date

November 4, 2026

Submission Date

June 16, 2026

Acceptance Date

September 27, 2026

Published in Issue

Year 2026 Volume: 52

DOI

https://doi.org/10.32708/uutfd.1972680

IZ

https://izlik.org/JA38PF42RU

Cite

RIS / Bibtex

APA

Kaya, G., Gürer Giray, B., Özgür, D., Kahraman Kılbaş, E. P., Solmaz, S., Oskay, M., Yilmaz Erbay, E., İncirkuş Küçük, H., Trabzon, Ş., Ergenç, H., & Aksaray, S. (2026). Changes in Respiratory Microorganism Distribution and Antimicrobial Resistance Patterns in Intensive Care Units: A Comparative Analysis Before and During the COVID-19 Pandemic. Journal of Uludağ University Medical Faculty, 52. https://doi.org/10.32708/uutfd.1972680

AMA

1.Kaya G, Gürer Giray B, Özgür D, et al. Changes in Respiratory Microorganism Distribution and Antimicrobial Resistance Patterns in Intensive Care Units: A Comparative Analysis Before and During the COVID-19 Pandemic. J Uludag Univ Med Fac. 2026;52. doi:10.32708/uutfd.1972680

Chicago

Kaya, Gülsüm, Burcu Gürer Giray, Didem Özgür, et al. 2026. “Changes in Respiratory Microorganism Distribution and Antimicrobial Resistance Patterns in Intensive Care Units: A Comparative Analysis Before and During the COVID-19 Pandemic”. Journal of Uludağ University Medical Faculty 52 (November). https://doi.org/10.32708/uutfd.1972680.

EndNote

Kaya G, Gürer Giray B, Özgür D, Kahraman Kılbaş EP, Solmaz S, Oskay M, Yilmaz Erbay E, İncirkuş Küçük H, Trabzon Ş, Ergenç H, Aksaray S (November 1, 2026) Changes in Respiratory Microorganism Distribution and Antimicrobial Resistance Patterns in Intensive Care Units: A Comparative Analysis Before and During the COVID-19 Pandemic. Journal of Uludağ University Medical Faculty 52

IEEE

[1]G. Kaya et al., “Changes in Respiratory Microorganism Distribution and Antimicrobial Resistance Patterns in Intensive Care Units: A Comparative Analysis Before and During the COVID-19 Pandemic”, J Uludag Univ Med Fac, vol. 52, Nov. 2026, doi: 10.32708/uutfd.1972680.

ISNAD

Kaya, Gülsüm - Gürer Giray, Burcu - Özgür, Didem - Kahraman Kılbaş, Elmas Pınar - Solmaz, Sinem - Oskay, Mehtap - Yilmaz Erbay, Ece et al. “Changes in Respiratory Microorganism Distribution and Antimicrobial Resistance Patterns in Intensive Care Units: A Comparative Analysis Before and During the COVID-19 Pandemic”. Journal of Uludağ University Medical Faculty 52 (November 1, 2026). https://doi.org/10.32708/uutfd.1972680.

JAMA

1.Kaya G, Gürer Giray B, Özgür D, Kahraman Kılbaş EP, Solmaz S, Oskay M, Yilmaz Erbay E, İncirkuş Küçük H, Trabzon Ş, Ergenç H, Aksaray S. Changes in Respiratory Microorganism Distribution and Antimicrobial Resistance Patterns in Intensive Care Units: A Comparative Analysis Before and During the COVID-19 Pandemic. J Uludag Univ Med Fac. 2026;52. doi:10.32708/uutfd.1972680.

MLA

Kaya, Gülsüm, et al. “Changes in Respiratory Microorganism Distribution and Antimicrobial Resistance Patterns in Intensive Care Units: A Comparative Analysis Before and During the COVID-19 Pandemic”. Journal of Uludağ University Medical Faculty, vol. 52, Nov. 2026, doi:10.32708/uutfd.1972680.

Vancouver

1.Gülsüm Kaya, Burcu Gürer Giray, Didem Özgür, Elmas Pınar Kahraman Kılbaş, Sinem Solmaz, Mehtap Oskay, Ece Yilmaz Erbay, Hülya İncirkuş Küçük, Şeyma Trabzon, Hasan Ergenç, Sebahat Aksaray. Changes in Respiratory Microorganism Distribution and Antimicrobial Resistance Patterns in Intensive Care Units: A Comparative Analysis Before and During the COVID-19 Pandemic. J Uludag Univ Med Fac. 2026 Nov. 1;52. doi:10.32708/uutfd.1972680

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Tables: Tables should be placed after the "References" section in the main text file. Each table should be written on a separate page, along with its title and footnotes. Each table should contain an appropriate title that explains its content, and the title should be placed above the table. Tables should be numbered consecutively in the order they appear in the main text, and mentions to the tables in the text should always follow the consecutive numbering order. In the numbering of tables, Roman numerals should be used (Table I, Table II, III, IV…). If abbreviations are used in the table, they should be explained as footnotes below the table.
Figures: Within the scope of the journal, photographs, graphs, and/or illustrations are defined as "Figures." All figures must be placed after the "Tables" section in the main text file and should also be prepared according to the specified features and uploaded separately to the system. Each figure should be numbered consecutively in the main text according to the order in which they appear (Figure 1, Figure 2,…). Figure files must be in JPEG or TIFF format. Other formats are not accepted. In figures with multiple sections, each section should be indicated with lowercase letters (a, b, c, etc.). Figures containing multiple sections should be prepared as a single combined figure and uploaded to the manuscript submission system as a single file.
The titles and descriptions of all figures should be provided on a separate page after the "Figures" section in the full text file, and the figure files uploaded to the system should not contain titles and descriptions. If an abbreviation is used in the figure, the abbreviations should be explained as a footnote under the figure. If the figure is a quotation from another source, the source should be cited in the figure caption.
Figures containing photographs should be saved at a minimum resolution of 600x600 pixels and scaled to fit one or two columns in magazine size.
Graphics and illustrations should be prepared with a resolution of at least 300x300 pixels and scaled to fit one or two columns.

CASE REPORT
Cases that contribute to the literature and have publication value should be submitted. Title (in English and Turkish), abstract (in English and Turkish), keywords (in English and Turkish) (at least 3, at most 6), introduction, case report (patient presentation, laboratory or other findings, diagnosis and explanation of the outcome), discussion and conclusion (what is new in this case report, how it differs from previously published cases, and how it is related), references, table titles and tables, figures and figure titles sections should be included.
For all case reports submitted to the journal, informed consent must be obtained from the patient. This consent must be specified in the 'case report' section of the main text.
The number of authors for case reports is limited to six.
REVIEW
The title (in English and Turkish), abstract (in English and Turkish), keywords (in English and Turkish), and main text sections should be included.
The number of authors for compilations is limited to three.
LETTER TO THE EDITOR
The title (in English and Turkish), abstract (in English and Turkish), keywords (in English and Turkish), and main text sections should be included.
Article Submission Checklist:
Before submitting the articles, compliance with writing rules should be checked, and any deficiencies should be addressed using the checklist below.
1. It should be ensured that the journal's writing rules, copyright, and author responsibilities are seen, read, and understood.
2. It should be ensured that the article has not been published or submitted to another journal and is not under review elsewhere.
3. It should be ensured that the study complies with research ethics rules.
4. It should be ensured that all authors' names are written.
5. Mandatory forms (Cover Letter, Title Page, Copyright Form, and Author Contribution Form) should be downloaded from the system, filled out, and then re-uploaded to the system.
6. Main Text:
It should consist of the following sections:
- Article Title (English and Turkish)
-Summary (in English and Turkish)
-Keywords (English and Turkish)
-Introduction
-Materials and Methods
-Results
-Discussion and Conclusion
-References (Must comply with the journal's guidelines.)
-Acknowledgement
-Tables
-Figures and figure captions with subtitles

ETHICAL PRINCIPLES
The Journal of Uludağ University Medical Faculty adopts and adheres to the ethical principles, frameworks, and standards established by the Committee on Publication Ethics (COPE)(https://publicationethics.org)(https://publicationethics.org/membership/code-of-conduct).
The Journal of Uludağ University Medical Faculty requires the documentation of the Ethics Committee Decision in clinical studies involving humans, experimental studies using laboratory animals, and survey studies. These documents must also include a page with the signatures of the Committee Members (a cover letter alone is insufficient). In the article text, the Ethics Committee information (Committee name, decision date, decision number) should be included in the "Materials and Methods" section.
In case reports, an ethics committee decision is not required, but consent must be obtained from the cases included in the article, and this must be stated within the article.
Ethics committee approval is not required for reviews, but it is expected that the corresponding author uploads a signed statement indicating this to the system.
Article authors must adhere to universal publication ethics rules.

Ethical Responsibilities of Authors
Authors must state that their articles are their original work and that all data in the article are real and original. Authors are responsible for ensuring that the data presented in their articles is accurate and representative of the article. To ensure transparency, authors may be asked to submit their raw data or additional data along with the article. Authors are responsible for providing supplementary and auxiliary materials. The articles submitted to the journal must not have been published elsewhere or be under consideration for publication. However, authors can submit their articles to the Journal after receiving a rejection letter from another publisher. Theses and graduation theses that are not archived online are considered original and unpublished. However, authors who submit articles using the content and data of their theses should mention this in the Acknowledgments section.

Authors must comply with the authorship criteria listed in the "Authorship" section. The level of their contributions should be defined in the 'Authorship Contribution Form' section. Authors are responsible for retracting and correcting errors. Authors must disclose and declare any conflicts of interest to the Editors. If there is no conflict of interest, the authors should also declare this in their article. Authors should specify all sources used in the creation of the articles. Authors should cite relevant and verified literature to support their scientific work and should not use unrelated sources that could assist other research/journals.

The corresponding author is the main owner of the article, so they can withdraw their articles before entering the review process or when a revision is requested. Authors cannot make significant changes to the article or withdraw it without a serious reason after the paper has been accepted.

Authors are obliged to inform the journal editor or publisher of any errors or mistakes in a published, preprint, or review-stage article and to cooperate with the chief editor to correct or retract the article. Authors should avoid submitting a manuscript based on the same dataset, study, or experiment for publication. The journal reserves the right to withhold publication or reject articles identified as plagiarism, ethical violations, undisclosed prior publication, or conflicts of interest, even after an editorial acceptance decision.

All articles are examined for similarity or plagiarism. Articles submitted to the journal for evaluation are examined using the "Plagiarism Detection Program" (iThenticate), and articles with a similarity rate above 20% are returned to the authors.

Authors should maintain open and constructive communication with other editors and reviewers. (Inappropriate language or destructive behavior is unacceptable. The journal follows COPE guidelines when dealing with such situations.

Ethical Responsibilities of Referees
Reviewers must keep all information related to the articles confidential and treat it as privileged information. Evaluations should be conducted objectively without personal criticism of the author. The authors' self-identification should not influence their comments and decisions. Reviewers may identify relevant published work that has not been cited by the authors. Reviewers should not review articles that have conflicts of interest arising from competitive, collaborative, or other relationships or connections with the authors, companies, or institutions connected to the articles.
Reviewers are obliged to complete the assigned tasks on time and to inform the journal in case of the need for an extension or withdrawal from the task.

The Ethical Responsibilities of Editors
Journal Editors (Chief Editor, Editor, or Editorial Board Members) have full responsibility and authority to reject/accept an article. Editors always consider the needs of authors and readers while striving to improve the publication. Editors take the necessary precautions to keep articles and editorial reports confidential. Articles, editorial reports, and obtained information are not shared or disclosed for any reason.
Editorial decisions in the journal are based solely on the significance, originality, clarity, and suitability of the articles for publication. Editors ensure that all research materials published in the Journal comply with internationally accepted ethical standards. Editors are obliged to take action and make all reasonable efforts to resolve the issue when they encounter any abuse, unethical behavior, or misconduct related to research and publication ethics, whether the article is published or unpublished.
In articles submitted by editors or members of the editorial board of the journal, the process is conducted in such a way that the editor or board member who is the author of the article does not participate in the evaluation and decision stages.
Editors, editorial staff, authors, reviewers, and committee members conduct the evaluation process in a manner that does not allow any conflicts of interest.
Editors are responsible for completing assigned tasks on time, facilitating the review process, remaining impartial, and ensuring that the review process progresses consistently and fairly.

PUBLISHING POLICY
The Journal of Uludağ University Medical Faculty is an open-access journal that publishes for scientific purposes and does not request any fees at any stage of the process. Articles submitted for evaluation to the journal are primarily subjected to a format review, and a similarity check is conducted at this stage. Subsequently, a priority assessment for publication in the journal is conducted by the chief editor, editor, and/or the relevant section editor. Due to the large number of articles submitted to our journal, in this evaluation, articles determined not to have priority are not considered for review and are returned to the author. A Section Editor from the Editorial Board is assigned to the articles that are accepted for review. The section editor obtains opinions from at least 2 scientific advisors and informs the editor of the decision. In the case of equal opinions from scientific advisors (1 rejection, 1 acceptance/revision), the article may be sent to a third reviewer by the section editor, or the section editor may provide her/his opinion based on her/his own evaluation. The final decision is made by the Chief Editor and/or the Editor and communicated to the author.
The review period in our journal is an average of 60 days. However, for various reasons, this period can vary between 15 days and 120 days.

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Changes in Respiratory Microorganism Distribution and Antimicrobial Resistance Patterns in Intensive Care Units: A Comparative Analysis Before and During the COVID-19 Pandemic

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Yoğun Bakım Ünitelerinde Solunum Yolu Mikroorganizma Dağılımı ve Antimikrobiyal Direnç Paternlerindeki Değişimler: COVID-19 Pandemisi Öncesi ve Pandemi Döneminin Karşılaştırmalı Analizi

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