A Comparative Study on Microbial Air Quality of Radiology and Patient Waiting Rooms of a Full-Equipped Hospital in Aydın Province

Yıl 2024, , 12 - 24, 30.04.2024

Bahadır Törün , Aykan Özgür , Hacı Halil Bıyık , Esin Poyrazoğlu

https://doi.org/10.53433/yyufbed.1329620

Öz

Every year many patients die due to hospital-acquired infections. These infections also put the lives of healthcare workers at risk. Additionally, hospitals are one of the main reservoirs of antimicrobial resistance. In this study, the effect of X-rays on species diversity and functions and antimicrobial resistance were observed. Metagenome analysis was performed on air samples taken from the x-ray room (radiation exposure) and the waiting room (non-radiation area) to examine whether the radiation affected the species present in the air. The diversity of microorganisms was analysed based on phylum, genus, and species levels. Functional profiling and resistance screening were also performed. X-ray radiation was found to have a major effect at the phylum level. It was observed that Proteobacteria species almost dominated the microbiome in the x-ray room (99%) while Actinobacteria species dominated the microbiome in the waiting room (84%). No significant differences were observed between the two areas in functional profiling. A total of thirty-eight functions were observed, twenty-four of which were overlapping. Antimicrobial resistance was not as diverse as expected. Only beta-lactam, penicillin, tetracycline, and lincomycin resistance genes were present (2364 reads belonging to four different genes). According to the results, it was observed that X-rays affected the air microbiome, as expected. A decrease in the number of microorganisms was expected, but it was also observed that the dominant microorganism types changed. On the other hand, no significant difference was found in terms of functional profiling and no significant antimicrobial resistance was observed.

Anahtar Kelimeler

Air microbiome, Air quality, Metagenome, X-Ray room

Teşekkür

This study was conducted at Aydın Adnan Menderes University, Faculty of Science and Literature, Microbiology Laboratory.

Aydın İlindeki Tam Teşekküllü Bir Hastanenin Radyoloji ve Hasta Bekleme Odalarının Mikrobiyal Hava Kalitesinin Karşılaştırmalı Olarak İncelenmesi

Öz

Her yıl çok sayıda hasta hastane kaynaklı enfeksiyonlar nedeniyle hayatını kaybetmektedir. Bu enfeksiyonlar sağlık çalışanlarının hayatını da riske atmaktadır. Ayrıca hastaneler, antimikrobiyal direncin ana rezervuarlarından biridir. Çalışmada X-ışınlarının tür çeşitliliği ve fonksiyonları üzerine etkisi ve antimikrobiyal direnç gözlemlenmiştir. Röntgen odasından (radyasyona maruz kalan) ve bekleme odasından (radyasyon olmayan alan) alınan hava örneklerine radyasyonun havada bulunan türleri etkileyip etkilemediğini görmek için metagenom analizi yapıldı. Mikroorganizmaların çeşitliliği şube, cins ve tür seviyelerinde analiz edildi. Ayrıca fonksiyonel profilleme ve direnç taraması yapıldı. X-ışını radyasyonunun şube düzeyinde büyük bir etkisi olduğu bulundu. Röntgen odasında Proteobacteria türleri mikrobiyomu neredeyse domine ettiği (%99), bekleme odasında Actinobacteria mikrobiyomu domine ettiği görüldü (%84). Fonksiyonel profillemede iki alan arasında önemli bir fark görülmedi. Yirmi dördü örtüşen toplam otuz sekiz fonksiyon gözlemlendi. Antimikrobiyal direnç beklenilen kadar çeşitli değildi. Sadece beta-laktam, penisilin, tetrasiklin ve lincomycin direnç genleri mevcuttu (dört farklı gene ait 2364 okuma). Çıkan sonuçlara göre, beklenti doğrultusunda, X-ışınlarının hava mikrobiyomunu etkilediği gözlemlendi. Mikroorganizma sayısında azalma bekleniyordu fakat baskın mikroorganizma türlerinin değiştiği de gözlemlendi. Fonksiyonel profilleme açısından önemli bir fark bulunamamış ve önemli bir antimikrobiyal direnç görülmemiştir.

Anahtar Kelimeler

Hava kalitesi, Hava mikrobiyomu, Metagenom, Röntgen odası

Kaynakça

• Adedeji, W. A. (2016). The treasure called antibiotics. Annals of Ibadan Postgraduate Medicine, 14(2), 56.
• Ahmad, H., Masroor, T., Parmar, S. A., & Panigrahi, D. (2021). Urinary tract infection by a rare pathogen Cedecea neteri in a pregnant female with Polyhydramnios: rare case report from UAE. BMC Infectious Diseases, 21, 1-6. doi:10.1186/s12879-021-06298-y
• Akinyemi, K. O., Atapu, A. D., Adetona, O. O., & Coker, A. O. (2009). The potential role of mobile phones in the spread of bacterial infections. The Journal of Infection in Developing Countries, 3(08), 628-632. doi:10.3855/jidc.556
• Anonymus. (2018). Picard Tools. http://broadinstitute.github.io/picard/ Access Date: 08.11.2024.
• Alrazeeni, D., & Al Sufi, M. S. (2014). Nosocomial infections in ambulances and effectiveness of ambulance fumigation techniques in Saudi Arabia: Phase I study. Saudi Medical Journal, 35(11), 1354.
• Bannert, N., Hofmann, H., & Hohn, O. (2018). HERVs new role in cancer: from accused perpetrators to cheerful protectors. Frontiers in Microbiology, 9, 338466. doi:10.3389/fmicb.2018.00178
• Barnett, D. W., Garrison, E. K., Quinlan, A. R., Strömberg, M. P., & Marth, G. T. (2011). BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics, 27(12), 1691-1692. doi:10.1093/bioinformatics/btr174
• Bures, S., Fishbain, J. T., Uyehara, C. F., Parker, J. M., & Berg, B. W. (2000). Computer keyboards and faucet handles as reservoirs of nosocomial pathogens in the intensive care unit. American Journal of Infection Control, 28(6), 465-471. doi:10.1067/mic.2000.107267
• Clark, G. L., & Boruff, C. S. (1929). The effect of X-rays on bacteria. Science, 70(1803), 74-75. doi:10.1126/science.70.1803.74
• Curty, G., Marston, J. L., de Mulder Rougvie, M., Leal, F. E., Nixon, D. F., & Soares, M. A. (2020). Human endogenous retrovirus K in cancer: a potential biomarker and immunotherapeutic target. Viruses, 12(7), 726. doi:10.3390/v12070726
• Dalamaga, M., & Vrioni, G. (2011). Cedecea. In: Liu D. (Ed.), Molecular Detection of Human Bacterial Pathogens (pp 817-825), Boca Raton, FL: CRC Press/Taylor and Francis Group.
• Delétoile, A., Decré, D., Courant, S., Passet, V., Audo, J., Grimont, P., ... & Brisse, S. (2009). Phylogeny and identification of Pantoea species and typing of Pantoea agglomerans strains by multilocus gene sequencing. Journal of Clinical Microbiology, 47(2), 300-310. doi:10.1128/jcm.01916-08
• Farkas, J., & Mohácsi-Farkas, C. (2011). History and future of food irradiation. Trends in Food Science & Technology, 22(2-3), 121-126. doi:10.1016/j.tifs.2010.04.002
• Girma, A., & Lamore, Y. (2022). Determination of the indoor air bacterial profile in Jimma University Specialized Hospital, Southwest Ethiopia. SAGE Open Medicine, 10. doi:10.1177/20503121221122405
• Grimont, P. A., Grimont, F., Farmer III, J. J., & Asbury, M. A. (1981). Cedecea davisae gen. nov., sp. no v. and Cedecea lapagei sp. nov., New Enterobacteriaceae from clinical specimens. International Journal of Systematic and Evolutionary Microbiology, 31(3), 317-326. doi:10.1099/00207713-31-3-317
• Ilyas, F., Burbridge, B., & Babyn, P. (2019). Health care–associated infections and the radiology department. Journal of Medical Imaging and Radiation Sciences, 50(4), 596-606. doi:10.1016/j.jmir.2019.07.011
• Karapetsa, M., Tsolaki, V., Arabatzis, M., Petinaki, E., Velegraki, A., & Zakynthinos, E. (2019). Septic shock due to Candida famata (Debaryomyces hansenii) candidemia in an ICU immunocompetent trauma-patient. Journal of Infection and Public Health, 12(4), 594-597. doi:10.1016/j.jiph.2018.12.015
• Klindworth, A., Pruesse, E., Schweer, T., Peplies, J., Quast, C., Horn, M., & Glöckner, F. O. (2013). Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Research, 41(1). doi:10.1093/nar/gks808
• Kumar, V., Singh C., Shukla V., & Bhargava, H.K. (2012). Gamma radiation and its effect on microbial growth. India: Babasaheb Bhimrao Ambedkar University.
• Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10, 1-10. doi:10.1186/gb-2009-10-3-r25
• Lax, S., Smith, D. P., Hampton-Marcell, J., Owens, S. M., Handley, K. M., Scott, N. M., ... & Gilbert, J. A. (2014). Longitudinal analysis of microbial interaction between humans and the indoor environment. Science, 345(6200), 1048-1052. doi:10.1126/science.1254529
• Lax, S., & Gilbert, J. A. (2015). Hospital-associated microbiota and implications for nosocomial infections. Trends in Molecular Medicine, 21(7), 427-432. doi:10.1016/j.molmed.2015.03.005
• Lax, S., Smith, D., Sangwan, N., Handley, K., Larsen, P., Richardson, M., ... & Gilbert, J. A. (2017). Colonization and succession of hospital-associated microbiota. Science Translational Medicine, 9(391).
• Leung, M., & Chan, A.H.S. (2006). Control and management of hospital indoor air quality. Medical Science Monitor, 12, SR17e23.
• Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., ... & Durbin, R. (2009). The sequence alignment/map format and SAMtools. Bioinformatics, 25(16), 2078-2079. doi:10.1093/bioinformatics/btp352
• Li, J., Cao, J., Zhu, Y. G., Chen, Q. L., Shen, F., Wu, Y., ... & Yao, M. (2018). Global survey of antibiotic resistance genes in air. Environmental Science & Technology, 52(19), 10975-10984. doi:10.1021/acs.est.8b02204
• Li, X., Wu, Z., Dang, C., Zhang, M., Zhao, B., Cheng, Z., ... & Xia, Y. (2021). A metagenomic-based method to study hospital air dust resistome. Chemical Engineering Journal, 406, 126854. doi:10.1016/j.cej.2020.126854
• Lohse, M., Bolger, A. M., Nagel, A., Fernie, A. R., Lunn, J. E., Stitt, M., & Usadel, B. (2012). R obi NA: A user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Research, 40(W1), W622-W627. doi:10.1093/nar/gks540
• Mahmoud, B. S. (2009). Effect of X-ray treatments on inoculated Escherichia coli O157: H7, Salmonella enterica, Shigella flexneri and Vibrio parahaemolyticus in ready-to-eat shrimp. Food Microbiology, 26(8), 860-864. doi:10.1016/j.fm.2009.05.013
• Mahmoud, B. S. (2010). The effects of X-ray radiation on Escherichia coli O157: H7, Listeria monocytogenes, Salmonella enterica and Shigella flexneri inoculated on whole Roma tomatoes. Food Microbiology, 27(8), 1057-1063. doi:10.1016/j.fm.2010.07.009
• Mahmoud, B. S. (2012). Effects of X-ray treatments on pathogenic bacteria, inherent microflora, color, and firmness on whole cantaloupe. International Journal of Food Microbiology, 156(3), 296-300. doi:10.1016/j.ijfoodmicro.2012.04.001
• Marinella, M. A., Pierson, C., & Chenoweth, C. (1997). The stethoscope: a potential source of nosocomial infection?. Archives of Internal Medicine, 157(7), 786-790. doi:10.1001/archinte.1997.00440280114010
• O’Hara, N. B., Reed, H. J., Afshinnekoo, E., Harvin, D., Caplan, N., Rosen, G., ... & Mason, C. E. (2017). Metagenomic characterization of ambulances across the USA. Microbiome, 5, 1-20. doi:10.1186/s40168-017-0339-6
• Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999). KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research, 27(1), 29-34. doi:10.1093/nar/27.1.29
• Oksanen, J., Kindt, R., Legendre, P., O’Hara, B., Stevens, M. H. H., Oksanen, M. J., & Suggests, M. A. S. S. (2007). The vegan package. Community Ecology Package, 10(631-637), 719.
• Ondov, B. D., Bergman, N. H., & Phillippy, A. M. (2011). Interactive metagenomic visualization in a Web browser. BMC Bioinformatics, 12, 1-10. doi:10.1186/1471-2105-12-385
• Oner, M. E., & Wall, M. M. (2013). Quality of fresh‐cut purple‐fleshed sweet potatoes after X‐ray irradiation treatment and refrigerated storage. International Journal of Food Science & Technology, 48(10), 2064-2070. doi:10.1111/ijfs.12187
• Oshoma, C., Ehigimamusoe, F. O., Emoghene, A., Osayande, A. O. (2010). Microbial air quality of x-ray rooms in private and public radiology unit in Benin City, Nigeria. Asian Journal of Microbiology, Biotechnology and Environmental Sciences, 12(4), 721-726.
• R Development Core Team. (2010). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
• Roux, S., Brum, J. R., Dutilh, B. E., Sunagawa, S., Duhaime, M. B., Loy, A., ... & Sullivan, M. B. (2016). Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature, 537(7622), 689-693. doi:10.1038/nature19366
• Tarasov, A., Vilella, A. J., Cuppen, E., Nijman, I. J., & Prins, P. (2015). Sambamba: fast processing of NGS alignment formats. Bioinformatics, 31(12), 2032-2034. doi:10.1093/bioinformatics/btv098
• Ventola, C. L. (2015). The antibiotic resistance crisis: part 1: causes and threats. Pharmacy and Therapeutics, 40(4), 277.
• Whon, T. W., Kim, M. S., Roh, S. W., Shin, N. R., Lee, H. W., & Bae, J. W. (2012). Metagenomic characterization of airborne viral DNA diversity in the near-surface atmosphere. Journal of Virology, 86(15), 8221-8231. doi:10.1128/jvi.00293-12
• Wiener-Well, Y., Galuty, M., Rudensky, B., Schlesinger, Y., Attias, D., & Yinnon, A. M. (2011). Nursing and physician attire as possible source of nosocomial infections. American Journal of Infection Control, 39(7), 555-559. doi:10.1016/j.ajic.2010.12.016
• Wood, D. E., & Salzberg, S. L. (2014). Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biology, 15, 1-12. doi:10.1186/gb-2014-15-3-r46
• Xie, J., Jin, L., Luo, X., Zhao, Z., & Li, X. (2018). Seasonal disparities in airborne bacteria and associated antibiotic resistance genes in PM2. 5 between urban and rural sites. Environmental Science & Technology Letters, 5(2), 74-79. doi:10.1021/acs.estlett.7b00561
• Yayla, B. D., Mutlu, B., & Gedudot, A. (2018). Invasive Trichosporon infection: a report of two cases. Klimik Dergisi, 31(1), 67-70.
• Yılmaz, F., Savcı, S., Pazar-Yıldırım, E., Gönüllü, N., Bavunoğlu, I., Köksal-Çakırlar, F., ... & Kiraz, N. (2015). Pantoea agglomerans ın neden olduğu kateter ilişkili bir sepsis olgusu. Türk Hijyen ve Deneysel Biyoloji Dergisi, 72(1), 59-62.
• Zhou, C. E., Smith, J., Lam, M., Zemla, A., Dyer, M. D., & Slezak, T. (2007). MvirDB—a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications. Nucleic Acids Research, 35, D391-D394. doi:10.1093/nar/gkl791