In Silico Analysis of Resistance Gene Identifiers on Plasmids of blaNDM-5 Producing Carbapenem-Resistant Escherichia coli Strains Isolated in Humans and Animals

Abstract

Due to their ability to resist endpoint antimicrobials such as carbapenem, it is very important to detect and monitor multi-drug resistant Gram negative strains with plasmids containing genes such as blaNDM-5 by new molecular methods. This study aimed to perform in silico analysis of resistance gene identifiers on human and animal-derived blaNDM-5 plasmids found in open databases, which were analyzed by new whole genome sequencing techniques and to compare these resistance genes. The plasmid genomic sequences of 4 human and 2 animal E. coli strains containing blaNDM-5 genes included in our study were analyzed in Silico using the Resistance Gene Identifier (RGI) option of the comprehensive antibiotic resistance gene database using default values. Human and animal strains included in our study were found to have different antimicrobial resistance genes in addition to blaNDM-5. All plasmids were found to have at least 8 perfect antimicrobial resistance gene sequences matches. When the resistance gene identifiers in all plasmids were examined, 35 resistance gene identifiers were found. Besides blaNDM-5, mphA, qacEdelta1 and sul1 were found in all plasmids. As a conclusion, it was determined by our study results that, regardless of the source, there may be different antimicrobial resistance gene identifiers besides the blaNDM-5 resistance gene in plasmids. We are of the opinion that routine molecular surveillance studies should be carried out considering the one health approach of Gram-negative pathogens such as E. coli, which can contain plasmids that cause multi-drug resistance and can be isolated from all sources.

Keywords

• bla-NDM5
• Carbapenem resistant E.coli
• in silico analysis
• resistance gene identifier

İnsanlardan ve Hayvanlardan İzole Edilen blaNDM-5 Üreten Karbapenem Dirençli Escherichia coli Kökenlerinin Plazmidlerı Üstünde Bulunan Direnç Gen Tanımlayıcılarının İn Silico Analizi

Öz

Karbapenem gibi son nokta antimikrobiyallere direnç yetenekleri dolayısıyla, blaNDM-5 gibi genler ihtiva eden plazmidlere sahip çoklu ilaç direnci gösteren Gram negatif kökenlerin yeni moleküler yöntemlerle tespiti önemlidir. Biz de çalışmamızda bu yeni tekniklerle tüm genom sekans analizi yapılan ve açık veritabanlarında bulunan insan ve hayvan kaynaklı blaNDM-5 plazmidleri üstünde bulunan direnç gen tanımlayıcılarının in silico analizini yapmayı ve bu direnç genlerini karşılaştırmayı amaçladık. Çalışmamıza dahil edilen 4 insan ve 2 hayvan kaynaklı, blaNDM-5 geni içeren E.coli kökenlerine ait plazmid genomik dizileri, varsayılan değerler kullanılarak kapsamlı antibiyotik direnç gen veritabanının, direnç geni tanımlayıcı (RGI) seçeneği kullanılarak bilgisayar ortamında analiz edildi. Çalışmamıza dahil edilen insan ve hayvan kaynaklı kökenlerde blaNDM-5 yanında farklı antimikrobiyal direnç genlerinin de olduğu tespit edildi. Tüm plazmidlerin en az 8 mükemmel antimikrobiyal direnç gen dizisi eşleşmesi gösterdiği saptandı. Tüm plazmidlerde bulunan direnç gen tanımlayıcıları incelendiğinde 35 direnç gen tanımlayıcısı saptandı. blaNDM-5 yanında, mphA, qacEdelta1 ve sul1’in bütün plazmidlerde olduğu tespit edildi. Sonuç olarak, kaynak fark etmeksizin, plazmidlerde, blaNDM-5 direnç geni yanında farklı antimikrobiyallere direnç gen tanımlayıcılarının da olabildiği çalışma sonucunda tespit edilmiştir. Çoklu ilaç direncine neden olan plazmidleri ihtiva edebilen ve tüm kaynaklardan izole edilebilen E. coli gibi Gram negatif patojenler üzerinde tek sağlık yaklaşımı düşünülerek rutin moleküler surveyans çalışmalarının yapılması gerektiği kanaatindeyiz.

Anahtar Kelimeler

• blaNDM-5
• direnç gen tanımlayıcıları
• in silico analiz Karbapenem dirençli E.coli

References

1. Aenishaenslin C, Häsler B, Ravel A, Parmley EJ, Mediouni S, Bennani H, Buckeridge DL. Evaluating the Integration of One Health in Surveillance Systems for Antimicrobial Use and Resistance: A Conceptual Framework. Frontiers in veterinary science. 2021; 8, 169.
2. Basu S. Variants of the New Delhi Metallo-β-lactamase: New kids on the block 1. 2020; 465-467.
3. Brown AC, Chen JC, Watkins LKF, Campbell D, Folster JP, Tate H, Friedman CR. CTX-M-65 extended-spectrum β-lactamase–producing Salmonella enterica serotype Infantis, United States. Emerging infectious diseases. 2018; 24(12), 2284.
4. Feng Y, Liu L, McNally A, Zong Z. Coexistence of two blaNDM-5 genes on an IncF plasmid as revealed by nanopore sequencing. Antimicrobial agents and chemotherapy. 2018; 62(5).
5. He T, Wei R, Zhang L, Sun L, Pang M, Wang R, Wang Y. Characterization of NDM-5-positive extensively resistant Escherichia coli isolates from dairy cows. Veterinary microbiology. 2017; 207, 153-158.
6. Huang YS, Tsai WC, Li JJ, Chen PY, Wang JT, Chen YT, Chang SC. Increasing New Delhi Metallo-β-lactamase-positive Escherichia coli among carbapenem non-susceptible Enterobacteriaceae in Taiwan during 2016 to 2018. Scientific reports. 2021; 11(1), 1-10
7. Hornsey M, Phee L, Wareham DW. A novel variant, NDM-5, of the New Delhi Metallo-β-lactamase in a multidrug-resistant Escherichia coli ST648 isolate recovered from a patient in the United Kingdom. Antimicrobial agents and chemotherapy. 2011; 55(12), 5952-5954.
8. Li X, Fu Y, Shen M, Huang D, Du X, Hu Q, Yu Y. Dissemination of bla NDM-5 gene via an IncX3-type plasmid among non-clonal Escherichia coli in China. Antimicrobial Resistance & Infection Control. 2018; 7(1), 1-9.

9. Liu BT, Zhang XY, Wan SW, Hao JJ, Jiang RD, Song FJ. Characteristics of carbapenem-resistant Enterobacteriaceae in ready-to-eat vegetables in China. Frontiers in microbiology. 2018; 9, 1147.
10. Liu Z, Xiao X, Li Y, Liu Y, Li R, Wang Z. Emergence of IncX3 Plasmid-Harboring blaNDM–5 Dominated by Escherichia coli ST48 in a Goose Farm in Jiangsu, China. Frontiers in microbiology. 2019;10, 2002.
11. Marchetti VM, Bitar I, Mercato A, Nucleo E, Bonomini A, Pedroni P, Migliavacca R. Complete Nucleotide Sequence of Plasmids of Two Escherichia coli Strains Carrying blaNDM–5 and blaNDM–5 and blaOXA–181 From the Same Patient. Frontiers in microbiology. 2020; 10, 3095.
12. Ramadan H, Gupta SK, Sharma P, Ahmed M, Hiott LM, Barrett JB, Jackson CR. Circulation of emerging NDM‐5‐producing Escherichia coli among humans and dogs in Egypt. Zoonoses and public health. 2020; 67(3), 324-329.
13. Sun P, Xia W, Liu G, Huang X, Tang C, Liu C, Pan S. Characterization of blaNDM-5-positive Escherichia coli prevalent in a university hospital in eastern China. Infection and drug resistance. 2019; 12, 3029. Tian D, Wang B, Zhang H, Pan F, Wang C, Shi Y, Sun Y. Dissemination of the blaNDM-5 gene via IncX3-type plasmid among Enterobacteriaceae in children. Msphere. 2020; 5(1).
14. Tyson GH, Li C, Ceric O, Reimschuessel R, Cole S, Peak L, Rankin SC. Complete genome sequence of a carbapenem-resistant Escherichia coli isolates with blaNDM-5 from a dog in the United States. Microbiology resource announcements. 2019; 8(34).
15. Yong D, Toleman MA, Giske CG, Cho HS, Sundman K, Lee K, Walsh TR. Characterization of a new Metallo-β-lactamase gene, blaNDM-1, and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Antimicrobial agents and chemotherapy. 2009; 53(12), 5046-5054.
16. Xie M, Li R, Liu Z, Chan EWC, Chen S. Recombination of plasmids in a carbapenem-resistant NDM-5-producing clinical Escherichia coli isolate. Journal of Antimicrobial Chemotherapy. 2018; 73(5), 1230-1234.
17. Zhao Q, Berglund B, Zou H, Zhou Z, Xia H, Zhao L, Li X. Dissemination of blaNDM-5 via IncX3 plasmids in carbapenem-resistant Enterobacteriaceae among humans and in the environment in an intensive vegetable cultivation area in eastern China. Environmental Pollution. 2021; 273, 116370.
18. Zhu YQ, Zhao JY, Xu C, Zhao H, Jia N, Li YN. Identification of an NDM-5-producing Escherichia coli sequence type 167 in a neonatal patient in China. Scientific reports. 2016; 6(1), 1-8.