STUDY OF GENE EXPRESSION IN RESPONSE TO SERIAL EXPOSURE TO MEROPENEM IN BACTEROIDES FRAGILIS
Main Article Content
Authors
D.S. Bayanbek
L.N. Gumilyov Eurasian National University, Astana, Kazakhstan, Kazhymukan str. 13, 010000
A. Bekbaeva
National Center for Biotechnology, Astana, Kazakhstan, 13/5, Kurgalzhyn road, 010000
S.S. Kozhahmetova
National Center for Biotechnology, Astana, Kazakhstan, 13/5, Kurgalzhyn road, 010000
B.R. Turdalina
NJSC “Astana Medical University”
E.V. Zholdybaeva
National Center for Biotechnology, Astana, Kazakhstan, 13/5, Kurgalzhyn road, 010000
Abstract
Antibiotic resistance is a major global health concern, and inappropriate antibiotic use contributes significantly to the development of resistance in pathogens. Bacteroides fragilis, an anaerobic bacterium, is commonly treated with β-lactam antibiotics like meropenem. B. fragilis possesses various antibiotic resistance mechanisms, including enzymatic modification of antibiotics, efflux systems, and reduction of cell membrane permeability. The primary mechanism of carbapenem resistance in B. fragilis is linked to the production of a metallo-β-lactamase encoded by the cfiA gene. However, this gene is frequently inactive and requires activation by insertion elements.
The study aimed to explore the expression of specific genes in B. fragilis associated with different metabolic pathways in response to exposure to sub-inhibitory concentrations of meropenem. The study used B. fragilis strain BFR KZ01, obtained from a patient with appendicitis and peritonitis. Serial exposure to meropenem was conducted, and gene expression was analyzed using quantitative RT-PCR. Significant and long-lasting alterations in gene expression patterns were observed in B. fragilis following exposure to meropenem, even after removal of the antibiotic. Genes such as cfiA, oxyR, and Ddl showed heightened expression levels even after discontinuation of meropenem.
The study discussed the implications of gene expression changes induced by meropenem exposure, highlighting the role of oxidative stress response (oxyR), D-Ala-D-Ala ligase (Ddl), and carbapenemase (cfiA) genes in antibiotic resistance mechanisms. The study concluded that exposure to meropenem induced lasting alterations in gene expression in B. fragilis, contributing to antibiotic resistance. Understanding these mechanisms is crucial for developing strategies to combat antibiotic resistance.
Keywords
Bacteroides fragilis, antibiotic resistance, gene expression, meropenem, β-lactamase, cfiA gene
Article Details
References
Nikaido H., Structure and mechanism of RND-type multidrug efflux pumps // Advances in Enzymology and Related Areas of Molecular Biology. – 2011. – Vol. 77. – P.1-60.
Jamal W., Khodakhast F.B., AlAzmi A., Sόki J., AlHashem G., Rotimi V.O. Prevalence and antimicrobial susceptibility of enterotoxigenic extra-intestinal Bacteroides fragilis among 13-year collection of isolates in Kuwait // BMC Microbiology. – 2020 Jan 15; – Vol. 20. – No. 1. – P.14 // doi: 10.1186/s12866-020-1703-4.
Pumbwe L., Ueda O., Yoshimura F., Chang A., Smith R. L., Wexler. H. M. Bacteroides fragilis BmeABC efflux systems additively confer intrinsic antimicrobial resistance // Journal of Antimicrobial Chemotherapy. – 2006 July. – Vol. 58. – No.1. P. 37–46 // doi.org/10.1093/jac/dkl202.
Ghotaslou R., Yekani M., Memar M. Y.. The role of efflux pumps in Bacteroides fragilis resistance to antibiotics // Microbiol Resistance. – 2018 May. – Vol. 210. – P.1-5. // doi: 10.1016/j.micres.2018.02.007.
Hartmeyer G. N., Soki J., Nagy E., Justesen U. S. Multidrug-resistant Bacteroides fragilis group on the rise in Europe? // Journal of Medical Microbiology. – 2012. – Vol. 61. –No.12. – P.1784-1788 // doi.org/10.1099/jmm.0.049825-0.
Sárvári K.P, Sóki J, Kristóf K, Juhász E, Miszti C, Melegh S.Z, et al. Molecular characterisation of multidrug-resistant Bacteroides isolates from Hungarian clinical samples // J Global Antimicrob Resist. – 2018. – Vol. 61. – P.65-69 // doi.org/10.1016/j.jgar.2017.10.020.
Wareham D., Wilks M., Ahmed D., Brazier J., Millar M., Anaerobic sepsis due to multidrug-resistant Bacteroides fragilis: microbiological cure and clinical response with linezolid therapy // Clin. Infect. Dis. – 2005. – Vol. 40. – No. 7. – P.67-68 // doi:10/1086/428623
Edwards R, Read P.N. Expression of the carbapenemase gene (cfiA) in Bacteroides fragilis // J Antimicrob Chemother. – 2000. – Vol. 46. – P. 1009–12 //doi.org/10.1093/jac/ 46.6.1009
de Freitas M.C.R. et al. Exploratory Investigation of Bacteroides fragilis Transcriptional Response during In vitro Exposure to Subinhibitory Concentration of Metronidazole // Frontiers in Microbiology - 2016. - Vol. 7. - P. 1-13 //doi: 10.3389/fmicb.2016.01465.
Eley A., Greenwood D., O’Grady F. Comparative growth of Bacteroides species in various anaerobic culture media // Journal of Medical Microbiology. – 1985. – Vol. 19, – No. 2. – P.195-201 // doi. 10.1099/00222615-19-2-195
Clinical and Laboratory Standards Institute. Methods for antimicrobial susceptibility testing of anaerobic bacteria; approved standard. 7th ed. CLSI document M11-A7. Wayne, PA: CLSI; 2007.
Lu G., Moriyama E. N., Vector NTI, a balanced all-in-one sequence analysis suite // Briefings in Bioinformatics. – 2004. – Vol. 5. – No. 4. – P. 378–388. //doi.org/10.1093/bib/5.4.378.
Kozhakhmetova S., Zholdybayeva E., Tarlykov P., Atavliyeva S., Syzdykov T., Daniyarov A., Mukhtarova K., Ramankulov Y. Determinants of resistance in Bacteroides fragilis strain BFR_KZ01 isolated from a patient with peritonitis in Kazakhstan // Journal of Global Antimicrobial Resistance. – 2021. – Vol. 25. – P.1–4. //doi.org/10.1016/j.jgar.2021.02.022.
Teixeira F.L., Costa S.B., Pauer H., de Almeida B.J., Oliveira A.C.S.C., Smith C.J., Domingues R.M.C.P., Rocha E.R., Lobo L.A. Characterization of the oxidative stress response regulatory network in Bacteroides fragilis: An interaction between BmoR and OxyR regulons promotes abscess formation in a model of intra-abdominal infection // Anaerobe. –2022. – Vol. 78. – P. 102668 // doi: 10.1016/j.anaerobe.2022.102668.
Kohanski M.A., Dwyer D.J., Hayete B., Lawrence C.A., Collins J.J. A common mechanism of cellular death induced by bactericidal antibiotics // Cell. – 2007. – Vol. 130. – P.797– 810 //doi.org/10.1016/j.cell.2007.06.049.
Dwyer D.J., Kohanski M.A., Hayete B., Collins J.J. Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli // Mol Syst Biol. – 2007. – Vol.3. – P. 91 //doi.org/10.1038/msb4100135.
Foti J.J., Devadoss B., Winkler J.A., Collins J.J., Walker G.C. Oxidation of the guanine nucleotide pool underlies cell death by bactericidal antibiotics // Science. – 2012. – Vol. 336. – No. 6079. – P. 315–319 //doi.org/10.1126/ science.1219192.
Degtyareva N.P., Heyburn L., Sterling J., Resnick M.A., Gordenin D.A., Doetsch P.W. Oxidative stress-induced mutagenesis in single-strand DNA occurs primarily at cytosines and is DNA polymerase zeta-dependent only for adenines and guanines // Nucleic Acids Res. – Oct. 2013. – Vol. 41. – No. 19. – P. 8995–9005 // doi.org/10.1093/NAR/GKT671.
Qi, W., Jonker, M.J., Teichmann, L. et al. The influence of oxygen and oxidative stress on de novo acquisition of antibiotic resistance in E. coli and Lactobacillus lactis // BMC Microbiol. – 2023. – Vol. 23. – P. 279 //doi.org/10.1186/s12866-023-03031-4.
Bouillaut L., Newton W., Sonenshein A.L., Belitsky B.R. DdlR, an essential transcriptional regulator of peptidoglycan biosynthesis in Clostridioides difficile // Molecular Microbiology. – 2019. – Vol. 112. – No. 5. – P. 1453–1470 // doi. 10.1111/mmi.14371.
Zhang S., Oh J.H., Alexander L.M., Özçam M., van Pijkeren J.P. D-Alanyl-d-Alanine Ligase as a Broad-Host-Range Counterselection Marker in Vancomycin-Resistant Lactic Acid Bacteria // Journal of Bacteriology. – July 2018. – Vol. 200. – No. 13. – P. 607-617 //doi.org/10.1128/JB.00607-17.
Soki J. Extended role for insertin sequence elements in the antibiotic resistance of Bacteroides // World J Clin Infect Dis. – 2013. – Vol. 3. – P. 1–12.
Soki J., Eitel Z., Urbán E., Nagy E. Molecular analysis of the carbapenem and metronidazole resistance mechanisms of Bacteroides strains reported in a Europe-wide antibiotic resistance survey // Int J Antimicrob Agents. – 2013. – Vol. 41. – P. 122–125 // doi: 10.1016/j.ijantimicag.2012.10.001.
Wexler H.M., Bacteroides: the good, the bad, and the nitty-gritty // Clin. Microbiol. Rev. – 2007. – Vol. 20. – No. 4. – P. 593-621// doi: 10.1128/CMR.00008-07
Veloo A.C.M., Baas W.H., Haan F.J., Coco J., Rossen J.W., Prevalence of antimicrobial resistance genes in Bacteroides spp. and Prevotella spp. Dutch clinical isolates // Clin. Microbiol. Infect. – 2019. – Vol. 25. – No.9. – P. 1156.e9-13 // doi: 10.1016/j.cmi.2019.02.017
Cordovana M., Kostrzewa M., Soki J., Witt E., Ambretti S., Pranada A.B., Bacteroides fragilis: a whole MALDI-based workflow from identification to confirmation of carbapenemase production for routine laboratories // Anaerobe. – 2018. – Vol. 54. – P. 246-253 // doi: 10.1016/j.anaerobe.2018.04.004
Gao Q., Wu S., Xu T., Zhao X., Huang H., Hu F., Emergence of carbapenem resistance in Bacteroides fragilis in China // Int. J. Antimicrob. Agents. – 2019. – Vol. 53. – No.6. – P. 859-863 // doi: 10.1016/j.ijantimicag.2019.02.017
Jeverica S., Soki J., Premru M.M., Nagy E., Papst L., High prevalence of division II (cfiA positive) isolates among blood stream Bacteroides fragilis in Slovenia as determined by MALDI-TOF MS // Anaerobe. – 2019. – Vol. 58. – P.30-34 //doi: 10.1016/j.anaerobe.2019.01.011
Wang Y., Han Y., Shen H., Lv Y., Zheng W., Wang J., Higher prevalence of multiantimicrobial resistant Bacteroides spp. strains isolated at a tertiary teaching hospital in China // Infect. Drug Resist. – 2020. – Vol.13. – P. 1537-1546 // doi: 10.2147/IDR.S246318
Toprak N.U., Akgul O., Bilgin H., Ozaydin A.N., Gelmez G.A., Sayin E., Sili U., Korten V., Soyletir G. Frequency and associated factors for carbapenem-non-susceptible Bacteroides fragilis group bacteria colonization in hospitalized patients: Case control study in a university hospital in Turkey // Indian Journal of Medical Microbiology. – 2021. – Vol. 39. – P. 518–522 // doi: 10.1016/j.ijmmb.2021.03.018
Pilmis B., Le Monnier A., Zahar J.R. Gut microbiota, antibiotic therapy and antimicrobial resistance: a narrative review // Microorganisms. – 2020. – Vol. 8. – No. 2. – P. 269. 8 // doi.org/10.3390/microorganisms8020269.
Snydman D.R., Jacobus N.V., McDermott L.A., Golan Y., Goldstein E.J., Harrell L., et al. Update on resistance of Bacteroides fragilis group and related species with special attention to carbapenems 2006-2009 // Anaerobe. – 2011. – Vol. 17. – No. 4. – P.147–51 // doi: 10.1016/j.anaerobe.2011.05.014
Jean S., Wallace M.J., Dantas G., Burnham C.D., Time for some group therapy: update on identification, antimicrobial resistance, taxonomy, and clinical significance of the Bacteroides fragilis group // J. Clin. Microbiol. – 2022. – Vol. 60. – No. 9. – P. e0236120. // doi: 10.1128/jcm.02361-20.
Wallace M.J., Jean S., Wallace M.A., Burnham C.D., Dantas G., Comparative genomics of Bacteroides fragilis group isolates reveals species-dependent resistance mechanisms and validates clinical tools for resistance prediction // mBio. – 2022. – Vol. 13. – No. 1. – P. e0360321 // doi: 10.1128/mbio.03603-21.
Nagy E., Becker S., Soki J., Urba E., Kostrzewa M. Differentiation of division I (cfiA-negative) and division II (cfiA-positive) Bacteroides fragilis strains by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry // J Med Microbiol. – 2011. – Vol. 60. – No. 11. – P. 1584-1590 // doi: 10.1099/jmm.0.031336-0.
Sóki J.; Edwards R.; Urbán E.; Fodor E.; Beer Z.; Nagy E. Screening of isolates from faeces for carbapenem-resistant Bacteroides strains; existence of strains with novel types of resistance mechanisms // Int. J. Antimicrob. Agents. – 2004. – Vol. 24. – P. 450–454 // doi: 10.1016/j.ijantimicag.2004.06.017.
Sóki J.; Fodor E.; Hecht D.W.; Edwards R.; Rotimi V.O.; Kerekes I.; Urbán E.; Nagy E. Molecular characterization of imipenemresistant, cfiA-positive Bacteroides fragilis isolates from the USA, Hungary and Kuwait // J. Med. Microbiol. – 2004. – Vol. 53. – P. 413–419 // doi: 10.1099/jmm.0.05452-0.
Sóki J.; Edwards R.; Hedberg M.; Fang H.; Nagy E.; Nord C.E. Examination of cfiA-mediated carbapenem resistance in Bacteroides fragilis strains from a European antibiotic susceptibility survey // Int. J. Antimicrob. Agents. – 2006. – Vol. 28. – P. 497–502 // doi: 10.1016/j.ijantimicag.2006.07.021.
Baaity Z., von Loewenich F.D., Nagy E., Orosz L., Burián K., Somogyvári F., Sóki J. Phenotypic and Molecular Characterization of Carbapenem-Heteroresistant Bacteroides fragilis Strains // Antibiotics. – 2022. – Vol.11. – P. 590 // doi.org/10.3390/antibiotics11050590.