Characterization of integrons in Escherichia coli infections isolated from pediatric fecal samples
DOI:
https://doi.org/10.34119/bjhrv9n1-084Keywords:
integrones, microbiota intestinal, muestras fecales, Escherichia coliAbstract
Integrons significantly contribute to horizontal gene transfer and resistance gene dissemination in human gut microbiota. In this study, we aimed to quantify the presence of class 1 and class 2 integrons and clinical integrons in pediatric fecal samples. It also seeks to estimate bacterial and Escherichia coli loads and determine the ratio of integrons to bacterial cells, thus shedding light on integron-mediated resistance under diarrheal and non-diarrheal conditions. Fecal samples from children treated at Hospital Infantil João Paulo II were collected and analyzed. In this study, E. coli strains were isolated from diarrheal and non-diarrheal samples, followed by DNA analysis. extraction. Quantitative PCR (qPCR) was used to quantify integron markers of E. coli 16S rRNA and bacterial 16S rRNA. The results were statistically analyzed using t-tests to compare integron prevalence between the diarrheal and non-diarrheal groups. Integrons were found in all fecal samples studied. Class 2 integrons were, on average, 2–4 times more abundant than class 1 integrons. There was no significant difference in integron counts between diarrheal and non-diarrheal samples. For every 10,000 bacterial cells, there were approximately 4.5, 7, and 15 copies of clinical integron, int1, and int2 markers in diarrheal samples, and 3, 8, and 30.5, respectively, in non-diarrheal samples. This study highlights the pervasive presence of integrons in pediatric fecal samples, even in children who have not been exposed to antimicrobial therapies. The higher abundance of class 2 integrons suggested a critical role in the dissemination of resistance genes in the gut microbiota.
References
Mir RA, Qadri H, Lee B. Integrons in the development of antimicrobial resistance : critical review and perspectives. Front Microbiol 2023;14:1231938. https://doi.org/10.3389/fmicb.2023.1231938.
Gillings MR. Integrons: Past, Present, and Future Structure of Integrons. Microbiol Mol Biol Rev 2014;78:257–77. https://doi.org/10.1128/MMBR.00056-13.
Pereira MB, Österlund T, Eriksson KM, Backhaus T, Axelson-fisk M, Kristiansson E. Open Access A comprehensive survey of integron-associated genes present in metagenomes. BMC Genomics 2020;21:495.
Ghaly TM, Penesyan A, Pritchard A, Qi Q, Rajabal V, Tetu SG. Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities. Microb Genomics 2022:000788. https://doi.org/10.1099/mgen.0.000788.
Lee K, Raguideau S, Sirén K, Asnicar F, Cumbo F, Hildebrand F, et al. Population-level impacts of antibiotic usage on the human gut microbiome. Nat Commun 2023;14:191. https://doi.org/10.1038/s41467-023-36633-7.
Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile Genetic Elements Associated with Antimicrobial Resistance. Clin Microbiol Rev 2018;31:61.
Larsson DGJ, Flach CF. Antibiotic resistance in the environment. Nat Rev Microbiol 2022;20:257–69. https://doi.org/10.1038/s41579-021-00649-x.
Matzaras R, Nikopoulou A, Protonotariou E, Christaki E. Gut Microbiota Modulation and Prevention of Dysbiosis as an Alternative Approach to Antimicrobial Resistance : A Narrative Review. Yale J Biol Med 2022;95:479–94.
Maddamsetti R, Yao Y, Wang T, Gao J, Huang VT, Hamrick GS, et al. Duplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria. Nat Commun 2024. https://doi.org/10.1038/s41467-024-45638-9.
Makowska N, Zawierucha K, Nadobna P, Pi K, Krajewska A, Szwedyk J, et al. Science of the Total Environment Occurrence of integrons and antibiotic resistance genes in cryoconite and ice of Svalbard , Greenland , and the Caucasus glaciers. Sci Total Environ 2020;716. https://doi.org/10.1016/j.scitotenv.2020.137022.
Amos GCA, Ploumakis S, Zhang L, Hawkey PM, Gaze WH, Wellington EMH. The widespread dissemination of integrons throughout bacterial communities in a riverine system. ISME J 2018:681–91. https://doi.org/10.1038/s41396-017-0030-8.
Su J, Shi L, Yang L, Xiao Z, Li X, Yamasaki S. Analysis of integrons in clinical isolates of Escherichia coli in China during the last six years. FEMS Microbiol Lett 2006;254:75–80. https://doi.org/10.1111/j.1574-6968.2005.00025.x.
Clímaco EC. Análise molecular de mecanismos determinantes de resistência a antibióticos em Pseudomonas aeruginosa e Acinetobacter spp . Análise molecular de mecanismos determinantes de resistência a antibióticos em Pseudomonas aeruginosa e Acinetobacter spp . 2011.
LEVESQUE C, PICHE L, LAROSE C, ROY PH. PCR Mapping of Integrons Reveals Several Novel Combinations of Resistance Genes. Antimicrob Agents Chemother 1995;39:185–91.
Ahmed AM, Motoi Y, Sato M, Maruyama A, Watanabe H, Fukumoto Y, et al. Zoo Animals as Reservoirs of Gram-Negative Bacteria Harboring Integrons and Antimicrobial Resistance Genes ᰔ. Appl Environ Microbiol 2007;73:6686–90. https://doi.org/10.1128/AEM.01054-07.
LIMA IFN, QUETZ JDS, RICHARD LITTLETON GUERRANT JPN, HOUPT ER, LIMA AAM, HAVT and A. Enteroaggregative Escherichia coli quantification in children stool samples using quantitative PCR. APMIS 2014;121:643–51. https://doi.org/10.1111/apm.12032.Enteroaggregative.
Cardinali-rezende J, Colturato LFDB, Colturato TDB, Chartone-souza E, Nascimento AMA, Sanz JL. Bioresource Technology Prokaryotic diversity and dynamics in a full-scale municipal solid waste anaerobic reactor from start-up to steady-state conditions. Bioresour Technol 2012;119:373–83. https://doi.org/10.1016/j.biortech.2012.05.136.
Kim DD, Park D, Yoon H, Yun T, Joon M, Yoon S. Quantification of nosZ genes and transcripts in activated sludge microbiomes with novel group-specific qPCR methods validated with metagenomic analyses. Water Res 2020;185:116261. https://doi.org/10.1016/j.watres.2020.116261.
Kim J, Lim J, Lee C. Quantitative real-time PCR approaches for microbial community studies in wastewater treatment systems : Applications and considerations. Biotechnol Adv 2013;31:1358–73. https://doi.org/10.1016/j.biotechadv.2013.05.010.
Klappenbach JA, Saxman PR, Cole JR, Schmidt TM. rrndb : the Ribosomal RNA Operon Copy Number Database. Nucleic Acids Res 2001;29:181–4.
Arrieta M, Stiemsma LT, Amenyogbe N, Brown EM, Finlay B, Finlay B, et al. The intestinal microbiome in early life : health and disease. Front Immunol 2014;5:427. https://doi.org/10.3389/fimmu.2014.00427.
Muyzer G, Waal ECDE, Uitierlinden AG. Profiling of Complex Microbial Populations by Denaturing Gradient Gel Electrophoresis Analysis of Polymerase Chain Reaction-Amplified Genes Coding for 16S rRNA. Appl Environ Microbiol 1993;59:695–700.
Saint-Cyr MJ, Perrin-guyoMard A, Houée P. Use of Accuracy Profile Procedure to Validate a Real-Time PCR Method to Quantify Bacteria in Feces. Microbiol Methods 2014;97:573–9. https://doi.org/10.5740/jaoacint.13-310.
Skurnik D, Le A, Zurakowski D, Mazel D, Courvalin P, Denamur E, et al. Integron-Associated Antibiotic Resistance and Phylogenetic Grouping of Escherichia coli Isolates from Healthy Subjects Free of Recent Antibiotic Exposure. Antimicrob Agents Chemother 2005;49:3062–5. https://doi.org/10.1128/AAC.49.7.3062.
Zeighami H, Haghi F, Masumian N, Hemmati F, Samei A, Naderi G. Distribution of Integrons and Gene Cassettes Among Uropathogenic and Diarrheagenic Escherichia coli Isolates in Iran. Microb Drug Resist 2015;00:1–6. https://doi.org/10.1089/mdr.2014.0147.
Ravi A, Avershina E, Foley SL, Ludvigsen J, Storrø O, Øien T, et al. The commensal infant gut meta-mobilome as a potential reservoir for persistent multidrug resistance integrons. Sci Rep 2015;5:15317. https://doi.org/10.1038/srep15317.
Hardwick SA, Stokes HW, Findlay S, Taylor M, Gillings MR. Quanti ¢ cation of class1integron abundance in natural environments using real-time quantitative PCR. FEMS Microbiol Lett 2008;278:207–12. https://doi.org/10.1111/j.1574-6968.2007.00992.x.
Oliveira C, Patrícia P, Mariana SC, Chartone E, Andréa S. Diversity of gene cassettes and the abundance of the class 1 integron ‑ integrase gene in sediment polluted by metals. Extremophiles 2016;20:283–9. https://doi.org/10.1007/s00792-016-0820-3.
