Diversidad genómica de Escherichia coli uropatógena en aislados clínicos de seis países de Latinoamérica, 2018-2023

Francesca Caballero; Anne Martinez-Ventura; Diego Cuicapuza Arteaga; Alex Fajardo-Loyola; Rosmery Gutierrez-Ajalcriña; Javier Soto-Pastrana; Percy Asmat-Marrufo; Evelyn Barco-Yaipen de Vera; Henry Meza-Fernandez; Mario Chambi-Quispe; Jimena Pino-Dueñas; Nicomedes Laura-Rivas; Alexander Briones-Alejo; Pilar Diaz-Rengifo; Carlos Peralta-Siesquen; Guillermo Salvatierra; Pablo Tsukayama Cisneros; Pool Marcos Carbajal

doi:10.17843/rpmesp.2025.422.14299

Authors

Francesca Caballero Universidad Peruana Cayetano Heredia, Laboratorio de Genómica Microbiana, Lima, Perú https://orcid.org/0009-0001-7241-4136
Anne Martinez-Ventura Universidad Peruana Cayetano Heredia, Laboratorio de Genómica Microbiana, Lima, Perú. Emerge (Emerging Diseases and Climate Change Research Unit), Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia, Lima, Perú https://orcid.org/0009-0008-5271-4319
Diego Cuicapuza Arteaga Universidad Peruana Cayetano Heredia, Laboratorio de Genómica Microbiana, Lima, Perú. Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Perú https://orcid.org/0000-0002-5735-4614
Alex Fajardo-Loyola Instituto Nacional de Salud, Centro Nacional de Salud Pública, Laboratorio de Biotecnología y Biología molecular, Lima, Perú https://orcid.org/0000-0002-8162-1321
Rosmery Gutierrez-Ajalcriña Hospital de Huaycán, Área de Epidemiología, Lima, Perú. https://orcid.org/0000-0001-8237-6092
Javier Soto-Pastrana Hospital Nacional Docente Madre Niño San Bartolomé, Departamento de Patología Clínica, Área de Microbiología, Lima, Perú. https://orcid.org/0000-0001-9534-5746
Percy Asmat-Marrufo Laboratorio de Referencia Regional Salud Pública, Servicio de microbiología, Trujillo, La Libertad, Perú https://orcid.org/0000-0003-3377-6713
Evelyn Barco-Yaipen de Vera Hospital JAMO, Área de microbiología, Tumbes, Perú https://orcid.org/0000-0003-3303-2087
Henry Meza-Fernandez Hospital Alberto Sabogal Sologuren, Departamento de Patología Clínica, Servicio de Microbiología, Bellavista, Callao, Perú https://orcid.org/0000-0003-4973-7794
Mario Chambi-Quispe Hospital Carlos Monge Medrano, Patología Clínica, Puno, Perú https://orcid.org/0000-0003-3303-2087
Jimena Pino-Dueñas Hospital Regional del Cusco, Patología Clínica, Cusco, Perú https://orcid.org/0000-0003-4563-5459
Nicomedes Laura-Rivas Laboratorio de Referencia Regional de Salud Pública Huancavelica, Servicio de microbiología, Huancavelica, Perú https://orcid.org/0000-0002-6413-3270
Alexander Briones-Alejo Hospital Regional de Loreto, Servicio de microbiología, Iquitos, Perú https://orcid.org/0000-0003-4849-6466
Pilar Diaz-Rengifo Laboratorio de Referencia Regional Salud Pública San Martín, Servicio de Microbiología, Tarapoto, Perú https://orcid.org/0000-0002-0929-4602
Carlos Peralta-Siesquen IPRESS Jorge Chávez, Área de microbiología, Madre de Dios, Perú https://orcid.org/0000-0002-9605-8324
Guillermo Salvatierra Universidad Peruana Cayetano Heredia, Laboratorio de Genómica Microbiana, Lima, Perú https://orcid.org/0000-0002-6887-2599
Pablo Tsukayama Cisneros Universidad Peruana Cayetano Heredia, Laboratorio de Genómica Microbiana, Lima, Perú. Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú https://orcid.org/0000-0002-1669-2553
Pool Marcos Carbajal Universidad Peruana Cayetano Heredia, Laboratorio de Genómica Microbiana, Lima, Perú. Universidad Peruana Unión, Escuela Profesional Medicina, Laboratorio de Investigación en Biología Molecular, Lima, Perú https://orcid.org/0000-0002-7741-0337

DOI:

https://doi.org/10.17843/rpmesp.2025.422.14299

Keywords:

Escherichia coli, Uropathogen, UPEC, Bacterial Resistance, Molecular Epidemiology

Abstract

Objective. To genetically characterize clinical isolates of uropathogenic Escherichia coli (UPEC) from hospitals in Peru and contextualize them against 127 additional UPEC genomes reported in six Latin American countries between 2018 and 2023. Materials and methods. The genomes of 16 Peruvian UPEC isolates were sequenced, assembled and supplemented with 127 genomes available in the NCBI public database. Serotypes, sequence types (STs), antimicrobial resistance (AMR) genes, and resistance-associated mutations were identified. A phylogenetic analysis was also conducted in order to determine evolutionary relations and distribution in phylogroups. Results. The ST131 clone was the most prevalent (42.7%), followed by ST1193 (13.3%). Phylogroup B2 was widely predominant (83.2%), with serotype O25:H4 standing out. The resistance genes
blaTEM-1, blaCTX-M-15, and blaCTX-M-27 were identified with high frequency, as well as mutations in gyrA and parC associated with fluoroquinolone resistance, especially in the ST131 clone. Conclusion. Our findings show high circulation of high-risk UPEC clones, such as ST131 and ST1193, in Latin America, along with a notable burden of genes and mutations linked to multidrug resistance, highlighting the need to strengthen regional genomic surveillance.

Downloads

Download data is not yet available.

References

Rodriguez-Angeles M. Principales características y diagnóstico de los grupos patógenos de Escherichia coli. Salud Pública México. 2002; 1;44. doi: 10.1590/S0036-36342002000500011.

Agarwal J, Srivastava S, Singh M. Pathogenomics of uropathogenic Escherichia coli. Indian J Med Microbiol. 2012; 30(2):141–9. doi:

4103/0255-0857.96657.

Spurbeck RR, Dinh PC, Walk ST, Stapleton AE, Hooton TM, Nolan LK, et al. Escherichia coli Isolates That Carry vat, fyuA, chuA, and yfcV Efficiently Colonize the Urinary Tract. Infect Immun. 2012; 80(12):4115–22. doi: 10.1128/IAI.00752-12.

Yang X, Chen H, Zheng Y, Qu S, Wang H, Yi F. Disease burden and longterm trends of urinary tract infections: A worldwide report. Front Public Health. 2022; 10:888205. doi: 10.3389/fpubh.2022.888205.

Whelan S, Lucey B, Finn K. Uropathogenic Escherichia coli (UPEC)-Associated Urinary Tract Infections: The Molecular Basis for

Challenges to Effective Treatment. Microorganisms. 2023; 11(9):2169. doi: 10.3390/microorganisms11092169.

Terlizzi ME, Gribaudo G, Maffei ME. UroPathogenic Escherichia coli (UPEC) Infections: Virulence Factors, Bladder Responses, Antibiotic,

and Non-antibiotic Antimicrobial Strategies. Front Microbiol. 2017; 8:1566. doi: 10.3389/fmicb.2017.01566.

Kot B. Antibiotic Resistance Among Uropathogenic Escherichia coli. Pol J Microbiol. 2019; 68(4):403–15. doi: 10.33073/pjm-2019-048.

Loyola S, Concha-Velasco F, Pino-Dueñas J, Vasquez-Luna N, Juarez P, Llanos C, et al. Antimicrobial Resistance Patterns and Dynamics of Extended-Spectrum β-Lactamase-Producing Uropathogenic Escherichia coli in Cusco, Peru. Antibiotics. 2021; 10(5):485. doi: 10.3390/antibiotics10050485.

Pavez M, Troncoso C, Osses I, Salazar R, Illesca V, Reydet P, et al. High prevalence of CTX-M-1 group in ESBL-producing enterobacteriaceae infection in intensive care units in southern Chile. Braz J Infect Dis Off Publ Braz Soc Infect Dis. 2019; 23(2):102–10. doi: 10.1016/j.bjid.2019.03.002.

Shenagari M, Bakhtiari M, Mojtahedi A, Atrkar Roushan Z. High frequency of mutations in gyrA gene associated with quinolones resistance in uropathogenic Escherichia coli isolates from the north of Iran. Iran J Basic Med Sci. 2018; 21(12):1226–31. doi: 10.22038/ijbms.2018.31285.7539.

Garallah ET, Al-Jubori SS. Molecular detection of glpT and uhpT genes as fosfomycin pathways in UTI infection patients. Gene Rep. 2020; 21:100930. doi: 10.1016/j.genrep.2020.100930.

Lin JC, Kristopher Siu LK, Chang FY, Wang CH. Mutations in the pmrB gene constitute the major mechanism underlying chromosomally encoded colistin resistance in clinical Escherichia coli. J Glob Antimicrob Resist. 2024; 38:275–80. doi: 10.1016/j.jgar.2024.06.013.

Yu L, Li W, Xue M, Li J, Chen X, Ni J, et al. Regulatory Role of the Two-Component System BasSR in the Expression of the EmrD Multidrug Efflux in Escherichia coli. Microb Drug Resist Larchmt N. 2020; 26(10):1163–73. doi: 10.1089/mdr.2019.0412.

Bunduki GK, Heinz E, Phiri VS, Noah P, Feasey N, Musaya J. Virulence factors and antimicrobial resistance of uropathogenic Escherichia coli (UPEC) isolated from urinary tract infections: a systematic review and meta-analysis. BMC Infect Dis. 2021; 21(1):753. doi: 10.1186/s12879-021-06435-7.

Al-Guranie DR, Al-Mayahie SM. Prevalence of E. coli ST131 among Uropathogenic E. coli Isolates from Iraqi Patients in Wasit Province,

Iraq. Int J Microbiol. 2020; 2020:8840561. doi: 10.1155/2020/8840561.

Kudinha T, Johnson JR, Andrew SD, Kong F, Anderson P, Gilbert GL. Escherichia coli Sequence Type 131 as a Prominent Cause of

Antibiotic Resistance among Urinary Escherichia coli Isolates from Reproductive-Age Women. J Clin Microbiol. 2013; 51(10):3270–6.

doi: 10.1128/JCM.01315-13.

Pitout J, Peirano G, Chen L, DeVinney R, Matsumura Y. Escherichia coli ST1193: Following in the Footsteps of E. coli ST131. Antimicrob Agents Chemother. 2022; 66. doi: 10.1128/aac.00511-22.

Marcos-Carbajal P, Salvatierra G, Yareta J, Pino J, Vásquez N, Diaz P, et al. Caracterización microbiológica y molecular de la resistencia

antimicrobiana de Escherichia coli uropatógenas de hospitales públicos peruanos. Rev Peru Med Exp Salud Pública. 2021; 38:119–23. doi:

17843/rpmesp.2021.381.6182.

Alqasim A, Abu Jaffal A, Alyousef A. Prevalence and molecular characteristics of sequence type 131 clone among clinical uropathogenic Escherichia coli isolates in Riyadh, Saudi Arabia. Saudi J Biol Sci. 2020; 27(1):296–302. doi: 10.1016/j.sjbs.2019.09.020.

Whitmer GR, Moorthy G, Arshad M. The pandemic Escherichia coli sequence type 131 strain is acquired even in the absence of antibiotic exposure. PLoS Pathog. 2019; 15(12):e1008162. doi: 10.1371/journal.ppat.1008162.

García-Meniño I, Lumbreras P, Lestón L, Álvarez-Álvarez M, García V, Hammerl JA, et al. Occurrence and Genomic Characterization

of Clone ST1193 Clonotype 14-64 in Uncomplicated Urinary Tract Infections Caused by Escherichia coli in Spain. Microbiol Spectr. 2022;

(3):e0004122. doi: 10.1128/spectrum.00041-22.

Nowrouzian FL, Wold AE, Adlerberth I. Escherichia coli Strains Belonging to Phylogenetic Group B2 Have Superior Capacity to Persist in the Intestinal Microflora of Infants. J Infect Dis. 2005; 191(7):1078–83. doi: 10.1086/427996.

Shahbazi R, Salmanzadeh-Ahrabi S, Aslani MM, Alebouyeh M, Falahi J, Nikbin VS. The genotypic and phenotypic characteristics contributing to high virulence and antibiotics resistance in Escherichia coli O25-B2-ST131 in comparison to non- O25-B2-ST131. BMC Pediatr. 2023; 23(1):59. doi: 10.1186/s12887-023-03866-w.

Rodriguez AOG, Pastor HJB, Villafuerte CAG, Barrón YLM de, Miranda DVHC de, Cunza SS. Clasificación filogenética de Escherichia coli

uropatógena y respuesta inmunometabólica en adultos mayores con infección urinaria en casas de reposo. Arch Med Col. 2019;19(2):238–46.

Ali SA, Al-Dahmoshi HOM. Detection of Efflux Pumps Gene and Relation with Antibiotics Resistance in Uropathogenic Escherichia coli

(UPEC) Isolated from Patients with Cystitis. Iraqi J Sci. 2022; 2388–97. doi: 10.24996/ijs.2022.63.6.7.

Boroumand M, Naghmachi M , Ghatee M A. Detection of Phylogenetic Groups and Drug Resistance Genes of Escherichia coli Causing Urinary Tract Infection in Southwest Iran. Jundishapur J Microbiol. 2021; 14(2):e112547. doi: 10.5812/jjm.112547.

Tchesnokova V, Radey M, Chattopadhyay S, Larson L, Weaver JL, Kisiela D, et al. Pandemic fluoroquinolone resistant Escherichia coli clone ST1193 emerged via simultaneous homologous recombinations in 11 gene loci. Proc Natl Acad Sci. 2019; 116(29):14740–8. doi: 10.1073/pnas.1903002116.

Zakaria AS, Edward EA, Mohamed NM. Genomic Insights into a Colistin-Resistant Uropathogenic Escherichia coli Strain of O23:H4-ST641 Lineage Harboring mcr-1.1 on a Conjugative IncHI2 Plasmid from Egypt. Microorganisms. 2021; 9(4):799. doi: 10.3390/microorganisms9040799.