Simultaneous detection of phylogroups and ESBL genes in E. coli using Multiplex PCR

Bushra B. Patoli, Atif A. Patoli, Iram Nabi Begum, Zarafshan Majeed

Abstract


Background: Escherichia coli (E. coli) strains harbor various allelic versions of beta lactamase genes and their identification using conventional phenotypic tests is a tedious and time consuming task. In the present study, multiplex PCR is performed for the simulatanoues detection of E. coli phylogroups and extended-spectrum β-lactamase- (ESBL) genes.

Methods: A total of 128 E. coli isolates from urine samples were screened for antibiotic resistance and expression of ESBL activity using phenotypic and genotypic methods. Uniplex and multiplex PCRs were used to detect E. coli phylogroup detrminants and blaCTX-M-15, blaOXA-1 and TEM1 genes. Chi Square test of independence was employed for evaluating significant levels at P value < 0.05. 

Results: Phylogroup B2 was detected as the predominant group (36%) followed by group D (30%), A (25%) and B1 (9%). The highest resistance was seen against nalidixic acid (100%) and the lowest against amoxicillin-clavulanic acid (55%). Significant P values were observed for resistance against cefotaxime and cefepime in the phylogroup B2 while resistance against cefoxitin, sulfamethoxazole and fosfomycin was significantly associated with group D. Combination disc diffusion test (CDDT) showed ESBL activity in 42% E. coli isolates. A significant association of blaCTX-M-15 gene was observed for phylogroup B2 (P = 0.007). Moreover, a combination genotype of blaCTX-M-15 and TEM1 was also found statistically prevalent in phylogroup B2 (P = 0.006).

Conclusion: The study highlights the alarming rise in antibiotic resistance and delineates B2 a predominant phylogoup with a high prevalence of blaCTX-M-15 and TEM1 genes in urinary E. coli isolates.

Keywords: UTI; E. Coli; Phylogenetic groups; ESBL genes; Multiplex PCR   


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References


Escobar-Páramo P, Grenet K, Le Menac’h A, Rode L, Salgado E, Amorin C, et al. Large-scale population structure of human commensal Escherichia coli isolates. Applied and Environmental Microbiology, (2004); 70(9):5698–700.

Kaper JB, Nataro JP, Mobley HLT. Pathogenic Escherichia coli. Nature Reviews Microbiololgy, (2004); 2(2):123–40.

Lindstedt BA, Finton MD, Porcellato D, Brandal LT. High frequency of hybrid Escherichia coli strains with combined Intestinal Pathogenic Escherichia coli ( IPEC ) and Extraintestinal Pathogenic Escherichia coli ( ExPEC ) virulence factors isolated from human faecal samples. BMC Infectious Diseases, (2018); 18(1):1–12.

Proença JT, Barral DC, Gordo I. Commensal-to-pathogen transition: One-single transposon insertion results in two pathoadaptive traits in Escherichia coli-macrophage interaction. Scientific Reports, (2017); 7(1):1–12.

Poolman JT, Wacker M. Extraintestinal pathogenic Escherichia coli, a common human pathogen: challenges for vaccine development and progress in the field. The Journal of Infectious Diseases, (2016); 213(1):6–13.

Clermont O, Bonacorsi S, Bingen E. Rapid and simple determination of the Escherichia coli phylogenetic group. Applied and Environmental Microbiology, (2000); 66(10):4555–8.

Iranpour D, Hassanpour M, Ansari H, Tajbakhsh S, Khamisipour G, Najafi A. Phylogenetic groups of escherichia coli strains from patients with urinary tract infection in Iran based on the new Clermont phylotyping method. BioMed Research International, (2015); (2015): 5–12.

Sacher-Pirklbauer A, Klein-Jöbstl D, Sofka D, Blanc-Potard AB, Hilbert F. Phylogenetic groups and antimicrobial resistance genes in escherichia coli from different meat species. Antibiotics, (2021); 10(12): 1543

Bush K, Jacoby GA. Updated functional classification of β-lactamases. Antimicrobial Agents and Chemotherapy, (2010); 54(3):969–76

Liaqat Z, Khan I, Azam S, Anwar Y, Althubaiti EH, Maroof L. Isolation and molecular characterization of extended spectrum beta lactamase producing Escherichia coli from chicken meat in Pakistan. PLoS ONE, (2022) ;17(6):1–15.

Ellington MJ, Kistler J, Livermore DM, Woodford N. Multiplex PCR for rapid detection of genes encoding acquired metallo-β-lactamases. Journal of Antimicrobial Chemotherapy, (2007); 59(2):321–2.

Dallenne C, da Costa A, Decré D, Favier C, Arlet G. Development of a set of multiplex PCR assays for the detection of genes encoding important β-lactamases in Enterobacteriaceae. Journal of Antimicrobial Chemotherapy, (2010); 65(3):490–5.

Walker RD. Standards for antimicrobial susceptibility testing. American journal of veterinary research, (1999); 60: 1034.

Drieux L, Brossier F, Sougakoff W, Jarlier V. Phenotypic detection of extended-spectrum β-lactamase production in Enterobacteriaceae: Review and bench guide. Clinical Microbiology and Infection, 2008; 14(1):90–103.

Changkaew K, Intarapuk A, Utrarachkij F, Nakajima C, Suthienkul O, Suzuki Y. Antimicrobial resistance, extended-spectrum b-Lactamase productivity, and class 1 integrons in Escherichia coli from healthy swine. Journal of Food Protection, (2015); 78(8):1443–50.

Halaji M, Fayyazi A, Rajabnia M, Zare D. Phylogenetic Group Distribution of Uropathogenic Escherichia coli and Related Antimicrobial Resistance Pattern : A Meta-Analysis and Systematic Review. Frontiers in Cellular and Infection Microbiology, (2022); 12:1–14.

Dadi BR, Abebe T, Zhang L, Mihret A, Abebe W, Amogne W. Distribution of virulence genes and phylogenetics of uropathogenic Escherichia coli among urinary tract infection patients in Addis Ababa, Ethiopia. BMC Infectious Diseases, (2020); 20(1):108.

Li B, Sun JY, Han LZ, Huang XH, Fu Q, Ni YX. Phylogenetic groups and pathogenicity island markers in fecal escherichia coli isolates from asymptomatic humans in china. Applied and Environmental Microbiology, (2010); 76(19):6698–700.

Munkhdelger Y, Gunregjav N, Dorjpurev A, Juniichiro N, Sarantuya J. Detection of virulence genes, phylogenetic group and antibiotic resistance of uropathogenic Escherichia coli in Mongolia. The Journal of Infection in Developing Countries, (2017);11(1):51–7.

Clermont, O., Christenson, J.K., Denamur, E. and Gordon, D.M. A new E. coli phylo-typing method. Environmental Microbiology Reports, (2013); 5: 5865.

Khairy RM, Mohamed ES, Abdel Ghany HM, Abdelrahim SS. Phylogenic classification and virulence genes profiles of uropathogenic E. coli and diarrhegenic E. coli strains isolated from community acquired infections. PLoS ONE, (2019); 14(9): 0222441.

Gordon, D.M., Clermont, O., Tolley, H. and Denamur, E. Assigning Escherichia coli strains to phylogenetic groups: multi-locus sequence typing versus the PCR triplex method. Environmental Microbiology, (2008); 10: 2484-2496.

Bashir S, Haque A, Sarwar Y, Ali A, Anwar MI. Virulence profile of different phylogenetic groups of locally isolated community acquired uropathogenic E. coli from Faisalabad region of Pakistan. Annals of Clinical Microbiology and Antimicrobials, (2012); 11:1–6.

Blango MG, Mulvey MA. Persistence of uropathogenic Escherichia coli in the face of multiple antibiotics. Antimicrobial Agents and Chemotherapy, (2010); 54(5):1855–63.

Bashir S, Haque A, Sarwar Y. Prevalence of Integrons and Antibiotic Resistance among Uropathogenic Escherichia Coli from Faisalabad Region of Pakistan. Archives of Clinal Microbiology, (2015); 6(4):1–7.

Rehman N, Azam S, Ali A, khan I, Asghar M, Ali M, et al. Molecular epidemiology of antibiotic-resistant genes and potent inhibitors against TEM, CTX-M-14, CTX-M-15, and SHV-1 proteins of Escherichia coli in district Peshawar, Pakistan. Saudi Journal of Biological Sciences, (2021); 28(11):6568–81.

Li F, Ye K, Li X, Ye L, Guo L, Wang L, et al. Genetic characterization of Carbapenem-Resistant Escherichia coli from China, 2015–2017. BMC Microbiology, (2021); 21(1):1–7.

Nasrollahian S, Halaji M, Hosseini A, Teimourian M, Armaki MT, Rajabnia M, et al. Genetic Diversity, Carbapenem Resistance Genes, and Biofilm Formation in UPEC Isolated from Patients with Catheter-Associated Urinary Tract Infection in North of Iran. International Journal of Clinical Practice, (2022); 2022: 62.

Ali I, Rafaque Z, Ahmed I, Tariq F, Graham SE, Salzman E, et al. Phylogeny, sequence-typing and virulence profile of uropathogenic Escherichia coli (UPEC) strains from Pakistan. BMC Infectious Diseases, (201); 19(1):1–9.

Khan FZ, Nawaz T, Mirani ZA, Khan S, Raza Y, Kazmi SU. Study of class integrons in multidrug-resistant uropathogenic Escherichia coli isolated from different hospitals in Karachi. Iranian Journal of Basic Medical Sciences, (2018); 21(10):1079–82.




DOI: http://dx.doi.org/10.62940/als.v11i2.2788

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