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. 2021 Mar;24(3):400-407.
doi: 10.22038/ijbms.2021.47095.10865.

Correlation between antibiotic resistance and phylogenetic types among multidrug-resistant Escherichia coli isolated from urinary tract infections

Humera Nazir  1   2 , Mubashar Aziz  2 , Zulfiqar Ali Mirani  3 , Ahsan Sattar Sheikh  4 , Muhammad Qamar Saeed  2 , Aleem Ahmed Khan  2 , Tahira Ruby  5 , Naseem Rauf  6
Affiliations

Correlation between antibiotic resistance and phylogenetic types among multidrug-resistant Escherichia coli isolated from urinary tract infections

Humera Nazir et al. Iran J Basic Med Sci. 2021 Mar.

Abstract

Objectives: Emergence of multidrug resistance has reduced the choice of antimicrobial regimens for UTIs. To understand the association of phenotype and genotype among uropathogens.

Materials and methods: Six hundred and twenty-eight (628) urine samples were collected and analyzed. Antibiotic sensitivity pattern was determined by the Kirby-Bauer Disc Diffusion Method and minimum inhibitory concentration (MIC) was tested by the E test. Fluoroquinolone resistant mutations in QRDR of gyrA and ParC, phylogenetic groups, and PAIusp subtype were detected by PCR.

Results: Most prevalent uropathogens were Escherichia coli (53.2%) followed by Klebsiella pneumoniae (21%). Multidrug- resistance was observed in > 50% cases for third-generation cephalosporins and ciprofloxacin and lowest in meropenem. E. coli (66.2%) and K. pneumonia (64.4%) were extended-spectrum β-lactamases (ESBLs) producers. MIC to trimethoprim-sulfamethoxazole was highest in E. coli (>1024 µg/ml). In 80 (24%) of the 334 E. coli isolates analyzed in detail, 54 fluoroquinolones (FQ) resistant isolates carried mutations (S83L, D87N, S80I, E84V) in QRDR of gyrA and ParC. Out of 54 FQ-resistant isolates, 43 (79.6%) isolates belonged to the phylogenetic group B2, and 11(20.4%) belonged to group D. Isolates belonged to group B2, 38 (88.4%) of the 43 isolates carried PAIusp subtype IIa and high frequency of mutation E84V in ParC was detected in 37 (97.4%). Other mutations, such as S80I, S83L in gyrA and D87N in ParC were found in all resistant isolates.

Conclusion: Correlations between phenotype and genotype provided a basis to understand the resistance development in uropathogens, and PAIusp subtyping indicated that E. coli belonged to the B2 group.

Keywords: ESBL; Escherichia coli; MDR; PCR; UTI.

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Figures

Figure 1
Figure 1
PCR profile specific for Escherichia coli phylogenetic groups. a: Each combination of ChuA, yjaA, and DNA fragment TspE4.C2 amplification allowed phylogenetic group determination of a strain. Lane M: 100 bp ladder, lane 1 chuA(-), lane 2 Yja A(+) and lane 3 TspE4.C2(-): Phylogenetic group A. b: Lane M: 100 bp ladder, lane 1 chuA(-), lane 2 Yja A(+) and lane 3 TspE4.C2(+): Phylogenetic group B1. c: Lane M: 100 bp ladder, lane 1 chuA(+), lane 2 Yja A(+) and lane 3 TspE4.C2(+): Phylogenetic group B2. d: Lane M: 100 bp ladder, lane 1 chuA(+), lane 2 Yja A(-) and lane 3 TspE4.C2 (-): Phylogenetic group D
Figure 2
Figure 2
Profile after 1% agarose gel electrophoresis of the PCR product amplified by three sets of primers for subtyping of PAI usp. M: 1 kb ladder, lanes 1, 2, and 3 contain PCR amplicons by pairs of primer USP81f andORFU1r, USP81f, and ORFU2r, USP81f and ORFU3: Type IIa
Figure 3
Figure 3
PCR amplification of gyrA and par C genes, lane M1, M2: 100 bp ladder, lanes 1-4: Escherichia coli clinical isolates (gyrA) and lanes 5-8 (par C)
See this image and copyright information in PMC

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