Longitudinal Genomic Characterization of Ciprofloxacin-Resistant Enterobacterales Recovered from Mother–Infant Fecal Samples: ST1193 and PMQR Determinants in Non-ST1193 Isolates

Escherichia coli sequence type 1193 (ST1193) is an emerging global high-risk clone, but its mother–infant gut carriage remains poorly characterized. Using selective culture, antimicrobial susceptibility testing, and whole-genome sequencing, we analyzed 244 samples collected twice, 6 months apart, from 61 mother–infant dyads in Jinan, China, in 2025. Ciprofloxacin-resistant Enterobacterales were recovered from 55 samples (35/122 maternal [28.69%]; 20/122 infant [16.39%]), yielding 58 isolates because three samples contained two species; 54 were E. coli, and 57 were multidrug resistant. ST1193 was most frequent (17/54, 31.48%); all harbored GyrA S83L/D87N and ParC S80I substitutions, whereas none carried screened plasmid-mediated quinolone resistance (PMQR) determinants. Core-genome multilocus sequence typing identified 11 related clusters among 25 E. coli, involving four of eight positive dyads and seven of 13 longitudinally positive individuals, suggesting sharing or repeated detection without proving transmission or continuous carriage. PMQR genes occurred in 15 non-ST1193 isolates. Five closed circular PMQR-positive plasmids had diverse replicons and resistance cargoes; all contained IS26. Four donors yielded target-gene-positive J53 recipient-background colonies at apparent endpoint frequencies of 4.46 × 10−7–3.69 × 10−6. These findings distinguish QRDR-mediated resistance in ST1193 from PMQR-positive non-ST1193 backgrounds; selected PMQR elements showed in vitro transfer potential in this selectively cultured mother–infant cohort.