Association of CRISPR-Cas Systems with Antimicrobial Resistance and MLST Types in Neonatal Invasive Escherichia coli

Background To investigate the distribution of CRISPR-Cas systems in Escherichia coli ( E. coli ) isolates and evaluate their associations with multilocus sequence types (MLST), antimicrobial resistance genes (ARGs), and plasmid features. Results ST1193 (16/65, 24.6%) and ST95 (11/65, 16.9%) were the predominant lineages. ST1193 showed a higher resistance gene burden than ST95, and bla _TEM−1 was detected in 87.5% of ST1193 isolates. CRISPR-Cas systems were detected in 22 isolates (33.8%), including 11 with type I-F (50.0%), 10 with type I-E (45.5%), and one with both types. Spacer sequences were primarily directed against plasmid DNA. Plasmid replicons were frequently detected, and plasmid burden varied across lineages. All the ST1193 isolates lacked detectable CRISPR-Cas systems, whereas 90.9% (10/11) of ST95 isolates harbored type I-F systems. Conclusions CRISPR-Cas carriage was strongly lineage-dependent and showed an inverse association with predicted resistance gene burden in this cohort; this pattern should be interpreted as a lineage-structured correlation rather than mechanistic evidence of CRISPR-mediated restriction of ARG acquisition.