Antimicrobial resistance profiles and genome characteristics of Klebsiella isolated from the faeces of neonates in the neonatal intensive care unit

<b>Introduction.</b> <i>Klebsiella</i> spp. are important bacteria that colonize the human intestine, especially in preterm infants; they can induce local and systemic disease under specific circumstances, including inflammatory bowel disease, necrotizing enterocolitis and colorectal cancer.<b>Hypothesis.</b> <i>Klebsiella</i> spp. colonized in the intestine of the neonates in the neonatal intensive care unit (NICU) may be associated with disease and antibiotic resistance, which will be hazardous to the children.<b>Aim.</b> Our aim was to know about the prevalence, antimicrobial resistance and genome characteristics of <i>Klebsiella</i> spp. in neonate carriers.<b>Methodology.</b> Genome sequencing and analysis, and antimicrobial susceptibility testing were mainly performed in this study.<b>Results.</b> The isolation rates of <i>Klebsiella</i> spp. strains were 3.7% (16/436) in 2014 and 4.3% (18/420) in 2021. Cases with intestinal-colonized <i>Klebsiella</i> spp. were mainly infants with low birth weights or those with pneumonia or hyperbilirubinemia. According to the core-pan genomic analysis, 34 stains showed gene polymorphism and a sequence type (ST) of an emerging high-risk clone (ST11). Eight strains (23.5%) were found to be resistant to 2 or more antibiotics, and 46 genes/gene families along with nine plasmids were identified that conferred resistance to antibiotics. In particular, the two strains were multidrug-resistant. Strain A1256 that is related to <i>Klebsiella quasipneumoniae subsp. similipneumoniae</i> was uncommon, carrying two plasmids similar to IncFII and IncX3 that included five antibiotic resistance genes.<b>Conclusion.</b> The prevention and control of neonatal <i>Klebsiella</i> spp. colonization in the NICU should be strengthened by paying increased attention to preventing antimicrobial resistance in neonates.