Molecular epidemiology and clinical profiles of carbapenem-resistant Enterobacterales in neonates from two large children’s hospitals in southwestern China

Introduction Carbapenem-resistant Enterobacterales (CRE) are a global health threat due to their high antimicrobial resistance and transmissibility. However, data on CRE infection in neonates in China are lacking. We collected non-duplicate CRE isolates from neonates between 2018 and 2022 in Chongqing and Kunming and investigated their antimicrobial resistance profiles, risk factors, and molecular epidemiology. Methods Antimicrobial susceptibility testing was performed using broth microdilution. Polymerase chain reaction (PCR) was performed to detect carbapenem-resistance genes, extended-spectrum β-lactamase (ESBL) genes, and virulence genes. Multilocus sequence typing (MLST) was used to analyze strain relatedness. Clinical data were collected and multivariable logistic regression analysis was used to identify risk factors. Results A total of 139 non-duplicate neonatal CRE isolates were collected from 2018 to 2022, comprising carbapenem-resistant Klebsiella pneumoniae (CRKP, 81.3%) and carbapenem-resistant Escherichia coli (CREC, 18.7%). New Delhi metallo-β-lactamase (NDM) was the predominant carbapenemase (83.5%) in neonates, followed by imipenemase (IMP, 11.5%) and Klebsiella pneumoniae carbapenemase (KPC, 4.3%). Extended-spectrum β-lactamase (ESBL) genes (including bla SHV , bla TEM, and bla CTX-M ) were widely distributed among these isolates. Sequence type 2 (ST2, 84.6%) was the most prevalent among CREC isolates, while ST2407 (15.9%) was the dominant sequence type among CRKP isolates. Four novel STs were identified. The detection rate of hypervirulent K. pneumoniae (hvKP) was 8.0% in neonatal CRKP isolates. All isolates exhibited high-level resistance to cephalosporins and carbapenems. However, resistance rates to amikacin, tigecycline, colistin, and aztreonam-avibactam remained relatively low. Cesarean section (OR 3.283; 95% CI 1.682–6.411), elevated white blood cell (WBC) count (OR 1.049; 95% CI 1.001–1.100), and patent ductus arteriosus (OR 2.758; 95% CI 1.374–5.534) were significantly associated with an increased risk of neonatal CRE infection, whereas increasing age was associated with reduced risk thereof (OR 0.965; 95% CI 0.934–0.998); all P < 0.05). Conclusion NDM is highly prevalent and transferable among CRE isolates in neonatal infections. The high-risk ST2407 NDM-producing K. pneumoniae clone warrants increased attention and monitoring of neonates. Aztreonam-avibactam (ATM/AVI) demonstrated potent in vitro activity against neonatal CRE isolates. Cesarean delivery, age, WBC count, and patent ductus arteriosus were identified as key risk factors for neonatal CRE infection.