Screening and drug resistance analysis of enterobacterales in neonatal gut microbiota in a hospital in Yunnan province, from December 2017 to May 2018

Objective  To investigate the colonization status and strain characteristics of resistant Enterobacterales in the intestine of neonates.

Methods  277 fecal samples of neonates in the maternity ward of a hospital were collected from September 2017 to May 2018 in Yunnan province. We analyzed the status of carriage of drug-resistant bacteria in the intestinal tract of neonates, strain resistance phenotypes, resistance genotypes and sequence types (STs) characteristics by isolation and culture in extended spectrum β-lactamase (ESBL) chromogenic medium, strain drug susceptibility testing and genome sequencing of Illumina, a representative strain.

Results  113 fecal samples out of 77 samples were ESBL-positive strains, with a positivity rate of 40.79%. 113 Enterobacterales strains of 11 species from 4 genera were isolated and identified, including Klebsiella 53.10% (60/113), Escherichia 30.10% (34/113), Enterobacter 15.04% (17/113), and Leuconostoc 1.77% (2/113). The strains presenting multidrug-resistant profiles. Except for highly resistant to second and third-generation cephalosporin, the resistance rates of carbapenems, sulfonamides, tetracyclines and ciprofloxacin were 52.21% (59/113), 72.57% (82/113), 65.49% (74/113), and 54.87% (62/113), respectively. The genome sequences of 84 representaive strains were screened, and al of 70 drug r(esis)tance genes were detected, including sul1 (84.52%, 71/84), fosA (71.43%, 60/84), tet(A) (67.86%, 57/84), bla_SHV (63.10%, 53/84) and bla_NDM (61.90%, 52/84). 53 Klebsiella pneumoniae showed a concentrated distribution of clones, ST17 carrying bla_NDM-1 gene accounted for 92.45% (49/53). The STs of other species were diverse. Enterobacter cloacae and Enterobacter hormaechei carrying bla_NDM-1, Klebsiella gordonii carrying bla_IMP-26, Leclercia carrying bla_IMP-1, and Enterobacter albus, E. hormaechei and Escherichia hermannii carrying mcr were detected.

Conclusion  It is found that a high proportion of neonates in a maternity ward carried ESBL-resistant enterobacters in their intestines, revealing that drug-resistant strains are highly susceptible to inter-neonatal transmission and intestinal colonization. Attention should be paid to the environmental exposure risk of neonatal drug-resistant bacteria and its impact on the establishment of intestinal microecology.