Multidrug-resistant Enterobacterales responsible for septicaemia in a neonatal intensive care unit in Morocco

Abstract

Neonatal sepsis with multidrug resistant (MDR) bacteria is an important cause of morbidity and mortality, especially in low- and middle-income countries. Here, the molecular mechanisms of MDR in bacteria responsible of sepsis in neonates was determined. From July to December 2019, documented bacteraemia from 524 neonates hospitalized in a neonatal intensive care unit (NICU) in Morocco were collected. WGS was used to determine the resistome, MLST and phylogeny. Among the 199 documented bacteraemia, 40 (20%) and 20 (10%) were due to MDR K. pneumoniae (Kp) and E. hormaechei (Eh), respectively. Of these, 23 (38.5%) were early neonatal infections (≤ 3 days of life). Twelve different STs were observed among Kp isolates with ST1805 (n=10), and ST307 (n=8), being the most prevalent. Twenty-one Kp (53%) possessed blaCTX-M-15 gene, of which 6 co-produced an OXA-48, 2 an NDM-7, and 2 OXA-48 and NDM-7. BlaOXA-48 gene was present in 11 (27.5%), blaNDM-1 in 13 (32.5%), and blaNDM-7 in 4 isolates of Kp (10.0%). Eighteen Eh (90.0%) produced an ESBL. Three SHV-12 that co-produced CMY-4 and NDM-1, and 15 CTXM-15 of which 6 co-produced OXA-48. Twelve different STs belonging to 3 different Eh subspecies were observed with one to 4 isolates. Kp and Eh isolates belonging to the same ST had less than 20 SNP differences, and were found throughout the study period, highlighting their endemic presence in the NICU. Thirty percent of neonatal sepsis (23 early- and 37 late-neonatal sepsis) were due to highly-drug resistant carbapenemase- and/or ESBL producing-Enterobacterales.