First identification of bla NDM-5 producing Escherichia coli from neonates and a HIV infected adult in Tanzania

Carbapenem-resistant members of the family Enterobacteriaceae are emerging as a global public-health threat and cause substantial challenges in clinical practice. There is a need for increased and continued genomic surveillance of antimicrobial resistance genes globally in order to detect outbreaks and dissemination of clinically important resistance genes and their associated mobile genetic elements in human pathogens. To describe the resistance mechanisms of carbapenem-resistant . Rectal swabs from neonates and newly diagnosed human immunodeficiency virus (HIV) infected adults were collected between April 2017 and May 2018 and screened for faecal carriage of carbapenamases and OXA-48 producing members of the family Enterobacteriaceae. Bacterial isolates were identified using matrix assisted laser desorption ionization time of flight mass spectrometry. Antimicrobial susceptibility testing was performed by E-test. Whole genomes of carbapenem-resistant were investigated using a hybrid assembly of Illumina and Oxford Nanopore Technologies sequencing reads. Three carbapenem-resistant were detected, two from neonates and one from an HIV infected adult. All three isolates carried . Two from neonates belonged to ST167 and co-existed with and , and all were carried on IncFIA type plasmids. The from the HIV infected adult belonged to ST2083, and carried on an IncX3 type plasmid and on an IncI type plasmid. All carrying plasmids contained conjugation related genes. In addition, from the HIV infected adult carried three more plasmid types; IncFIA, IncFIB and Col(BS512). One from a neonate also carried one extra plasmid Col(BS512). All three harboured resistance genes to fluoroquinolone, aminoglycosides, sulfamethoxazole, trimethoprim, macrolides and tetracycline, carried on the IncFIA type plasmid. Furthermore, from the neonates carried a chloramphenicol resistance gene ( ), also on the IncFIA plasmid. All three isolates were susceptible to colistin. This is the first report, to our knowledge, from Tanzania detecting producing The carbapenemase gene was carried on an IncFIA and IncX3 type plasmids. Our findings highlight the urgent need for a robust antimicrobial resistance (AMR) surveillance system to monitor and rapidly report on the incidence and spread of emerging resistant bacteria in Tanzania.