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

Abstract

Introduction. Carbapenem-resistant members of the family Enterobacteriaceae are emerging as a global public-health threat and cause substantial challenges in clinical practice. Gap Statement. 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. Aim. To describe the resistance mechanisms of carbapenem-resistant Escherichia coli . Methods. 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 E. coli were investigated using a hybrid assembly of Illumina and Oxford Nanopore Technologies sequencing reads. Results. Three carbapenem-resistant E. coli were detected, two from neonates and one from an HIV infected adult. All three isolates carried bla NDM-5. Two E. coli from neonates belonged to ST167 and bla NDM-5 co-existed with bla CTX-M-15 and bla OXA-01, and all were carried on IncFIA type plasmids. The E. coli from the HIV infected adult belonged to ST2083, and carried bla NDM-5 on an IncX3 type plasmid and bla CMY-42 on an IncI type plasmid. All bla NDM-5 carrying plasmids contained conjugation related genes. In addition, E. coli from the HIV infected adult carried three more plasmid types; IncFIA, IncFIB and Col(BS512). One E. coli from a neonate also carried one extra plasmid Col(BS512). All three E. coli harboured resistance genes to fluoroquinolone, aminoglycosides, sulfamethoxazole, trimethoprim, macrolides and tetracycline, carried on the IncFIA type plasmid. Furthermore, E. coli from the neonates carried a chloramphenicol resistance gene (catB3), also on the IncFIA plasmid. All three isolates were susceptible to colistin. Conclusion. This is the first report, to our knowledge, from Tanzania detecting bla NDM-5 producing E. coli. 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.

Phenotypic and genotypic characterizations of antimicrobial resistance among gram-negative bacilli of clinical isolates

“…Four isolates showed co-existence with blaNDM-1 and blaOXA-1 producing E. coli in the molecular characterization; two isolates were associated with blaNDM-1 and blaOXA-1, and one was blaNDM-4 co-existing with blaOXA-1 among K. pneumonia; one isolate was associated with blaNDM-5 and blaOXA-1, and one was blaNDM-1 co-existing with blaOXA-1. The previously discovered blaNDM and blaOXA-1.15NDM-5, which were first discovered in E. coli, are also found in Bangladesh (Manyahi et al 2022). These alterations were responsible for the high resistance of NDM-5 bacteria compared to NDM-1 bacteria (Hornsey, Phee, & Wareham 2011).…”

Genomic analysis of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli colonising adults in Blantyre, Malawi reveals previously undescribed diversity

“…ESBL-producing Gram-negative infections are an increasing clinical problem in Malawi, and there is a significant unmet need for access to carbapenem antimicrobials to treat them. Carbapenemase producing Enterobacterales including E. coli (bla NDM-5 in E. coli ST636) have recently been described in other regions of Malawi [52], and bla NDM-5 is increasingly being identified across sSA [53]. The presence of carbapenemases in this collection despite minimal local carbapenem use highlights the need for ongoing surveillance as these last-line antimicrobials are introduced.…”

“…coli ( bla NDM-5 in E. coli ST636) have recently been described in other regions of Malawi [52], and bla NDM-5 is increasingly being identified across sSA [53]. The presence of carbapenemases in this collection despite minimal local carbapenem use highlights the need for ongoing surveillance as these last-line antimicrobials are introduced.…”

Whole-genome sequence analysis of clinically isolated carbapenem resistant Escherichia coli from Iran

“…MLST showed that the two CREC isolates (CREC-18 and 19) belonged to ST167, and the remaining 2 isolates were characterized with ST361 (CREC-20) and ST648 (CREC-17). The E. coli ST167 clone is emerging throughout the world, being frequently recognized for having a link with carbapenem resistance [ 15 , 16 ] and for being involved in the transmission of the bla NDM-1 and bla NDM-5 genes in hospitals [ 17 ]. It has been demonstrated that the ST167 has peculiar virulence characteristics which facilitate its evolution to a high-risk clone with widespread colonization and infection capabilities [ 18 ].…”