Molecular investigation of an outbreak associated with total parenteral nutrition contaminated with NDM-producing Leclercia adecarboxylata

• Main Authors: Elvira Garza-González, Paola Bocanegra-Ibarias, Eduardo Rodríguez-Noriega, Esteban González-Díaz, Jesús Silva-Sanchez, Ulises Garza-Ramos, Iván Fernando Contreras-Coronado-Tovar, José Ecil Santos-Hernández, David Gutiérrez-Bañuelos, Juan Pablo Mena-Ramirez, Saúl Ramírez-De-los-Santos, Adrián Camacho-Ortiz, Rayo Morfín-Otero
• Format: Article
• Language: English
• Published: BMC 2021-02-01
• Series: BMC Infectious Diseases
• Subjects: NDM-carrying Leclercia adecarboxylata; Outbreak of L. adecarboxylata; Carbapenem-resistant L. adecarboxylata; Contaminated total parenteral nutrition; Bloodstream infections
• Online Access: https://doi.org/10.1186/s12879-021-05923-0

Abstract Background This study aimed to determine the epidemiological, microbiological, and molecular characteristics of an outbreak of carbapenem-resistant Leclercia adecarboxylata in three hospitals associated with the unintended use of contaminated total parental nutrition (TPN). Methods For 10 days, 25 patients who received intravenous TPN from the same batch of a formula developed sepsis and had blood cultures positive for L. adecarboxylata. Antimicrobial susceptibility and carbapenemase production were performed in 31 isolates, including one from an unopened bottle of TPN. Carbapenemase-encoding genes, extended-spectrum β-lactamase–encoding genes were screened by PCR, and plasmid profiles were determined. Horizontal transfer of carbapenem resistance was performed by solid mating. Clonal diversity was performed by pulsed-field gel electrophoresis. The resistome was explored by whole-genome sequencing on two selected strains, and comparative genomics was performed using Roary. Results All 31 isolates were resistant to aztreonam, cephalosporins, carbapenems, trimethoprim/sulfamethoxazole, and susceptible to gentamicin, tetracycline, and colistin. Lower susceptibility to levofloxacin (51.6%) and ciprofloxacin (22.6%) was observed. All the isolates were carbapenemase producers and positive for bla NDM-1, bla TEM-1B, and bla SHV-12 genes. One main lineage was detected (clone A, 83.9%; A1, 12.9%; A2, 3.2%). The bla NDM-1 gene is embedded in a Tn125-like element. Genome analysis showed genes encoding resistance for aminoglycosides, quinolones, trimethoprim, colistin, phenicols, and sulphonamides and the presence of IncFII (Yp), IncHI2, and IncHI2A incompatibility groups. Comparative genomics showed a major phylogenetic relationship among L. adecarboxylata I1 and USDA-ARS-USMARC-60222 genomes, followed by our two selected strains. Conclusion We present epidemiological, microbiological, and molecular evidence of an outbreak of carbapenem-resistant L. adecarboxylata in three hospitals in western Mexico associated with the use of contaminated TPN.