Genomic characterization of carbapenem-resistant Gram-negative bacilli isolated from hospital wastewater in Niamey, Niger.

OBJECTIVES

This study aims to characterize the resistance gene profiles in cultured isolates and clonal diversity of bacterial isolates from wastewater collected at three major hospitals in Niamey.

METHODS

Samples of raw and treated wastewater were collected at the Niamey National Hospital, the Amirou Boubacar Diallo National Hospital, and the General Referral Hospital. An approach combining classical microbiology and whole-genome sequencing was used to identify bacterial species and characterize their carbapenem resistance mechanisms.

RESULTS

Analysis revealed a strong predominance of Acinetobacter baumannii clones and carbapenemase-producing Enterobacteriaceae. A total of 459 antimicrobial resistance genes occurrences corresponding to 57 distinct resistance genes identified were detected by whole-genome sequencing. Wastewater resistance gene profiles in cultured isolates analysis revealed a high diversity of antibiotic resistance genes. The most frequent gene was sul1 (6.1%, 95% confidence interval: 3.9-8.3), conferring resistance to sulfonamides. The detection of several carbapenemase genes was particularly noteworthy, with bla NDM-1 being the most frequent (3.3%, 95% confidence interval: 1.6-4.9). The use of flow diagrams demonstrated active gene and plasmid circulation among the three hospital sites. The detection of epidemic clones co-carrying bla OXA-23 and bla NDM-1 in the effluents confirms the persistence of these super pathogens despite existing treatment systems.

CONCLUSION

This preliminary study provides crucial baseline data on carbapenem resistance in hospital wastewater in Niamey. This study provides the first baseline genomic data on carbapenemases dynamics in hospital wastewater in Niamey. The persistence of international elite clones (ST11, ST773) and epidemic plasmids (IncFII, IncL, IncX3) throughout the treatment process underscores the ineffectiveness of current sanitation barriers. These findings necessitate the following actions: (i) the adoption of environmental genomic surveillance as an early warning system for emerging clinical clones, (ii) the revision of disinfection protocols to target the stability of mobile genetic elements, and (iii) the urgent integration of this approach into national action plans for combating antimicrobial resistance in Niger and West Africa to prevent irreversible environmental dissemination.