A set of antibiotic-resistance mechanisms and virulence factors in GES-16-producing Klebsiella quasipneumoniae subsp. similipneumoniae from hospital wastewater revealed by whole-genome sequencing

Author(s)

Zagui, Guilherme Sgobbi ; Almeida, Otavio Guiherme Goncalves de ; Moreira, Natalia Columbaro ; Abichalki, Nathalia ; Machado, Gabriel Pinheiro ; Martinis, Elaine Cristina Pereira De ; Darini, Ana Lucia Costa ; Andrade, Leonardo Neves ; Segura-Munoz, Susana Ines

• Document type: Journal article
• Source: Environmental Pollution; v. 316, p. 8-pg., 2023-01-01.

Abstract

Klebsiella quasipneumoniae subsp. similipneumoniae has emerged as a human pathogen and sporadic isolates from non-clinical sources were reported. Here, we described the phenotypic-and genomic-characteristics of a multidrug-resistant (MDR) and potentially hypervirulent (MDR-hv) Klebsiella quasipneumoniae subsp. sim-ilipneumoniae (KqA1) isolated from hospital wastewater. The antibiotic susceptibility profile of KqA1 was investigated using disk-diffusion method, broth microdilution method, and agar dilution method, and the genetic characteristics of antimicrobial resistance, mobile genetics elements, and virulence were evaluated by genomic DNA sequencing on the Illumina (R) NovaSeq6000 platform as well as by bioinformatic analysis. Resistome ana-lyses revealed the presence of genes related to resistance to beta-lactams, aminoglycosides, quinolones, tetracy-clines, sulfonamides, trimethoprim, chloramphenicol, macrolides, and fosfomycin. New genetic contexts to blaGES-16 (carbapenemase gene) and to fosA (fosfomycin resistance gene) were described. A set of mechanisms that can contribute to antibiotic resistance, commonly detected in Klebsiella spp., was also found including chromosomal mutations, efflux systems, proteins, and regulators. Moreover, KqA1 presented genes related to tolerance to metals (arsenic, copper, nickel, cobalt, magnesium, cadmium, zinc, tellurium, selenium) and to biocides (quaternary-ammonium compounds). The isolate was classified as potentially hypervirulent due to a wide range of virulence factors found associated to regulation, motility, biofilm, effector delivery systems, im-mune modulation, nutritional/metabolic factors, adherence, invasion, and competitive advantage. The occur-rence of MDR-hv KqA1 in hospital wastewater points out how this environment matrix plays a crucial role in the maintenance and selection of critical bacterial pathogens. Regarding One Health perspective, it is evident the need for multidisciplinary implementation of control measures for antibiotic-resistant bacteria, not only in hospital settings but also in a general environmental context to mitigate the dissemination of MDR and hv bacteria. (AU)

• FAPESP's process: 18/13564-3 - Metagenomic prospection of bacteria linked to quorum sensing during spontaneous cocoa fermentation
• Grantee: Elaine Cristina Pereira de Martinis
• Support Opportunities: Regular Research Grants
• FAPESP's process: 19/18663-2 - Antibiotics, toxic metals and multiresistant bacteria in hospital and urban sewage and their potential impact on receiving water ecosystems
• Grantee: Susana Segura Muñoz
• Support Opportunities: Regular Research Grants
• FAPESP's process: 19/05938-3 - Antibiotics, toxic metals and multiresistant bacteria in hospital and urban sewage and their potential impact on receiving water ecosystems
• Grantee: Guilherme Sgobbi Zagui
• Support Opportunities: Scholarships in Brazil - Doctorate