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| Author(s): |
João Pedro Rueda Furlan
Total Authors: 1
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| Document type: | Doctoral Thesis |
| Press: | Ribeirão Preto. |
| Institution: | Universidade de São Paulo (USP). Faculdade de Ciências Farmacêuticas de Ribeirão Preto (PCARP/BC) |
| Defense date: | 2022-06-24 |
| Examining board members: |
Eliana Guedes Stehling;
Doroti de Oliveira Garcia;
Gerson Nakazato
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| Advisor: | Eliana Guedes Stehling |
| Abstract | |
The occurrence of multidrug-resistant (MDR) pathogens has become a threat to the ability to treat infections and the rapid spread of these pathogens at the human-animal-environmental interface causes concern. Escherichia coli remains one of the main pathogens associated with healthcare-related infections and has a great ability to acquire and transfer antimicrobial resistance genes (ARGs). The environment is commonly affected by pollution resulting from human activities, which favor the selection of antimicrobial-resistant bacteria and the horizontal transfer of ARGs. Thus, this study aimed to characterize E. coli isolates recovered from environmental samples regarding antimicrobial resistance, virulence, and epidemiological profiles. Soil (n=300) and water (n=200) samples were collected in different cities in the Southeast region of Brazil and were used to isolate E. coli. The isolates obtained were submitted to phenotypic and molecular tests to characterize the profiles and genes of antimicrobial resistance, while virulence genes, mobile genetic elements, and typing were determined by molecular methods. Accordingly, 105 MDR isolates were obtained and showed resistance mainly to extended-spectrum cephalosporins, fluoroquinolones, and colistin. The typing and subtyping of the isolates revealed a great genetic diversity, highlighting the sequence types (STs) of the clonal complex 10 and the high-risk clones ST10, ST131, ST354, ST648, and ST744. Several ARGs were detected, evidencing the presence of blaCTX-M, blaCMY, and qnrB genes in isolates from soil and water, and mcr-1 (mcr-1.1, mcr-1.26) and qnrS in isolates from water. In some isolates, the genes blaCTX-M-2, blaCTXM- 14, and blaCTX-M-15 were located on the chromosome and were associated with the Tn21-like element and ISEcp1, while the genes blaCMY, qnrB, qnrS, and mcr-1 were located on plasmids IncI1-ST12, Col(pHAD28), IncR, and IncX4, respectively. IncX4 plasmids were highly similar; however, a new genetic environment attributed by the insertion of the ΔIS5-like (258 bp) in the opposite orientation upstream of the mcr-1.1 gene was evidenced. Differences in the adjacent regions of the mcr-1.26 gene, as well as the underestimation and first description in the world of the mcr-1.26 gene in the environment were determined in this study. Different gene cassettes inserted into the class 1 integron in isolates from soil and the presence of a module of antimicrobial resistance and metal tolerance in isolates from water were observed. In addition, mutations in the resistance determinants to fluoroquinolones (GyrA, ParC, ParE) and to colistin (PmrAB, PhoPQ, MgrB) were also identified. Virulence genes related to diarrheogenic E. coli (DEC) and extra-intestinal pathogenic E. coli strains were detected among the isolates, spotlighting the presence of Shiga toxin-producing E. coli and the prevalence of DEC in soils. Furthermore, a hybrid and multireplicon plasmid IncF [F2:A-B1]-ΔIncQ1 carrying ARGs and virulence genes was detected in a ST131-H22 lineage from water that was also positive for the mcr-1.26 gene. On that account, these results show a high genetic diversity in lineages of E. coli MDR and potentially pathogenic in the environment, which come mainly from contamination of human origin and animals in the food production chain. Therefore, the presence of these lineages in the environment represents a potential risk to public and environmental health, as well as food safety. (AU) | |
| FAPESP's process: | 18/01890-3 - Study of resistance, virulence and epidemiological profile of Escherichia coli isolated from environment |
| Grantee: | João Pedro Rueda Furlan |
| Support Opportunities: | Scholarships in Brazil - Doctorate |