Identification and characterization of antimicrobial resistant genes in the microbiome of seabirds of the Brazilian coast

Author(s)

Ana Carolina Ewbank

• Document type: Doctoral Thesis
• Press: São Paulo.
• Institution: Universidade de São Paulo (USP). Faculdade de Medicina Veterinária e Zootecnia (FMVZ/SBD)
• Defense date: 2021-03-02

Examining board members

José Luiz Catão Dias; Lilian Silva Catenacci; Marcos Paulo Vieira Cunha; Terezinha Knöbl; Carlos Gonçalo Afonso Rolhas Fernandes das Neves

• Advisor: José Luiz Catão Dias; Fernando Esperón Fajardo

Abstract

Antimicrobial resistance is a quintessential One Health issue. Microbial resistance results from bacteria genetic plasticity and interactions among microbials, hosts and the environment, enhanced by anthropogenic pressure. The consequent remodeling of the existing microbiomes, associated with their dissemination capacity, confer antimicrobial resistance genes (ARGs) the role of environmental pollutants and, alongside antimicrobial resistant bacteria (ARB), indicators of environmental anthropization. Seabirds are excellent sentinels of the marine ecosystem health. We used genotypic (i.e., gelled real-time PCR [rtPCR] and whole genome sequencing [WGS]) and phenotypic techniques (bacterial culture and antimicrobial sensitivity tests) to evaluate the presence and diversity of ARGs and ARB of critical priority (extended-spectrum beta-lactamase [ESBL]-producing Escherichia coli [ESBL-EC] and AmpC-producing E.coli [AmpC-EC]) in the microbiome of wild seabirds inhabiting coastal and insular environments in Brazil. Gelled rtPCR reactions detected and quantified selected plasmid-mediated ARGs in enemas of (1) 25 seabirds (kelp gull [Larus dominicanus, n = 14] and Magellanic penguin [Spheniscus magellanicus, n = 11]) upon admission to a rehabilitation center in southern Brazil, and (2) 308 individuals: 104 from the Fernando de Noronha Archipelago (FNA), Pernambuco (masked boobies [Sula dactylatra, n = 48], brown boobies [Sula leucogaster, n = 31] and magnificent frigatebirds [Fregata magnificens, n = 25]), and 204 from Rocas Atoll (ROA), Rio Grande do Norte (masked boobies [n = 33], brown boobies [n = 33], magnificent frigatebirds [n = 35], red-footed boobies [Sula sula, n = 33], sooty terns [Onychoprion fuscatus, n = 36], and brown noddies [Anous stolidus, n = 34]) to compare the highly anthropized (FNA) versus the pristine biome (ROA), northeastern Brazil. Additionally, we used phenotypic techniques and WGS to survey ESBL-/AmpC-EC in cloacal swabs of (1) the same 204 ROA individuals, and (2) 20 magnificent frigatebirds from an uninhabited site (Alcatrazes Archipelago, São Paulo) Brazil), inserted in the anthropized southeastern Brazilian coast. Our goals were to use seabirds as environmental bioindicators of anthropization to assess the occurrence and dissemination of ARGs and ESBL-/AmpC-EC in the Brazilian coast, and their epidemiology and persistence through a One Health approach. Our findings showed their wide occurrence and diversity throughout the evaluated scenarios, especially in the anthropized (FNA), which presented results consistent with anthropogenic pressure: statistically significant higher prevalence of sulfonamide- and quinolone-encoding ARGs in comparison with ROA, and higher sulII gene prevalence. To our knowledge, this is the first detection of mecA in seabirds in the Americas, and of mcr-1 gene in wild free-ranging seabirds in Brazil and in free-ranging migratory non- synanthropic seabirds worldwide. This is the first description of the pandemic and public health relevant ST131-O25b harboring blaCTX-M-8, and the first report of ST648 harboring blaCTX-M-2 and blaCMY-2, ST117 harboring blaSHV-12, and of a novel ST11350 (ST349 clonal complex) harboring blaCTX-M-55 and fosA3 in wild birds. We showed the key role of species- specific biological and ecological characteristics (e.g., migration, foraging strategies) and the relevance of anthropization in the study of antimicrobial resistance. Finally, we highlight the role of seabirds as anthropization sentinels and their involvement in the One Health chain of antimicrobial resistance. (AU)

• FAPESP's process: 16/20956-0 - Identification and quantification of antimicrobial resistance genes in the microbiome of seabirds from the Southern-Southeastern coast of Brazil
• Grantee: Ana Carolina Ewbank
• Support Opportunities: Scholarships in Brazil - Doctorate