Genomic Features of an MDR Escherichia coli ST5506 Harboring an IncHI2/In 229/ blaCTX-M-2 Array Isolated from a Migratory Black Skimmer

Quézia Moura; Miriam R Fernandes; Fábio P Sellera; Brenda Cardoso; Cristiane L Nascimento; Gustavo H P Dutra; Nilton Lincopan

doi:10.3390/pathogens13010063

Genomic Features of an MDR Escherichia coli ST5506 Harboring an IncHI2/In 229/ bla_CTX-M-2 Array Isolated from a Migratory Black Skimmer

Pathogens. 2024 Jan 9;13(1):63. doi: 10.3390/pathogens13010063.

Authors

Quézia Moura^{1

2}, Miriam R Fernandes³, Fábio P Sellera^{4

5}, Brenda Cardoso^{6

7}, Cristiane L Nascimento⁸, Gustavo H P Dutra⁸, Nilton Lincopan^{6

7

9}

Affiliations

¹ Federal Institute of Espírito Santo, Vila Velha 29106-010, Brazil.
² Postgraduate Program in Infectious Diseases, Federal University of Espírito Santo, Vitória 29047-105, Brazil.
³ Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-9760, USA.
⁴ Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo 05508-270, Brazil.
⁵ School of Veterinary Medicine, Metropolitan University of Santos, Santos 11045-002, Brazil.
⁶ Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil.
⁷ One Health Brazilian Resistance Project (OneBR), São Paulo 05508-000, Brazil.
⁸ Veterinary Unit of Santos Aquarium, Santos 11030-600, Brazil.
⁹ Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, São Paulo 05508-000, Brazil.

Abstract

Migratory birds have contributed to the dissemination of multidrug-resistant (MDR) bacteria across the continents. A CTX-M-2-producing Escherichia coli was isolated from a black skimmer (Rynchops niger) in Southeast Brazil. The whole genome was sequenced using the Illumina NextSeq platform and de novo assembled by CLC. Bioinformatic analyses were carried out using tools from the Center for Genomic Epidemiology. The genome size was estimated at 4.9 Mb, with 4790 coding sequences. A wide resistome was detected, with genes encoding resistance to several clinically significant antimicrobials, heavy metals, and biocides. The bla_CTX-M-2 gene was inserted in an In229 class 1 integron inside a ∆TnAs3 transposon located in an IncHI2/ST2 plasmid. The strain was assigned to ST5506, CH type fumC19/fimH32, serotype O8:K87, and phylogroup B1. Virulence genes associated with survival in acid conditions, increased serum survival, and adherence were also identified. These data highlight the role of migratory seabirds as reservoirs and carriers of antimicrobial resistance determinants and can help to elucidate the antimicrobial resistance dynamics under a One Health perspective.

Keywords: ESBL; biocides; heavy metals; seabirds; whole-genome sequencing; wildlife.

Grants and funding

This research was funded by Bill and Melinda Gates Foundation, Grand Challenges Explorations Brazil–New approaches to characterize the global burden of antimicrobial resistance (grant number OPP1193112), Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP; grant number 2016/08593-9), and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq; grant number 462042/2014-6).