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First Report of a Wastewater Treatment-Adapted Enterococcus faecalis ST21 Harboring vanA Gene in Brazil

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Abstract

Enterococcus faecalis has emerged as an important opportunistic pathogen due to its increasing resistance to antimicrobials, mainly to vancomycin, which leads substantial cases of therapeutic failures. Wastewater treatment plants (WWTP), in turn, are considered hotpots in the spread of antimicrobial resistance according to One Health perspective. In this study, we present the first report of a vancomycin-resistant E. faecalis strain recovered from treated effluent in Brazil. For this purpose, the whole-genome sequencing (WGS) was carried out aiming to elucidate its molecular mechanisms of antimicrobial resistance and its phylogenetic relationships amongst strains from other sources and countries. According to Multilocus Sequence Typing (MLST) analysis this strain belongs to ST21. The WGS pointed the presence of vanA operon, multiple antibiotic resistance and virulence genes, and a significant pathogenic potential for humans. The phylogenomic analysis of E. faecalis 6805 was performed with ST21 representatives from the PubMLST database, including the E. faecalis IE81 strain from clinical sample in Brazil, which had its genome sequenced in this study. Our results demonstrated a strain showing resistance to vancomycin in treated effluent. To the best of our knowledge, this is an unprecedented report of vanA-carrying E. faecalis ST21. Furthermore, it is the first description of a vanA-harboring strain of this species from environmental sample in Brazil. Our data highlight the role of WWTP in the spread of AMR, since these environments are favorable for the selection of multidrug-resistant pathogens and the treated effluents, carrying antibiotic resistance genes, are directed to receiving water bodies.

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Fig. 1

Data Availability

The datasets generated during and/or analysed during the current study are available in GenBank under BioProject PRJNA708321.

Code Availability

Not applicable.

References

  1. Hamiwe T, Kock MM, Magwira CA, Antiabong JF, Ehlers MM (2019) Occurrence of enterococci harbouring clinically important antibiotic resistance genes in the aquatic environment in Gauteng, South Africa. Environ Pollut 245:1041–1049. https://doi.org/10.1016/j.envpol.2018.11.040

    Article  CAS  PubMed  Google Scholar 

  2. Zaheer R, Cook SR, Barbieri R, Goji N, Cameron A, Petkau A et al (2020) Surveillance of Enterococcus spp. reveals distinct species and antimicrobial resistance diversity across a One-Health continuum. Sci Rep 10(1):1–16. https://doi.org/10.1038/s41598-020-61002-5

    Article  CAS  Google Scholar 

  3. Sanderson H, Ortega-Polo R, Zaheer R, Goji N, Amoako KK, Brown RS et al (2020) Comparative genomics of multidrug-resistant Enterococcus spp. isolated from wastewater treatment plants. BMC Microbiol 20(1):1–17. https://doi.org/10.1186/s12866-019-1683-4

    Article  CAS  Google Scholar 

  4. Gouliouris T, Raven KE, Moradigaravand D et al (2019) Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment. Genome Res 29:626–634. https://doi.org/10.1101/gr.232629.117

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Gotkowska-Płachta A (2021) The prevalence of virulent and multidrug-resistant enterococci in river water and in treated and untreated municipal and hospital wastewater. Int J Environ Res Public Health 18(2):1–19. https://doi.org/10.3390/ijerph18020563

    Article  Google Scholar 

  6. Kuch A, Willems RJ, Werner G, Coque TM, Hammerum AM, Sundsfjord A, Klare I, Ruiz-Garbajosa P, Simonsen GS, van Luit-Asbroek M, Hryniewicz W, Sadowy E (2012) Insight into antimicrobial susceptibility and population structure of contemporary human Enterococcus faecalis isolates from Europe. J Antimicrob Chemother 67(3):551–558. https://doi.org/10.1093/jac/dkr544

    Article  CAS  PubMed  Google Scholar 

  7. Zischka M, Künne CT, Blom J et al (2015) Comprehensive molecular, genomic and phenotypic analysis of a major clone of Enterococcus faecalis MLST ST40. BMC Genomics 16:175. https://doi.org/10.1186/s12864-015-1367-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Bakshi U, Sarkar M, Paul S, Dutta C (2016) Assessment of virulence potential of uncharacterized Enterococcus faecalis strains using pan genomic approach - Identification of pathogen-specific and habitat-specific genes. Sci Rep. https://doi.org/10.1038/srep38648

    Article  PubMed  PubMed Central  Google Scholar 

  9. Dai D, Wang H, Xu X, Chen C, Song C, Jiang D, Du P, Zhang Y, Zeng H (2018) The emergence of multi-resistant Enterococcus faecalis clonal complex, CC4, causing nosocomial infections. J Med Microbiol 67(8):1069–1077. https://doi.org/10.1099/jmm.0.000761

    Article  CAS  PubMed  Google Scholar 

  10. De FBO, Bianco K, Nascimento APA, Gonçalves De Brito AS, Moreira TC, Clementino MM (2022) Genomic analysis of multidrug-resistant Enterococcus faecium harboring vanA gene from wastewater treatment plants. Microb Drug Resist 28:444–452. https://doi.org/10.1089/mdr.2021.0254

    Article  CAS  Google Scholar 

  11. Santos BA, Oliveira JS, Cardoso NT, Barbosa AV, Superti SV, Teixeira LM, Neves FPG (2017) Major globally disseminated clonal complexes of antimicrobial resistant enterococci associated with infections in cancer patients in Brazil. Infect Genet Evol 55:56–62. https://doi.org/10.1016/j.meegid.2017.08.027

    Article  PubMed  Google Scholar 

  12. Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

  13. Schmieder R, Edwards R (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27(6):863–864. https://doi.org/10.1093/bioinformatics/btr026

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Wick RR, Judd LM, Gorrie CL, Holt KE (2017) Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13(6):1–22. https://doi.org/10.1371/journal.pcbi.1005595

    Article  CAS  Google Scholar 

  15. Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29(8):1072–1075. https://doi.org/10.1093/bioinformatics/btt086

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R (2014) The SEED and the rapid annotation of microbial genomes using Subsystems Technology (RAST). Nucl Acids Res 42(Database issue):D206–D214. https://doi.org/10.1093/nar/gkt1226

    Article  CAS  PubMed  Google Scholar 

  17. Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A et al (2020) CARD 2020: Antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 48(D1):D517–D525. https://doi.org/10.1093/nar/gkz935

    Article  CAS  PubMed  Google Scholar 

  18. Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V et al (2020) ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 75(12):3491–500. https://doi.org/10.1093/jac/dkaa345

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Jolley KA, Bray JE, Maiden MCJ (2018) Open-access bacterial population genomics: BIGSdb software, the PubMLST. org website and their applications. Wellcome Open Res 3:1–20. https://doi.org/10.12688/wellcomeopenres.14826.10

    Article  Google Scholar 

  20. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454

    Article  CAS  PubMed  Google Scholar 

  21. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16(2):111–120. https://doi.org/10.1007/BF01731581

    Article  CAS  PubMed  Google Scholar 

  22. Farman M, Yasir M, Al-Hindi RR, Farraj SA, Jiman-Fatani AA, Alawi M et al (2019) Genomic analysis of multidrug-resistant clinical Enterococcus faecalis isolates for antimicrobial resistance genes and virulence factors from the western region of Saudi Arabia. Antimicrob Resist Infect Control 8(1):1–11. https://doi.org/10.1186/s13756-019-0508-4

    Article  Google Scholar 

  23. Hirt H, Greenwood-Quaintance KE, Karau MJ, Till LM, Kashyap PC, Patel R, Dunny GM (2018) Enterococcus faecalis sex pheromone cCF10 enhances conjugative plasmid transfer in vivo. mBio 9:e00037-18. https://doi.org/10.1128/mBio.00037-18

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Mbanga J, Amoako DG, Abia ALK, Allam M, Ismail A, Essack SY (2021) Genomic Analysis of Enterococcus spp. isolated from a wastewater treatment plant and its associated waters in Umgungundlovu district. South Africa Front Microbiol 12:1–13. https://doi.org/10.3389/fmicb.2021.648454

    Article  Google Scholar 

  25. Fatoba DO, Amoako DG, Akebe ALK, Ismail A, Essack SY (2022) Genomic analysis of antibiotic-resistant Enterococcus spp. reveals novel enterococci strains and the spread of plasmid-borne Tet(M), Tet(L) and Erm(B) genes from chicken litter to agricultural soil in South Africa. J Environ Manag 302(Pt B):114101. https://doi.org/10.1016/j.jenvman.2021.114101

    Article  CAS  Google Scholar 

  26. Founou RC, Founou LL, Allam M, Ismail A, Essack SY (2021) Enterococcus faecalis ST21 harbouring Tn6009 isolated from a carriage sample in South Africa. South African Med J 111(2):98–99. https://doi.org/10.7196/samj.2021.v111i2.15454

    Article  CAS  Google Scholar 

  27. Soge OO, Beck NK, White TM, No DB, Roberts MC (2008) A novel transposon, Tn6009, composed of a Tn916 element linked with a Staphylococcus aureus mer operon. J Antimicrob Chemother 62(4):674–80. https://doi.org/10.1093/jac/dkn255

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. d’Azevedo PA, Kacman SB, Schmalfuss T, Silva A, Rodrigues LF (2000) Primeiro caso de Enterococcus resistente à vancomicina isolado em Porto Alegre. RS J Bras Patol 36:258

    Google Scholar 

  29. Resende M, Caierão J, Prates JG, Narvaez GA, Dias CA, d’Azevedo PA (2014) Emergence of vanA vancomycin-resistant Enterococcus faecium in a hospital in Porto Alegre, South Brazil. J Infect Dev Ctries 8(2):160–167. https://doi.org/10.3855/jidc.4126

    Article  PubMed  Google Scholar 

  30. Medeiros AW, Pereira RI, Oliveira DV, Martins PD, D’azevedo PA, Van Der Sand S, Frazzon J, Frazzon APG (2014) Molecular detection of virulence factors among food and clinical Enterococcus faecalis strains in South. Braz J Microbiol 45(1):327–332. https://doi.org/10.1590/S1517-83822014005000031

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Almeida LM, Gaca A, Bispo PM et al (2020) Coexistence of the Oxazolidinone resistance-associated genes cfr and optrA in Enterococcus faecalis from a healthy piglet in Brazil. Front Public Health. https://doi.org/10.3389/fpubh.2020.00518

    Article  PubMed  PubMed Central  Google Scholar 

  32. Sims N, Kasprzyk-Hordern B (2020) Future perspectives of wastewater-based epidemiology: monitoring infectious disease spread and resistance to the community level. Environ Int 139:105689. https://doi.org/10.1016/j.envint.2020.105689

    Article  PubMed  PubMed Central  Google Scholar 

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Funding

This work was supported by the Oswaldo Cruz Foundation [grant numbers VPPCB-007-FIO-18-2-68].

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Authors and Affiliations

  1. Instituto Nacional de Controle de Qualidade Em Saúde, Fundação Oswaldo Cruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, Brazil

    Beatriz O. Farias, Ana Paula A. Nascimento, Mariana Magaldi, Andressa S. Gonçalves-Brito, Claudia Flores, Thais C. Moreira, Kayo Bianco & Maysa M. Clementino

  2. Escola Nacional de Saúde Pública, Fundação Oswaldo Cruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, Brazil

    Kaylanne S. Montenegro

  3. Departamento de Microbiologia E Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Alameda Barros Terra, S/N. São Domingos, Niterói, RJ, 24020-150, Brazil

    Felipe P. G. Neves

  4. Fiocruz Genomic Network, Oswaldo Cruz Foundation - FIOCRUZ, Rio de Janeiro, RJ, 4365, Brazil

    Beatriz O. Farias, Andressa S. Gonçalves-Brito, Kayo Bianco & Maysa M. Clementino

  5. COVID-19 Monitoring Network in Wastewater, São Paulo, Brazil

    Kayo Bianco & Maysa M. Clementino

Authors
  1. Beatriz O. Farias
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  2. Kaylanne S. Montenegro
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  3. Ana Paula A. Nascimento
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  4. Mariana Magaldi
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  7. Thais C. Moreira
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  8. Felipe P. G. Neves
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  9. Kayo Bianco
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  10. Maysa M. Clementino
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Contributions

BF and KB: experimental works, data analysis and wrote the manuscript; KSM, APAN, MM, ASGB, CF, and TCM: field and experimental works; FPGN: collected data and availability of E. faecalis IE81 strain; MMC: project administration and revised the final draft. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Kayo Bianco.

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Farias, B.O., Montenegro, K.S., Nascimento, A.P.A. et al. First Report of a Wastewater Treatment-Adapted Enterococcus faecalis ST21 Harboring vanA Gene in Brazil. Curr Microbiol 80, 313 (2023). https://doi.org/10.1007/s00284-023-03418-6

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