1887

Abstract

. Carbapenem-resistant (CRAB) is the primary pathogen causing hospital-acquired infections. The spread of CRAB is mainly driven by the dissemination of resistant clones, and in Latin America, International Clones IC-1 (also known as clonal complex CC1), IC-4 (CC15) and IC-5 (CC79) are the most prevalent.

There are no documented outbreaks of CRAB International Clone 2 (IC-2) reported in Brazil.

To describe a large outbreak of CRAB caused by the uncommon IC-2 in a Brazilian COVID-19 hospital.

From May 2020 to May 2021, 224 patients infected or colonized with CRAB were identified in a single hospital; 92 % of them were also infected with SARS-CoV-2. From these patients, 137 isolates were recovered and subjected to antimicrobial susceptibility testing, PCR analysis and molecular typing. Whole-genome sequencing and downstream analysis were carried out on a representative isolate (the first available isolate).

In 76 % of the patients, a single OXA-23-producing CRAB IC-2 was identified. All the isolates were susceptible to polymyxin B, but highly resistant (>95 %) to aminoglycosides, fluoroquinolones and beta-lactams. Genomic analysis revealed that the representative isolate also carried the 16S rRNA Methylase ArmA, which was detected for the first time in this species in Brazil.

We report the rapid spread of an emerging CRAB clone responsible for causing a large outbreak in a hospital in Brazil, a country with predominance of other CRAB clones. Continuous and prospective surveillance is warranted to evaluate the impact of this clone in Brazilian hospital settings.

Funding
This study was supported by the:
  • Conselho Nacional de Desenvolvimento Científico e Tecnológico (Award Productivity Research Fellows)
    • Principle Award Recipient: CarlosHenrique Camargo
  • Fundação de Amparo à Pesquisa do Estado de São Paulo (Award 2017/16988-6, 2017/50333-7, 2018/21192-9, 2018/21193-5, 2020/06157-2)
    • Principle Award Recipient: CarlosHenrique Camargo
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. The Microbiology Society waived the open access fees for this article.
Loading

Article metrics loading...

/content/journal/jmm/10.1099/jmm.0.001509
2022-04-13
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/jmm/71/4/jmm001509.html?itemId=/content/journal/jmm/10.1099/jmm.0.001509&mimeType=html&fmt=ahah

References

  1. Wong D, Nielsen TB, Bonomo RA, Pantapalangkoor P, Luna B et al. Clinical and pathophysiological overview of Acinetobacter infections: a century of challenges. Clin Microbiol Rev 2017; 30:409–447 [View Article] [PubMed]
    [Google Scholar]
  2. Fortaleza CMCB, Padoveze MC, Kiffer CRV, Barth AL, Carneiro IC do RS et al. Multi-state survey of healthcare-associated infections in acute care hospitals in Brazil. J Hosp Infect 2017; 96:139–144 [View Article] [PubMed]
    [Google Scholar]
  3. Levy-Blitchtein S, Roca I, Plasencia-Rebata S, Vicente-Taboada W, Velásquez-Pomar J et al. Emergence and spread of carbapenem-resistant Acinetobacter baumannii international clones II and III in Lima, Peru. Emerg Microbes Infect 2018; 7:119 [View Article] [PubMed]
    [Google Scholar]
  4. Camargo CH, Tiba MR, Saes MR, Vasconcellos F de, Santos LFD et al. Population structure analysis of carbapenem-resistant Acinetobacter baumannii clinical isolates from clinical isolates from Brazil reveals predominance of clonal complexes 1, 15, and 79. Antimicrob Agents Chemother 2016; 60:2545–2547 [View Article] [PubMed]
    [Google Scholar]
  5. Zarrilli R, Pournaras S, Giannouli M, Tsakris A. Global evolution of multidrug-resistant Acinetobacter baumannii clonal lineages. Int J Antimicrob Agents 2013; 41:11–19 [View Article] [PubMed]
    [Google Scholar]
  6. Martins N, Dalla-Costa L, Uehara AA, Riley LW, Moreira BM. Emergence of Acinetobacter baumannii international clone II in Brazil: reflection of a global expansion. Infect Genet Evol 2013; 20:378–380 [View Article] [PubMed]
    [Google Scholar]
  7. Pagano M, Nunes LS, Niada M, Barth AL, Martins AF. Comparative analysis of carbapenem-resistant Acinetobacter baumannii sequence types in Southern Brazil: from the first outbreak (2007-2008) to the Endemic period (2013-2014). Microb Drug Resist 2019; 25:538–542 [View Article]
    [Google Scholar]
  8. Brazilian Committee on Antimicrobial Susceptibility Testing (BrCAST) BR Cast. BrCAST; 2021 http://brcast.org.br accessed 27 August 2020
  9. Woodford N, Ellington MJ, Coelho JM, Turton JF, Ward ME et al. Multiplex PCR for genes encoding prevalent OXA carbapenemases in Acinetobacter spp. Int J Antimicrob Agents 2006; 27:351–353 [View Article] [PubMed]
    [Google Scholar]
  10. Higgins PG, Lehmann M, Seifert H. Inclusion of OXA-143 primers in a multiplex polymerase chain reaction (PCR) for genes encoding prevalent OXA carbapenemases in Acinetobacter spp. Int J Antimicrob Agents 2010; 35:305 [View Article] [PubMed]
    [Google Scholar]
  11. Cayô R, Merino M, Ruiz Del Castillo B, Cano ME, Calvo J et al. OXA-207, a novel OXA-24 variant with reduced catalytic efficiency against carbapenems in Acinetobacter pittii from Spain. Antimicrob Agents Chemother 2014; 58:4944–4948 [View Article] [PubMed]
    [Google Scholar]
  12. Donald HM, Scaife W, Amyes SGB, Young H-K. Sequence analysis of ARI-1, a novel OXA beta-lactamase, responsible for imipenem resistance in Acinetobacter baumannii 6B92. Antimicrob Agents Chemother 2000; 44:196–199 [View Article]
    [Google Scholar]
  13. Seifert H, Dolzani L, Bressan R, van der Reijden T, van Strijen B et al. Standardization and interlaboratory reproducibility assessment of pulsed-field gel electrophoresis-generated fingerprints of Acinetobacter baumannii. J Clin Microbiol 2005; 43:4328–4335 [View Article] [PubMed]
    [Google Scholar]
  14. Turton JF, Gabriel SN, Valderrey C, Kaufmann ME, Pitt TL. Use of sequence-based typing and multiplex PCR to identify clonal lineages of outbreak strains of Acinetobacter baumannii. Clin Microbiol Infect 2007; 13:807–815 [View Article] [PubMed]
    [Google Scholar]
  15. Martins N, Picão RC, Cerqueira-Alves M, Uehara A, Barbosa LC et al. A new trilocus sequence-based multiplex-PCR to detect major Acinetobacter baumannii clones. Infect Genet Evol 2016; 42:41–45 [View Article] [PubMed]
    [Google Scholar]
  16. Héritier C, Poirel L, Fournier P-E, Claverie J-M, Raoult D et al. Characterization of the naturally occurring oxacillinase of Acinetobacter baumannii. Antimicrob Agents Chemother 2005; 49:4174–4179 [View Article] [PubMed]
    [Google Scholar]
  17. Wyres KL, Cahill SM, Holt KE, Hall RM, Kenyon JJ. Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with kaptive. Microb Genomics 2020; 6: [PubMed]
    [Google Scholar]
  18. Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications [version 1; referees: 2 approved]. Wellcome Open Res 2018; 3:124 [View Article] [PubMed]
    [Google Scholar]
  19. Iacono M, Villa L, Fortini D, Bordoni R, Imperi F et al. Whole-genome pyrosequencing of an epidemic multidrug-resistant Acinetobacter baumannii strain belonging to the European clone II group. Antimicrob Agents Chemother 2008; 52:2616–2625 [View Article] [PubMed]
    [Google Scholar]
  20. Blackwell GA, Holt KE, Bentley SD, Hsu LY, Hall RM. Variants of AbGRI3 carrying the armA gene in extensively antibiotic-resistant Acinetobacter baumannii from Singapore. J Antimicrob Chemother 2017; 72:1031–1039 [View Article] [PubMed]
    [Google Scholar]
  21. Higgins PG, Dammhayn C, Hackel M, Seifert H. Global spread of carbapenem-resistant Acinetobacter baumannii. J Antimicrob Chemother 2010; 65:233–238 [View Article] [PubMed]
    [Google Scholar]
  22. Stietz MS, Ramírez MS, Vilacoba E, Merkier AK, Limansky AS et al. Acinetobacter baumannii extensively drug resistant lineages in Buenos Aires hospitals differ from the international clones I-III. Infect Genet Evol 2013; 14:294–301 [View Article] [PubMed]
    [Google Scholar]
  23. Nodari CS, Cayô R, Streling AP, Lei F, Wille J et al. Genomic analysis of carbapenem-resistant Acinetobacter baumannii isolates belonging to major endemic clones in South America. Front Microbiol 2020; 11:584603 [View Article] [PubMed]
    [Google Scholar]
  24. Cerezales M, Xanthopoulou K, Wille J, Bustamante Z, Seifert H et al. Acinetobacter baumannii analysis by core genome multi-locus sequence typing in two hospitals in Bolivia: endemicity of international clone 7 isolates (CC25). Int J Antimicrob Agents 2019; 53:844–849 [View Article] [PubMed]
    [Google Scholar]
  25. Vasconcelos ATR, Barth AL, Zavascki AP, Gales AC, Levin AS et al. The changing epidemiology of Acinetobacter spp. producing OXA carbapenemases causing bloodstream infections in Brazil: a BrasNet report. Diagn Microbiol Infect Dis 2015; 83:382–385 [View Article] [PubMed]
    [Google Scholar]
  26. Medeiros M, Lincopan N. Oxacillinase (OXA)-producing Acinetobacter baumannii in Brazil: clinical and environmental impact and therapeutic options. J Bras Patol Med Lab 2013; 49:391–405 [View Article]
    [Google Scholar]
  27. Tada T, Miyoshi-Akiyama T, Shimada K, Shimojima M, Kirikae T. Dissemination of 16S rRNA methylase ArmA-producing Acinetobacter baumannii and emergence of OXA-72 carbapenemase coproducers in Japan. Antimicrob Agents Chemother 2014; 58:2916–2920 [View Article] [PubMed]
    [Google Scholar]
  28. Doi Y, Wachino J-I, Arakawa Y. Aminoglycoside resistance: the emergence of acquired 16S ribosomal RNA methyltransferases. Infect Dis Clin North Am 2016; 30:523–537 [View Article] [PubMed]
    [Google Scholar]
  29. Camargo CH, Cunha MPV, de Barcellos TAF, Bueno MS, de Jesus Bertani AM et al. Genomic and phenotypic characterisation of antimicrobial resistance in carbapenem-resistant Acinetobacter baumannii hyperendemic clones CC1, CC15, CC79 and CC25. Int J Antimicrob Agents 2020; 56:106195 [View Article] [PubMed]
    [Google Scholar]
  30. Hawkey PM, Warren RE, Livermore DM, McNulty CAM, Enoch DA et al. Treatment of infections caused by multidrug-resistant Gram-negative bacteria: report of the British Society for antimicrobial chemotherapy/healthcare infection society/British infection association joint working party. J Antimicrob Chemother 2018; 73:iii2–iii78 [View Article] [PubMed]
    [Google Scholar]
  31. Durante-Mangoni E, Utili R, Zarrilli R. Combination therapy in severe Acinetobacter baumannii infections: an update on the evidence to date. Future Microbiol 2014; 9:773–789 [View Article] [PubMed]
    [Google Scholar]
  32. Isler B, Doi Y, Bonomo RA, Paterson DL. New treatment options against carbapenem-resistant Acinetobacter baumannii infections. Antimicrob Agents Chemother 2019; 63: Epub ahead of print 1 January 2019 [View Article]
    [Google Scholar]
  33. Hornsey M, Ellington MJ, Doumith M, Thomas CP, Gordon NC et al. AdeABC-mediated efflux and tigecycline MICs for epidemic clones of Acinetobacter baumannii. J Antimicrob Chemother 2010; 65:1589–1593 [View Article] [PubMed]
    [Google Scholar]
  34. Perez S, Innes GK, Walters MS, Mehr J, Arias J et al. Increase in hospital-acquired carbapenem-resistant Acinetobacter baumannii infection and colonization in an acute care hospital during a surge in COVID-19 admissions - New Jersey, February-July 2020. MMWR Morb Mortal Wkly Rep 2020; 69:1827–1831 [View Article] [PubMed]
    [Google Scholar]
  35. Shinohara DR, Santos Saalfeld SM, Martinez HV, Altafini DD, Costa BB et al. Outbreak of endemic carbapenem-resistant A. baumannii in a COVID-19-specific intensive care unit. Infect Control Hosp Epidemiol 20211–7 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jmm/10.1099/jmm.0.001509
Loading
/content/journal/jmm/10.1099/jmm.0.001509
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error