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Morgado SM, Fonseca ÉL, Freitas FS, Bighi NS, Oliveira PPC, Monteiro PM, Lima LS, Santos BP, Sousa MAR, Assumpção AO, Mascarenhas LA, Vicente ACP. Erratum to "Outbreak of high-risk XDR CRAB of international clone 2 (IC2) in Rio Janeiro, Brazil" [Journal of Global Antimicrobial Resistance 34 (2023) 91-98]. J Glob Antimicrob Resist 2024; 36:495. [PMID: 38521552 DOI: 10.1016/j.jgar.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024] Open
Affiliation(s)
- Sérgio M Morgado
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.
| | - Érica L Fonseca
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Fernanda S Freitas
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Nathalia S Bighi
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Priscila P C Oliveira
- Hospital Infection Control Committee, São Francisco na Providência de Deus Hospital, Rio de Janeiro, Brazil
| | - Priscilla M Monteiro
- Hospital Infection Control Committee, São Francisco na Providência de Deus Hospital, Rio de Janeiro, Brazil
| | - Lorena S Lima
- Hospital Infection Control Committee, São Francisco na Providência de Deus Hospital, Rio de Janeiro, Brazil
| | - Bianca P Santos
- Hospital Infection Control Committee, São Francisco na Providência de Deus Hospital, Rio de Janeiro, Brazil
| | - Maria A R Sousa
- Hospital Infection Control Committee, São Francisco na Providência de Deus Hospital, Rio de Janeiro, Brazil
| | - Adriana O Assumpção
- Hospital Infection Control Committee, São Francisco na Providência de Deus Hospital, Rio de Janeiro, Brazil
| | - Luiz A Mascarenhas
- Hospital Infection Control Committee, São Francisco na Providência de Deus Hospital, Rio de Janeiro, Brazil
| | - Ana Carolina P Vicente
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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Morgado SM, Fonseca ÉL, Freitas FS, Bighi NS, Oliveira PPC, Monteiro PM, Lima LS, Santos BP, Sousa MAR, Assumpção AO, Mascarenhas LA, Vicente ACP. Outbreak of high-risk XDR CRAB of international clone 2 (IC2) in Rio Janeiro, Brazil. J Glob Antimicrob Resist 2023; 34:91-98. [PMID: 37419183 DOI: 10.1016/j.jgar.2023.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/13/2023] [Accepted: 06/24/2023] [Indexed: 07/09/2023] Open
Abstract
OBJECTIVES Among the high-risk clones of Acinetobacter baumannii, called international clones (ICs), IC2 represents the main lineage causing outbreaks worldwide. Despite the successful global spread of IC2, the occurrence of IC2 is rarely reported in Latin America. Here, we aimed to evaluate the susceptibility and genetic relatedness of isolates from a nosocomial outbreak in Rio de Janeiro/Brazil (2022) and perform genomic epidemiology analyses of the available genomes of A. baumannii. METHODS Sixteen strains of A. baumannii were subjected to antimicrobial susceptibility tests and genome sequencing. These genomes were compared phylogenetically with other IC2 genomes from the NCBI database, and virulence and antibiotic resistance genes were searched. RESULTS The 16 strains represented carbapenem-resistant A. baumannii (CRAB) with an extensively drug-resistant profile. In silico analysis established the relationship between the Brazilian CRAB genomes and IC2/ST2 genomes in the world. The Brazilian strains belonged to three sub-lineages, associated with genomes from countries in Europe, North America, and Asia. These sub-lineages presented three distinct capsules, KL7, KL9, and KL56. The Brazilian strains were characterised by the co-presence of blaOXA-23 and blaOXA-66, in addition to the genes APH(6), APH(3"), ANT(3"), AAC(6'), armA, and the efflux pumps adeABC and adeIJK. A large set of virulence genes was also identified: adeFGH/efflux pump; the siderophores barAB, basABCDFGHIJ, and bauBCDEF; lpxABCDLM/capsule; tssABCDEFGIKLM/T6SS; and pgaABCD/biofilm. CONCLUSION Widespread extensively drug-resistant CRAB IC2/ST2 is currently causing outbreaks in clinical settings in southeastern Brazil. This is due to at least three sub-lineages characterised by an enormous apparatus of virulence and resistance to antibiotics, both intrinsic and mobile.
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Affiliation(s)
- Sérgio M Morgado
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.
| | - Érica L Fonseca
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Fernanda S Freitas
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Nathalia S Bighi
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Priscila P C Oliveira
- Hospital Infection Control Committee, São Francisco na Providência de Deus Hospital, Rio de Janeiro, Brazil
| | - Priscilla M Monteiro
- Hospital Infection Control Committee, São Francisco na Providência de Deus Hospital, Rio de Janeiro, Brazil
| | - Lorena S Lima
- Hospital Infection Control Committee, São Francisco na Providência de Deus Hospital, Rio de Janeiro, Brazil
| | - Bianca P Santos
- Hospital Infection Control Committee, São Francisco na Providência de Deus Hospital, Rio de Janeiro, Brazil
| | - Maria A R Sousa
- Hospital Infection Control Committee, São Francisco na Providência de Deus Hospital, Rio de Janeiro, Brazil
| | - Adriana O Assumpção
- Hospital Infection Control Committee, São Francisco na Providência de Deus Hospital, Rio de Janeiro, Brazil
| | - Luiz A Mascarenhas
- Hospital Infection Control Committee, São Francisco na Providência de Deus Hospital, Rio de Janeiro, Brazil
| | - Ana Carolina P Vicente
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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Fonseca ÉL, Vicente AC. Integron Functionality and Genome Innovation: An Update on the Subtle and Smart Strategy of Integrase and Gene Cassette Expression Regulation. Microorganisms 2022; 10:microorganisms10020224. [PMID: 35208680 PMCID: PMC8876359 DOI: 10.3390/microorganisms10020224] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/14/2022] [Accepted: 01/15/2022] [Indexed: 12/22/2022] Open
Abstract
Integrons are considered hot spots for bacterial evolution, since these platforms allow one-step genomic innovation by capturing and expressing genes that provide advantageous novelties, such as antibiotic resistance. The acquisition and shuffling of gene cassettes featured by integrons enable the population to rapidly respond to changing selective pressures. However, in order to avoid deleterious effects and fitness burden, the integron activity must be tightly controlled, which happens in an elegant and elaborate fashion, as discussed in detail in the present review. Here, we aimed to provide an up-to-date overview of the complex regulatory networks that permeate the expression and functionality of integrons at both transcriptional and translational levels. It was possible to compile strong shreds of evidence clearly proving that these versatile platforms include functions other than acquiring and expressing gene cassettes. The well-balanced mechanism of integron expression is intricately related with environmental signals, host cell physiology, fitness, and survival, ultimately leading to adaptation on the demand.
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Fonseca ÉL, Morgado SM, Caldart RV, Freitas F, Vicente ACP. Emergence of a VIM-2-producing XDR Pseudomonas aeruginosa ST309 in South America: a comparative genomic analysis. Int J Antimicrob Agents 2021; 59:106507. [PMID: 34958864 DOI: 10.1016/j.ijantimicag.2021.106507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/14/2021] [Accepted: 12/18/2021] [Indexed: 11/18/2022]
Abstract
Pseudomonas aeruginosa has been considered a top priority pathogen associated with elevated morbidity and mortality. Worldwide outbreaks have been associated with few high-risk epidemic P. aeruginosa lineages. However, the biological features involved with the persistence and spread of such lineages among clinical settings remain to be unraveled. This study reports the emergence of an XDR ST309 P. aeruginosa in South America/Brazil, more precisely, in the Amazon region. Genomic analyses were performed with 42 complete and draft ST309 genomes, giving insights into its epidemiology, resistome, and mobilome. Heterogeneous distribution of acquired antimicrobial resistance genes among ST309 genomes was observed, which included blaVIM-2, blaIMP-15, and qnrVC1, all of them associated with class 1 integrons. The mobilome mining showed the presence of Integrative and Conjugative Elements, transposons, and genomic islands harbouring a huge arsenal of heavy metal resistance determinants, which probably provided adaptive advantages to ST309 lineage.
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Affiliation(s)
- Érica L Fonseca
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Avenida Brasil 4365, Manguinhos, Rio de Janeiro, RJ, 21040-900, Brazil.
| | - Sérgio M Morgado
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Avenida Brasil 4365, Manguinhos, Rio de Janeiro, RJ, 21040-900, Brazil
| | | | - Fernanda Freitas
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Avenida Brasil 4365, Manguinhos, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Ana Carolina P Vicente
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Avenida Brasil 4365, Manguinhos, Rio de Janeiro, RJ, 21040-900, Brazil
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Fonseca ÉL, Caldart RV, Freitas FS, Morgado SM, Rocha LT, dos Santos RC, Vicente ACP. Emergence of extensively drug-resistant international clone IC-6 Acinetobacter baumannii carrying blaOXA-72 and blaCTX-M-115 in the Brazilian Amazon region. J Glob Antimicrob Resist 2020; 20:18-21. [DOI: 10.1016/j.jgar.2019.06.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/11/2019] [Accepted: 06/17/2019] [Indexed: 11/26/2022] Open
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Fonseca ÉL, Vicente ACP. Polycistronic transcription of fused cassettes and identification of translation initiation signals in an unusual gene cassette array from Pseudomonas aeruginosa. F1000Res 2015; 2:99. [PMID: 26674490 PMCID: PMC4670013 DOI: 10.12688/f1000research.2-99.v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/25/2015] [Indexed: 11/15/2023] Open
Abstract
The gene cassettes found in class 1 integrons are generally promoterless units composed by an open reading frame (ORF), a short 5' untranslated region (UTR) and a 3' recombination site ( attC). Fused gene cassettes are generated by partial or total loss of the attC from the first cassette in an array, creating, in some cases, a fusion with the ORF from the next cassette. These structures are rare and little is known about their mechanisms of mobilization and expression. The aim of this study was to evaluate the dynamic of mobilization and transcription of the gcu14-bla GES-1 /aacA4 gene cassette array, which harbours a fused gene cassette represented by bla GES-1 /aacA4. The cassette array was analyzed by Northern blot and real-time reverse transcription-polymerase chain reaction (RT-PCR) in order to assess the transcription mechanism of bla GES-1 /aacA4 fused cassette. Also, inverse polymerase chain reactions (PCR) were performed to detect the free circular forms of gcu14, bla GES-1 and aacA4. The Northern blot and real time RT-PCR revealed a polycistronic transcription, in which the fused cassette bla GES-1 /aacA4 is transcribed as a unique gene, while gcu14 (with a canonical attC recombination site) has a monocistronic transcription. The gcu14 cassette, closer to the weak configuration of cassette promoter (PcW), had a higher transcription level than bla GES-1/ aacA4, indicating that the cassette position affects the transcript amounts. The presence of ORF-11 at attI1, immediately preceding gcu14, and of a Shine-Dalgarno sequence upstream bla GES-1/ aacA4 composes a scenario for the occurrence of array translation. Inverse PCR generated amplicons corresponding to gcu14, gcu14-aacA4 and gcu14-bla GES-1/ aacA4 free circular forms, but not to bla GES-1 and aacA4 alone, indicating that the GES-1 truncated attC is not substrate of integrase activity and that these genes are mobilized together as a unique cassette. This study was original in showing the transcription of fused cassettes and in correlating cassette position with transcription.
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Affiliation(s)
- Érica L. Fonseca
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Rio de Janeiro, 4365, Brazil
| | - Ana Carolina Paulo Vicente
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Rio de Janeiro, 4365, Brazil
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Barroso DE, Castiñeiras TMPP, Freitas FS, Marsh JW, Krauland MG, Tulenko MM, Fonseca ÉL, Vicente ACP, Rebelo MC, Cerqueira EO, Xavier AC, Cardozo APCM, da Silva SEM, Harrison LH. Three outbreak-causing Neisseria meningitidis serogroup C clones, Brazil(1.). Emerg Infect Dis 2014. [PMID: 24229563 PMCID: PMC3837672 DOI: 10.3201/eid1911.130610] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
During 2003–2012, 8 clusters of meningococcal disease were identified in Rio de Janeiro State, Brazil, all caused by serogroup C Neisseria meningitidis. The isolates were assigned to 3 clonal complexes (cc): cc11, cc32, and cc103. These hyperinvasive disease lineages were associated with endemic disease, outbreaks, and high case-fatality rates.
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Barroso DE, Castiñeiras TMPP, Freitas FS, Marsh JW, Krauland MG, Tulenko MM, Fonseca ÉL, Vicente ACP, Rebelo MC, Cerqueira EO, Xavier AC, Cardozo APCM, da Silva SEM, Harrison LH. Three outbreak-causing Neisseria meningitidis serogroup C clones, Brazil(1.). Emerg Infect Dis 2014; 19:1847-50. [PMID: 24229563 DOI: 10.3201/13-0610] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
During 2003-2012, 8 clusters of meningococcal disease were identified in Rio de Janeiro State, Brazil, all caused by serogroup C Neisseria meningitidis. The isolates were assigned to 3 clonal complexes (cc): cc11, cc32, and cc103. These hyperinvasive disease lineages were associated with endemic disease, outbreaks, and high case-fatality rates.
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Fonseca ÉL, Vicente ACP. Polycistronic transcription of fused cassettes and identification of translation initiation signals in an unusual gene cassette array from Pseudomonas aeruginosa. F1000Res 2013; 2:99. [PMID: 26674490 PMCID: PMC4670013 DOI: 10.12688/f1000research.2-99.v3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/25/2015] [Indexed: 11/20/2022] Open
Abstract
The gene cassettes found in class 1 integrons are generally promoterless units composed by an open reading frame (ORF), a short 5’ untranslated region (UTR) and a 3’ recombination site (
attC). Fused gene cassettes are generated by partial or total loss of the
attC from the first cassette in an array, creating, in some cases, a fusion with the ORF from the next cassette. These structures are rare and little is known about their mechanisms of mobilization and expression. The aim of this study was to evaluate the dynamic of mobilization and transcription of the
gcu14-blaGES-1/aacA4 gene cassette array, which harbours a fused gene cassette represented by
blaGES-1/aacA4. The cassette array was analyzed by Northern blot and real-time reverse transcription-polymerase chain reaction (RT-PCR) in order to assess the transcription mechanism of
blaGES-1/aacA4 fused cassette. Also, inverse polymerase chain reactions (PCR) were performed to detect the free circular forms of
gcu14, blaGES-1 and aacA4. The Northern blot and real time RT-PCR revealed a polycistronic transcription, in which the fused cassette
blaGES-1/aacA4 is transcribed as a unique gene, while
gcu14 (with a canonical
attC recombination site) has a monocistronic transcription. The
gcu14 cassette, closer to the weak configuration of cassette promoter (PcW), had a higher transcription level than
blaGES-1/
aacA4, indicating that the cassette position affects the transcript amounts. The presence of ORF-11 at
attI1, immediately preceding
gcu14, and of a Shine-Dalgarno sequence upstream
blaGES-1/
aacA4 composes a scenario for the occurrence of array translation. Inverse PCR generated amplicons corresponding to
gcu14, gcu14-aacA4 and gcu14-blaGES-1/
aacA4 free circular forms, but not to
blaGES-1 and
aacA4 alone, indicating that the GES-1 truncated
attC is not substrate of integrase activity and that these genes are mobilized together as a unique cassette. This study was original in showing the transcription of fused cassettes and in correlating cassette position with transcription.
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Affiliation(s)
- Érica L Fonseca
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Rio de Janeiro, 4365, Brazil
| | - Ana Carolina Paulo Vicente
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Rio de Janeiro, 4365, Brazil
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