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Camargo CH, Yamada AY, Nagamori FO, de Souza AR, Tiba-Casas MR, de Moraes França FA, Porto MHTN, de Lima Garzon ML, Higgins P, Madalosso G, de Assis DB. Clonal spread of ArmA- and OXA-23-coproducing Acinetobacter baumannii International Clone 2 in Brazil during the first wave of the COVID-19 pandemic. J Med Microbiol 2022; 71. [PMID: 35417321 DOI: 10.1099/jmm.0.001509] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Carbapenem-resistant Acinetobacter baumannii (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.Gap Statement. There are no documented outbreaks of CRAB International Clone 2 (IC-2) reported in Brazil.Aim. To describe a large outbreak of CRAB caused by the uncommon IC-2 in a Brazilian COVID-19 hospital.Methodology. 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).Results. 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.Conclusion. 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.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Paul Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner site Bonn-Cologne, Cologne, Germany
| | - Geraldine Madalosso
- Divisão de Infecção Hospitalar, Centro de Vigilância Epidemiológica, São Paulo, Brazil
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2
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Spread of multidrug-resistant Acinetobacter baumannii isolates belonging to IC1 and IC5 major clones in Rondônia state. Braz J Microbiol 2022; 53:795-799. [PMID: 35141834 PMCID: PMC9151963 DOI: 10.1007/s42770-022-00706-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/01/2022] [Indexed: 02/01/2023] Open
Abstract
In Brazil, carbapenem-resistant A. baumannii (CRAB) is a critical pathogen showing high carbapenem resistance rates. Currently, there is little epidemiological data on A. baumannii isolated in the Northern Brazilian region. Herein, this study aimed to characterize the resistance mechanisms of CRAB isolates recovered from hospitalized patients in the state of Rondônia in 2019. Most of CRAB were considered as extensively drug-resistant, and some of them showed high MICs for minocycline. Only polymyxins showed a satisfactory activity. All isolates carried blaOXA-23 and were included in 14 distinct clusters, with the predominance of clonal group A (29%). The IC1 was the most frequent clonal group, followed by IC5 and IC4. Here, we firstly reported the epidemiological scenario of CRAB in the state of Rondônia, located in the Brazilian Amazon region. The high frequency of CRAB presenting XDR phenotype is of great concern, due to limited therapeutical options, especially in the actual pandemic scenario, in which we observed an overcrowding of ICU beds. Such results are essential to better characterize the epidemiology of CRAB in the entire Brazilian territory.
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de Barcellos TAF, Bueno MS, Cunha MPV, Nagamori FO, de Carvalho E, Takagi EH, Moreno LZ, Moreno AM, Chimara E, Tiba-Casas MR, Camargo CH. Silent mutations in ribosomal protein genes are associated with high-risk clones of carbapenem-resistant Acinetobacter baumannii prevalent in Brazil. INFECTION GENETICS AND EVOLUTION 2020; 88:104686. [PMID: 33359045 DOI: 10.1016/j.meegid.2020.104686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/09/2020] [Accepted: 12/19/2020] [Indexed: 11/18/2022]
Abstract
OBJECTIVES To analyze the relationship of ribosomal protein mutations and clonality of high-risk clones Acinetobacter baumannii. METHODS Seventy-nine carbapenem-resistant A. baumannii were subjected to whole-genome sequencing (Illumina NextSeq), and codifying sequences of ribosomal proteins were extracted and screened for mutations. MALDI-TOF MS analysis (Bruker Biotyper) and Spectra data from MALDI-TOF was employed to generate a dendrogram based on principal component analysis (PCA) data. Clones were identified by Multilocus sequencing typing (MLST) based on WGS. RESULTS Ribosomal RNA protein sequences extracted from the genomes identified mutations that were associated with clonal complexes, but most of them were silent. PCA did not cluster the isolates according to their clonality identified by MLST. CONCLUSIONS By comparing the nucleotide and amino acid sequences of diversified A. baumannii, and Bruker Biotyper profiles, we showed that silent mutations in ribosomal RNA nucleotides are associated with clonal complexes, but since most of the mutations were silent, MALDI-TOF MS raw data was not a useful tool for typing the high-risk clones of this species.
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Affiliation(s)
| | - Mariana Sardinha Bueno
- Instituto Adolfo Lutz, São Paulo, SP 01246-902, Brazil; Universidade de São Paulo, São Paulo, SP 01246-903, Brazil.
| | | | | | | | | | | | | | - Erica Chimara
- Instituto Adolfo Lutz, São Paulo, SP 01246-902, Brazil.
| | | | - Carlos Henrique Camargo
- Instituto Adolfo Lutz, São Paulo, SP 01246-902, Brazil; Universidade de São Paulo, São Paulo, SP 01246-903, Brazil.
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Antibiotic Susceptibility, Clonality, and Molecular Characterization of Carbapenem-Resistant Clinical Isolates of Acinetobacter baumannii from Washington DC. Int J Microbiol 2020; 2020:2120159. [PMID: 32695174 PMCID: PMC7368205 DOI: 10.1155/2020/2120159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/10/2020] [Indexed: 12/18/2022] Open
Abstract
The occurrence of carbapenem-resistant (CR) strains of Acinetobacter baumannii is reported to contribute to the severity of several nosocomial infections, especially in critically ill patients in intensive care units. The present study aims to determine the antibiotic susceptibility, clonality, and genetic mechanism of carbapenem resistance in twenty-eight Acinetobacter baumannii isolates from four hospitals in Washington DC. The antibiotic susceptibility of the isolates was determined by VITEK 2 analyses, while PCR was used to examine the presence of antibiotic-resistant genes and mobile genetic elements. Trilocus multiplex-PCR was used along with pulsed-field gel electrophoresis (PFGE) for strain typing and for accessing clonal relationships among the isolates. Antimicrobial susceptibility testing indicated that 46% of the isolates were carbapenem-resistant and possessed MDR and XDR phenotypes. PFGE clustered the 28 isolates into seven clonal (C1–C7) complexes based on >75% similarity cut-off. Thirty-six percent of the isolates belonged to international clone II, while 29% were assigned to Group 4 by trilocus multiplex-PCR. Although the blaOXA-51-like gene was found in all the isolates, only 36% were positive for the blaOXA-23-like gene. PCR analysis also found a metallo-β-lactamase (MBL) gene (blaVIM) in 71% of the isolates. Of the 13 CR isolates, 8 were PCR positive for both blaVIM and blaOXA-23-like genes, while 5 harbored only blaVIM gene. This study revealed the emergence of VIM carbapenemase-producing A. baumannii isolates, which has not been previously reported in the United States.
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Rafei R, Osman M, Dabboussi F, Hamze M. Update on the epidemiological typing methods for Acinetobacter baumannii. Future Microbiol 2019; 14:1065-1080. [DOI: 10.2217/fmb-2019-0134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The outstanding ability of Acinetobacter baumannii to cause outbreaks and acquire multidrug resistance motivated the development of a plethora of typing techniques, which can help infection preventionists and hospital epidemiologists to more efficiently implement intervention controls. Nowadays, the world is witnessing a gradual transition from traditional typing methodology to whole genome sequencing-based approaches. Such approaches are opening new prospects and applications never achieved by existing typing methods. Herein, we provide the reader with an updated review on A. baumannii typing methods recapping the added value of well-established techniques previously applied for A. baumannii and detailing new ones (as clustered regularly interspaced short palindromic repeats-based typing) with a special focus on whole genome sequencing.
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Affiliation(s)
- Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
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Romanin P, Palermo RL, Cavalini JF, Fávaro LDS, De Paula-Petroli SB, Fernandes EV, Dos Anjos Szczerepa MM, Tognim MCB, Yamada-Ogatta SF, Carrara-Marroni FE, Yamauchi LM. Multidrug- and Extensively Drug-Resistant Acinetobacter baumannii in a Tertiary Hospital from Brazil: The Importance of Carbapenemase Encoding Genes and Epidemic Clonal Complexes in a 10-Year Study. Microb Drug Resist 2019; 25:1365-1373. [PMID: 31361565 DOI: 10.1089/mdr.2019.0002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
This study aimed to characterize the main mechanisms of acquired antimicrobial resistance of 103 multidrug-resistant Acinetobacter baumannii isolated from bloodstream from 2006 to 2016 from a hospital in Londrina, Brazil. All 103 isolates were identified as A. baumannii by amplification of the blaOXA-51-like and rpoB genes. Mortality was observed in the majority (81.6%) of the patients. High non-susceptibility rates (100.0-10.7%) were obtained for the evaluated antimicrobials, including colistin, polymyxin B, and tigecycline, and most isolates were classified as extensively drug-resistant (78.6%). Carbapenemase production was observed in 92.2% of the isolates. All carbapenem-resistant isolates showed a carbapenem-hydrolyzing class D β-lactamase being either blaOXA-23-like (97.9%) or blaOXA-143-like (2.1%). None of the isolates had the genes blaOXA-24-like, blaOXA-58-like, blaOXA-48, blaKPC, blaNDM, blaSPM-1, blaSIM-1, blaVIM, blaIMP, blaGIM, blaGES, mcr-1, qnrA, qnrB, qnrC, qnrS, and qnrVc. As a genetic context of the blaOXA-23-like gene, Tn2006 was predominated (86.0%), and Tn2008 was less frequent (12.9%). Isolates harboring the blaOXA-143-like gene showed the blaOXA-253-like variant. A polyclonal profile was observed among the A. baumannii isolates. The presence of the international clonal complexes CC113/79, CC109/1, CC110/25, and CC103/15 was detected, with prevalence of CC113/79 (38.8%). This study provides essential information to understand the antimicrobial resistance patterns of A. baumannii and can be used to strengthen infection control measures in our hospital. Also, the study reinforces the urgent need to develop stewardship programs to avoid the spread and potential outbreaks by this pathogen.
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Affiliation(s)
- Priscila Romanin
- Laboratório de Estudos Moleculares e Resistência aos Antimicrobianos, Departamento de Patologia, Análises Clínicas e Toxicológicas, Universidade Estadual de Londrina, Londrina, Brazil.,Laboratório de Biologia Molecular de Microrganismos, Departamento de Microbiologia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Raquel Lima Palermo
- Laboratório de Estudos Moleculares e Resistência aos Antimicrobianos, Departamento de Patologia, Análises Clínicas e Toxicológicas, Universidade Estadual de Londrina, Londrina, Brazil.,Laboratório de Biologia Molecular de Microrganismos, Departamento de Microbiologia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Jônatas Fernando Cavalini
- Laboratório de Estudos Moleculares e Resistência aos Antimicrobianos, Departamento de Patologia, Análises Clínicas e Toxicológicas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Larissa Dos Santos Fávaro
- Laboratório de Estudos Moleculares e Resistência aos Antimicrobianos, Departamento de Patologia, Análises Clínicas e Toxicológicas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Suelen Balero De Paula-Petroli
- Laboratório de Estudos Moleculares e Resistência aos Antimicrobianos, Departamento de Patologia, Análises Clínicas e Toxicológicas, Universidade Estadual de Londrina, Londrina, Brazil.,Laboratório de Biologia Molecular de Microrganismos, Departamento de Microbiologia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Eduardo Vignoto Fernandes
- Laboratório de Estudos Moleculares e Resistência aos Antimicrobianos, Departamento de Patologia, Análises Clínicas e Toxicológicas, Universidade Estadual de Londrina, Londrina, Brazil
| | | | - Maria Cristina Bronharo Tognim
- Laboratório de Microbiologia, Departamento de Ciências Básicas da Saúde, Universidade Estadual de Maringá, Maringá, Brazil
| | - Sueli Fumie Yamada-Ogatta
- Laboratório de Biologia Molecular de Microrganismos, Departamento de Microbiologia, Universidade Estadual de Londrina, Londrina, Brazil
| | - Floristher Elaine Carrara-Marroni
- Laboratório de Estudos Moleculares e Resistência aos Antimicrobianos, Departamento de Patologia, Análises Clínicas e Toxicológicas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Lucy Megumi Yamauchi
- Laboratório de Biologia Molecular de Microrganismos, Departamento de Microbiologia, Universidade Estadual de Londrina, Londrina, Brazil
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Opazo-Capurro A, San Martín I, Quezada-Aguiluz M, Morales-León F, Domínguez-Yévenes M, Lima CA, Esposito F, Cerdeira L, Bello-Toledo H, Lincopan N, González-Rocha G. Evolutionary dynamics of carbapenem-resistant Acinetobacter baumannii circulating in Chilean hospitals. INFECTION GENETICS AND EVOLUTION 2019; 73:93-97. [PMID: 31029791 DOI: 10.1016/j.meegid.2019.04.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 04/16/2019] [Accepted: 04/21/2019] [Indexed: 12/31/2022]
Abstract
We analyze the evolutionary dynamics of ninety carbapenem-resistant Acinetobacter baumannii (CRAB) isolates collected between 1990 and 2015 in Chile. CRAB were identified at first in an isolate collected in 2005, which harbored the ISAba1-blaOXA-69 arrangement. Later, OXA-58- and OXA-23-producing A. baumannii strains emerged in 2007 and 2009, respectively. This phenomenon was associated with variations in the epidemiology of OXA-type carbapenemases, linked to nosocomial lineages belonging to ST109, ST162, ST15 (CC15) and ST318 (CC15).
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Affiliation(s)
- Andrés Opazo-Capurro
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile; Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Chile
| | - Iván San Martín
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
| | - Mario Quezada-Aguiluz
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
| | - Felipe Morales-León
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile; Departamento de Farmacia, Facultad de Farmacia, Universidad de Concepción, Chile
| | - Mariana Domínguez-Yévenes
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
| | - Celia A Lima
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
| | - Fernanda Esposito
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Louise Cerdeira
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Helia Bello-Toledo
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
| | - Nilton Lincopan
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA-UdeC), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile; Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Chile.
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Tavares LCB, de Vasconcellos FM, Sant'Ana DA, Tiba-Casas MR, Camargo CH. Acinetobacter baumannii ST317 can be identified with Martins' trilocus sequence-based multiplex-PCR. INFECTION GENETICS AND EVOLUTION 2018; 58:251-252. [PMID: 29331669 DOI: 10.1016/j.meegid.2018.01.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/06/2018] [Accepted: 01/09/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Laís Calissi Brisolla Tavares
- Bacteriology Division, Adolfo Lutz Institute, Sao Paulo, Brazil; School of Medicine, University of Sao Paulo, Sao Paulo, Brazil
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9
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Vasconcellos FMD, Tiba-Casas MR, Tavares LCB, Souza WVD, Garcia DDO, Camargo CH. Evaluation of a new trilocus sequence-based multiplex-PCR to detect major Acinetobacter baumannii clonal complexes circulating in Brazil. INFECTION GENETICS AND EVOLUTION 2017. [DOI: 10.1016/j.meegid.2017.06.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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