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      Diversity of metallo-β-lactamase-encoding genes found in distinct species of Acinetobacter isolated from the Brazilian Amazon Region

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          Abstract

          BACKGROUND

          The multidrug resistance (MDR) phenotype is frequently observed in Acinetobacter baumannii, the most clinically relevant pathogenic species of its genus; recently, other species belonging to the A. calcoaceticus-A. baumannii complex have emerged as important MDR nosocomial pathogens.

          OBJECTIVES

          The present study aimed to verify the occurrence of metallo-β-lactamase genes among distinct Acinetobacter species in a hospital located in the Brazilian Amazon Region.

          METHODS

          Antimicrobial susceptibility profiles were determined by broth microdilution. The genetic relationships among these isolates were assessed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Pyrosequencing reads of plasmids carrying the bla NDM-1 gene were generated using the Ion Torrent™ platform sequencing.

          FINDINGS

          A total of six isolates carried bla NDM-1: A. baumannii (n = 2), A. nosocomialis (n = 3), and A. pittii (n = 1); three carried bla IMP-1: A. baumannii, A. nosocomialis , and A. bereziniae. Resistance to colistin was observed for an NDM-1-producing A. nosocomialis isolate. Diverse PFGE patterns and sequence types were found among A. nosocomialis and A. baumannii isolates. The bla NDM-1 sequence was inserted in a Tn 125 transposon, while the bla IMP-1 was found as a gene cassette of the class 1 integron In 86.

          MAIN CONCLUSIONS

          To the best of our knowledge, this is the first report describing the dissemination of bla NDM-1 among distinct Acinetobacter species recovered from the same hospital in South America.

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          Sequencing of the rpoB gene and flanking spacers for molecular identification of Acinetobacter species.

          Vijay A. K. B. Gundi, Atieh Khamis, Bernard La Scola … (2006)
          Acinetobacter species are defined on the basis of several phenotypic characters, results of DNA-DNA homology, and more recently, similarities or dissimilarities in 16S rRNA gene sequences. However, the 16S rRNA gene is not polymorphic enough to clearly distinguish all Acinetobacter species. We used an RNA polymerase beta-subunit gene (rpoB)-based identification scheme for the delineation of species within the genus Acinetobacter, and towards that end, we determined the complete rpoB gene and flanking spacer (rplL-rpoB and rpoB-rpoC) sequences of the 17 reference strains of Acinetobacter species and 7 unnamed genomospecies. By using complete gene sequences (4,089 bp), we clearly separated all species and grouped them into different clusters. A phylogenetic tree constructed using these sequences was supported by bootstrap values higher than those obtained with 16S rRNA or the gyrB or recA gene. Four pairs of primers enabled us to amplify and sequence two highly polymorphic partial sequences (350 and 450 bp) of the rpoB gene. These and flanking spacers were designed and tested for rapid identification of the 17 reference strains of Acinetobacter species and 7 unnamed genomospecies. Each of these four variable sequences enabled us to delineate most species. Sequences of at least two polymorphic sequences should be used to distinguish Acinetobacter grimontii, Acinetobacter junii, Acinetobacter baylyi, and genomic species 9 from one another. Finally, 21 clinical isolates of Acinetobacter baumannii were tested for intraspecies relationships and assigned correctly to the same species by comparing the partial sequences of the rpoB gene and its flanking spacers.
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            The epidemiology of carbapenemases in Latin America and the Caribbean.

            Kevin Escandón-Vargas, Sergio Reyes, Sergio Gutierrez … (2017)
            Enterobacteriaceae, Pseudomonas spp., and Acinetobacter spp. infections are major causes of morbidity and mortality, especially due to the emergence and spread of β-lactamases. Carbapenemases, which are β-lactamases with the capacity to hydrolyze or inactivate carbapenems, have become a serious concern as they have the largest hydrolytic spectrum and therefore limit the utility of most β-lactam antibiotics. Areas covered: Here, we present an update of the current status of carbapenemases in Latin America and the Caribbean. Expert commentary: The increased frequency of reports on carbapenemases in Latin America and the Caribbean shows that they have successfully spread and have even become endemic in some countries. Countries such as Brazil, Colombia, Argentina, and Mexico account for the majority of these reports. Early suspicion and detection along with implementation of antimicrobial stewardship programs in all healthcare settings are crucial for the control and prevention of carbapenemase-producing bacteria.
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              Genomic Epidemiology of NDM-1-Encoding Plasmids in Latin American Clinical Isolates Reveals Insights into the Evolution of Multidrug Resistance

              Ricaurte Alejandro Márquez-Ortiz, Leanne Haggerty, Narda Olarte … (2017)
              Abstract Bacteria that produce the broad-spectrum Carbapenem antibiotic New Delhi Metallo-β-lactamase (NDM) place a burden on health care systems worldwide, due to the limited treatment options for infections caused by them and the rapid global spread of this antibiotic resistance mechanism. Although it is believed that the associated resistance gene bla NDM-1 originated in Acinetobacter spp., the role of Enterobacteriaceae in its dissemination remains unclear. In this study, we used whole genome sequencing to investigate the dissemination dynamics of bla NDM-1-positive plasmids in a set of 21 clinical NDM-1-positive isolates from Colombia and Mexico (Providencia rettgeri, Klebsiella pneumoniae, and Acinetobacter baumannii) as well as six representative NDM-1-positive Escherichia coli transconjugants. Additionally, the plasmids from three representative P. rettgeri isolates were sequenced by PacBio sequencing and finished. Our results demonstrate the presence of previously reported plasmids from K. pneumoniae and A. baumannii in different genetic backgrounds and geographically distant locations in Colombia. Three new previously unclassified plasmids were also identified in P. rettgeri from Colombia and Mexico, plus an interesting genetic link between NDM-1-positive P. rettgeri from distant geographic locations (Canada, Mexico, Colombia, and Israel) without any reported epidemiological links was discovered. Finally, we detected a relationship between plasmids present in P. rettgeri and plasmids from A. baumannii and K. pneumoniae. Overall, our findings suggest a Russian doll model for the dissemination of bla NDM-1 in Latin America, with P. rettgeri playing a central role in this process, and reveal new insights into the evolution and dissemination of plasmids carrying such antibiotic resistance genes.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Mem Inst Oswaldo Cruz
                Journal ID (iso-abbrev): Mem. Inst. Oswaldo Cruz
                Journal ID (publisher-id): mioc
                Title: Memórias do Instituto Oswaldo Cruz
                Publisher: Instituto Oswaldo Cruz, Ministério da Saúde
                ISSN (Print): 0074-0276
                ISSN (Electronic): 1678-8060
                Publication date (Electronic): 30 May 2019
                Publication date Collection: 2019
                Volume: 114
                Electronic Location Identifier: e190020
                Affiliations
                [1 ]Instituto Evandro Chagas, Seção de Bacteriologia e Micologia, Ananindeua, PA, Brasil
                [2 ]Universidade Federal de São Paulo, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Departamento de Ciências Biológicas, Setor de Biologia Molecular, Microbiologia e Imunologia, Diadema, SP, Brasil
                [3 ]Universidade Federal de São Paulo, Departamento de Medicina, Escola Paulista de Medicina, Laboratório Alerta, Disciplina de Infectologia, São Paulo, SP, Brasil
                [4 ]Instituto Evandro Chagas, Centro de Inovação Tecnológica, Ananindeua, PA, Brasil
                [5 ]Hospital Fundação Santa Casa de Misericórdia do Pará, Belém, PA, Brasil
                Author notes
                + Corresponding-author: daniellemurici@ 123456iec.gov.br

                DB, RC and ACG conceived and supervised the project; RS provided the Acinetobacter isolates for the study; DB, RC, APS, CSN, RRB, PSL and JMM carried out the experimental procedures; YC and IM collected patient clinical data; DB, RC, APS, CSN and ACG drafted the manuscript. All authors read and approved the final manuscript. Competing interests: ACG recently received research funding and/or consultation fees from Bayer, Eurofarma, Pfizer, and MSD. Other authors have nothing to declare. This study was not financially supported by any Diagnostic/Pharmaceutical company.

                Author information
                http://orcid.org/0000-0003-2772-639X
                Article
                Other ID: 00330
                DOI: 10.1590/0074-02760190020
                PMC ID: 6543903
                PubMed ID: 31166421
                SO-VID: 8bcd8365-26dc-4e51-909e-f9f5cfcb1545
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution License

                History
                Date received : 17 January 2019
                Date accepted : 29 April 2019
                Page count
                Figures: 2, Tables: 1, Equations: 0, References: 20
                Categories
                Subject: Original Article

                Keywords: metallo-β-lactamase,non-baumannii acinetobacter species,polymyxin resistance,nosocomial infection,icu,tn125
                Data availability:
                Keywords: metallo-β-lactamase, non-baumannii acinetobacter species, polymyxin resistance, nosocomial infection, icu, tn125

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