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Sequino G, Cobo-Diaz JF, Valentino V, Tassou C, Volpe S, Torrieri E, Nychas GJ, Álvarez Ordóñez A, Ercolini D, De Filippis F. Microbiome mapping in beef processing reveals safety-relevant variations in microbial diversity and genomic features. Food Res Int 2024; 186:114318. [PMID: 38729711 DOI: 10.1016/j.foodres.2024.114318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/05/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024]
Abstract
The microbiome of surfaces along the beef processing chain represents a critical nexus where microbial ecosystems play a pivotal role in meat quality and safety of end products. This study offers a comprehensive analysis of the microbiome along beef processing using whole metagenomics with a particular focus on antimicrobial resistance and virulence-associated genes distribution. Our findings highlighted that microbial communities change dynamically in the different steps along beef processing chain, influenced by the specific conditions of each micro-environment. Brochothrix thermosphacta, Carnobacterium maltaromaticum, Pseudomonas fragi, Psychrobacter cryohalolentis and Psychrobacter immobilis were identified as the key species that characterize beef processing environments. Carcass samples and slaughterhouse surfaces exhibited a high abundance of antibiotic resistance genes (ARGs), mainly belonging to aminoglycosides, β-lactams, amphenicols, sulfonamides and tetracyclines antibiotic classes, also localized on mobile elements, suggesting the possibility to be transmitted to human pathogens. We also evaluated how the initial microbial contamination of raw beef changes in response to storage conditions, showing different species prevailing according to the type of packaging employed. We identified several genes leading to the production of spoilage-associated compounds, and highlighted the different genomic potential selected by the storage conditions. Our results suggested that surfaces in beef processing environments represent a hotspot for beef contamination and evidenced that mapping the resident microbiome in these environments may help in reducing meat microbial contamination, increasing shelf-life, and finally contributing to food waste restraint.
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Affiliation(s)
- Giuseppina Sequino
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055 Portici, (NA), Italy
| | - José F Cobo-Diaz
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Vincenzo Valentino
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055 Portici, (NA), Italy
| | - Chrysoula Tassou
- Hellenic Agricultural Organization - DIMITRA, Institute of Technology of Agricultural Products, Sofokli Venizelou 1, 14123 Lycovrissi, Attica, Greece
| | - Stefania Volpe
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055 Portici, (NA), Italy
| | - Elena Torrieri
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055 Portici, (NA), Italy
| | | | - Avelino Álvarez Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055 Portici, (NA), Italy; Task Force on Microbiome Studies, University of Naples Federico II, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055 Portici, (NA), Italy; Task Force on Microbiome Studies, University of Naples Federico II, Italy.
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Genomic Analysis of Acinetobacter baumannii Isolates Carrying OXA-23 and OXA-58 Genes from Animals Reveals ST1 and ST25 as Major Clonal Lineages. Antibiotics (Basel) 2022; 11:antibiotics11081045. [PMID: 36009914 PMCID: PMC9404926 DOI: 10.3390/antibiotics11081045] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 02/04/2023] Open
Abstract
Acinetobacter baumannii is increasingly being recognized as a relevant pathogen for animals with a putative zoonotic impact. This study aimed at identifying and characterizing carbapenemase-producing A. baumannii from animals. Among 503 A. baumannii, mainly isolated from dogs/cats (75.7%) between 2013 and 2018, 42 isolates from 22 veterinary clinics (VCs) harboured blaOXA-58 (n = 29) or blaOXA-23 (n = 13). The blaOXA-58 gene was located on plasmids (11.4–21.1 kb) within different genetic surroundings (patterns A–D). BlaOXA-23 was embedded in Tn2006 on the chromosome (n = 4; pattern a) or Tn2008 on plasmids (n = 9; 41.2–71.3 kb; patterns b–e). The predominant IC1-ST1P-OXA-58 (66.7%; 96.4% cgMLST complex type (CT)-1808) was disseminated among 11 VCs in Germany. Resistance islands AbaR3-like (n = 15) and AbaR10 (n = 1) have emerged among ST1-isolates since 2016. IC7-ST25P-OXA-23 isolates (21.4%) occurred in seven VCs in Germany, France and Italy and differed in their resistance gene patterns from those of OXA-58 isolates. They were separated into six CTs, basically according to their regional origin. Other STs observed were ST10, ST578 and ST602. In conclusion, OXA-23 and OXA-58 were linked with ST1 and ST25, two globally distributed lineages in humans. The suggested transmission of certain lineages within and among VCs together with the acquisition of AbaR islands hints at a successful dissemination of multidrug-resistant strains in the VC environment.
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Unger F, Eisenberg T, Prenger-Berninghoff E, Leidner U, Semmler T, Ewers C. Imported Pet Reptiles and Their “Blind Passengers”—In-Depth Characterization of 80 Acinetobacter Species Isolates. Microorganisms 2022; 10:microorganisms10050893. [PMID: 35630338 PMCID: PMC9144363 DOI: 10.3390/microorganisms10050893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 11/16/2022] Open
Abstract
Reptiles are popular pet animals and important food sources, but the trade of this vertebrate class is—besides welfare and conservation—under debate due to zoonotic microbiota. Ninety-two shipments of live reptiles were sampled during border inspections at Europe’s most relevant transshipment point for the live animal trade. Acinetobacter spp. represented one significant fraction of potentially MDR bacteria that were further analyzed following non-selective isolation or selective enrichment from feces, urinate, or skin samples. Taxonomic positions of respective isolates were confirmed by MALDI-TOF MS and whole-genome sequencing analysis (GBDP, dDDH, ANIb, and rMLST). The majority of the 80 isolates represented established species; however, a proportion of potentially novel taxa was found. Antimicrobial properties and genome-resistance gene screening revealed novel and existing resistance mechanisms. Acinetobacter spp. strains were most often resistant to 6–10 substance groups (n = 63) in vitro. Resistance to fluorchinolones (n = 4) and colistin (n = 7), but not to carbapenems, was noted, and novel oxacillinase variants (n = 39) were detected among other genes. Phylogenetic analysis (MLST) assigned few isolates to the known STs (25, 46, 49, 220, and 249) and to a number of novel STs. No correlation was found to indicate that MDR Acinetobacter spp. in reptiles were associated with harvesting mode, e.g., captive-bred, wild-caught, or farmed in natural ecosystems. The community of Acinetobacter spp. in healthy reptiles turned out to be highly variable, with many isolates displaying a MDR phenotype or genotype.
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Affiliation(s)
- Franziska Unger
- Institute of Hygiene and Infectious Diseases of Animals, Faculty of Veterinary Medicine, Justus-Liebig University Giessen, 35392 Giessen, Germany; (F.U.); (E.P.-B.); (U.L.)
| | | | - Ellen Prenger-Berninghoff
- Institute of Hygiene and Infectious Diseases of Animals, Faculty of Veterinary Medicine, Justus-Liebig University Giessen, 35392 Giessen, Germany; (F.U.); (E.P.-B.); (U.L.)
| | - Ursula Leidner
- Institute of Hygiene and Infectious Diseases of Animals, Faculty of Veterinary Medicine, Justus-Liebig University Giessen, 35392 Giessen, Germany; (F.U.); (E.P.-B.); (U.L.)
| | - Torsten Semmler
- NG1 Microbial Genomics, Robert Koch Institute, 13353 Berlin, Germany;
| | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Faculty of Veterinary Medicine, Justus-Liebig University Giessen, 35392 Giessen, Germany; (F.U.); (E.P.-B.); (U.L.)
- Correspondence: ; Tel.: +49-641-9938300
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Davies YM, Franco LS, Barbosa FB, Vanin CL, Gomes VTM, Moreno LZ, Barbosa MRF, Sato MIZ, Moreno AM, Knöbl T. Use of MALDI-TOF for identification and surveillance of gram-negative bacteria in captive wild psittacines. BRAZ J BIOL 2021; 82:e233523. [PMID: 33787713 DOI: 10.1590/1519-6984.233523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 08/08/2020] [Indexed: 11/22/2022] Open
Abstract
Microbiological studies of the sanitary and health status of psittacine birds that will be reintroduced is important in evaluating whether these animals act as carriers of pathogenic agents to other animals and humans. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a faster and more accurate method to identify bacteria than conventional microbiology methods. The aim of this study was to evaluate the health status of psittacines housed in captivity, by assessment of Gram-negative bacteria from fecal microbiota through MALDI- TOF MS identification. The results indicate high frequency of Gram-negative bacteria in feces (96.5%), especially from the Enterobacteriaceae family (88.7%). The most prevalent bacteria were Escherichia coli (39.0%), Proteus vulgaris (12.2%), Klebsiella spp. (12.1%) and Raoultella ornithinolytica (8.7%). Proteus hauseri, Citrobacter spp., Morganella morgannii, Providencia rettgeri, Enterobacter spp. and Escherichia hermannii were isolated with lower frequency. . All these agents are potentially pathogenic for parrots and can cause systemic infections in other animals and humans. These findings reinforce that MALDI- TOF MS proved to be a rapid and accurate method of identification of the microorganism and evaluation of the health status of psittacines, providing relevant data to assist decision-making regarding the sanitary protocols in wildlife centers, and possible future reintroduction of wild birds.
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Affiliation(s)
- Y M Davies
- Universidade de São Paulo - USP, Departamento de Patologia da Faculdade de Medicina Veterinária e Zootecnia, São Paulo, SP, Brasil
| | - L S Franco
- Universidade de São Paulo - USP, Departamento de Patologia da Faculdade de Medicina Veterinária e Zootecnia, São Paulo, SP, Brasil
| | - F B Barbosa
- Universidade de São Paulo - USP, Departamento de Patologia da Faculdade de Medicina Veterinária e Zootecnia, São Paulo, SP, Brasil
| | - C L Vanin
- Departamento de Fauna da Secretaria de Infraestrutura e Meio Ambiente do estado de São Paulo, São Paulo, SP, Brasil
| | - V T M Gomes
- Universidade de São Paulo - USP, Departamento de Medicina Veterinária Preventiva e Saúde Animal da Faculdade de Medicina Veterinária e Zootecnia, São Paulo, SP, Brasil
| | - L Z Moreno
- Universidade de São Paulo - USP, Departamento de Medicina Veterinária Preventiva e Saúde Animal da Faculdade de Medicina Veterinária e Zootecnia, São Paulo, SP, Brasil
| | - M R F Barbosa
- Companhia Ambiental do Estado de São Paulo - CETESB, São Paulo, SP, Brasil
| | - M I Z Sato
- Companhia Ambiental do Estado de São Paulo - CETESB, São Paulo, SP, Brasil
| | - A M Moreno
- Universidade de São Paulo - USP, Departamento de Medicina Veterinária Preventiva e Saúde Animal da Faculdade de Medicina Veterinária e Zootecnia, São Paulo, SP, Brasil
| | - T Knöbl
- Universidade de São Paulo - USP, Departamento de Patologia da Faculdade de Medicina Veterinária e Zootecnia, São Paulo, SP, Brasil
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Łopińska A, Indykiewicz P, Skiebe E, Pfeifer Y, Trček J, Jerzak L, Minias P, Nowakowski J, Ledwoń M, Betleja J, Wilharm G. Low Occurrence of Acinetobacter baumannii in Gulls and Songbirds. Pol J Microbiol 2020; 69:1-6. [PMID: 32162853 PMCID: PMC7256842 DOI: 10.33073/pjm-2020-011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/24/2020] [Accepted: 02/11/2020] [Indexed: 12/24/2022] Open
Abstract
Acinetobacter baumannii is a worldwide occurring nosocomial pathogen, the natural habitats of which remain to be defined. Recently, white stork nestlings have been described as a recurring source of A. baumannii. Here, we challenged the hypothesis of a general preference of A. baumannii for avian hosts. Taking advantage of campaigns to ring free-living birds, we collected cloacal swab samples from 741 black-headed gulls (Chroicocephalus ridibundus) in Poland, tracheal and cloacal swabs from 285 songbirds in Poland as well as tracheal swabs from 25 songbirds in Slovenia and screened those for the growth of A. baumannii on CHROMagar™ Acinetobacter. Of the 1,051 samples collected only two yielded A. baumannii isolates. Each carried one variant of the blaOXA-51-like gene, i.e. OXA-71 and OXA-208, which have been described previously in clinical isolates of A. baumannii. In conclusion, our data do not support a general preference of A. baumannii for avian hosts.
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Affiliation(s)
- Andżelina Łopińska
- Robert Koch Institute , Wernigerode Branch, Wernigerode , Germany ; Institute of Biological Sciences , University of Zielona Góra , Zielona Góra , Poland
| | - Piotr Indykiewicz
- Department of Biology and Animal Environment , Faculty of Animal Breeding and Biology , UTP University of Science and Technology , Bydgoszcz , Poland
| | - Evelyn Skiebe
- Robert Koch Institute , Wernigerode Branch, Wernigerode , Germany
| | - Yvonne Pfeifer
- Robert Koch Institute , Wernigerode Branch, Wernigerode , Germany
| | - Janja Trček
- Department of Biology , Faculty of Natural Sciences and Mathematics , University of Maribor , Maribor , Slovenia
| | - Leszek Jerzak
- Institute of Biological Sciences , University of Zielona Góra , Zielona Góra , Poland
| | - Piotr Minias
- Department of Biodiversity Studies and Bioeducation , Faculty of Biology and Environmental Protection , University of Łódź , Łódź , Poland
| | - Jacek Nowakowski
- Department of Ecology and Environmental Protection , Faculty of Biology and Biotechnology , University of Warmia and Mazury in Olsztyn , Olsztyn , Poland
| | - Mateusz Ledwoń
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences , Kraków , Poland
| | - Jacek Betleja
- Upper Silesian Museum , Department of Natural History , Bytom , Poland
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6
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Malta RCR, Ramos GLDPA, Nascimento JDS. From food to hospital: we need to talk about Acinetobacter spp. Germs 2020; 10:210-217. [PMID: 33134199 DOI: 10.18683/germs.2020.1207] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 06/18/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023]
Abstract
Some species of the genus Acinetobacter are admittedly important hospital pathogens. Additionally, various animal and plant foods have been linked to the presence of Acinetobacter, including resistant strains. However, due to isolation difficulties and the lack of official standard methods, there is a dearth of work and epidemiological data on foodborne diseases caused by this microorganism. Considering that Acinetobacter spp. may represent a serious public health problem, especially because of their resistance to carbapenems and colistin, and because of the fact that these pathogens may transfer resistance genes to other bacteria, studies are needed to evaluate the pathogenicity of both food and clinical isolates and to search for them using control strategies, such as the adoption of more efficient disinfection measures and use of antimicrobial substances (AMS). In contrast, AMS production by strains of the genus Acinetobacter has already been described, and its potential for application against other Gram-negative food or clinical pathogens, reveals a new field to be explored.
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Affiliation(s)
- Rogerio Caldeira Rodrigues Malta
- Departamento de Microbiologia, Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro (IFRJ), Rua Senador Furtado, 121 - Laboratório 412 - Maracanã, Rio de Janeiro, RJ, CEP 20270-021, Brazil
| | - Gustavo Luis de Paiva Anciens Ramos
- MD, Departamento de Bromatologia, Faculdade de Farmácia, Universidade Federal Fluminense (UFF), Rua Doutor Mário Viana, 523 - Santa Rosa - Niterói, CEP 24241-002, Brazil
| | - Janaína Dos Santos Nascimento
- PhD, Departamento de Microbiologia, Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro (IFRJ), Rua Senador Furtado, 121 - Laboratório 412 - Maracanã, Rio de Janeiro, RJ, CEP 20270-021, Brazil
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Schwarz S, Mensing N, Hörmann F, Schneider M, Baumgärtner W. Polyarthritis Caused by Acinetobacter kookii in a Rothschild's Giraffe Calf (Giraffa camelopardalis rothschildi). J Comp Pathol 2020; 178:56-60. [PMID: 32800110 DOI: 10.1016/j.jcpa.2020.06.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 06/04/2020] [Accepted: 06/29/2020] [Indexed: 11/19/2022]
Abstract
We report the first isolation of Acinetobacter kookii from a Rothschild's giraffe calf (Giraffa camelopardalis rothschildi) that had severe polyarthritis. The isolate was resistant to more than one representative of each of four classes of antibiotics (penicillins, macrolides, lincosamides and tetracyclines). As A. kookii has not been previously associated with disease in humans or animals, it may be an emerging opportunistic pathogen posing a threat to immunocompromised patients. Furthermore, as transmission of Acinetobacter spp. with similar patterns of antimicrobial resistance has been previously reported in human and animal populations, special care should be taken when handling infected animals.
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Affiliation(s)
- S Schwarz
- Department of Pathology, University of Veterinary Medicine, Hannover, Germany
| | - N Mensing
- Veterinary Practice Dr. Niels Mensing, Magdeburg, Germany
| | - F Hörmann
- Veterinary Practice Dr. Niels Mensing, Magdeburg, Germany
| | - M Schneider
- LABOKLIN GMBH & CO.KG, Bad Kissingen, Germany
| | - W Baumgärtner
- Department of Pathology, University of Veterinary Medicine, Hannover, Germany.
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Narciso AC, Martins WMBS, Almeida LGP, Cayô R, Santos SV, Ramos PL, Lincopan N, Vasconcelos ATR, Gales AC. Healthcare-associated carbapenem-resistant OXA-72-producing Acinetobacter baumannii of the clonal complex CC79 colonizing migratory and captive aquatic birds in a Brazilian Zoo. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 726:138232. [PMID: 32304941 DOI: 10.1016/j.scitotenv.2020.138232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
Carbapenem resistance in Acinetobacter baumannii is a public health issue globally, mainly due to the production of carbapenem hydrolyzing class D β-lactamases (CHDLs). In Brazil, OXA-23 and OXA-143 CHDLs have been prevalent in A. baumannii from clinical settings, with some OXA-23 reports in the environmental samples, whereas OXA-72 has begun to be increasingly reported. This study aims to perform the genomic and microbiological characterization of carbapenem-resistant A. baumannii isolates recovered from migratory birds and captive birds inhabiting a lake within a Brazilian Zoo. Four hundred and eighty-one gram-negative bacilli were recovered from choanal and cloacal swabs obtained from 50 migratory birds and 37 captive birds present at the zoo's lake between July and August of 2012. Among all GNB, nine OXA-72-producing A. baumannii were detected from the microbiota of four migratory and five captive aquatic birds. The OXA-72-producing A. baumannii isolates were submitted to antimicrobial susceptibility test and PFGE, exhibiting a multidrug-resistant profile and clonal relatedness with OXA-72-positive human isolates circulating for eighteen years in a hospital setting. MLST, plasmid analysis and whole-genome sequencing revealed which all carbapenem-resistant A. baumannii from bird and human hosts belonged to clonal complex 79, and harboured a small plasmid (⁓16.6-kb in size), named pAC1-BRL, which carried blaOXA-72 gene, macrolide resistance genes msrE and mphE, and the toxin-antitoxin system AbkAB. To determine the impact of pAC1-BRL acquisition in the the capacity of a microorganism to survive in a competitive environment (in the following called fitness), the laboratory strain A. baumannii ATCC 19606 was used in the fitness experiments and suggested an increase of its relative fitness after the pAC1-BRL acquisition. In summary, the detection of OXA-72-producing A. baumannii strains belonging to CC79 in aquatic birds is a piece of epidemiological evidence demonstrating that dissemination of high-risk bacteria is extending beyond the hospital.
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Affiliation(s)
- Ana Clara Narciso
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo - UNIFESP, São Paulo, Brazil
| | - Willames M B S Martins
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo - UNIFESP, São Paulo, Brazil.
| | - Luiz G P Almeida
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica - LNCC, Petrópolis, Brazil
| | - Rodrigo Cayô
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo - UNIFESP, São Paulo, Brazil; Universidade Federal de São Paulo, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Departamento de Ciências Biológicas, Laboratório de Bacteriologia e Imunologia, Diadema, SP, Brazil
| | - Stéfanie Vanessa Santos
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo - UNIFESP, São Paulo, Brazil
| | - Patrícia Locosque Ramos
- Departamento de Pesquisas Aplicadas, Fundação Parque Zoológico de São Paulo - FPZSP, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo - USP, São Paulo, Brazil
| | - Ana Tereza R Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica - LNCC, Petrópolis, Brazil
| | - Ana Cristina Gales
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo - UNIFESP, São Paulo, Brazil
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The Current Burden of Carbapenemases: Review of Significant Properties and Dissemination among Gram-Negative Bacteria. Antibiotics (Basel) 2020; 9:antibiotics9040186. [PMID: 32316342 PMCID: PMC7235769 DOI: 10.3390/antibiotics9040186] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/29/2020] [Accepted: 04/01/2020] [Indexed: 11/16/2022] Open
Abstract
Carbapenemases are β-lactamases belonging to different Ambler classes (A, B, D) and can be encoded by both chromosomal and plasmid-mediated genes. These enzymes represent the most potent β-lactamases, which hydrolyze a broad variety of β-lactams, including carbapenems, cephalosporins, penicillin, and aztreonam. The major issues associated with carbapenemase production are clinical due to compromising the activity of the last resort antibiotics used for treating serious infections, and epidemiological due to their dissemination into various bacteria across almost all geographic regions. Carbapenemase-producing Enterobacteriaceae have received more attention upon their first report in the early 1990s. Currently, there is increased awareness of the impact of nonfermenting bacteria, such as Acinetobacter baumannii and Pseudomonas aeruginosa, as well as other Gram-negative bacteria that are carbapenemase-producers. Outside the scope of clinical importance, carbapenemases are also detected in bacteria from environmental and zoonotic niches, which raises greater concerns over their prevalence, and the need for public health measures to control consequences of their propagation. The aims of the current review are to define and categorize the different families of carbapenemases, and to overview the main lines of their spread across different bacterial groups.
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Jia H, Sun Q, Ruan Z, Xie X. Characterization of a small plasmid carrying the carbapenem resistance gene bla OXA-72 from community-acquired Acinetobacter baumannii sequence type 880 in China. Infect Drug Resist 2019; 12:1545-1553. [PMID: 31239730 PMCID: PMC6559137 DOI: 10.2147/idr.s202803] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/22/2019] [Indexed: 12/20/2022] Open
Abstract
Background Acinetobacter baumannii has emerged as an important pathogen associated with hospital- and community-acquired infections. Community-acquired A. baumannii pneumonia is characterized by a fulminant course and high mortality rates. In this study, we report the identification of a community-acquired carbapenem-resistant A. baumannii strain carrying the bla OXA-72 gene. Methods This A. baumannii isolate was recovered from a male patient diagnosed with community-acquired pneumonia, septic shock, and respiratory failure. Antimicrobial susceptibility testing were performed and the minimum inhibitory concentrations were determined by the broth microdilution method. Whole-genome sequencing was performed using both long-read MinION and short-read Illumina platforms to fully characterize the bla OXA-72-carrying plasmid of the A. baumannii A52. The in silico multilocus sequence typing and genomic epidemiological analysis of the closely related isolates were further elucidated by our recently updated BacWGSTdb server. Results The isolate was resistant to meropenem and remained susceptible to several other antimicrobial agents. Whole-genome sequencing and bioinformatics analysis indicated that this A. baumannii isolate belonged to the rare sporadic clone sequence type 880 and the bla OXA-72 gene was located on the 8,493-bp plasmid pA52-OXA-72. This plasmid exhibited only partial similarity to different OXA-72-encoding plasmids (size range: 8,771-12,056 bp) in various Acinetobacter spp. recovered from patients and other reservoirs in different countries. Conclusion This study described the first case of fulminant carbapenem-resistant community-acquired A. baumannii pneumonia caused by a rare sporadic clone in China. Adequate surveillance is warranted to monitor the emergence of A. baumannii as a community pathogen.
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Affiliation(s)
- Huiqiong Jia
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Qingyang Sun
- Department of Clinical Laboratory, The 117th hospital of People's Liberation Army, Hangzhou, People's Republic of China
| | - Zhi Ruan
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Xinyou Xie
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
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Püntener-Simmen S, Zurfluh K, Schmitt S, Stephan R, Nüesch-Inderbinen M. Phenotypic and Genotypic Characterization of Clinical Isolates Belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) Complex Isolated From Animals Treated at a Veterinary Hospital in Switzerland. Front Vet Sci 2019; 6:17. [PMID: 30805352 PMCID: PMC6370676 DOI: 10.3389/fvets.2019.00017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 01/17/2019] [Indexed: 11/25/2022] Open
Abstract
Objectives: We investigated a collection of strains belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex obtained from a veterinary clinic with regard to their genetic relatedness, presence of antibiotic resistance genes and antimicrobial susceptibility profiles. Methods: Fifty-eight ACB-complex strains from animals treated at a veterinary clinic between 2006 and 2017, and seven strains collected from the hospital environment during 2012 were analyzed. Assignment to sequence types (ST) and international complexes (IC) was done by multilocus sequence typing (MLST) according to the Pasteur scheme. Genes encoding carbapenemases, aminoglycoside-modifying enzymes, macrolide-, quinolone- and co-trimoxazole resistance genes, the ISAba1 element, virulence associated intI1 genes and plasmid associated toxin-antitoxin markers were identified by microarray. Genes encoding blaOXA−51-like carbapenemases were amplified by PCR and sequenced. Susceptibility profiles were determined by disc diffusion or by broth microdilution. Results: Among 50 A. baumannii isolates from animals, two predominant clones were observed linked to CC1 (n = 27/54% of the isolates) and CC25 (n = 14/28%), respectively. Strains of IC I harbored blaOXA−69, aac(3′)-la, aadA1, sul1, intI1, and splA/T genes. Isolates belonging to CC25 possessed blaOXA−64. Six (12%) isolates belonging to CC2 and carrying blaOXA−66 were also noted. One isolate belonged to CC10 (blaOXA−68), one to CC149 (blaOXA−104), the remaining isolate was assigned to ST1220 and possessed blaOXA−116. Of six environmental A. baumannii, four (66.7%) belonged to CC25 (blaOXA−64), one (16.7%) to CC2 (blaOXA−66) and one to CC3 (blaOXA−71). Nine isolates (eight from animals and one environmental strain) were non-baumannii strains and did not harbor blaOXA−51-like genes. None of the isolates carried blaOXA−23, blaOXA−48, or blaOXA−58, and none were resistant to carbapenems. Conclusions: Clonal lineages of the veterinary A. baumannii isolates in our collection are identical to those globally emerging in humans but do not harbor blaOXA−23. A. baumannii CC25 may be specific for this particular veterinary clinic environment.
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Affiliation(s)
- Sabrina Püntener-Simmen
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Katrin Zurfluh
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Sarah Schmitt
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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Wareth G, Neubauer H, Sprague LD. Acinetobacter baumannii - a neglected pathogen in veterinary and environmental health in Germany. Vet Res Commun 2018; 43:1-6. [PMID: 30591981 DOI: 10.1007/s11259-018-9742-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/06/2018] [Indexed: 01/01/2023]
Abstract
The emergence and global spread of drug resistant Acinetobacter (A.) baumannii is a cause of great concern. The current knowledge on antibiotic resistance in A. baumannii from animal origin is mostly based on few internationally published case reports, investigations of strain collections and several whole genome analyses. This lack of data results in a somewhat sketchy picture on how to assess the possible impact of drug resistant A. baumannii strains on veterinary and public health in Germany. Consequently, there is an urgent need to intensify the surveillance of A. baumannii in pet animals, the farm animal population and wildlife.
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Affiliation(s)
- Gamal Wareth
- Institut für bakterielle Infektionen und Zoonosen, Friedrich-Loeffler-Institut, Jena, Germany
| | - Heinrich Neubauer
- Institut für bakterielle Infektionen und Zoonosen, Friedrich-Loeffler-Institut, Jena, Germany
| | - Lisa D Sprague
- Institut für bakterielle Infektionen und Zoonosen, Friedrich-Loeffler-Institut, Jena, Germany.
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Acinetobacter in veterinary medicine, with an emphasis on Acinetobacter baumannii. J Glob Antimicrob Resist 2018; 16:59-71. [PMID: 30144636 DOI: 10.1016/j.jgar.2018.08.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 08/11/2018] [Accepted: 08/14/2018] [Indexed: 12/21/2022] Open
Abstract
Acinetobacter spp. are aerobic, rod-shaped, Gram-negative bacteria belonging to the Moraxellaceae family of the class Gammaproteobacteria and are considered ubiquitous organisms. Among them, Acinetobacter baumannii is the most clinically significant species with an extraordinary ability to accumulate antimicrobial resistance and to survive in the hospital environment. Recent reports indicate that A. baumannii has also evolved into a veterinary nosocomial pathogen. Although Acinetobacter spp. can be identified to species level using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS) coupled with an updated database, molecular techniques are still necessary for genotyping and determination of clonal lineages. It appears that the majority of infections due to A. baumannii in veterinary medicine are nosocomial. Such isolates have been associated with several types of infection such as canine pyoderma, feline necrotizing fasciitis, urinary tract infection, equine thrombophlebitis and lower respiratory tract infection, foal sepsis, pneumonia in mink, and cutaneous lesions in hybrid falcons. Given the potential multidrug resistance of A. baumannii, treatment of diseased animals is often supportive and should preferably be based on in vitro antimicrobial susceptibility testing results. It should be noted that animal isolates show high genetic diversity and are in general distinct in their sequence types and resistance patterns from those found in humans. However, it cannot be excluded that animals may occasionally play a role as a reservoir of A. baumannii. Thus, it is of importance to implement infection control measures in veterinary hospitals to avoid nosocomial outbreaks with multidrug-resistant A. baumannii.
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OXA-72-Mediated Carbapenem Resistance in Sequence Type 1 Multidrug (Colistin)-Resistant Acinetobacter baumannii Associated with Urinary Tract Infection in a Dog from Serbia. Antimicrob Agents Chemother 2018; 62:AAC.00219-18. [PMID: 29760134 DOI: 10.1128/aac.00219-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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