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Gaetano AS, Semeraro S, Greco S, Greco E, Cain A, Perrone MG, Pallavicini A, Licen S, Fornasaro S, Barbieri P. Bioaerosol Sampling Devices and Pretreatment for Bacterial Characterization: Theoretical Differences and a Field Experience in a Wastewater Treatment Plant. Microorganisms 2024; 12:965. [PMID: 38792794 PMCID: PMC11124041 DOI: 10.3390/microorganisms12050965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Studies on bioaerosol bacterial biodiversity have relevance in both ecological and health contexts, and molecular methods, such as 16S rRNA gene-based barcoded sequencing, provide efficient tools for the analysis of airborne bacterial communities. Standardized methods for sampling and analysis of bioaerosol DNA are lacking, thus hampering the comparison of results from studies implementing different devices and procedures. Three samplers that use gelatin filtration, swirling aerosol collection, and condensation growth tubes for collecting bioaerosol at an aeration tank of a wastewater treatment plant in Trieste (Italy) were used to determine the bacterial biodiversity. Wastewater samples were collected directly from the untreated sewage to obtain a true representation of the microbiological community present in the plant. Different samplers and collection media provide an indication of the different grades of biodiversity, with condensation growth tubes and DNA/RNA shieldTM capturing the richer bacterial genera. Overall, in terms of relative abundance, the air samples have a lower number of bacterial genera (64 OTUs) than the wastewater ones (75 OTUs). Using the metabarcoding approach to aerosol samples, we provide the first preliminary step toward the understanding of a significant diversity between different air sampling systems, enabling the scientific community to orient research towards the most informative sampling strategy.
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Affiliation(s)
- Anastasia Serena Gaetano
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
- INSTM National Interuniversity Consortium of Materials Science and Technology, Via G. Giusti, 9, 50121 Firenze, Italy
| | - Sabrina Semeraro
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
- INSTM National Interuniversity Consortium of Materials Science and Technology, Via G. Giusti, 9, 50121 Firenze, Italy
| | - Samuele Greco
- Department of Life Sciences, University of Trieste, Via L. Giorgieri, 5, 34127 Trieste, Italy;
| | - Enrico Greco
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
- INSTM National Interuniversity Consortium of Materials Science and Technology, Via G. Giusti, 9, 50121 Firenze, Italy
| | - Andrea Cain
- ACEGAS APS AMGA S.p.a., Via degli Alti Forni, 11, 34121 Trieste, Italy;
| | | | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via L. Giorgieri, 5, 34127 Trieste, Italy;
| | - Sabina Licen
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
| | - Stefano Fornasaro
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
| | - Pierluigi Barbieri
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
- INSTM National Interuniversity Consortium of Materials Science and Technology, Via G. Giusti, 9, 50121 Firenze, Italy
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Costa-Ribeiro A, Azinheiro S, Mota S, Prado M, Lamas A, Garrido-Maestu A. Assessment of the presence of Acinetobacter spp. resistant to β-lactams in commercial ready-to-eat salad samples. Food Microbiol 2024; 118:104410. [PMID: 38049272 DOI: 10.1016/j.fm.2023.104410] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 12/06/2023]
Abstract
Acinetobacter baumannii is a well-known nosocomial infection causing agent. However, other Acinetobacter spp. have also been implicated in cases of human infection. Additionally, these bacteria are known for the development of antibiotic resistance thus making the treatment of the infections they cause, challenging. Due to their relevance in clinical setups less attention has been paid to their presence in foods, and its relation with infection/dissemination routes. In the current study commercial Ready-To-Eat (RTE) salads were analyzed seeking for antibiotic resistant Acinetobacter spp. A preliminary screening allowed us to recover Gram-negative bacteria resistant to β - lactams using cefotaxime, third generation cephalosporins, as the selective agent, and this was followed by identification with CHROMagar™ Acinetobacter and 16S rDNA sequencing. Finally, the isolates identified as Acinetobacter spp. were reanalyzed by PCR to determine the presence of nine potential Extended Spectrum β Lactamases (ESBL). Two commercial RTE salad brands were included in the study (2 batches per brand and 8 samples of each batch making a total of 32 independent samples), and compared against an organic lettuce. High concentrations of β - lactam, resistant bacteria were found in all the samples tested (5 log CFU/g). Additionally, 209 isolates were phenotypically characterized on CHROMagar Acinetobacter. Finally, PCR analysis identified the presence of different ESBL genes, being positive for blaACC, blaSHV, blaDHA and blaVEB; out of these, blaACC was the most prevalent. None of the isolates screened were positive for more than one gene. To conclude, it is important to highlight the fact that pathogenic species within the genus Acinetobacter spp., other than A. baumannii, have been identified bearing resistance genes not typically associated to these microorganisms highlight the importance of continuous surveillance.
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Affiliation(s)
- Ana Costa-Ribeiro
- Health and Environment Research Center, School of Health, Polytechnic Institute of Porto, R. Dr. Roberto Frias 712, 4200-465, Porto, Portugal; International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal; Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
| | - Sarah Azinheiro
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal; College of Pharmacy/School of Veterinary Sciences, University of Santiago de Compostela, Campus Vida, E-15782, Santiago de Compostela, Spain
| | - Sandra Mota
- Health and Environment Research Center, School of Health, Polytechnic Institute of Porto, R. Dr. Roberto Frias 712, 4200-465, Porto, Portugal
| | - Marta Prado
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal; Food Hygiene, Inspection and Control Laboratory (Lhica), Department of Analytical Chemistry, Nutrition and Bromatology, Veterinary School, Campus Terra, University of Santiago de Compostela, 27002, Lugo, Spain
| | - Alexandre Lamas
- Food Hygiene, Inspection and Control Laboratory (Lhica), Department of Analytical Chemistry, Nutrition and Bromatology, Veterinary School, Campus Terra, University of Santiago de Compostela, 27002, Lugo, Spain.
| | - Alejandro Garrido-Maestu
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal.
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Li C, Nyaruaba R, Zhao X, Xue H, Li Y, Yang H, Wei H. Thermosensitive Hydrogel Wound Dressing Loaded with Bacteriophage Lysin LysP53. Viruses 2022; 14:v14091956. [PMID: 36146767 PMCID: PMC9502541 DOI: 10.3390/v14091956] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/14/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
Wound infections are prone to attacks from infectious pathogens, including multidrug resistant bacteria that render conventional antimicrobials ineffective. Recently, lysins have been proposed as alternatives to conventional antimicrobials to tackle the menace of multidrug resistance pathogens. The coupling of lysins with a material that will cover the wound may prove beneficial in both protecting and treating wound infections. Hence, in this study, a Gram-negative lysin, LysP53, was coupled with a thermosensitive hydrogel, poloxamer P407, and its efficacy to treat wound infection was tested. In vitro, the addition of LysP53 to the poloxamer did not affect its thermosensitive characteristics, nor did it affect the hydrogel structure. Moreover, the lysin hydrogel could hydrolyze the peptidoglycan, demonstrating that it may have bactericidal activity. Up to 10.4% of LysP53 was released from the hydrogel gradually within 24 h, which led to a 4-log reduction of stationary phase Acinetobacter baumannii. Lastly, the lysin hydrogel was found safe with no cytotoxic effects observed in cells. Ex vivo, LysP53 hydrogel could inhibit bacterial growth on a pig skin decolonization model, with 3-log differences compared to non-treated groups. Overall, our results suggest that lysin-loaded hydrogels may provide a novel solution to treat wound infections caused by resistant bacteria.
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Affiliation(s)
- Changchang Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Raphael Nyaruaba
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaowei Zhao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine, Ministry of Education, School of Stomatology, Wuhan University, Wuhan 430079, China
| | - Heng Xue
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhong Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine, Ministry of Education, School of Stomatology, Wuhan University, Wuhan 430079, China
| | - Hang Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: ; Tel.: +86-27-51861077
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Zurawski DV, Black CC, Alamneh YA, Biggemann L, Banerjee J, Thompson MG, Wise MC, Honnold CL, Kim RK, Paranavitana C, Shearer JP, Tyner SD, Demons ST. A Porcine Wound Model of Acinetobacter baumannii Infection. Adv Wound Care (New Rochelle) 2019; 8:14-27. [PMID: 30705786 PMCID: PMC6350066 DOI: 10.1089/wound.2018.0786] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/24/2018] [Indexed: 01/25/2023] Open
Abstract
Objective: To better understand Acinetobacter baumannii pathogenesis and to advance drug discovery against this pathogen, we developed a porcine, full-thickness, excisional, monospecies infection wound model. Approach: The research was facilitated with AB5075, a previously characterized, extensively drug-resistant A. baumannii isolate. The model requires cyclophosphamide-induced neutropenia to establish a skin and soft tissue infection (SSTI) that persists beyond 7 days. Multiple, 12-mm-diameter full-thickness wounds were created in the skin overlying the cervical and thoracic dorsum. Wound beds were inoculated with 5.0 × 104 colony-forming units (CFU) and covered with dressing. Results:A. baumannii was observed in the wound bed and on the dressing in what appeared to be biofilm. When bacterial burdens were measured, proliferation to at least 106 CFU/g (log106) wound tissue was observed. Infection was further characterized by scanning electron microscopy (SEM) and peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) staining. To validate as a treatment model, polymyxin B was applied topically to a subset of infected wounds every 2 days. Then, the treated and untreated wounds were compared using multiple quantitative and qualitative techniques to include gross pathology, CFU burden, histopathology, PNA-FISH, and SEM. Innovation: This is the first study to use A. baumannii in a porcine model as the sole infectious agent. Conclusion: The porcine model allows for an additional preclinical assessment of antibacterial candidates that show promise against A. baumannii in rodent models, further evaluating safety and efficacy, and serve as a large animal in preclinical assessment for the treatment of SSTI.
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Affiliation(s)
- Daniel V. Zurawski
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Chad C. Black
- Experimental Therapeutics Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Yonas A. Alamneh
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Lionel Biggemann
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Jaideep Banerjee
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Mitchell G. Thompson
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Matthew C. Wise
- Veterinary Services Program, Department of Pathology, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Cary L. Honnold
- Veterinary Services Program, Department of Pathology, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Robert K. Kim
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Chrysanthi Paranavitana
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Jonathan P. Shearer
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Stuart D. Tyner
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Samandra T. Demons
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
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Ramanathan S, Arunachalam K, Chandran S, Selvaraj R, Shunmugiah K, Arumugam V. Biofilm inhibitory efficiency of phytol in combination with cefotaxime against nosocomial pathogen Acinetobacter baumannii. J Appl Microbiol 2018; 125:56-71. [DOI: 10.1111/jam.13741] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 02/11/2018] [Accepted: 02/18/2018] [Indexed: 12/29/2022]
Affiliation(s)
- S. Ramanathan
- Department of Biotechnology; Science Campus; Alagappa University; Karaikudi Tamil Nadu India
| | - K. Arunachalam
- Department of Biotechnology; Science Campus; Alagappa University; Karaikudi Tamil Nadu India
| | - S. Chandran
- Department of Biotechnology; Science Campus; Alagappa University; Karaikudi Tamil Nadu India
| | - R. Selvaraj
- Department of Biotechnology; Science Campus; Alagappa University; Karaikudi Tamil Nadu India
| | - K.P. Shunmugiah
- Department of Biotechnology; Science Campus; Alagappa University; Karaikudi Tamil Nadu India
| | - V.R. Arumugam
- Department of Biotechnology; Science Campus; Alagappa University; Karaikudi Tamil Nadu India
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Silva AS, Quintelas C, Ferreira EC, Lopes JA, Sousa C. Exploiting intrinsic fluorescence spectroscopy to discriminate between Acinetobacter calcoaceticus–Acinetobacter baumannii complex species. RSC Adv 2017. [DOI: 10.1039/c6ra27531a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Spectroscopy for bacterial typing purposes. Instrisinc fluorescence versus FTIR-ATR and MALDI-TOF MS.
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Affiliation(s)
- Ana Sofia Silva
- CEB-Centre of Biological Engineering
- University of Minho
- Braga
- Portugal
| | | | | | - João A. Lopes
- Research Institute for Medicines (iMed.ULisboa)
- Faculdade de Farmácia
- Universidade de Lisboa
- Lisboa
- Portugal
| | - Clara Sousa
- LAQV/REQUIMTE
- Departamento de Ciências Químicas
- Faculdade de Farmácia
- Universidade do Porto
- 4050-313 Porto
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Genomic and phenotypic characterization of the species Acinetobacter venetianus. Sci Rep 2016; 6:21985. [PMID: 26902269 PMCID: PMC4763211 DOI: 10.1038/srep21985] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/01/2016] [Indexed: 11/10/2022] Open
Abstract
Crude oil is a complex mixture of hydrocarbons and other organic compounds that can produce serious environmental problems and whose removal is highly demanding in terms of human and technological resources. The potential use of microbes as bioremediation agents is one of the most promising fields in this area. Members of the species Acinetobacter venetianus have been previously characterized for their capability to degrade n-alkanes and thus may represent interesting model systems to implement this process. Although a preliminary experimental characterization of the overall hydrocarbon degradation capability has been performed for five of them, to date, the genetic/genomic features underlying such molecular processes have not been identified. Here we have integrated genomic and phenotypic information for six A. venetianus strains, i.e. VE-C3, RAG-1T, LUH 13518, LUH 7437, LUH 5627 and LUH 8758. Besides providing a thorough description of the A. venetianus species, these data were exploited to infer the genetic features (presence/absence patterns of genes) and the short-term evolutionary events possibly responsible for the variability in n-alkane degradation efficiency of these strains, including the mechanisms of interaction with the fuel droplet and the subsequent catabolism of this pollutant.
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Grosso F, Silva L, Sousa C, Ramos H, Quinteira S, Peixe L. Extending the reservoir of bla IMP-5: the emerging pathogen Acinetobacter bereziniae. Future Microbiol 2015; 10:1609-13. [PMID: 26439605 DOI: 10.2217/fmb.15.88] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Acinetobacter bereziniae clinical relevance is starting to be recognized; however, very few descriptions of its carbapenem resistance currently exist. Here we characterize two carbapenem-resistant A. bereziniae isolates. MATERIALS & METHODS Isolates were obtained from environmental and clinical samples. Carbapenemases were searched by phenotypic, biochemical and PCR assays. Clonality was studied by ApaI-PFGE and genetic location for carbapenemase genes were assessed by I-CeuI and S1 hybridizations. RESULTS Isolates were not clonally related but both produced the 'exclusively Portuguese' IMP-5, with the clinical isolate also producing an OXA-58. The carbapenemase genes were plasmid located. CONCLUSION Our results emphasize the role of non-baumannii Acinetobacter species as important reservoirs of clinically relevant resistance genes that could also contribute to their emergence as nosocomial pathogens.
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Affiliation(s)
- Filipa Grosso
- UCIBIO-REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Liliana Silva
- UCIBIO-REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal.,Escola Superior de Saúde Dr. Lopes Dias, Instituto Politécnico de Castelo Branco, Castelo Branco, Portugal
| | - Clara Sousa
- CEB- Centro de Engenharia Biológica, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Helena Ramos
- Hospital Geral de Santo António, Porto, Portugal
| | - Sandra Quinteira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos. Universidade do Porto (CIBIO/UP)/InBio Laboratório Associado, Vairão, Portugal.,Faculdade de Ciências da Universidade do Porto, Departamento de Biologia, Porto, Portugal.,CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Gandra PRD, Portugal
| | - Luísa Peixe
- UCIBIO-REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
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Stojowska K, Krawczyk B. A new double digestion ligation mediated suppression PCR method for simultaneous bacteria DNA-typing and confirmation of species: an Acinetobacter sp. model. PLoS One 2014; 9:e115181. [PMID: 25522278 PMCID: PMC4270756 DOI: 10.1371/journal.pone.0115181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 11/19/2014] [Indexed: 11/18/2022] Open
Abstract
We have designed a new ddLMS PCR (double digestion Ligation Mediated Suppression PCR) method based on restriction site polymorphism upstream from the specific target sequence for the simultaneous identification and differentiation of bacterial strains. The ddLMS PCR combines a simple PCR used for species or genus identification and the LM PCR strategy for strain differentiation. The bacterial identification is confirmed in the form of the PCR product(s), while the length of the PCR product makes it possible to differentiate between bacterial strains. If there is a single copy of the target sequence within genomic DNA, one specific PCR product is created (simplex ddLMS PCR), whereas for multiple copies of the gene the fingerprinting patterns can be obtained (multiplex ddLMS PCR). The described ddLMS PCR method is designed for rapid and specific strain differentiation in medical and microbiological studies. In comparison to other LM PCR it has substantial advantages: enables specific species' DNA-typing without the need for pure bacterial culture selection, is not sensitive to contamination with other cells or genomic DNA, and gives univocal "band-based" results, which are easy to interpret. The utility of ddLMS PCR was shown for Acinetobacter calcoaceticus-baumannii (Acb) complex, the genetically closely related and phenotypically similar species and also important nosocomial pathogens, for which currently, there are no recommended methods for screening, typing and identification. In this article two models are proposed: 3' recA-ddLMS PCR-MaeII/RsaI for Acb complex interspecific typing and 5' rrn-ddLMS PCR-HindIII/ApaI for Acinetobacter baumannii intraspecific typing. ddLMS PCR allows not only for DNA-typing but also for confirmation of species in one reaction. Also, practical guidelines for designing a diagnostic test based on ddLMS PCR for genotyping different species of bacteria are provided.
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Affiliation(s)
- Karolina Stojowska
- Department of Microbiology, Faculty of Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Beata Krawczyk
- Department of Microbiology, Faculty of Chemistry, Gdansk University of Technology, Gdansk, Poland
- * E-mail:
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Donelli G, Vuotto C. Biofilm-based infections in long-term care facilities. Future Microbiol 2014; 9:175-88. [PMID: 24571072 DOI: 10.2217/fmb.13.149] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The recent trend in the early admittance to long-term care facilities (LTCFs) of severely injured patients transferred from general hospitals has given a new dynamic to the incidence of healthcare-associated infections, including biofilm-based infections related to the implant of urinary and intravascular catheters, and the onset of pressure ulcers. Catheter-associated urinary tract infections lead in most of the surveys on LTCFs, approximately 80% of urinary tract infections in these settings being due to the short- or long-term insertion of a urinary catheter. Furthermore, the implantation of intravascular catheters is often responsible for catheter-related bloodstream infections caused by the development of an intraluminal biofilm. Pressure ulcers, frequently occurring in bedridden patients admitted to LTCFs, are also susceptible to infection by biofilm-growing aerobic and anaerobic bacteria, the biofilm formation on the wound being the main reason for its delayed healing.
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Identification of Acinetobacter baumannii serum-associated antibiotic efflux pump inhibitors. Antimicrob Agents Chemother 2014; 58:6360-70. [PMID: 25114126 DOI: 10.1128/aac.03535-14] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Adaptive antibiotic resistance is a newly described phenomenon by which Acinetobacter baumannii induces efflux pump activity in response to host-associated environmental cues that may, in part, account for antibiotic treatment failures against clinically defined susceptible strains. To that end, during adaptation to growth in human serum, the organism induces approximately 22 putative efflux-associated genes and displays efflux-mediated minocycline tolerance at antibiotic concentrations corresponding to patient serum levels. Here, we show that in addition to minocycline, growth in human serum elicits A. baumannii efflux-mediated tolerance to the antibiotics ciprofloxacin, meropenem, tetracycline, and tigecycline. Moreover, using a whole-cell high-throughput screen and secondary assays, we identified novel serum-associated antibiotic efflux inhibitors that potentiated the activities of antibiotics toward serum-grown A. baumannii. Two compounds, Acinetobacter baumannii efflux pump inhibitor 1 (ABEPI1) [(E)-4-((4-chlorobenzylidene)amino)benezenesulfonamide] and ABEPI2 [N-tert-butyl-2-(1-tert-butyltetrazol-5-yl)sulfanylacetamide], were shown to lead to minocycline accumulation within A. baumannii during serum growth and inhibit the efflux potential of the organism. While both compounds also inhibited the antibiotic efflux properties of the bacterial pathogen Pseudomonas aeruginosa, they did not display significant cytotoxicity toward human cells or mammalian Ca(2+) channel inhibitory effects, suggesting that ABEPI1 and ABEPI2 represent promising structural scaffolds for the development of new classes of bacterial antibiotic efflux pump inhibitors that can be used to potentiate the activities of current and future antibiotics for the therapeutic intervention of Gram-negative bacterial infections.
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MALDI-TOF MS and chemometric based identification of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex species. Int J Med Microbiol 2014; 304:669-77. [PMID: 24877727 DOI: 10.1016/j.ijmm.2014.04.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 03/07/2014] [Accepted: 04/27/2014] [Indexed: 11/21/2022] Open
Abstract
MALDI-TOF MS is becoming the technique of choice for rapid bacterial identification at species level in routine diagnostics. However, some drawbacks concerning the identification of closely related species such as those belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii (Acb) complex lead to high rates of misidentifications. In this work we successfully developed an approach that combines MALDI-TOF MS and chemometric tools to discriminate the six Acb complex species (A. baumannii, Acinetobacter nosocomialis, Acinetobacter pittii, A. calcoaceticus, genomic species "Close to 13TU" and genomic species "Between 1 and 3"). Mass spectra of 83 taxonomically well characterized clinical strains, reflecting the breadth of currently known phenetic diversity within the Acb complex, were achieved from intact cells and cell extracts and analyzed with hierarchical cluster analysis (HCA) and partial least squares discriminant analysis (PLSDA). This combined approach lead to 100% of correct species identification using mass spectra obtained from intact cells. Moreover, it was possible to discriminate two Acb complex species (genomic species "Close to 13TU" and genomic species "Between 1 and 3") not included in the MALDI Biotyper database.
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Sousa C, Silva L, Grosso F, Lopes J, Peixe L. Development of a FTIR-ATR based model for typing clinically relevant Acinetobacter baumannii clones belonging to ST98, ST103, ST208 and ST218. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 133:108-14. [PMID: 24727403 DOI: 10.1016/j.jphotobiol.2014.02.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 02/13/2014] [Accepted: 02/22/2014] [Indexed: 11/16/2022]
Abstract
In this work we developed and validated a FTIR-ATR (Fourier transform infrared spectroscopy with attenuated total reflectance) based model for typing Acinetobacter baumannii clinical isolates belonging to ST98, ST208 and ST218 included into the worldwide spread clonal complex (CC) 92 and ST103. FTIR-ATR spectra of seventy-seven previously characterized isolates (Multi Locus Sequence Type-MLST, Pulsed-Field Gel Electrophoresis-PFGE and carbapenem-hydrolyzing class D β-lactamase-CHDL) were acquired and modeled by partial least squares discriminant analysis (PLSDA). The model was tested and successfully validated with a diverse collection of isolates (n=148) recovered from different countries and periods of time belonging to modeled and non-modeled STs.
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Affiliation(s)
- Clara Sousa
- REQUIMTE, Microbiology Laboratory, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, R. Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
| | - Liliana Silva
- REQUIMTE, Microbiology Laboratory, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, R. Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Filipa Grosso
- REQUIMTE, Microbiology Laboratory, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, R. Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - João Lopes
- REQUIMTE, Applied Chemistry Laboratory, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, R. Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Luísa Peixe
- REQUIMTE, Microbiology Laboratory, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, R. Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
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Validation of a novel murine wound model of Acinetobacter baumannii infection. Antimicrob Agents Chemother 2013; 58:1332-42. [PMID: 24342634 DOI: 10.1128/aac.01944-13] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Patients recovering from traumatic injuries or surgery often require weeks to months of hospitalization, increasing the risk for wound and surgical site infections caused by ESKAPE pathogens, which include A. baumannii (the ESKAPE pathogens are Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species). As new therapies are being developed to counter A. baumannii infections, animal models are also needed to evaluate potential treatments. Here, we present an excisional, murine wound model in which a diminutive inoculum of a clinically relevant, multidrug-resistant A. baumannii isolate can proliferate, form biofilms, and be effectively treated with antibiotics. The model requires a temporary, cyclophosphamide-induced neutropenia to establish an infection that can persist. A 6-mm-diameter, full-thickness wound was created in the skin overlying the thoracic spine, and after the wound bed was inoculated, it was covered with a dressing for 7 days. Uninoculated control wounds healed within 13 days, whereas infected, placebo-treated wounds remained unclosed beyond 21 days. Treated and untreated wounds were assessed with multiple quantitative and qualitative techniques that included gross pathology, weight loss and recovery, wound closure, bacterial burden, 16S rRNA community profiling, histopathology, peptide nucleic acid-fluorescence in situ hybridization, and scanning electron microscopy assessment of biofilms. The range of differences that we are able to identify with these measures in antibiotic- versus placebo-treated animals provides a clear window within which novel antimicrobial therapies can be assessed. The model can be used to evaluate antimicrobials for their ability to reduce specific pathogen loads in wounded tissues and clear biofilms. Ultimately, the mouse model approach allows for highly powered studies and serves as an initial multifaceted in vivo assessment prior to testing in larger animals.
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Chan JZM, Halachev MR, Loman NJ, Constantinidou C, Pallen MJ. Defining bacterial species in the genomic era: insights from the genus Acinetobacter. BMC Microbiol 2012; 12:302. [PMID: 23259572 PMCID: PMC3556118 DOI: 10.1186/1471-2180-12-302] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 12/18/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microbial taxonomy remains a conservative discipline, relying on phenotypic information derived from growth in pure culture and techniques that are time-consuming and difficult to standardize, particularly when compared to the ease of modern high-throughput genome sequencing. Here, drawing on the genus Acinetobacter as a test case, we examine whether bacterial taxonomy could abandon phenotypic approaches and DNA-DNA hybridization and, instead, rely exclusively on analyses of genome sequence data. RESULTS In pursuit of this goal, we generated a set of thirteen new draft genome sequences, representing ten species, combined them with other publically available genome sequences and analyzed these 38 strains belonging to the genus. We found that analyses based on 16S rRNA gene sequences were not capable of delineating accepted species. However, a core genome phylogenetic tree proved consistent with the currently accepted taxonomy of the genus, while also identifying three misclassifications of strains in collections or databases. Among rapid distance-based methods, we found average-nucleotide identity (ANI) analyses delivered results consistent with traditional and phylogenetic classifications, whereas gene content based approaches appear to be too strongly influenced by the effects of horizontal gene transfer to agree with previously accepted species. CONCLUSION We believe a combination of core genome phylogenetic analysis and ANI provides an appropriate method for bacterial species delineation, whereby bacterial species are defined as monophyletic groups of isolates with genomes that exhibit at least 95% pair-wise ANI. The proposed method is backwards compatible; it provides a scalable and uniform approach that works for both culturable and non-culturable species; is faster and cheaper than traditional taxonomic methods; is easily replicable and transferable among research institutions; and lastly, falls in line with Darwin's vision of classification becoming, as far as is possible, genealogical.
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Affiliation(s)
- Jacqueline Z-M Chan
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Mihail R Halachev
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Chrystala Constantinidou
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Mark J Pallen
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
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Chen Z, Liu W, Zhang Y, Li Y, Jian Z, Deng H, Zou M, Liu Y. Molecular epidemiology of carbapenem-resistantAcinetobacterspp. from XiangYa Hospital, in Hunan Province, China. J Basic Microbiol 2012; 53:121-7. [PMID: 22581767 DOI: 10.1002/jobm.201100420] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 12/12/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Zhenhua Chen
- Department of Clinical Laboratory; Xiangya Hospital of Central South University; Changsha; China
| | - Wenen Liu
- Department of Clinical Laboratory; Xiangya Hospital of Central South University; Changsha; China
| | - Yunli Zhang
- Department of Clinical Laboratory; Xiangya Hospital of Central South University; Changsha; China
| | - Yanbing Li
- Department of Clinical Laboratory; Xiangya Hospital of Central South University; Changsha; China
| | - Zijuan Jian
- Department of Clinical Laboratory; Xiangya Hospital of Central South University; Changsha; China
| | - Hongli Deng
- Department of Clinical Laboratory; Xiangya Hospital of Central South University; Changsha; China
| | - Mingxiang Zou
- Department of Clinical Laboratory; Xiangya Hospital of Central South University; Changsha; China
| | - Yuanyuan Liu
- Department of Clinical Laboratory; Xiangya Hospital of Central South University; Changsha; China
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Grosso F, Quinteira S, Peixe L. Understanding the dynamics of imipenem-resistant Acinetobacter baumannii lineages within Portugal. Clin Microbiol Infect 2011; 17:1275-9. [PMID: 21375660 DOI: 10.1111/j.1469-0691.2011.03469.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A recent collection of 213 imipenem-resistant Acinetobacter baumannii (IRAB) clinical isolates was characterized for the presence of acquired carbapenem-hydrolysing class D β-lactamases (CHDLs) and clonality. A population structure analysis of IRAB was also conducted, with five molecular typing methods. Three main clusters, each one associated with a specific CHDL, were observed with multilocus sequence typing. Overall, our results suggest a switch in the dominant clone, with sequence type (ST) 92, carrying bla(OXA-23) (63.4%), replacing the closely related ST98, carrying bla(OXA-24/40) (22%). In addition, ST103, an independent lineage, was associated with bla(OXA-58) -carrying isolates (14.6%).
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Affiliation(s)
- F Grosso
- REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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