1
|
Afonso AC, Botting J, Gomes IB, Saavedra MJ, Simões LC, Liu J, Simões M. Elucidating bacterial coaggregation through a physicochemical and imaging surface characterization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174872. [PMID: 39032752 DOI: 10.1016/j.scitotenv.2024.174872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/10/2024] [Accepted: 07/16/2024] [Indexed: 07/23/2024]
Abstract
Bacterial coaggregation is a highly specific type of cell-cell interaction, well-documented among oral bacteria, and involves specific characteristics of the cell surface of the coaggregating strains. However, the understanding of the mechanisms promoting coaggregation in aquatic systems remains limited. This gap is critical to address, given the broad implications of coaggregation for multispecies biofilm formation, water quality, the performance of engineered systems, and diverse biotechnological applications. Therefore, this study aims to comprehensively characterize the cell surface of the coaggregating strain Delftia acidovorans 005P, isolated from drinking water, alongside a non-coaggregating strain, D. acidovorans 009P. By analyzing two strains of the same species, we aim to identify the factors contributing to the coaggregation ability of strain 005P. To achieve this, we employed a combination of physicochemical characterization, Fourier-transform infrared spectroscopy (FTIR), and advancing imaging techniques [transmission electron microscopy and cryo-electron tomography (cryo-ET)]. The coaggregating strain (005P) exhibited higher surface hydrophobicity, negative surface charge, and cell surface and co-adhesion energies than the non-coaggregating strain (009P). The chemical characterization of bacterial surfaces through FTIR revealed subtle differences, particularly in spectral regions linked to carbohydrates and phosphodiesters/amide III of proteins (860-930 cm-1 and 1212-1240 cm-1, respectively). Cryo-ET highlighted significant differences in pili structures between the strains, such as variations in length, frequency, and arrangement. The pili in the 005P strain, identified as pili-like adhesins, serve as key mediators of coaggregation. By integrating physicochemical analyses and high-resolution imaging techniques, this study conclusively links the coaggregation ability of D. acidovorans 005P to its unique pili characteristics, emphasizing their crucial role in microbial coaggregation in aquatic environments.
Collapse
Affiliation(s)
- Ana C Afonso
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal; ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal; CITAB, Department of Veterinary Sciences, University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal; CEB-LABBELS, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Jack Botting
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, United States; New Haven Microbial Sciences Institute, Yale University, West Haven, CT 06516, United States
| | - Inês B Gomes
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal; ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal
| | - Maria J Saavedra
- CITAB, Department of Veterinary Sciences, University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal
| | - Lúcia C Simões
- CEB-LABBELS, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, United States; New Haven Microbial Sciences Institute, Yale University, West Haven, CT 06516, United States
| | - Manuel Simões
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal; ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal.
| |
Collapse
|
2
|
Novais Â, Gonçalves AB, Ribeiro TG, Freitas AR, Méndez G, Mancera L, Read A, Alves V, López-Cerero L, Rodríguez-Baño J, Pascual Á, Peixe L. Development and validation of a quick, automated, and reproducible ATR FT-IR spectroscopy machine-learning model for Klebsiella pneumoniae typing. J Clin Microbiol 2024; 62:e0121123. [PMID: 38284762 PMCID: PMC10865814 DOI: 10.1128/jcm.01211-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/18/2023] [Indexed: 01/30/2024] Open
Abstract
The reliability of Fourier-transform infrared (FT-IR) spectroscopy for Klebsiella pneumoniae typing and outbreak control has been previously assessed, but issues remain in standardization and reproducibility. We developed and validated a reproducible FT-IR with attenuated total reflectance (ATR) workflow for the identification of K. pneumoniae lineages. We used 293 isolates representing multidrug-resistant K. pneumoniae lineages causing outbreaks worldwide (2002-2021) to train a random forest classification (RF) model based on capsular (KL)-type discrimination. This model was validated with 280 contemporaneous isolates (2021-2022), using wzi sequencing and whole-genome sequencing as references. Repeatability and reproducibility were tested in different culture media and instruments throughout time. Our RF model allowed the classification of 33 capsular (KL)-types and up to 36 clinically relevant K. pneumoniae lineages based on the discrimination of specific KL- and O-type combinations. We obtained high rates of accuracy (89%), sensitivity (88%), and specificity (92%), including from cultures obtained directly from the clinical sample, allowing to obtain typing information the same day bacteria are identified. The workflow was reproducible in different instruments throughout time (>98% correct predictions). Direct colony application, spectral acquisition, and automated KL prediction through Clover MS Data analysis software allow a short time-to-result (5 min/isolate). We demonstrated that FT-IR ATR spectroscopy provides meaningful, reproducible, and accurate information at a very early stage (as soon as bacterial identification) to support infection control and public health surveillance. The high robustness together with automated and flexible workflows for data analysis provide opportunities to consolidate real-time applications at a global level. IMPORTANCE We created and validated an automated and simple workflow for the identification of clinically relevant Klebsiella pneumoniae lineages by FT-IR spectroscopy and machine-learning, a method that can be extremely useful to provide quick and reliable typing information to support real-time decisions of outbreak management and infection control. This method and workflow is of interest to support clinical microbiology diagnostics and to aid public health surveillance.
Collapse
Affiliation(s)
- Ângela Novais
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ana Beatriz Gonçalves
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Teresa G. Ribeiro
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- CCP, Culture Collection of Porto, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ana R. Freitas
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
| | - Gema Méndez
- CLOVER Bioanalytical Software, Granada, Spain
| | | | - Antónia Read
- Clinical Microbiology Laboratory, Local Healthcare Unit, Matosinhos, Portugal
| | - Valquíria Alves
- Clinical Microbiology Laboratory, Local Healthcare Unit, Matosinhos, Portugal
| | - Lorena López-Cerero
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Vírgen Macarena, Instituto de Biomedicina de Sevilla (IBIS; CSIC/Hospital Virgen Macarena/Universidad de Sevilla), Sevilla, Spain
- Departamentos de Microbiología y Medicina, Universidad de Sevilla, Sevilla, Spain
| | - Jesús Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Vírgen Macarena, Instituto de Biomedicina de Sevilla (IBIS; CSIC/Hospital Virgen Macarena/Universidad de Sevilla), Sevilla, Spain
- Departamentos de Microbiología y Medicina, Universidad de Sevilla, Sevilla, Spain
| | - Álvaro Pascual
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Vírgen Macarena, Instituto de Biomedicina de Sevilla (IBIS; CSIC/Hospital Virgen Macarena/Universidad de Sevilla), Sevilla, Spain
- Departamentos de Microbiología y Medicina, Universidad de Sevilla, Sevilla, Spain
| | - Luísa Peixe
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- CCP, Culture Collection of Porto, Faculty of Pharmacy, University of Porto, Porto, Portugal
| |
Collapse
|
3
|
Eales BM, Bai B, Merlau PR, Tam VH. Growth of Acinetobacter baumannii impacted by iron chelation. Lett Appl Microbiol 2023; 76:ovad019. [PMID: 36731874 PMCID: PMC9990167 DOI: 10.1093/lambio/ovad019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/26/2023] [Accepted: 02/01/2023] [Indexed: 02/04/2023]
Abstract
Acinetobacter baumannii (AB) has become multidrug-resistant (MDR) in recent years, and, currently, there are limited effective treatment options. Nutrient metals (e.g. iron) are essential to the metabolic functions of AB. This study examined the impact of iron chelation on the growth of AB in vitro and in vivo. Susceptible and MDR-AB bloodstream isolates (n = 9) were recovered from different patients between 2011 and 2018. Clonal diversity was ascertained by Fourier-transform infrared spectroscopy. In vitro bacterial densities were measured over 20 h to determine growth profiles. Variable amounts of a chelating agent [deferiprone (DFP)] were added to create a concentration gradient. Galleria mellonella larvae were inoculated with an isolate, with and without DFP. Quantitative culture was used to ascertain the bacterial burden of aggregate larvae immediately and 4 h post-infection. Increasing concentrations of DFP caused a transient and concentration-dependent hindrance to in vitro growth, compared to the no-treatment group. In vivo bacterial burden immediately post-infection in both groups was comparable. After 4 h, the burden was much higher in the control group comparatively (8.7 and 6.7 log CFU g-1). These results support that micro-nutrient limitation has the potential of being a novel approach for treating high-risk infections due to MDR-AB.
Collapse
Affiliation(s)
- Brianna M Eales
- Department of Pharmacy Practice and Translational Research, University of Houston, Houston, TX 77204, USA
| | - Bing Bai
- Department of Pharmacy Practice and Translational Research, University of Houston, Houston, TX 77204, USA
- Department of Infectious Diseases and Shenzhen Key Laboratory for Endogenous Infections, The 6th Affiliated Hospital of Shenzhen University Health Center, Shenzhen, Guangdong 518052, China
| | - Paul R Merlau
- Department of Pharmacy Practice and Translational Research, University of Houston, Houston, TX 77204, USA
| | - Vincent H Tam
- Department of Pharmacy Practice and Translational Research, University of Houston, Houston, TX 77204, USA
| |
Collapse
|
4
|
Lombardo D, Cordovana M, Deidda F, Pane M, Ambretti S. Application of Fourier transform infrared spectroscopy for real-time typing of Acinetobacter baumannii outbreak in intensive care unit. Future Microbiol 2021; 16:1239-1250. [PMID: 34674538 DOI: 10.2217/fmb-2020-0276] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Acinetobacter baumannii is a pathogen of serious concern, often exhibiting multiple antibiotic resistance, frequently associated with hospital outbreaks in intensive care units. A prompt detection and tracking of these isolates is crucial. Reference methods for typing (pulsed-field gel electrophoresis, whole-genome sequencing) are accurate, but expensive and time-consuming, therefore limited to retrospective analysis. Materials & methods: In this study, the application of the FTIR-based IR Biotyper® (IRBT) to track and monitor in real-time the spread of a multidrug-resistant A. baumannii outbreak was investigated. The index case and the multidrug-resistant A. baumannii isolates collected in the following 3 weeks were investigated. Results: IR Biotyper® clustering results were fully confirmed by pulsed-field gel electrophoresis results. Conclusions: IR Biotyper represent a promising tool for real-time hospital hygiene, enabling a prompt and reliable typing.
Collapse
Affiliation(s)
- Donatella Lombardo
- Operative Unit of Microbiology, University Hospital Policlinico Sant'Orsola-Malpighi, Bologna, Italy
| | - Miriam Cordovana
- Operative Unit of Microbiology, University Hospital Policlinico Sant'Orsola-Malpighi, Bologna, Italy
| | | | - Marco Pane
- Probiotical Research s.r.l., Novara, Italy
| | - Simone Ambretti
- Operative Unit of Microbiology, University Hospital Policlinico Sant'Orsola-Malpighi, Bologna, Italy
| |
Collapse
|
5
|
Hu Y, Zhou H, Lu J, Sun Q, Liu C, Zeng Y, Zhang R. Evaluation of the IR Biotyper for Klebsiella pneumoniae typing and its potentials in hospital hygiene management. Microb Biotechnol 2021; 14:1343-1352. [PMID: 33205912 PMCID: PMC8313285 DOI: 10.1111/1751-7915.13709] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/29/2020] [Indexed: 02/02/2023] Open
Abstract
Klebsiella pneumoniae has emerged as one of the most important pathogens that frequently encounter in community-acquired or hospital-acquired infections. Timely epidemiological surveillance could greatly facilitate infection control of K. pneumoniae and many deadly pathogens alike. In this study, we evaluated the performance of the IR Biotyper, a Fourier transform infrared (FTIR) spectroscopy system for K. pneumoniae isolates typing through (i) optimizing the culture scheme and defining the cutoff value (COV) range and (ii) comparing with commonly used typing tools such as multi-locus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS). We found that a non-selective and non-chromogenic medium with 24 ± 2 h incubation gives the best discriminatory power for the IR Biotyper (IRBT). COV evaluation indicated that the IRBT is a robust typing method with good reproducibility. Besides, we observed that the modified H2 O-EtOH suspensions preparation method could enhance the quality of the spectrum, especially for those hypermucoviscous strains. For the method comparison study, our data demonstrated that FTIR spectroscopy could accurately cluster K. pneumoniae strains. The typing results of the IRBT were almost entirely in concordance with those from PFGE and WGS. Together with the advantages such as low costs and short turnaround time (less than 3h), the IRBT is a promising tool for strain typing that could make real-time outbreak investigation a reality.
Collapse
Affiliation(s)
- Yanyan Hu
- Clinical Microbiology LaboratorySchool of Medicine2nd Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhouChina
| | - Hongwei Zhou
- Clinical Microbiology LaboratorySchool of Medicine2nd Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhouChina
| | - Jiayue Lu
- Clinical Microbiology LaboratorySchool of Medicine2nd Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhouChina
| | - Qiaoling Sun
- Clinical Microbiology LaboratorySchool of Medicine2nd Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhouChina
| | - Congcong Liu
- Clinical Microbiology LaboratorySchool of Medicine2nd Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhouChina
| | - Yu Zeng
- Clinical Microbiology LaboratorySchool of Medicine2nd Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhouChina
| | - Rong Zhang
- Clinical Microbiology LaboratorySchool of Medicine2nd Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhouChina
| |
Collapse
|
6
|
Silva L, Grosso F, Rodrigues C, Ksiezarek M, Ramos H, Peixe L. The success of particular Acinetobacter baumannii clones: accumulating resistance and virulence inside a sugary shield. J Antimicrob Chemother 2021; 76:305-311. [PMID: 33150386 DOI: 10.1093/jac/dkaa453] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 10/05/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND In Portugal, carbapenem-resistant Acinetobacter baumannii (CRAB) has been associated with ST98, ST103 and ST208 (Oxford Scheme, Oxf) and a clone has usually been associated with a particular period of time. These clonal shifts were primarily explained by an increased antimicrobial resistance profile. Here we explore genomic and biochemical differences among these and more recent clones, which could further explain the diversity and evolution of this species. METHODS A total of 116 CRAB isolates (2010-15), together with representatives of a previously described CRAB collection (4 isolates, 2001-06) were characterized by attenuated total reflection Fourier transform infrared spectroscopy (FTIR-ATR) and MLST. Representatives of different FTIR-ATR/MLST clusters were selected for WGS (n = 13), which allowed the in silico extraction of resistance and virulence genes, capsule locus and SNP analysis. RESULTS A. baumannii clonal shifts of OXA-58-producing ST103Oxf (2001-04), OXA-40-producing ST98Oxf (2002-06), OXA-23-producing ST208Oxf (2006-10) and OXA-23-producing ST218Oxf (2010-15) were accompanied by an increase in AMR genes and virulence factors. FTIR-ATR clustering was congruent with sugar composition predicted from the capsular locus: a fucosamine cluster comprising ST98Oxf, ST103Oxf and a single ST218Oxf isolate; a pseudaminic acid cluster of ST208Oxf and ST1557Oxf isolates; and legionaminic acid, resembling the sialic acid from mammalian cells, in a cluster comprising ST218Oxf isolates. The whole-genome phylogenetic tree was congruent with MLST, with isolates presenting 5-28 938 SNPs. ST208Oxf and ST218Oxf presented ∼1900 SNPs while ST103Oxf and ST1557Oxf showed a greater number of SNPs (∼28 000). CONCLUSIONS Clonal shifts of CRAB were promoted, in our country, by consecutive virulence and AMR gene pool enlargement, together with features increasing pathogen-host adaptation. Worldwide dominance of ST218Oxf is supported by the combination of high AMR and virulence levels.
Collapse
Affiliation(s)
- Liliana Silva
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- ESALD, Instituto Politécnico de Castelo Branco, Castelo Branco, Portugal
| | - Filipa Grosso
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Carla Rodrigues
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Magdalena Ksiezarek
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Helena Ramos
- Hospital Geral de Santo António (HGSA), Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| |
Collapse
|
7
|
Hao JW, Chen Y, Chen ND, Qin CF. Rapid Detection of Adulteration in Dendrobium huoshanense Using NIR Spectroscopy Coupled with Chemometric Methods. J AOAC Int 2021; 104:854-859. [PMID: 33064805 DOI: 10.1093/jaoacint/qsaa138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/30/2020] [Accepted: 09/18/2020] [Indexed: 11/14/2022]
Abstract
BACKGROUND Dendrobium huoshanense (DHS) is a typical traditional Chinese medicine with unique medical and high economic values; however, it may easily be adulterated with cheaper alternatives (e.g. Dendrobium henanese, DHN), because of their similar appearances and tastes. OBJECTIVE In this study, adulteration of DHN in DHS was detected by near infrared (NIR) spectroscopy combined with chemometric methods. METHODS By performing partial least squares (PLS) analysis, PLS multivariate methods including partial least-squares discriminant analysis (PLS-DA), and partial least-squares regressions (PLSR) were applied to the obtained spectral data to build models. The PLS-DA model was employed to differentiate between pure DHS samples and those adulterated with DHN. RESULTS The R2 value obtained for the PLS-DA model was 0.4898 with an RMSEP error of 0.1554, resulting in a 100% accuracy of validation sample sets. Similarly, a PLSR model was also developed to quantify the amount of DHN adulterant in DHS samples. Experimental results indicated that the good performance of the multiplicative scattering correction (MSC) model is the better model showing a prediction performance of RMSEP of 2.38 and R2 of 0.9946. CONCLUSIONS These results suggest that the combination of NIR spectroscopy and chemometric method provides a fast, simple and reliable method for detecting adulteration of DHS. HIGHLIGHTS The method of classification allowed identification of both authentic and adulterated DHS samples. Comparison of six different techniques for spectra preprocessing to improve quantitative model performance was obtained with MSC derivative spectra. The method can detect most of the current DHS adulterations in the Chinese market.
Collapse
Affiliation(s)
- Jing-Wen Hao
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu'an City 237012, China
| | - Yue Chen
- Institute of Pharmaceutical Science, China Pharmaceutical University, Tong Jia Xiang, Nanjing, Jiangsu 210009, China
| | - Nai-Dong Chen
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu'an City 237012, China.,Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resource, Lu'an City 237012, China
| | - Chao-Feng Qin
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu'an City 237012, China
| |
Collapse
|
8
|
Dickstein Y, Lellouche J, Schwartz D, Nutman A, Rakovitsky N, Dishon Benattar Y, Altunin S, Bernardo M, Iossa D, Durante-Mangoni E, Antoniadou A, Skiada A, Deliolanis I, Daikos GL, Daitch V, Yahav D, Leibovici L, Rognås V, Friberg LE, Mouton JW, Paul M, Carmeli Y. Colistin Resistance Development Following Colistin-Meropenem Combination Therapy Versus Colistin Monotherapy in Patients With Infections Caused by Carbapenem-Resistant Organisms. Clin Infect Dis 2021; 71:2599-2607. [PMID: 31758195 DOI: 10.1093/cid/ciz1146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/21/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND We evaluated whether carbapenem-colistin combination therapy reduces the emergence of colistin resistance, compared to colistin monotherapy, when given to patients with infections due to carbapenem-resistant Gram-negative organisms. METHODS This is a pre-planned analysis of a secondary outcome from a randomized, controlled trial comparing colistin monotherapy with colistin-meropenem combination for the treatment of severe infections caused by carbapenem-resistant, colistin-susceptible Gram-negative bacteria. We evaluated rectal swabs taken on Day 7 or later for the presence of new colistin-resistant (ColR) isolates. We evaluated the emergence of any ColR isolate and the emergence of ColR Enterobacteriaceae (ColR-E). RESULTS Data were available for 214 patients for the primary analysis; emergent ColR organisms were detected in 22 (10.3%). No difference was observed between patients randomized to treatment with colistin monotherapy (10/106, 9.4%) versus patients randomized to colistin-meropenem combination therapy (12/108, 11.1%; P = .669). ColR-E organisms were detected in 18/249 (7.2%) patients available for analysis. No difference was observed between the 2 treatment arms (colistin monotherapy 6/128 [4.7%] vs combination therapy 12/121 [9.9%]; P = .111). Enterobacteriaceae, as the index isolate, was found to be associated with development of ColR-E (hazard ratio, 3.875; 95% confidence interval, 1.475-10.184; P = .006). CONCLUSIONS Carbapenem-colistin combination therapy did not reduce the incidence of colistin resistance emergence in patients with infections due to carbapenem-resistant organisms. Further studies are necessary to elucidate the development of colistin resistance and methods for its prevention.
Collapse
Affiliation(s)
- Yaakov Dickstein
- Institute of Infectious Diseases, Rambam Health Care Campus, Haifa, Israel
| | - Jonathan Lellouche
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv, Israel.,Molecular Epidemiology Laboratory, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - David Schwartz
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv, Israel.,Molecular Epidemiology Laboratory, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - Amir Nutman
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Ramat-Aviv, Israel
| | - Nadya Rakovitsky
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv, Israel.,Molecular Epidemiology Laboratory, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | | | - Sergey Altunin
- Institute of Infectious Diseases, Rambam Health Care Campus, Haifa, Israel
| | - Mariano Bernardo
- University of Campania "L. Vanvitelli," Monaldi Hospital, Naples, Italy
| | - Domenico Iossa
- University of Campania "L. Vanvitelli," Monaldi Hospital, Naples, Italy
| | | | - Anastasia Antoniadou
- Fourth Department of Medicine, Attikon University General Hospital, Athens, Greece.,National and Kapodistrian University of Athens, Athens, Greece
| | - Anna Skiada
- National and Kapodistrian University of Athens, Athens, Greece.,First Department of Medicine, Laikon General Hospital, Athens, Greece
| | - Ioannis Deliolanis
- National and Kapodistrian University of Athens, Athens, Greece.,First Department of Medicine, Laikon General Hospital, Athens, Greece
| | - George L Daikos
- National and Kapodistrian University of Athens, Athens, Greece.,First Department of Medicine, Laikon General Hospital, Athens, Greece
| | - Vered Daitch
- Sackler Faculty of Medicine, Tel Aviv University, Ramat-Aviv, Israel.,Department of Medicine E, Beilinson Hospital, Rabin Medical Center, Petah Tikva, Israel
| | - Dafna Yahav
- Sackler Faculty of Medicine, Tel Aviv University, Ramat-Aviv, Israel.,Infectious Diseases Unit, Beilinson Hospital, Rabin Medical Center, Petah Tikva, Israel
| | - Leonard Leibovici
- Sackler Faculty of Medicine, Tel Aviv University, Ramat-Aviv, Israel.,Department of Medicine E, Beilinson Hospital, Rabin Medical Center, Petah Tikva, Israel
| | - Viktor Rognås
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Lena E Friberg
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Johan W Mouton
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Mical Paul
- Institute of Infectious Diseases, Rambam Health Care Campus, Haifa, Israel.,Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Yehuda Carmeli
- National Institute for Antibiotic Resistance and Infection Control, Ministry of Health, Tel Aviv, Israel.,Molecular Epidemiology Laboratory, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Ramat-Aviv, Israel
| | | |
Collapse
|
9
|
Lavrinenko A, Sheck E, Kolesnichenko S, Azizov I, Turmukhambetova A. Antibiotic Resistance and Genotypes of Nosocomial Strains of Acinetobacter baumannii in Kazakhstan. Antibiotics (Basel) 2021; 10:antibiotics10040382. [PMID: 33916831 PMCID: PMC8065490 DOI: 10.3390/antibiotics10040382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/25/2021] [Accepted: 04/01/2021] [Indexed: 12/17/2022] Open
Abstract
The aim of this study was to determine the prevalence of A. baumannii antibiotic-resistant strains in Kazakhstan and to characterize genotypes related to epidemic “high-risk” clones. Two hundred and twenty four A. baumannii isolates from four cities of Kazakhstan in 2011–2019 were studied. Antibiotic susceptibility testing was performed by using broth microdilutions method according to EUCAST (v 11.0) recommendations. The presence of blaOXA-23-like, blaOXA-24/40-like,blaOXA-58-like,blaVIM,blaIMP, and blaNDM genes was determined by PCR. Genotyping was performed using high-throughput real-time PCR detection of 21 SNPs at 10 chromosomal loci used in existing MLST schemes. Resistance rates to imipenem, meropenem, amikacin, gentamicin, and ciprofloxacin were 81.3%, 78.6%, 79.9%, 65.2%, and 89.3%, respectively. No colistin resistant isolates were detected. The values of the MIC 50% and the MIC 90% of tigecycline were 0.125 mg/L, only four isolates (1.8%) had the ECOFF value >0.5 mg/L. The presence of acquired carbapenemase genes was found in 82.2% strains, including blaOXA-23-like (78.6%) or blaOXA-58-like (3.6%) genes. The spreading of carbapenem resistant A. baumannii strains in Kazakhstan was associated with epidemic “high-risk” clonal groups, predominantly, CG208(92)OXF/CG2PAS (80.8%) and less often CG231(109)OXF/CG1PAS (1.8%).
Collapse
Affiliation(s)
- Alyona Lavrinenko
- Share Resource Laboratory, Karaganda Medical University, Karaganda 100008, Kazakhstan; (A.L.); (A.T.)
| | - Eugene Sheck
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214014 Smolensk, Russia; (E.S.); (I.A.)
| | - Svetlana Kolesnichenko
- Share Resource Laboratory, Karaganda Medical University, Karaganda 100008, Kazakhstan; (A.L.); (A.T.)
- Correspondence: ; Tel.: +7-721-251-3479
| | - Ilya Azizov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214014 Smolensk, Russia; (E.S.); (I.A.)
| | - Anar Turmukhambetova
- Share Resource Laboratory, Karaganda Medical University, Karaganda 100008, Kazakhstan; (A.L.); (A.T.)
| |
Collapse
|
10
|
Karah N, Wai SN, Uhlin BE. CRISPR-based subtyping to track the evolutionary history of a global clone of Acinetobacter baumannii. INFECTION GENETICS AND EVOLUTION 2021; 90:104774. [PMID: 33618003 DOI: 10.1016/j.meegid.2021.104774] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 01/14/2021] [Accepted: 02/15/2021] [Indexed: 11/16/2022]
Abstract
Acinetobacter baumannii global clone 1 (GC1) is the second most common clone in the global population of A. baumannii isolates and a key cause of hospital-acquired infections. In this study, comparative analysis of the clustered regularly interspaced short palindromic repeats (CRISPR)-based sequence types (CST) was performed to determine the genetic relatedness and track patterns of descent among 187 GC1 isolates, as a complement to the evolutionary inferences from their multilocus sequence types and genome-wide single nucleotide polymorphism (SNP)-based phylogeny. The CST2 cluster, CST2 and all the CSTs descending from CST2, corresponded to GC1 lineage 1. This cluster included 143 of the 187 isolates showing a prevalent geographical distribution worldwide. A well-demarcated group of 13 CSTs, accounting for 33 of the 187 isolates, corresponded to GC1 lineage 2. All the CSTs of this group were characterized by the absence of spacer Ab-18. Many of the GC1 lineage 2 isolates had an epidemiological link to the Middle East and/or were obtained in military healthcare facilities. GC1 lineage 3 was a novel lineage that has so far been limited to Afghanistan, Pakistan and India. Diversification of A. baumannii GC1 into lineages and clades has probably been related to a dynamic expansion after passing a migration bottleneck to enter the hospital environment. We conclude that CRISPR-based subtyping is a convenient method to trace the evolutionary history of particular bacterial clones, such as A. baumannii GC1.
Collapse
Affiliation(s)
- Nabil Karah
- Department of Molecular Biology, the Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.
| | - Sun Nyunt Wai
- Department of Molecular Biology, the Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Bernt Eric Uhlin
- Department of Molecular Biology, the Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.
| |
Collapse
|
11
|
Locke A, Fitzgerald S, Mahadevan-Jansen A. Advances in Optical Detection of Human-Associated Pathogenic Bacteria. Molecules 2020; 25:E5256. [PMID: 33187331 PMCID: PMC7696695 DOI: 10.3390/molecules25225256] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
Bacterial infection is a global burden that results in numerous hospital visits and deaths annually. The rise of multi-drug resistant bacteria has dramatically increased this burden. Therefore, there is a clinical need to detect and identify bacteria rapidly and accurately in their native state or a culture-free environment. Current diagnostic techniques lack speed and effectiveness in detecting bacteria that are culture-negative, as well as options for in vivo detection. The optical detection of bacteria offers the potential to overcome these obstacles by providing various platforms that can detect bacteria rapidly, with minimum sample preparation, and, in some cases, culture-free directly from patient fluids or even in vivo. These modalities include infrared, Raman, and fluorescence spectroscopy, along with optical coherence tomography, interference, polarization, and laser speckle. However, these techniques are not without their own set of limitations. This review summarizes the strengths and weaknesses of utilizing each of these optical tools for rapid bacteria detection and identification.
Collapse
Affiliation(s)
- Andrea Locke
- Vanderbilt Biophotonics Center, Nashville, TN 37232, USA; (A.L.); (S.F.)
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA
| | - Sean Fitzgerald
- Vanderbilt Biophotonics Center, Nashville, TN 37232, USA; (A.L.); (S.F.)
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA
| | - Anita Mahadevan-Jansen
- Vanderbilt Biophotonics Center, Nashville, TN 37232, USA; (A.L.); (S.F.)
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA
| |
Collapse
|
12
|
A Front Line on Klebsiella pneumoniae Capsular Polysaccharide Knowledge: Fourier Transform Infrared Spectroscopy as an Accurate and Fast Typing Tool. mSystems 2020; 5:5/2/e00386-19. [PMID: 32209717 PMCID: PMC7093823 DOI: 10.1128/msystems.00386-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Klebsiella pneumoniae is nowadays recognized as one of the most defiant human pathogens, whose infections are increasingly more challenging to treat and control. Whole-genome sequencing (WGS) has been key for clarifying the population structure of K. pneumoniae, and it is still instrumental to provide insights into potential pathogenicity and evolutionary markers, such as the capsular locus. However, this information and WGS are still far from being accessible and translated into routine clinical microbiology laboratories as quick and cost-efficient strain diagnostic tools. Here, we propose a biochemical fingerprinting approach based on Fourier transform infrared spectroscopy (FT-IR) and multivariate data analysis tools for K. pneumoniae capsular typing that, because of its high resolution, speed, and low cost, can be an asset to provide enough information to support real-time epidemiology and infection control decisions. Besides, it provides a simple framework for phenotypic/biochemical validation of K. pneumoniae capsular diversity. Genomics-based population analysis of multidrug-resistant (MDR) Klebsiella pneumoniae motivated a renewed interest on the capsule as an evolutionary and virulence marker of clinically relevant strains. Whole-genome sequencing (WGS)-based approaches have provided great insights into the genetic variability of the capsular locus, but genotypic-biochemical capsular (K)-type correlations are lacking, hindering the establishment of a reliable framework for K-type characterization and typing. To fill this gap, we combined molecular, comparative genomics, and multivariate data analysis tools with biochemical data on the capsular locus to support the usefulness of Fourier transform infrared (FT-IR) spectroscopy as a reliable K typing tool. To validate our approach, we used a representative collection of well-defined MDR K. pneumoniae lineages involved in local or nationwide epidemics in multiple countries. With this, we demonstrate a high accuracy and resolution of our FT-IR-based spectroscopy approach for K-type discrimination that is even higher than that provided by WGS. Moreover, the specific associations established between certain K types and specific K. pneumoniae lineages with high clinical relevance, together with the accuracy, simplicity, short time to result, and inexpensive features of the method, support the value of the developed FT-IR-based approach for an easy, fast, and cost-effective strain typing. This fulfills a still unmet need for tools to support real-time monitoring and control of K. pneumoniae infections. In addition, the genotypic-biochemical correlations established provide insights on sugar composition/structure of newly defined K. pneumoniae capsular types. IMPORTANCEKlebsiella pneumoniae is nowadays recognized as one of the most defiant human pathogens, whose infections are increasingly more challenging to treat and control. Whole-genome sequencing (WGS) has been key for clarifying the population structure of K. pneumoniae, and it is still instrumental to provide insights into potential pathogenicity and evolutionary markers, such as the capsular locus. However, this information and WGS are still far from being accessible and translated into routine clinical microbiology laboratories as quick and cost-efficient strain diagnostic tools. Here, we propose a biochemical fingerprinting approach based on Fourier transform infrared spectroscopy (FT-IR) and multivariate data analysis tools for K. pneumoniae capsular typing that, because of its high resolution, speed, and low cost, can be an asset to provide enough information to support real-time epidemiology and infection control decisions. Besides, it provides a simple framework for phenotypic/biochemical validation of K. pneumoniae capsular diversity.
Collapse
|
13
|
Attenuated total reflection: Fourier transform infrared spectroscopy for detection of heterogeneous vancomycin—intermediate Staphylococcus aureus. World J Microbiol Biotechnol 2020; 36:22. [DOI: 10.1007/s11274-019-2788-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 12/17/2019] [Indexed: 10/25/2022]
|
14
|
Vogt S, Löffler K, Dinkelacker AG, Bader B, Autenrieth IB, Peter S, Liese J. Fourier-Transform Infrared (FTIR) Spectroscopy for Typing of Clinical Enterobacter cloacae Complex Isolates. Front Microbiol 2019; 10:2582. [PMID: 31781074 PMCID: PMC6851243 DOI: 10.3389/fmicb.2019.02582] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/24/2019] [Indexed: 12/24/2022] Open
Abstract
Members of the Enterobacter (E.) cloacae complex have emerged as important pathogens frequently encountered in nosocomial infections. Several outbreaks with E. cloacae complex have been reported in recent years, especially in neonatal units. Fast and reliable strain typing methods are crucial for real-time surveillance and outbreak analysis to detect pathogen reservoirs and transmission routes. The aim of this study was to evaluate the performance of Fourier-transform infrared (FTIR) spectroscopy as a fast method for typing of clinical E. cloacae complex isolates, when whole genome sequencing (WGS) analysis was used as reference. First, the technique was used retrospectively on 24 first isolates of E. cloacae complex strains from neonatal patients and showed good concordance with SNP-based clustering [adjusted rand index (ARI) = 0.818] and with the sequence type (ST) (ARI = 0.801). 29 consecutive isolates from the same patients were shown by WGS analysis to almost always belong to the same SNP cluster as the first isolates, which was only inconsistently recognized by FTIR spectroscopy. Training of an artificial neural network (ANN) with all FTIR spectra from sequenced strains markedly improved the recognition of related and unrelated isolate spectra. In a second step, FTIR spectroscopy was applied on 14 strains during an outbreak with E. cloacae complex and provided fast typing results that were confirmed by WGS analysis. In conclusion, FTIR spectroscopy is a promising tool for strain typing of clinical E. cloacae complex strains. Discriminatory power can be improved by implementing an ANN for spectrum analysis. Due to its low costs and fast turnaround times, the method presents a valuable tool for real-time surveillance as well as outbreak analysis.
Collapse
Affiliation(s)
- Sophia Vogt
- Institute of Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Kim Löffler
- Institute of Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Ariane G Dinkelacker
- Institute of Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Baris Bader
- Institute of Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Ingo B Autenrieth
- Institute of Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Jan Liese
- Institute of Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| |
Collapse
|
15
|
Biswas D, Tiwari M, Tiwari V. Molecular mechanism of antimicrobial activity of chlorhexidine against carbapenem-resistant Acinetobacter baumannii. PLoS One 2019; 14:e0224107. [PMID: 31661500 PMCID: PMC6818764 DOI: 10.1371/journal.pone.0224107] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 10/04/2019] [Indexed: 02/07/2023] Open
Abstract
Acinetobacter baumannii causes hospital-acquired infections, especially in those with impaired immune function. Biocides or disinfectants are widely used antibacterial agents used to eradicate the effect of A. baumannii on inanimate objects and health care environments. In the current study, the antimicrobial activity of chlorhexidine has been investigated against carbapenem-resistant (RS-307, RS-7434, RS-6694, and RS-122), and sensitive (ATCC-19606 and RS-10953) strains of A. baumannii. We have determined growth kinetics, antimicrobial susceptibility, ROS production, lipid peroxidation, cell viability using flow cytometry assay (FACS), and membrane integrity by scanning electron microscope (SEM). The effect of chlorhexidine on the bacterial membrane has also been investigated using Fourier transform infrared (FTIR) spectroscopy. The present study showed that 32μg/ml chlorhexidine treatment results in the decreased bacterial growth, CFU count and cell viability. The antibacterial activity of chlorhexidine is due to the elevated ROS production and higher lipid peroxidation. These biochemical changes result in the membrane damage and alteration in the membrane proteins, phospholipids, carbohydrates, nucleic acids as evident from the FTIR and SEM data. Therefore, chlorhexidine has the potential to be used in the hospital setups to remove the spread of A. baumannii.
Collapse
Affiliation(s)
- Deepika Biswas
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
| | - Monalisa Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
| | - Vishvanath Tiwari
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
- * E-mail: ,
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Martak D, Valot B, Sauget M, Cholley P, Thouverez M, Bertrand X, Hocquet D. Fourier-Transform InfraRed Spectroscopy Can Quickly Type Gram-Negative Bacilli Responsible for Hospital Outbreaks. Front Microbiol 2019; 10:1440. [PMID: 31293559 PMCID: PMC6606786 DOI: 10.3389/fmicb.2019.01440] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/07/2019] [Indexed: 12/19/2022] Open
Abstract
The typing of epidemic bacterial pathogens in hospitals relies on DNA-based, expensive, and time-consuming techniques, that are often limited to retrospective studies. However, the quick identification of epidemic pathogens in the routine of the microbiology laboratories would expedite infection control procedures that limit the contamination of new patients. IR Biotyper (Bruker Daltonics GmbH) is a new typing machine based on Fourier-transform infrared (FTIR) spectroscopy which generates spectra, aiming at typing the micro-organisms within 3 h. This technique discriminates the isolates by exploring the differences of the surface cell polysaccharides. In this work, we evaluated the ability of the FTIR spectroscopy to recognize Gram-negative bacilli clones responsible for hospital outbreaks. Isolates of Pseudomonas aeruginosa (n = 100), Klebsiella pneumoniae (n = 16), Enterobacter cloacae (n = 23), and Acinetobacter baumannii (n = 20) were typed by the reference methods Multi-Locus Sequence Typing (defining sequence types – STs) along with or without pulsed field gel electrophoresis (PFGE) (defining pulsotypes), and by FTIR spectroscopy. The congruence of FTIR spectroscopy clustering was compared to those of MLST and PFGE by Adjusted Rand index and Adjusted Wallace coefficient. We found that FTIR spectroscopy accurately clustered P. aeruginosa, K. pneumoniae, and E. cloacae isolates belonging to the same ST. The performance of the FTIR spectroscopy was slightly lower for A. baumannii. Furthermore, FTIR spectroscopy also correctly clustered P. aeruginosa isolates having a similar pulsotype. Overall, the IR Biotyper can quickly (in less than 3 h) detect the spread of clones of P. aeruginosa, K. pneumoniae, E. cloacae, and A. baumannii. The use of this technique by clinical microbiology laboratories may help to tackle the spread of epidemic clones by the quick implementation of infection control measures.
Collapse
Affiliation(s)
- Daniel Martak
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France
| | - Benoît Valot
- UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France
| | - Marlène Sauget
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France.,Centre de Ressources Biologiques - Filière Microbiologique de Besançon, Centre Hospitalier Régional Universitaire, Besançon, France
| | - Pascal Cholley
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France
| | - Michelle Thouverez
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France
| | - Xavier Bertrand
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France
| | - Didier Hocquet
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France.,Centre de Ressources Biologiques - Filière Microbiologique de Besançon, Centre Hospitalier Régional Universitaire, Besançon, France
| |
Collapse
|
18
|
Teixeira AM, Nemec A, Sousa C. Differentiation of Taxonomically Closely Related Species of the Genus Acinetobacter Using Raman Spectroscopy and Chemometrics. Molecules 2019; 24:molecules24010168. [PMID: 30621147 PMCID: PMC6337300 DOI: 10.3390/molecules24010168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/18/2018] [Accepted: 12/26/2018] [Indexed: 11/16/2022] Open
Abstract
In recent years, several efforts have been made to develop quick and low cost bacterial identification methods. Genotypic methods, despite their accuracy, are laborious and time consuming, leaving spectroscopic methods as a potential alternative. Mass and infrared spectroscopy are among the most reconnoitered techniques for this purpose, with Raman having been practically unexplored. Some species of the bacterial genus Acinetobacter are recognized as etiological agents of nosocomial infections associated with high rates of mortality and morbidity, which makes their accurate identification important. The goal of this study was to assess the ability of Raman spectroscopy to discriminate between 16 Acinetobacter species belonging to two phylogroups containing taxonomically closely related species, that is, the Acinetobacter baumannii-Acinetobacter calcoaceticus complex (six species) and haemolytic clade (10 species). Bacterial spectra were acquired without the need for any sample pre-treatment and were further analyzed with multivariate data analysis, namely partial least squares discriminant analysis (PLSDA). Species discrimination was achieved through a series of sequential PLSDA models, with the percentage of correct species assignments ranging from 72.1% to 98.7%. The obtained results suggest that Raman spectroscopy is a promising alternative for identification of Acinetobacter species.
Collapse
Affiliation(s)
- A Margarida Teixeira
- LAQV/REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
| | - Alexandr Nemec
- Laboratory of Bacterial Genetics, Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, 100 42 Prague 10, Czech Republic.
- Department of Laboratory Medicine, Third Faculty of Medicine, Charles University, Šrobárova 50, 100 34 Prague 10, Czech Republic.
| | - Clara Sousa
- LAQV/REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
| |
Collapse
|
19
|
Novais Â, Freitas AR, Rodrigues C, Peixe L. Fourier transform infrared spectroscopy: unlocking fundamentals and prospects for bacterial strain typing. Eur J Clin Microbiol Infect Dis 2018; 38:427-448. [DOI: 10.1007/s10096-018-3431-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/11/2018] [Indexed: 01/25/2023]
|
20
|
Teixeira AM, Sousa C. A review on the application of vibrational spectroscopy to the chemistry of nuts. Food Chem 2018; 277:713-724. [PMID: 30502208 DOI: 10.1016/j.foodchem.2018.11.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 10/12/2018] [Accepted: 11/05/2018] [Indexed: 11/18/2022]
Abstract
Nuts are highly appreciated due to their nutritional relevance and flavour, being the source of many desirable and healthy compounds as polyunsaturated fatty acids and antioxidants. Their characterization became the target of many studies in the last years through conventional analytical techniques as chromatographic ones. Due to the limitations associated to these techniques, as time, cost and environmental concerns, spectroscopic techniques have been increasingly pointed as reliable alternatives. Either applied to raw materials quality control or to more complex process, as industrial in-line monitoring, spectroscopic techniques, namely vibrational spectroscopy, are gathering strong acceptance. This paper presents a review on the application of vibrational spectroscopy, infrared and Raman, to nuts characterization. Estimates of several qualitative and quantitative parameters, origin authentication and/or adulteration in almonds, peanuts, pine nuts, hazelnuts, walnuts, Brazil nuts, cashews, chestnuts and pistachios will be covered. Advantages and limitations of these techniques and future trends will also be discussed.
Collapse
Affiliation(s)
- A Margarida Teixeira
- LAQV/REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Clara Sousa
- LAQV/REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Portugal.
| |
Collapse
|
21
|
Campos J, Sousa C, Mourão J, Lopes J, Antunes P, Peixe L. Discrimination of non-typhoid Salmonella serogroups and serotypes by Fourier Transform Infrared Spectroscopy: A comprehensive analysis. Int J Food Microbiol 2018; 285:34-41. [PMID: 30015261 DOI: 10.1016/j.ijfoodmicro.2018.07.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/30/2018] [Accepted: 07/03/2018] [Indexed: 01/11/2023]
Abstract
Simpler, quick and low-cost methods for routine Salmonella enterica typing are required for epidemiologic surveillance of this important zoonotic pathogen. In this study, using a comprehensive isolate collection, we investigated the potential of Fourier transform infrared spectroscopy (FTIRS) to discriminate the most clinically-relevant serogroups and serotypes of non-typhoid Salmonella. Moreover, the role of O-units composition on the FTIRS Salmonella discrimination was also explored. S. enterica isolates (n = 325; 2002-2015; different sources and countries), of 57 serotypes and 15 serogroups [including the most frequent ones, B-n = 122; C-n = 108; D-n = 43 and E-n = 33)] were analysed by FTIRS. Infrared spectra were analysed by Partial Least Square Discriminant Analysis (PLSDA) and/or Principal Component Analysis (PCA). The polysaccharides region provided the spectral sharpest differences being used in the subsequent Salmonella typing. Serogroups (B, C, D and E) discrimination was achieved with high accuracy (99.6% of correct assignments; PLSDA model). Differences in the O-unit structures composition of those serogroups are likely justifying the discrimination achieved. Other serogroups (G, H, K, L, M, N, O, T, U, Y, Z) were correctly predicted as not belonging to serogroups B, C, D nor E, except for 3 isolates of serogroups H (S. Sundsvall, n = 1) and K (S. Cerro, n = 2). In fact, O-unit structure of serogroup H and K shows some similarity with sub-serogroup C1 with the remaining serogroups presenting marked differences in this cellular component. The sub-serogroups discrimination was successfully achieved for C1, C2 and C3 (using PCA), and for E1-E2-E3 and E4 (by PLSDA). Appropriate serotype discrimination was obtained for most of S. Rissen from the remaining C1 serotypes (91.5%-PLSDA), and S. Enteritidis (D1) from the remaining D1/D2 serotypes (93.4%-PLSDA). The lack of available O-unit composition for particular serotypes prevents the elucidation of the role of this cellular component on the discrimination at serotype level obtained. FTIRS was able to discriminate relevant serogroups (B, C, D and E), sub-serogroups (C1, C2 and C3; E1-E2-E3 and E4) and particular important serotypes (S. Enteritidis, S. Rissen and S. Senftenberg). Further studies on O-antigen composition would clarify the fundaments of discrimination obtained by FTIRS.
Collapse
Affiliation(s)
- Joana Campos
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Clara Sousa
- LAQV/REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Joana Mourão
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - João Lopes
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Patrícia Antunes
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal; Faculdade de Ciências da Nutrição e Alimentação, Universidade do Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal.
| |
Collapse
|
22
|
Lasch P, Stämmler M, Zhang M, Baranska M, Bosch A, Majzner K. FT-IR Hyperspectral Imaging and Artificial Neural Network Analysis for Identification of Pathogenic Bacteria. Anal Chem 2018; 90:8896-8904. [DOI: 10.1021/acs.analchem.8b01024] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter Lasch
- ZBS6 Proteomics and Spectroscopy, Robert Koch-Institute, Seestrasse 10, Berlin, D-13353, Germany
| | - Maren Stämmler
- ZBS6 Proteomics and Spectroscopy, Robert Koch-Institute, Seestrasse 10, Berlin, D-13353, Germany
| | - Miao Zhang
- ZBS6 Proteomics and Spectroscopy, Robert Koch-Institute, Seestrasse 10, Berlin, D-13353, Germany
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-060 Krakow, Poland
| | - Alejandra Bosch
- CINDEFI,
CONICET-CCT
La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 1900 La Plata, Buenos Aires, Argentina
| | - Katarzyna Majzner
- ZBS6 Proteomics and Spectroscopy, Robert Koch-Institute, Seestrasse 10, Berlin, D-13353, Germany
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-060 Krakow, Poland
| |
Collapse
|
23
|
Abstract
Fourier transform infrared spectroscopy (FT-IR) was used to scan whole bacterial cells as well as lipopolysaccharides (LPSs, endotoxins) isolated from them. Proteus mirabilis cells, with chemically defined LPSs, served as a model for the ATR FT-IR method. The paper focuses on three steps of infrared spectroscopy: (1) sample preparation, (2) IR scanning, and (3) multivariate analysis of IR data (principal component analysis, PCA).
Collapse
|
24
|
Quintelas C, Ferreira EC, Lopes JA, Sousa C. An Overview of the Evolution of Infrared Spectroscopy Applied to Bacterial Typing. Biotechnol J 2017; 13. [DOI: 10.1002/biot.201700449] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/18/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Cristina Quintelas
- Dr. C. Quintelas, Dr. E. C. Ferreira; CEB − Centro de Engenharia Biológica; Universidade do Minho; Braga Portugal
| | - Eugénio C. Ferreira
- Dr. C. Quintelas, Dr. E. C. Ferreira; CEB − Centro de Engenharia Biológica; Universidade do Minho; Braga Portugal
| | - João A. Lopes
- Dr. J. A. Lopes; Research Institute for Medicines (iMed.ULisboa); Faculdade de Farmácia; Universidade de Lisboa; Lisboa Portugal
| | - Clara Sousa
- Dr. C. Sousa; LAQV/REQUIMTE; Departamento de Ciências Químicas Faculdade de Farmácia; Universidade do Porto; Rua Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
| |
Collapse
|
25
|
GES-14-Producing Acinetobacter baumannii Isolates in a Neonatal Intensive Care Unit in Tunisia Are Associated with a Typical Middle East Clone and a Transferable Plasmid. Antimicrob Agents Chemother 2017; 61:AAC.00142-17. [PMID: 28348158 DOI: 10.1128/aac.00142-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
|
26
|
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.
Collapse
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
| |
Collapse
|
27
|
Zenati K, Touati A, Bakour S, Sahli F, Rolain J. Characterization of NDM-1- and OXA-23-producing Acinetobacter baumannii isolates from inanimate surfaces in a hospital environment in Algeria. J Hosp Infect 2016; 92:19-26. [DOI: 10.1016/j.jhin.2015.09.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/28/2015] [Indexed: 01/29/2023]
|
28
|
Silva S, Tobaldini-Valerio F, Costa-de-Oliveira S, Henriques M, Azeredo J, Ferreira EC, Lopes JA, Sousa C. Discrimination of clinically relevant Candida species by Fourier-transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR). RSC Adv 2016. [DOI: 10.1039/c6ra16769a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Accurate Candida species identification remains a challenge due to their phenotypic and genotypic similarity.
Collapse
Affiliation(s)
- Sónia Silva
- CEB-Centro de Engenharia Biológica
- Universidade do Minho
- Braga
- Portugal
| | - Flávia Tobaldini-Valerio
- CEB-Centro de Engenharia Biológica
- Universidade do Minho
- Braga
- Portugal
- Departamento de Análises Clínicas e Biomedicina
| | | | - Mariana Henriques
- CEB-Centro de Engenharia Biológica
- Universidade do Minho
- Braga
- Portugal
| | - Joana Azeredo
- CEB-Centro de Engenharia Biológica
- Universidade do 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
| |
Collapse
|
29
|
Sousa C, Botelho J, Grosso F, Silva L, Lopes J, Peixe L. Unsuitability of MALDI-TOF MS to discriminate Acinetobacter baumannii clones under routine experimental conditions. Front Microbiol 2015; 6:481. [PMID: 26042113 PMCID: PMC4436932 DOI: 10.3389/fmicb.2015.00481] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/01/2015] [Indexed: 11/13/2022] Open
Abstract
MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry) is now in the forefront for routine bacterial species identification methodologies, being its value for clonality assessment controversial. In this work we evaluated the potential of MALDI-TOF MS for assisting infection control by depicting Acinetobacter baumannii clones. Mass spectra of 58 A. baumannii clinical isolates belonging to the worldwide spread lineages (ST98, ST103, ST208, and ST218) isolated in our country, were obtained and analyzed with several chemometric tools (pseudo gel views, peakfind function, and partial least squares discriminant analysis). The clonal lineages were obtained using the “Oxford” scheme, belonging ST98, ST208, and ST218 to the international clone II and ST103 to an epidemic clonal lineage (SG5). Additionally, mass spectra of a highly diverse international collection of 38 isolates belonging to 22 sequence types (STs) were obtained for further comparisons. Pseudo gel views and direct peak pattern analysis did not allow the discrimination of A. baumannii isolates belonging to ST98, ST103, ST208, or ST218. Moreover, a partial least square discriminant analysis of the mass spectra considering two spectral ranges (2–20 kDa and 4–10 kDa) revealed a poor degree of discrimination with only 64.6 and 65.8% of correct ST assignments, respectively. Also, mass spectra of the international isolates (n = 38, 22STs) revealed a very congruent peak pattern among them as well as among the four lineages included in this work. Despite the increasing interest of MALDI-TOF MS for bacterial typing at different taxonomical levels, we demonstrated, using routine experimental conditions, the unsuitability of this methodology for A. baumannii clonal discrimination.
Collapse
Affiliation(s)
- Clara Sousa
- Centro de Engenharia Biológica, Universidade do Minho Braga, Portugal
| | - João Botelho
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto Porto, Portugal
| | - Filipa Grosso
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto Porto, Portugal
| | - Liliana Silva
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto Porto, Portugal
| | - João Lopes
- Departamento de Farmácia Galénica e Tecnologia Farmacêutica, Faculdade de Farmácia, Universidade de Lisboa Lisboa, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto Porto, Portugal
| |
Collapse
|
30
|
Gheorghe I, Novais Â, Grosso F, Rodrigues C, Chifiriuc MC, Lazar V, Peixe L. Snapshot on carbapenemase-producing Pseudomonas aeruginosa and Acinetobacter baumannii in Bucharest hospitals reveals unusual clones and novel genetic surroundings for blaOXA-23. J Antimicrob Chemother 2015; 70:1016-20. [PMID: 25630639 DOI: 10.1093/jac/dku527] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES The present study was designed to provide a snapshot on carbapenemase-producing Pseudomonas aeruginosa (n=11) and Acinetobacter baumannii (n=7) isolates in hospitalized patients (November 2011, January-March 2012) from two main hospitals in Bucharest, south Romania. METHODS Clonality among isolates was established by PFGE, MLST and Fourier transform infrared spectroscopy. Carbapenemases were screened by the Blue-Carba test, PCR and sequencing. Transferability of blaOXA-23 was tested by conjugation and plasmid typing (number, size and identity) was assessed by S1-PFGE, replicon typing, hybridization and PCR mapping. RESULTS All P. aeruginosa isolates carried chromosomally located blaVIM-2, associated with a common class 1 integron (aacA7-blaVIM-2) or an atypical configuration (aacA7-blaVIM-2-dfrB5-tniC). These isolates belonged to unusual lineages; mostly ST233 disseminated in one hospital unit, with ST364 and ST1074 also being detected. A. baumannii isolates carried blaOXA-23 in Tn2008, which was found truncating a TnaphA6 transposon located in a common 60 kb GR6 (aci6) pABKp1-like conjugative plasmid in highly related CC92 clones (ST437, ST764 and ST765), where CC stands for clonal complex. CONCLUSIONS Our results show the spread of VIM-2-producing P. aeruginosa and OXA-23-producing A. baumannii clinical isolates in two hospitals from Bucharest and highlight a peculiar population structure in this Eastern European country. Also, we demonstrate the dissemination of a common and conjugative aci6 pABKp1-like plasmid scaffold in different A. baumannii clones and we report the first known identification of Tnaph6-carrying pACICU2-like plasmids in Europe.
Collapse
Affiliation(s)
- Irina Gheorghe
- Department of Microbiology, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Ângela Novais
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Filipa Grosso
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Carla Rodrigues
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | | | - Veronica Lazar
- Department of Microbiology, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| |
Collapse
|
31
|
Awad F, Ramprasath C, Mathivanan N, Aruna PR, Ganesan S. Optical Fiber-Based Steady State and Fluorescence Lifetime Spectroscopy for Rapid Identification and Classification of Bacterial Pathogens Directly from Colonies on Agar Plates. INTERNATIONAL SCHOLARLY RESEARCH NOTICES 2014; 2014:430412. [PMID: 27379265 PMCID: PMC4897486 DOI: 10.1155/2014/430412] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 07/09/2014] [Indexed: 11/17/2022]
Abstract
Fluorescence spectroscopy was examined as a potential technique for identification and classification of bacterial pathogens. Colonies of Staphylococcus aureus, Pseudomonas aeruginosa, Salmonella typhi, and Klebsiella pneumoniae on agar plates were measured directly using a laboratory spectrofluorimeter coupled with optical fiber. Steady state fluorescence spectra were collected following excitation at 280 nm (tryptophan) and 380 nm (NADH). Results showed that fluorescence lifetime decays of tryptophan at 280 nm excitation from the four organisms were best described with triexponential fit and it reveals the existence of different protein conformation. The emission spectroscopy of the four bacteria at 380 nm excitation (NADH) provided better classification (100% of original grouped cases correctly classified and 98.1% of cross-validated grouped cases correctly classified) than that of 280 nm excitation (tryptophan). Our results demonstrated that optical fiber-based fluorescence identification and classification of bacteria is rapid, easy to perform, and of low cost compared to standard methods.
Collapse
Affiliation(s)
- Fathi Awad
- Department of Medical Physics, Anna University, Chennai 600025, India; Department of Medical Physics, Red Sea University, P.O. Box 24, Port Sudan, Sudan
| | | | | | - Prakasa Rao Aruna
- Department of Medical Physics, Anna University, Chennai 600025, India
| | | |
Collapse
|
32
|
Szalontai B, Zimányi L. Chemometrics meets cytometry. Analysis of multivariate spectral data to organize and discriminate biological information. Cytometry A 2014; 85:660-2. [PMID: 24895023 DOI: 10.1002/cyto.a.22493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 05/15/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Balázs Szalontai
- Institute of Biophysics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6701, Hungary
| | | |
Collapse
|