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Fonton P, Hassoun-Kheir N, Harbarth S. Epidemiology of Citrobacter spp. infections among hospitalized patients: a systematic review and meta-analysis. BMC Infect Dis 2024; 24:662. [PMID: 38956542 PMCID: PMC11221093 DOI: 10.1186/s12879-024-09575-8] [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: 02/16/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Infections due to Citrobacter species are increasingly observed in hospitalized patients and are often multidrug-resistant. Yet, the magnitude and burden of Citrobacter spp. resistance in the hospital setting have not been reported. We aimed to evaluate the epidemiology of Citrobacter spp. infections among hospitalized patients, their main resistance patterns and Citrobacter spp. involvement in hospital outbreaks. METHODS We conducted a systematic review and meta-analysis of published literature (PROSPERO registration Jan-2023, CRD42023390084). We searched Embase, Medline and grey literature for studies on hospitalized patients diagnosed with Citrobacter spp. infections, and nosocomial outbreaks due to Citrobacter spp. published during the years 2000-2022. We included observational, interventional, surveillance studies and outbreak reports. Outcomes of interest were the frequency of Citrobacter spp. infections among hospitalized patients and 3rd generation cephalosporin and/or carbapenem resistance percentages in these infections. We used random-effects models to generate pooled outcome estimates and evaluated risk of bias and quality of reporting of outbreaks. RESULTS We screened 1609 deduplicated publications, assessed 148 full-texts, and included 41 studies (15 observational, 13 surveillance and 13 outbreak studies). Citrobacter spp. urinary tract- and bloodstream infections were most frequently reported, with Citrobacter freundii being the main causative species. Hospital-acquired infection occurred in 85% (838/990) of hospitalized patients with Citrobacter infection. After 2010, an increasing number of patients with Citrobacter spp. infections was reported in observational studies. Pooled frequency estimates for Citrobacter spp. infections could not be generated due to lack of data. The pooled prevalence of ESBL and carbapenemase producers among Citrobacter isolates were 22% (95%CI 4-50%, 7 studies) and 18% (95%CI 0-63%, 4 studies), respectively. An increased frequency of reported Citrobacter outbreaks was observed after 2016, with an infection/colonization ratio of 1:3 and a case-fatality ratio of 7% (6/89 patients). Common outbreak sources were sinks, toilets, contaminated food and injection material. Implemented preventive measures included environmental cleaning, isolation of positive patients and reinforcement of hand hygiene. Only seven out of 13 outbreaks (54%) were definitively controlled. CONCLUSION This review highlights the clinical importance of endemic and epidemic Citrobacter spp. in healthcare settings. As an emerging, multidrug‑resistant nosocomial pathogen it requires heightened awareness and further dedicated surveillance efforts.
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Affiliation(s)
- Pérince Fonton
- Infection Control Program, Geneva University Hospitals and Faculty of Medicine, WHO Collaborating Center, Rue Gabrielle-Perret-Gentil 4, CH-1205, Geneva, Switzerland
| | - Nasreen Hassoun-Kheir
- Infection Control Program, Geneva University Hospitals and Faculty of Medicine, WHO Collaborating Center, Rue Gabrielle-Perret-Gentil 4, CH-1205, Geneva, Switzerland
| | - Stephan Harbarth
- Infection Control Program, Geneva University Hospitals and Faculty of Medicine, WHO Collaborating Center, Rue Gabrielle-Perret-Gentil 4, CH-1205, Geneva, Switzerland.
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Alvaro A, Piazza A, Papaleo S, Perini M, Pasala AR, Panelli S, Nardi T, Nodari R, Sterzi L, Pagani C, Merla C, Castelli D, Olivieri E, Bracco S, Ferrando ML, Saluzzo F, Rimoldi SG, Corbella M, Cavallero A, Prati P, Farina C, Cirillo DM, Zuccotti G, Comandatore F. Cultivation and sequencing-free protocol for Serratia marcescens detection and typing. iScience 2024; 27:109402. [PMID: 38510115 PMCID: PMC10952028 DOI: 10.1016/j.isci.2024.109402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/08/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Serratia marcescens is an opportunistic pathogen that survives in inhospitable environments causing large outbreaks, particularly in neonatal intensive care units (NICUs). Genomic studies revealed that most S. marcescens nosocomial infections are caused by a specific clone (here "Infectious clone"). Whole genome sequencing (WGS) is the only portable method able to identify this clone, but it requires days to obtain results. We present a cultivation-free hypervariable-locus melting typing (HLMT) protocol for the fast detection and typing of S. marcescens, with 100% detection capability on mixed samples and a limit of detection that can reach the 10 genome copies. The protocol was able to identify the S. marcescens infectious clone with 97% specificity and 96% sensitivity when compared to WGS, yielding typing results portable among laboratories. The protocol is a cost and time saving method for S. marcescens detection and typing for large environmental/clinical surveillance screenings, also in low-middle income countries.
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Affiliation(s)
- Alessandro Alvaro
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
- Department of Biosciences and Pediatric Clinical Research Center "Romeo Ed Enrica Invernizzi", University of Milan, 20133 Milan, Italy
| | - Aurora Piazza
- Unit of Microbiology and Clinical Microbiology, Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia 27100, Italy
| | - Stella Papaleo
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
| | - Matteo Perini
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Ajay Ratan Pasala
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
- Biochemistry, Microbiology and Immunology Department, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Centre for Innovation, Canadian Blood Services, Ottawa, ON K1G 4J5, Canada
| | - Simona Panelli
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
| | - Tiago Nardi
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Riccardo Nodari
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
| | - Lodovico Sterzi
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
| | - Cristina Pagani
- Laboratorio di Microbiologia Clinica, Virologia e Diagnostica delle Bioemergenze, ASST Fatebenefratelli Sacco, 20157 Milan, Italy
| | - Cristina Merla
- Department of Microbiology & Virology, Fondazione IRCCS Policlinico San Matteo, Viale Camillo Golgi 19, 27100 Pavia, Italy
| | - Daniele Castelli
- Microbiology Unit, Fondazione IRCCS San Gerardo, 20900 Monza, Italy
| | - Emanuela Olivieri
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), 27100 Pavia, Italy
| | - Silvia Bracco
- Laboratory of Microbiology and Virology, Azienda Socio-Sanitaria Territoriale (ASST) Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Maria Laura Ferrando
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Francesca Saluzzo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Sara Giordana Rimoldi
- Laboratorio di Microbiologia Clinica, Virologia e Diagnostica delle Bioemergenze, ASST Fatebenefratelli Sacco, 20157 Milan, Italy
| | - Marta Corbella
- Department of Microbiology & Virology, Fondazione IRCCS Policlinico San Matteo, Viale Camillo Golgi 19, 27100 Pavia, Italy
| | | | - Paola Prati
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), 27100 Pavia, Italy
| | - Claudio Farina
- Laboratory of Microbiology and Virology, Azienda Socio-Sanitaria Territoriale (ASST) Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Gianvincenzo Zuccotti
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
- Department of Paediatrics, Children’s Hospital "V. Buzzi", 20154 Milano, Italy
| | - Francesco Comandatore
- Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center “Romeo and Enrica Invernizzi”, University of Milan, 20157 Milan, Italy
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Abdrabou AMM, Sy I, Bischoff M, Arroyo MJ, Becker SL, Mellmann A, von Müller L, Gärtner B, Berger FK. Discrimination between hypervirulent and non-hypervirulent ribotypes of Clostridioides difficile by MALDI-TOF mass spectrometry and machine learning. Eur J Clin Microbiol Infect Dis 2023; 42:1373-1381. [PMID: 37721704 PMCID: PMC10587247 DOI: 10.1007/s10096-023-04665-y] [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: 02/20/2023] [Accepted: 09/03/2023] [Indexed: 09/19/2023]
Abstract
Hypervirulent ribotypes (HVRTs) of Clostridioides difficile such as ribotype (RT) 027 are epidemiologically important. This study evaluated whether MALDI-TOF can distinguish between strains of HVRTs and non-HVRTs commonly found in Europe. Obtained spectra of clinical C. difficile isolates (training set, 157 isolates) covering epidemiologically relevant HVRTs and non-HVRTs found in Europe were used as an input for different machine learning (ML) models. Another 83 isolates were used as a validation set. Direct comparison of MALDI-TOF spectra obtained from HVRTs and non-HVRTs did not allow to discriminate between these two groups, while using these spectra with certain ML models could differentiate HVRTs from non-HVRTs with an accuracy >95% and allowed for a sub-clustering of three HVRT subgroups (RT027/RT176, RT023, RT045/078/126/127). MALDI-TOF combined with ML represents a reliable tool for rapid identification of major European HVRTs.
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Affiliation(s)
- Ahmed Mohamed Mostafa Abdrabou
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße 100, Building 43, D-66421, Homburg, Saar, Germany.
- Medical Microbiology and Immunology Department, Faculty of Medicine, Mansoura University, El Gomhouria Street, Mansoura, 35516, Egypt.
- National Reference Center for Clostridioides (Clostridium) difficile, Homburg-Münster-Coesfeld, Germany.
| | - Issa Sy
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße 100, Building 43, D-66421, Homburg, Saar, Germany
| | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße 100, Building 43, D-66421, Homburg, Saar, Germany
- National Reference Center for Clostridioides (Clostridium) difficile, Homburg-Münster-Coesfeld, Germany
| | - Manuel J Arroyo
- Clover Bioanalytical Software, Av. del Conocimiento, 41, 18016, Granada, Spain
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße 100, Building 43, D-66421, Homburg, Saar, Germany
| | - Alexander Mellmann
- National Reference Center for Clostridioides (Clostridium) difficile, Homburg-Münster-Coesfeld, Germany
- Institute of Hygiene, University of Münster, Robert-Koch-Straße 41, 48149, Münster, Germany
| | - Lutz von Müller
- National Reference Center for Clostridioides (Clostridium) difficile, Homburg-Münster-Coesfeld, Germany
- Christophorus Kliniken Coesfeld, Coesfeld, Germany
| | - Barbara Gärtner
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße 100, Building 43, D-66421, Homburg, Saar, Germany
- National Reference Center for Clostridioides (Clostridium) difficile, Homburg-Münster-Coesfeld, Germany
| | - Fabian K Berger
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße 100, Building 43, D-66421, Homburg, Saar, Germany
- National Reference Center for Clostridioides (Clostridium) difficile, Homburg-Münster-Coesfeld, Germany
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Zhang G, Zhao Q, Ye K, Ye L, Ma Y, Yang J. Molecular analysis of clinical Citrobacter spp. isolates: Acquisition of the Yersinia high-pathogenicity island mediated by ICEkp in C. freundii. Front Microbiol 2023; 14:1056790. [PMID: 37007518 PMCID: PMC10060806 DOI: 10.3389/fmicb.2023.1056790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
BackgroundStudies on Citrobacter spp. are limited, hindering our understanding of its species evolution and medical relevance.MethodsA total of 164 clinical Citrobacter spp. isolates were collected from 2017 to 2020 and identified by VITEK MALDI-TOF MS or VITEK-2 Gram-Negative Identification Card. All isolates were further analyzed by whole-genome sequencing using a HiSeq sequencer. All sequences were processed using different modules of the PGCGAP integrated package: Prokka and fastANI were used for annotation and average nucleotide identification (ANI), respectively. Antibiotic resistance and virulence genes were identified by searching CARD, ResFinder, and VFDB databases, respectively. Strains were identified using Ribosomal Multi-locus Sequence Typing (rMLST) classification based on 53 ribosome protein subunits (rps). The evolutionary relationship was analyzed using kSNP3 and visualized by iTOL editor v1_1. Genetic environments were compared by BLAST and visualized by Easyfig 2.2.5. The pathogenicity of some Citrobacter freundii isolates was confirmed by Galleria mellonella larvae infection test.ResultsA total of 14 species of Citrobacter spp. were identified from 164 isolates. However, 27 and 11 isolates were incorrectly identified as C. freundii and Citrobacter braakii by MALDI-TOF MS, respectively. In addition, MS also failed to identify Citrobacter portucalensis. The virulence genes mainly encoded proteins related to flagella and iron uptake systems. Citrobacter koseri isolates (n = 28) contained two iron uptake systems, coding yersiniabactin and aerobactin, respectively. C. braakii isolates (n = 32), like Salmonella, carried Vi capsule polysaccharide synthesis genes. The yersiniabactin gene clusters identified in five C. freundii isolates are located on various ICEkp elements and have not been reported previously. Moreover, ICEkp-carrying C. freundii showed diverse pathogenic features.ConclusionConventional methods have significant defects in identifying Citrobacter spp. ICEkp-like elements-mediated acquirement of the Yersinia high-pathogenicity island was identified for the first time in C. freundii.
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Development and Evaluation of a Core Genome Multilocus Sequencing Typing (cgMLST) Scheme for Serratia marcescens Molecular Surveillance and Outbreak Investigations. J Clin Microbiol 2022; 60:e0119622. [PMID: 36214584 PMCID: PMC9667775 DOI: 10.1128/jcm.01196-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Serratia marcescens can cause a range of severe infections and contributes to nosocomial outbreaks. Although whole-genome sequencing (WGS)-based typing is the standard method for molecular surveillance and outbreak investigation, there is no standardized analytic scheme for S. marcescens core genome multilocus sequence typing (cgMLST). Here, the development and evaluation of a S. marcescens cgMLST scheme is reported with the goal of enabling a standardized methodology and typing nomenclature. Four hundred ninety-one high-quality S. marcescens WGS data sets were extracted from public databases and-using the genomic sequence of NCBI reference strain S. marcescens Db11 (NZ_HG326223.1) as a starting point-all Db11 genes present in ≥97% data sets used to create a cgMLST scheme. The novel scheme was evaluated using WGS data from 24 outbreak investigations (n = 175 isolates) distributed over three continents. Analysis of Db11 genes within the 491 data sets identified 2,692 target genes present in ≥97% of genomes (mean, 99.1%; median, 99.9%). These genes formed the novel cgMLST scheme, covering 47.8% of nucleotides in the Db11 genome. Analyzing 175 isolates from 24 outbreaks using the novel scheme gave comparable results to previous typing efforts for both general groupings and allelic distances within clusters. In summary, a novel cgMLST scheme for S. marcescens was developed and evaluated. The scheme and its associated nomenclature will improve standardization of typing efforts for molecular surveillance and outbreak investigation, allowing better understanding of S. marcescens genomic epidemiology and facilitating interlaboratory comparisons.
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Wang L, Li Z, Xiao N, Tang J, He Y, Guo J, Zhao X. Genetic Characterization of bla NDM-1-Carrying Citrobacter portucalensis Sequence Type 328 and Citrobacter freundii Sequence Type 98. Infect Drug Resist 2022; 15:2235-2242. [PMID: 35510156 PMCID: PMC9059874 DOI: 10.2147/idr.s361761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/16/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose NDM-1-producing Citrobacter portucalensis and Citrobacter freundii simultaneously occurred in a hospital. This study aims to characterize the blaNDM-1-carrying plasmids in these Citrobacter strains. Methods Cf7303, Cf7308, and Cf7313 were recovered from three patients in a teaching hospital from September 24 to October 1, 2021. Bacteria were identified by MALDI-TOF mass spectrometry, and antibiotics susceptibility tests were determined by VITEK® 2 compact system. Whole-genome sequencing (WGS) was performed using the HiSeq Illumina and QNome platform to characterize the genomes. Results Cf7303 was identified as C. portucalensis Sequence Type 328 by WGS, and harbored two plasmids, namely pCf7303 and a novel IncFIB pNDM-Cf7303 on which antibiotic-resistant genes (blaTEM-1, blaCTX-M-14, blaNDM-1, aac (3)-IId, aadA2, fosA3, sul1, sul2, catA2, tetD, dfrA12, qacEdelta1, mph(A), and bleMBL) are located. C. freundii strain Cf7308 and Cf7313 belonged to the same Sequence Type 98. Cf7308 contained two plasmids, pCf7308, and an IncN1 pNDM-Cf7308 with homology to pNDM-BTR in E. coli and pNDM-CWH001 in C. freundii. Conclusion We characterized a putatively novel IncFIB plasmid carrying blaNDM-1 in C. portucalensis. In addition, the closely related blaNDM-1-carrying IncN1 plasmids in E. coli and C. freundii suggest that interspecies or intraspecies horizontal transfer occurs in China.
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Affiliation(s)
- Lijun Wang
- Department of Clinical Laboratory, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 102218, People's Republic of China
| | - Ziyao Li
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, 100029, People's Republic of China
| | - Nan Xiao
- Department of Clinical Laboratory, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 102218, People's Republic of China
| | - Jie Tang
- Department of Clinical Laboratory, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 102218, People's Republic of China
| | - Yu He
- Qitan Technology Ltd., Chengdu, Sichuan Province, 610044, People's Republic of China
| | - Jun Guo
- Department of Geriatrics, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 102218, People's Republic of China
| | - Xiuying Zhao
- Department of Clinical Laboratory, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 102218, People's Republic of China
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Microbial Reduction of Fumonisin B1 by the New Isolate Serratia marcescens 329-2. Toxins (Basel) 2021; 13:toxins13090638. [PMID: 34564642 PMCID: PMC8473028 DOI: 10.3390/toxins13090638] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/21/2022] Open
Abstract
The mycotoxin fumonisin (FB) has become a major problem in maize products in southeastern Asia. Fumonisin can affect the health of humans and many animals. Fumonisin contamination can be reduced by detoxifying microbial enzyme. Screening of 95 potent natural sources resulted in 5.3% of samples yielding a total of five bacterial isolates that were a promising solution, reducing approximately 10.0-30.0% of fumonisin B1 (FB1). Serratia marcescens, one of the dominant degrading bacteria, was identified with Gram staining, 16S rRNA gene, and MALDI-TOF/TOF MS. Cell-free extract showed the highest fumonisin reduction rates, 30.3% in solution and 37.0% in maize. Crude proteins from bacterial cells were analyzed with a label-free quantification technique. The results showed that hydrolase enzymes and transferase enzymes that can cooperate in the fumonisin degradation process were highly expressed in comparison to their levels in a control. These studies have shown that S. marcescens 329-2 is a new potential bacterium for FB1 reduction, and the production of FB1-reducing enzymes should be further explored.
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Fu M, Zhang X, Chen B, Li M, Zhang G, Cui L. Characteristics of Isolates of Pseudomonas aeruginosa and Serratia marcescens Associated With Post-harvest Fuzi ( Aconitum carmichaelii) Rot and Their Novel Loop-Mediated Isothermal Amplification Detection Methods. Front Microbiol 2021; 12:705329. [PMID: 34489893 PMCID: PMC8417746 DOI: 10.3389/fmicb.2021.705329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/05/2021] [Indexed: 11/13/2022] Open
Abstract
Fuzi (the lateral root of Aconitum carmichaelii Debx.) is a traditional Chinese medicine that is cultivated in more than eight provinces in China. However, it can be easily devastated by post-harvest rot, causing huge losses. Therefore, it is extremely important that the primary causal pathogens of post-harvest Fuzi rot are identified and appropriate detection methods for them are developed to prevent and control losses. In this study, two bacterial strains (X1 and X2) were isolated from rotten post-harvest Fuzi. Based on their morphological, physiological, and biochemical characteristics, housekeeping gene homologies, and matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF MS) results, these isolates were identified as Pseudomonas aeruginosa and Serratia marcescens. The pathogenicities of these isolates were confirmed by fulfilling Koch's postulates demonstrating that they were post-harvest Fuzi rot pathogens. Two loop-mediated isothermal amplification (LAMP) methods targeting the gyrase B subunit (gyrB) gene of P. aeruginosa and the phosphatidylinositol glycan C (pigC) gene of S. marcescens were successfully developed, and it was found that the target genes were highly specific to the two pathogens. These LAMP methods were used to detect P. aeruginosa and S. marcescens in 46 naturally occurring Fuzi and their associated rhizosphere soil samples of unknown etiology. The two bacterial assays were positive in some healthy and rotten samples and could be accomplished within 1 h at 65°C without the need for complicated, expensive instruments. To our knowledge, this is the first report of P. aeruginosa and S. marcescens causing post-harvest Fuzi rot. The newly developed methods are expected to have applications in point-of-care testing for the two pathogens under different Fuzi planting procedures and will significantly contribute to the control and prevention of Fuzi rot.
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Affiliation(s)
- Meng Fu
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xin Zhang
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Bei Chen
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Mingzhu Li
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Guoyan Zhang
- Chenggu County Qunli Traditional Chinese Medicine Cooperative, Chenggu, China
| | - Langjun Cui
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, China
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Huber CA, Reed SJ, Paterson DL. Bacterial Sub-Species Typing Using Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry: What Is Promising? Curr Issues Mol Biol 2021; 43:749-757. [PMID: 34294671 PMCID: PMC8929012 DOI: 10.3390/cimb43020054] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/07/2021] [Accepted: 07/16/2021] [Indexed: 11/28/2022] Open
Abstract
Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is routinely used for bacterial identification. It would be highly beneficial to also be able to use the technology as a fast way to detect clinically relevant clones of bacterial species. However, studies to this aim have often had limited success. The methods used for data acquisition, processing and data interpretation are highly diverse amongst studies on MALDI-TOF MS sub-species typing. In addition to this, feasibility may depend on the bacterial species and strains investigated, making it difficult to determine what methods may or may not work. In our paper, we have reviewed recent research on MALDI-TOF MS typing of bacterial strains. Although we found a lot of variation amongst the methods used, there were approaches shared by multiple research groups. Multiple spectra of the same isolate were often combined before further analysis for strain distinction. Many groups used a protein extraction step to increase resolution in their MALDI-TOF MS results. Peaks at a high mass range were often excluded for data interpretation. Three groups have found ways to determine feasibility of MALDI-TOF MS typing for their set of strains at an early stage of their project.
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Räisänen K, Sarvikivi E, Arifulla D, Pietikäinen R, Forsblom-Helander B, Tarkka E, Anttila VJ, Grönroos JO, Rintala E, Kauranen J, Ahlsved M, Broas M, Mikkola J, Sieberns J, Jalava J, Lyytikäinen O. Three clusters of carbapenemase-producing Citrobacter freundii in Finland, 2016-20. J Antimicrob Chemother 2021; 76:2697-2701. [PMID: 34164687 DOI: 10.1093/jac/dkab209] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/31/2021] [Indexed: 12/28/2022] Open
Abstract
OBJECTIVES Carbapenemase-producing Enterobacterales (CPE) have spread widely into health care facilities (HCF) but clusters caused by carbapenemase-producing (CP) Citrobacter freundii have been uncommon until recent years. Here we describe CP C. freundii clusters detected in Finland during 2016-20. METHODS As a part of the national CPE surveillance, clinical microbiology laboratories send potential CP C. freundii isolates to the reference laboratory for confirmation and further characterization. Whole genome sequencing (WGS) with Illumina MiSeq sequencer was used to detect clusters. Resistance genes and STs were analysed using SRST2 and typing with core genome (cg) MLST. A case was defined as a patient with a CP C. freundii isolate belonging to one of the detected clusters. RESULTS We detected three CP C. freundii clusters: cluster 1 included 16 cases in five HCFs during 2016-20, cluster 2 had two cases in two HCFs during 2018-19 and cluster 3 had two cases in one HCF in 2020. The isolates (11 clinical and 5 screening) in cluster 1 had KPC-2 carbapenemase and were sequence type (ST)18. Cluster 2 (2 clinical isolates) had OXA-181/GES-5 carbapenemases and were ST604 and cluster 3 (two screening isolates) had KPC-3 carbapenemase and were ST116. None of the cases had a history of recent travel abroad. CONCLUSIONS CP C. freundii also causes outbreaks and can be a reservoir of carbapenemase genes. The long intervals between successive cases, mostly found in clinical specimens in two clusters, suggest that besides unknown carriers, environmental contamination may play a role in transmission.
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Affiliation(s)
- Kati Räisänen
- Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Emmi Sarvikivi
- Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Dinah Arifulla
- Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Risto Pietikäinen
- Department of Internal medicine, Kymenlaakso Central Hospital, Kotka, Finland
| | - Benita Forsblom-Helander
- Clinical Microbiology, University of Helsinki, Helsinki, Finland.,Helsinki University Hospital, Helsinki, Finland
| | - Eveliina Tarkka
- Clinical Microbiology, University of Helsinki, Helsinki, Finland.,Helsinki University Hospital, Helsinki, Finland
| | | | - Juha O Grönroos
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Esa Rintala
- Department of Hospital Hygiene & Infection Control, Turku University Hospital, Turku, Finland
| | | | - Matias Ahlsved
- Infection-Hospital Hygiene Unit, Lapland Central Hospital, Rovaniemi, Finland
| | - Markku Broas
- Infection-Hospital Hygiene Unit, Lapland Central Hospital, Rovaniemi, Finland
| | - Janne Mikkola
- Department of Hospital Hygiene and Infection Control, Kanta-Häme Central Hospital, Hämeenlinna, Finland
| | - Jennifer Sieberns
- Joint Municipal Authority for North Karelia Social and Health Services (Siun Sote), Joensuu, Finland
| | - Jari Jalava
- Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Outi Lyytikäinen
- Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
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11
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Fang L, Xu H, Ren X, Li X, Ma X, Zhou H, Hong G, Liang X. Epidemiology and Risk Factors for Carbapenem-Resistant Klebsiella Pneumoniae and Subsequent MALDI-TOF MS as a Tool to Cluster KPC-2-Producing Klebsiella Pneumoniae, a Retrospective Study. Front Cell Infect Microbiol 2020; 10:462. [PMID: 33042858 PMCID: PMC7521130 DOI: 10.3389/fcimb.2020.00462] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/28/2020] [Indexed: 12/21/2022] Open
Abstract
Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) appeared recently and now presents a particularly critical problem to hospitalized patients worldwide. We aim to investigate the epidemiology and the risk factors for CRKP colonization and infections, and to evaluate the application performance of MALDI-TOF MS in clustering CRKP. Results: CRKP colonization and infections incidence was 2.7 (35/1,319,427) per 100,000 patient-days. Inpatients in CRKP group had higher medical expense than CSKP group. Inpatients with underlying conditions, particularly with pulmonary diseases, and with antimicrobial use prior to culture within 30 days, especially with carbapenem use, were risk factors for CRKP acquisition. All CRKP isolates were detected producing KPC-2. The MALDI-TOF MS system and PFGE system provided similar results, with a good concordance between the two methods (adjusted Rand's coefficient, 0.846) and a high probability of MALDI-TOF MS to predict PFGE results (Wallace coefficient, 0.908). Conclusions: Underlying conditions, particularly pulmonary diseases, and antimicrobial use prior to culture within 30 days, especially carbapenem use, are risk factors for CRKP acquisition. BlaKPC−2 is the mainstream gene of CRKP in our geographic area of analysis. As only simple sample preparation is needed and the results can be obtained in a short time, MALDI-TOF MS may be considered a probable alternative to PFGE in clustering KPC-2-producing CRKP.
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Affiliation(s)
- Lili Fang
- Department of Clinical Laboratory, The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Genetic Testing, Xiamen, China.,School of Public Health, Xiamen University, Xiamen, China
| | - Heping Xu
- Department of Clinical Laboratory, The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Genetic Testing, Xiamen, China.,School of Public Health, Xiamen University, Xiamen, China
| | - Xiaoying Ren
- Department of Clinical Laboratory, The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Genetic Testing, Xiamen, China.,School of Public Health, Xiamen University, Xiamen, China
| | - Xun Li
- Department of Clinical Laboratory, The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Genetic Testing, Xiamen, China.,School of Public Health, Xiamen University, Xiamen, China
| | - Xiaobo Ma
- Department of Clinical Laboratory, The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Genetic Testing, Xiamen, China.,School of Public Health, Xiamen University, Xiamen, China
| | - Haijian Zhou
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Guolin Hong
- Department of Clinical Laboratory, The First Affiliated Hospital, School of Medicine, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Genetic Testing, Xiamen, China.,School of Public Health, Xiamen University, Xiamen, China
| | - Xianming Liang
- Center of Clinical Laboratory, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, China.,Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
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12
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Welker M, Van Belkum A, Girard V, Charrier JP, Pincus D. An update on the routine application of MALDI-TOF MS in clinical microbiology. Expert Rev Proteomics 2019; 16:695-710. [PMID: 31315000 DOI: 10.1080/14789450.2019.1645603] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has entered clinical diagnostics and is today a generally accepted and integral part of the workflow for microbial identification. MALDI-TOF MS identification systems received approval from national and international institutions, such as the USA-FDA, and are continuously improved and adopted to other fields like veterinary and industrial microbiology. The question is whether MALDI-TOF MS also has the potential to replace other conventional and molecular techniques operated in routine diagnostic laboratories. Areas covered: We give an overview of new advancements of mass spectral analysis in the context of microbial diagnostics. In particular, the expansion of databases to increase the range of readily identifiable bacteria and fungi, the refined discrimination of species complexes, subspecies, and types, the testing for antibiotic resistance or susceptibility, progress in sample preparation including automation, and applications of other mass spectrometry techniques are discussed. Expert opinion: Although many new approaches of MALDI-TOF MS are still in the stage of proof of principle, it is expectable that MALDI-TOF MS will expand its role in the clinical microbiology laboratory of the future. New databases, instruments and analytical software modules will continue to be developed to further improve diagnostic efficacy.
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Affiliation(s)
- Martin Welker
- bioMérieux, Microbiology R&D , La Balme Les Grottes , France
| | - Alex Van Belkum
- bioMérieux, Microbiology R&D , La Balme Les Grottes , France
| | - Victoria Girard
- bioMérieux, Microbiology R&D , La Balme Les Grottes , France
| | | | - David Pincus
- bioMérieux, Microbiology Innovation , Hazelwood , MO , USA
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