1
|
Sheng Z, Li J, Han G, Fan R, Zhu P, Fang X. Molecular epidemiological and clinical infection characteristics analysis of Ralstonia. Eur J Clin Microbiol Infect Dis 2024:10.1007/s10096-024-04823-w. [PMID: 38639850 DOI: 10.1007/s10096-024-04823-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/02/2024] [Indexed: 04/20/2024]
Abstract
PURPOSE This study was to clarify the molecular epidemiology and clinical infection characteristics of Ralstonia pickettii and establish sequence typing system. METHODS 48 nonrepetitive Ralstonia pickettii strains were collected from January 2008 to December 2013 at the Chinese People's Liberation Army General Hospital (PLAGH) and were identified through a specific PCR experiment, 16 S rDNA experiment and VITEK 2 system to compare the identification accuracy. The sequence types of the strains were analyzed by multilocus sequence typing (MLST) method. The antibiotic sensitivity of these strains was determined with disc diffusion tests and broth microdilution method. The clinical data of Ralstonia pickettii infected patients were collected. RESULTS All of the 48 strains were identified as Ralstonia pickettii by VITEK 2 system. 30 and 34 strains were identified as Ralstonia pickettii by PCR and 16 S rDNA experiment respectively. ST9 was the most sequence types (STs) in these 18 STs of 42 strains. 42 strains were divided into 2 groups (A and B) and 18 genotypes. Ralstonia pickettii was sensitive to some cephalosporins, β-lactam/β-lactamase inhibitor, levofloxacin and trimethoprim/sulfamethoxazole. Cough, sputum, shortness of breath and pulmonary rales were the common clinical symptoms of most Ralstonia pickettii infected patients. CONCLUSION We established a sequence typing system with a relatively fine resolution and the PCR assay is a faster and more sensitive method for clinical identification of Ralstonia pickettii. ST9 is the most common sequence types of Ralstonia pickettii. The most common clinical characteristics of Ralstonia pickettii infected patients were cough, sputum, shortness of breath and pulmonary rales.
Collapse
Affiliation(s)
- Zhaojun Sheng
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Jiaxin Li
- Department of Respiratory and Critical Care Medicine, Aerospace Center Hospital, Beijing, China
| | - Guojing Han
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Ru Fan
- College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing, China
| | - Pingjun Zhu
- Department of Respiratory and Critical Care Medicine, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.
| | - Xiangqun Fang
- Department of Respiratory and Critical Care Medicine, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.
| |
Collapse
|
2
|
Chen Q, Tan S, Long S, Wang K, Liu Q. Vagococcus fluvialis isolation from the urine of a bladder cancer patient: a case report. BMC Infect Dis 2024; 24:261. [PMID: 38409020 PMCID: PMC10898091 DOI: 10.1186/s12879-024-09082-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/01/2024] [Indexed: 02/28/2024] Open
Abstract
Vagococcus fluvialis infection is rare in humans, and there is limited research on the clinical manifestations and antimicrobial susceptibility testing of Vagococcus fluvialis infection. Here, We isolated Vagococcus fluvialis from the urine samples of bladder cancer patients at Hunan Provincial People's Hospital, and it is the first reported case of Vagococcus fluvialis isolated from the urine. The fully automated microbial identification system and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) identified the bacterium as Vagococcus fluvialis with a confidence level of 99.9%. The VITEK-2Compact fully automated microbial susceptibility analysis system indicated that it was most sensitive to tigecycline, vancomycin, quinupristin/dalfopristin, linezolid, and showed moderate sensitivity to erythromycin, levofloxacin, ciprofloxacin, ampicillin/sulbactam, and tetracycline. Additionally, it exhibited synergy when combined with high-level gentamicin and vancomycin, showing sensitivity. However, it displayed poor activity against penicillin and furanth. According to our knowledge, this is the first study to isolate and identify Vagococcus fluvialis from the urine of bladder cancer patients and the systematically reviewed other reported Vagococcus infections on human, which provide an experimental basis for guiding the rational use of drugs in the clinical treatment and diagnose of Vagococcus fluvialis infection and related pathogenic mechanism research. Meanwhile, we have systematically reviewed other reported.
Collapse
Affiliation(s)
- Qian Chen
- Department of Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, 410005, Changsha, Hunan, P.R. China
| | - Siwen Tan
- Department of Comprehensive Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, 410005, Changsha, Hunan, P.R. China
| | - Sheng Long
- Department of Clinical Laboratory, Hunan Province People's Hospital, The First Affiliated Hospital of Hunan Normal University, 410005, Changsha, Hunan, P.R. China
| | - Kaixuan Wang
- Department of Comprehensive Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, 410005, Changsha, Hunan, P.R. China
| | - Qi Liu
- Department of Comprehensive Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, 410005, Changsha, Hunan, P.R. China.
| |
Collapse
|
3
|
Xie L, Yang M, Liu M, Li Q, Luo C, Luo J. Integrating rapid pathogen identification and antimicrobial susceptibility testing through multiplex TaqMan qPCR assay. J Microbiol Methods 2024; 217-218:106888. [PMID: 38176658 DOI: 10.1016/j.mimet.2023.106888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/23/2023] [Accepted: 12/28/2023] [Indexed: 01/06/2024]
Abstract
Timely bacterial identification (ID) and antimicrobial susceptibility testing (AST) are of significance for therapy of bacteria-infected patients. In the present study, we developed a multiplex TaqMan qPCR assay for rapid and accurate ID and AST of three common hospital acquired pneumonia species, namely Acinetobacter baumannii, Klebsiella pneumoniae and Staphylococcus aureus. In this assay, DNA extraction and bacterial co-incubation with antibiotics are accomplished based on a common PCR instrument. ID of three bacteria is based on specific conserved DNA sequence fragment (gltA for A. baumannii, phoE for K. pneumoniae and nuc for S. aureus) detection through multiplex TaqMan qPCR assay within 80 min. AST of three bacteria could be acquired within 200 min based on genomic DNA fold change detection after 2 h of antibiotic exposure. Testing of 23 bronchoalveolar lavage fluid samples spiked by different A. baumannii isolates, 20 bronchoalveolar lavage fluid samples spiked by different K. pneumoniae isolates, and 14 bronchoalveolar lavage fluid samples spiked by different S. aureus isolates showed that the multiplex TaqMan qPCR assay had 100% (95% CI: 85.69-100), 100% (95% CI: 83.89-100) and 100% (95% CI:78.47-100) identification agreement with the initial spiked bacteria. Subsequent AST results compared with the standard broth microdilution method showed an overall agreement of 91.30% (95% CI: 73.20 to 97.58) for A. baumannii, 90% (95% CI: 69.90 to 97.21) for K. pneumoniae and 92.86% (95% CI: 68.53 to 98.73) for S. aureus based on the current multiplex TaqMan assay. Due to the high rapidity, good agreement, simplicity, and high throughput, this multiplex TaqMan assay could be helpful for ID and broad-spectrum AST in A. baumannii, K. pneumoniae and S. aureus, as well as potentially applicable for other clinical bacteria by changing the primers and probes.
Collapse
Affiliation(s)
- Libo Xie
- The First College of Clinical Medical Science, China Three Gorges University, Yichang 443000, China; Yichang Central People's Hospital, China
| | - Min Yang
- Yunnan Center for Disease Control and Prevention, Yunnan, China
| | - Min Liu
- The First College of Clinical Medical Science, China Three Gorges University, Yichang 443000, China; Yichang Central People's Hospital, China
| | - Qianyuan Li
- The First College of Clinical Medical Science, China Three Gorges University, Yichang 443000, China; Yichang Central People's Hospital, China
| | - Chunhua Luo
- The First College of Clinical Medical Science, China Three Gorges University, Yichang 443000, China; Yichang Central People's Hospital, China.
| | - Jun Luo
- The First College of Clinical Medical Science, China Three Gorges University, Yichang 443000, China; Yichang Central People's Hospital, China.
| |
Collapse
|
4
|
da Silva RR, Tomachewski D, Karas LP, Galvão CW, da Rocha JCF, Miyoshi E, Etto RM. The new Ribopeaks (RPK-II): Updated and enlarged tool for bacterial classification based on r-protein m/z data. J Proteomics 2023; 289:105008. [PMID: 37775078 DOI: 10.1016/j.jprot.2023.105008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/29/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023]
Abstract
Ribopeaks is a rapid, sensitive, and economic web tool for bacterial identification based on m/z data from MALDI-TOF MS. To provide greater accuracy and robustness in the Ribopeaks analyzes we present an updated bacterial identification tool version, called Ribopeaks II (RPK-II). RPK-II contains a larger database, with r-protein data from fully sequenced bacterial genomes and optimized algorithms. Furthermore, this new version provides additional information about the identified bacterium, regarding antibiotic resistance.
Collapse
Affiliation(s)
- Renann Rodrigues da Silva
- Postgraduate Program in Agronomy, State University of Ponta Grossa, Paraná, Brazil; Microbial Molecular Biology Laboratory, State University of Ponta Grossa, Paraná, Brazil
| | - Douglas Tomachewski
- Postgraduate Program in Agronomy, State University of Ponta Grossa, Paraná, Brazil; Microbial Molecular Biology Laboratory, State University of Ponta Grossa, Paraná, Brazil
| | - Laís Priscila Karas
- Microbial Molecular Biology Laboratory, State University of Ponta Grossa, Paraná, Brazil; Postgraduate Program in Biomedical Sciences, State University of Ponta Grossa, Paraná, Brazil
| | - Carolina Weigert Galvão
- Postgraduate Program in Agronomy, State University of Ponta Grossa, Paraná, Brazil; Microbial Molecular Biology Laboratory, State University of Ponta Grossa, Paraná, Brazil
| | - José Carlos Ferreira da Rocha
- Microbial Molecular Biology Laboratory, State University of Ponta Grossa, Paraná, Brazil; Postgraduate Program in Applied Computing, State University of Ponta Grossa, Paraná, Brazil
| | - Edmar Miyoshi
- Microbial Molecular Biology Laboratory, State University of Ponta Grossa, Paraná, Brazil; Postgraduate Program in Biomedical Sciences, State University of Ponta Grossa, Paraná, Brazil
| | - Rafael Mazer Etto
- Postgraduate Program in Agronomy, State University of Ponta Grossa, Paraná, Brazil; Microbial Molecular Biology Laboratory, State University of Ponta Grossa, Paraná, Brazil; Postgraduate Program in Applied Computing, State University of Ponta Grossa, Paraná, Brazil.
| |
Collapse
|
5
|
Zhang D, Wang X, Yu J, Dai Z, Li Q, Zhang L. A case of Vagococcus fluvialis isolated from the bile of a patient with calculous cholecystitis. BMC Infect Dis 2023; 23:689. [PMID: 37845605 PMCID: PMC10578025 DOI: 10.1186/s12879-023-08696-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 10/11/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND Chronic cholecystitis, characterized by persistent inflammation of the gallbladder, predominantly stems from the prolonged presence of gallstones. Calculous cholecystitis has demonstrated a consistent escalation in its incidence over time.Gallbladder stones have been recognized as a predisposing factor for the development of biliary tract infections.Concomitantly, there have been substantial shifts in the distribution and resistance profiles of pathogenic microorganisms responsible for biliary tract infections. The timely acquisition of bile samples for pathogen analysis is of paramount importance, given its critical role in guiding judicious clinical pharmacotherapy and enhancing patient prognosis. CASE PRESENTATION We present a case involving a 66-year-old female patient who had previously undergone subtotal gastrectomy due to diffuse large B-cell lymphoma. The patient was admitted to our institution with complaints of abdominal pain. Subsequent diagnostic evaluation revealed concurrent choledocholithiasis and cholecystolithiasis. The patient underwent surgical cholecystectomy as the therapeutic approach. Histopathological examination of the excised gallbladder disclosed characteristic features indicative of chronic cholecystitis. Subsequent laboratory analysis of the patient's bile specimen yielded Gram-positive cocci, subsequently identified through biochemical assays, mass spectrometry, and 16 S rRNA analysis as Vagococcus fluvialis. Further in vitro antimicrobial susceptibility testing using disk diffusion and microfluidic dilution showed that this strain exhibited inhibition zone diameters ranging from 12.0 to 32.0 mm in response to 26 antibiotics, including ampicillin, cefazolin, cefuroxime, cefotaxime, ceftriaxone, cefepime, ampicillin/sulbactam, piperacillin, ciprofloxacin, cefoperazone/sulbactam, imipenem, meropenem, piperacillin/tazobarb, penicillin, erythromycin, chloramphenicol, vancomycin, methotrexate/sulfamethoxazole, teicoplanin, linezolid, tigecycline, cefoxitin, ceftazidime, levofloxacin, minocycline and tobramycin. However, the inhibition zone diameters were 6.0 mm for amikacin, oxacillin, clindamycin, and tetracycline. The patient received ceftazidime anti-infective therapy both preoperatively and within 24 h postoperatively and was discharged successfully one week after surgery. CONCLUSION In this study, we present the inaugural isolation and identification of Vagococcus fluvialis from bile specimens of patients afflicted with calculous cholecystitis. This novel finding lays a substantial experimental groundwork for guiding clinically rational antimicrobial therapy and advancing the exploration of relevant pathogenic mechanisms pertaining to Vagococcus fluvialis infections.
Collapse
Affiliation(s)
- Dan Zhang
- Department of Clinical Laboratory, Wuhan Asia General Hospital, Wuhan Asia General Hospital, Wuhan University of Science and Technology, Wuhan, Hubei Province, 430056, People's Republic of China
| | - Xiaosu Wang
- Department of Clinical Laboratory, Wuhan Asia General Hospital, Wuhan Asia General Hospital, Wuhan University of Science and Technology, Wuhan, Hubei Province, 430056, People's Republic of China
| | - Jingdan Yu
- Department of Clinical Laboratory, Wuhan Asia General Hospital, Wuhan Asia General Hospital, Wuhan University of Science and Technology, Wuhan, Hubei Province, 430056, People's Republic of China
| | - Zheng Dai
- Department of Clinical Laboratory, Wuhan Asia General Hospital, Wuhan Asia General Hospital, Wuhan University of Science and Technology, Wuhan, Hubei Province, 430056, People's Republic of China
| | - Qichao Li
- Department of Clinical Laboratory, Wuhan Asia General Hospital, Wuhan Asia General Hospital, Wuhan University of Science and Technology, Wuhan, Hubei Province, 430056, People's Republic of China
| | - Litao Zhang
- Department of Clinical Laboratory, Wuhan Asia General Hospital, Wuhan Asia General Hospital, Wuhan University of Science and Technology, Wuhan, Hubei Province, 430056, People's Republic of China.
| |
Collapse
|
6
|
Pinthanon A, Nithitarnwat C, Pintapin C, Siripanee C, Yindee J, Am-In N, Kesdangsakonwut S, Surachetpong S, Prapasarakul N. Rapid identification of canine uropathogens by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry and the clinical factors that correlated bacterial species and antimicrobial resistance. Vet Res Commun 2023; 47:1457-1469. [PMID: 37036600 DOI: 10.1007/s11259-023-10096-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/04/2023] [Indexed: 04/11/2023]
Abstract
Using the matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) method for bacterial diagnosis, rapid urine sample preparation can reduce time relapsing of diagnosis and improve discriminatory power in coinfection cases. We aimed to evaluate rapid urine preparation procedures before MALDI-TOF MS application using dog clinical urine samples in comparison with standard microbiological diagnostic methods by agreement analysis. We determined the frequency and distribution of bacteria and bacterial resistance and their correlations to clinical history. Three experimental procedures comprising direct centrifugation, 10% sodium dodecyl sulfate digestion, and ultrasonic preparation were performed for method validation and sensitivity. Sterile urine containing Escherichia coli and/or Staphylococcus aureus were used as simulated samples. By ultrasonic preparation, the microorganisms could be detected 1.46-1.51 × 105 CFU, which was considered the most suitable technique. This preparation was significantly consistent with the routine method based on data from Hospital Information Systems for 50 urine samples from canine cystitis. By standard protocol, Enterobacteriaceae and Staphylococcus pseudintermedius were found in most of the 155 urine samples with cystitis. Extended-spectrum beta-lactamase-producing Enterobacteriaceae was found in 25-30% of the samples. Imipenem resistance was found in 70% of Acinetobacter baumannii cases; almost all were resistant to second-generation fluoroquinolones and tetracyclines. The most efficient antibiotic for treating bacterial urinary tract infection was amoxicillin plus clavulanic acid. A. baumannii and Pseudomonas aeruginosa were susceptible to pradofloxacin. Prolonged urine catheterization was linked to lower urinary tract infections by Enterobacter spp., which also correlated with chronic kidney disease.
Collapse
Affiliation(s)
- Artitaya Pinthanon
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chayanan Nithitarnwat
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chadaporn Pintapin
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chonradee Siripanee
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Jitrapa Yindee
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nutthee Am-In
- Department of Veterinary Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Sawang Kesdangsakonwut
- Department of Veterinary Pathology and Veterinary Diagnostic Laboratory, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Sirilak Surachetpong
- Department of Veterinary Medicine, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nuvee Prapasarakul
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
- Center of Excellence in Diagnostic and Monitoring of Animal Pathogens, Chulalongkorn University, Bangkok, Thailand.
| |
Collapse
|
7
|
Liang J, Wang S, Luo X, Zhang Y, Chen F, Mi Z, Zhang L, Wang G, Zhang W, Liu Z, Ma X, Ye Z, Zhu Z, Yin W, Jia S. Non-contact bacterial identification and decontamination based on laser-induced breakdown spectroscopy. J Photochem Photobiol B 2023; 244:112719. [PMID: 37201319 DOI: 10.1016/j.jphotobiol.2023.112719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/21/2023] [Accepted: 05/03/2023] [Indexed: 05/20/2023]
Abstract
As a new kind of modern military biological weapon, bacterial agents pose a serious threat to the public health security of human beings. Existing bacterial identification requires manual sampling and testing, which is time-consuming, and may also introduce secondary contamination or radioactive hazards during decontamination. In this paper, a non-contact, nondestructive and "green" bacterial identification and decontamination technology based on laser-induced breakdown spectroscopy (LIBS) is proposed. The principal component analysis (PCA) combined with support vector machine (SVM) based on radial basis kernel function is used to establish the classification model of bacteria, and the two-dimensional decontamination test of bacteria is carried out using laser-induced low-temperature plasma combined with a vibration mirror. The experimental results show that the average identification rate of the seven types of bacteria, including Escherichia coli, Bacillus subtilis, Pseudomonas fluorescens, Bacillus megatherium, Pseudomonas aeruginosa, Bacillus thuringiensis and Enterococcus faecalis reaches 98.93%, and the corresponding true positive rate, precision, recall and F1-score reaches 0.9714, 0.9718, 0.9714 and 0.9716, respectively. The optimal decontamination parameters are laser defocusing amount of -50 mm, laser repetition rate of 15-20 kHz, scanning speed of 150 mm/s and number of scans of 10. In this way, the decontamination speed can reach 25.6 mm2/min, and the inactivation rates for both Escherichia coli and Bacillus subtilis are higher than 98%. In addition, it is confirmed that the inactivation rate of plasma is 4 times higher than that of thermal ablation, meaning that the decontamination ability of LIBS mainly relies on the plasma rather than the thermal ablation effect. The new non-contact bacterial identification and decontamination technology does not require sample pretreatment, and can quickly identify bacteria in situ and decontaminate the surfaces of precision instruments, sensitive materials, etc., which has potential application value in modern military, medical and public health fields.
Collapse
Affiliation(s)
- Jiahui Liang
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy, Shanxi University, Taiyuan, China; Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, China
| | - Shuqing Wang
- SINOPEC Research Institute of Petroleum Processing Co., Ltd., Beijing, China
| | - Xuebin Luo
- Shanxi Xinhua Chemical Defense Equipment Research Institute Co., Ltd., Taiyuan, China
| | - Yan Zhang
- School of Optoelectronic Engineering, Xi'an Technological University, Xian, China
| | - Fei Chen
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy, Shanxi University, Taiyuan, China; Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, China
| | - Ziqi Mi
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy, Shanxi University, Taiyuan, China; Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, China
| | - Lei Zhang
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy, Shanxi University, Taiyuan, China; Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, China.
| | - Gang Wang
- Shanxi Xinhua Chemical Defense Equipment Research Institute Co., Ltd., Taiyuan, China
| | - Wanfei Zhang
- Shanxi Xinhua Chemical Defense Equipment Research Institute Co., Ltd., Taiyuan, China
| | - Zhenrong Liu
- Shanxi Xinhua Chemical Defense Equipment Research Institute Co., Ltd., Taiyuan, China
| | - Xiaofei Ma
- Shanxi Xinhua Chemical Defense Equipment Research Institute Co., Ltd., Taiyuan, China
| | - Zefu Ye
- Shanxi Gemeng US-China Clean Energy R&D Center Co., Ltd., Taiyuan, China
| | - Zhujun Zhu
- Shanxi Gemeng US-China Clean Energy R&D Center Co., Ltd., Taiyuan, China
| | - Wangbao Yin
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy, Shanxi University, Taiyuan, China; Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, China.
| | - Suotang Jia
- State Key Laboratory of Quantum Optics and Quantum Optics Devices, Institute of Laser Spectroscopy, Shanxi University, Taiyuan, China; Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, China
| |
Collapse
|
8
|
Donnars A, Mahieu R, Declerck C, Chenouard R, Lemarié C, Pailhoriès H, Requin J, Kempf M, Eveillard M. BIOFIRE® Blood Culture IDentification 2 (BCID2) panel for early adaptation of antimicrobial therapy in adult patients with bloodstream infections: a real-life experience. Diagn Microbiol Infect Dis 2023; 105:115858. [PMID: 36442386 DOI: 10.1016/j.diagmicrobio.2022.115858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/24/2022] [Accepted: 11/05/2022] [Indexed: 11/13/2022]
Abstract
Our objective was to assess the effectiveness of a multiplex PCR panel for blood culture identification (BCID2) on the implementation of appropriate antimicrobial therapy. We conducted a monocentric pre/post study comparing the time to result from direct microscopic examination (DE) to bacterial identification (BI) in positive blood cultures between 2 different periods: P1 without BCID2 and P2 with BCID2. Appropriate treatments prescribed before DE and after DE / BCID2 and after BI / BCID2 were compared using direct proportion comparison and survival analysis. For mono-microbial bloodstream infections, the proportion of appropriate antimicrobial treatment after DE was 50% in P1 vs. 87.5% after BCID2 in P2 (P < 0.001) for Gram-negative bacteria and 33.0% in P1 vs. 64.4% in P2 (P < 0.01) for Gram-positive bacteria. A significant difference (P = 0.04) was recorded with survival curves for Gram positive bacteria. BCID2 seems effective in reducing the time for prescribing appropriate antimicrobials.
Collapse
Affiliation(s)
- Anne Donnars
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France
| | - Rafael Mahieu
- Service des Maladies Infectieuses et Tropicales, CHU Angers, Angers, France; Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, INCIT, Angers, France
| | - Charles Declerck
- Service des Maladies Infectieuses et Tropicales, CHU Angers, Angers, France
| | - Rachel Chenouard
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France
| | - Carole Lemarié
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France
| | - Hélène Pailhoriès
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France
| | - Jim Requin
- Service des Maladies Infectieuses et Tropicales, CHU Angers, Angers, France
| | - Marie Kempf
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France; Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, INCIT, Angers, France
| | - Matthieu Eveillard
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France; Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, INCIT, Angers, France.
| |
Collapse
|
9
|
Saelens G, Houf K. Systematic review and critical reflection on the isolation and identification methods for spoilage associated bacteria in fresh marine fish. J Microbiol Methods 2022; 203:106599. [PMID: 36243229 DOI: 10.1016/j.mimet.2022.106599] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/28/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022]
Abstract
Consumers demand more fresh, safe, and high-quality food. As this is partiallycorrelated to the microbial profile, several microbiological examination tools are available. Incontrast to meat, no microbiological normalized methods to assess the microbiological quality of fresh marine fish have been agreed on. As a result, studies on the detection and diversity of spoilage associated organisms (SAOs) in fish often apply various detection, isolation, and identification techniques. This complicates the comparison and interpretation of data reported, and often results in different or inconclusive results. Therefore, the present review aimed to present a critical overview of the isolation/cultivation and detection techniques currently applied in fish microbiology. After a comprehensive search in the PubMed, Web of Science and Scopus databases, a total of 111 studies fulfilled the review selection criteria. Results revealed that when relying on culture media for the isolation of SAOs in fish, it is essential to include a salt-containing medium next to plate count agar that is currently used as the reference medium for the enumeration of bacteria on fish. In terms of identification, MALDI-TOF MS and 16S rRNA gene sequencing are currently the most promising tools, though other housekeeping genes should be targeted as well, and, the biggest challenge at this point is still the lack of comprehensive proteomic and sequence databases for SAOs. A full replacement of cultivation by next generation sequencing is difficult to recommend due to the absence of a standardized experimental methodology, especially for fish, and the relatively high sequencing costs. Additionally, a discrepancy between culture-dependent and independent methods in revealing the bacterial diversity, and abundancy, from marine fish was demonstrated by several authors. It is therefore recommended to consider both approaches as complements of one another, rather than substitutes, and to include them simultaneously to yield more complete results regarding the SAOs in fresh marine fish. As such, a thorough understanding of the biology of spoilage organisms and process will be obtained to prolong the shelf-life and deliver a high-quality product.
Collapse
Affiliation(s)
- Ganna Saelens
- Laboratory of Foodborne Parasites, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
| | - Kurt Houf
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium; Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Karel Lodewijk Ledeganckstraat 35, 9000 Ghent, Belgium
| |
Collapse
|
10
|
Costa LVD, Miranda RVDSLD, Reis CMFD, Andrade JMD, Cruz FV, Frazão AM, Fonseca ELD, Ramos JN, Brandão MLL, Vieira VV. MALDI-TOF MS database expansion for identification of Bacillus and related genera isolated from a pharmaceutical facility. J Microbiol Methods 2022; 203:106625. [PMID: 36403787 DOI: 10.1016/j.mimet.2022.106625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
Bacillus and related genera are among the main bacterial groups isolated from pharmaceutical production areas. The identification of Bacillus species and related genera by classical methods is particularly difficult, due to similarities between closely related species. The Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) is one of the most promising techniques for chemotaxonomic characterization of microorganisms, being an alternative to genotypic methods. This study aimed to identify Bacillus strains and related genera isolated from immunobiological production areas by phylogenetic analysis of housekeeping genes and expand the database associated with MALDI-TOF MS to improve their identification. In a previous study, 97 aerobic endospore-forming bacteria isolated from a pharmaceutical facility were analyzed by MALDI-TOF MS and 16S rRNA gene full-length sequencing. All strains were identified as Bacillus and related genera by the latest methodology. Among the 97 strains, 22 were unidentified and 2 strains were misidentified by MALDI-TOF MS. In the present study, these 24 strains were subjected to 16S rRNA gene phylogenetic analysis. Strains not identified at species level by this methodology were submitted to rpoB gene phylogenetic analysis. After identifying the strains, 19 of the 24 strains were incubated for 24, 48, and 72 h on Tryptic Soy Agar and Sheep Blood Agar and subjected to analysis by MALDI-TOF MS. A SuperSpectrum for each strain was created and entered into the equipment database. Finally, the 24 strains were again submitted to proteomic analysis by MALDI-TOF MS, and, at this time, all were correctly identified. The genotypic identification of in-house isolated strains and the introduction of these spectra in MALDI-TOF MS, in order to obtain a customized database, proved to be an extremely effective tool in the identification of Bacillus and related genera from pharmaceutical industry origin.
Collapse
Affiliation(s)
- Luciana Veloso da Costa
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Microbiological Control Laboratory, Brazil.
| | | | | | - Joyce Modesto de Andrade
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Microbiological Control Laboratory, Brazil
| | - Fernanda Ventura Cruz
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Microbiological Control Laboratory, Brazil
| | - Adriana Marques Frazão
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Microbiological Control Laboratory, Brazil
| | - Erica Louro da Fonseca
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Microbiological Control Laboratory, Brazil
| | - Juliana Nunes Ramos
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz (IOC), Interdisciplinary Medical Research Laboratory, Brazil
| | - Marcelo Luiz Lima Brandão
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Microbiological Control Laboratory, Brazil
| | - Verônica Viana Vieira
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz (IOC), Interdisciplinary Medical Research Laboratory, Brazil
| |
Collapse
|
11
|
Hu S, Li X, Yin X, Li R, Zhang R, Zang J, Liu Y. Species-specific identification of Pseudomonas based on 16S-23S rRNA gene internal transcribed spacer (ITS) and its combined application with next-generation sequencing. BMC Microbiol 2022; 22:188. [PMID: 35915434 PMCID: PMC9341087 DOI: 10.1186/s12866-022-02607-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/26/2022] [Indexed: 11/10/2022] Open
Abstract
Background Pseudomonas species are widely distributed in the human body, animals, plants, soil, fresh water, seawater, etc. Pseudomonas aeruginosa is one of the main pathogens involved in nosocomial infections. It can cause endocarditis, empyema, meningitis, septicaemia and even death. However, the Pseudomonas classification system is currently inadequate and not well established. Results In this study, the whole genomes of 103 Pseudomonas strains belonging to 62 species available in GenBank were collected and the specificity of the 16S–23S ribosomal RNA internal transcribed spacer (ITS) sequence was analysed. Secondary structures of ITS transcripts determining where the diversity bases were located were predicted. The alignment results using BLAST indicated that the ITS sequence is specific for most species in the genus. The remaining species were identified by additional frequency analyses based on BLAST results. A double-blind experiment where 200 ITS sequences were randomly selected indicated that this method could identify Pseudomonas species with 100% sensitivity and specificity. In addition, we applied a universal primer to amplify the Pseudomonas ITS of DNA extracts from fish samples with next-generation sequencing. The ITS analysis results were utilized to species-specifically identify the proportion of Pseudomonas species in the samples. Conclusions The present study developed a species-specific method identification and classification of Pseudomonas based on ITS sequences combined NGS. The method showed its potential application in other genera. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02607-w.
Collapse
Affiliation(s)
- Shuqian Hu
- The school of medicine, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Xiang Li
- The school of medicine, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Xin Yin
- The school of medicine, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Runmeng Li
- The school of medicine, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Ruiyang Zhang
- The school of medicine, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Junhao Zang
- The school of medicine, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China
| | - Yin Liu
- The school of medicine, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, China.
| |
Collapse
|
12
|
Zhang X, Sun J, Zhu Y, Han Z, Hu X, Lv A, Guo Y. First record of isolation and characterization of Vibrio sinaloensis from diseased orange-spotted grouper Epinephelus coioides. Dis Aquat Organ 2022; 149:71-76. [PMID: 35608511 DOI: 10.3354/dao03665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A dominant bacterium, ZYL-12, isolated from the liver of a diseased orange-spotted grouper Epinephelus coioides, was identified as Vibrio sinaloensis, based on phenotypic and molecular analysis. The median lethal dosage of ZYL-12 was calculated as 1.6 × 105 CFU g-1 fish weight. The infection experiment indicated that ZYL-12 caused noticeable histological lesions to the liver, kidney and spleen of the fish. Growth characteristics showed that ZYL-12 possessed strong environmental adaptability. This note is the first report about the pathogenicity of V. sinaloensis isolated from diseased fish.
Collapse
Affiliation(s)
- Xue Zhang
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin 300380, PR China
| | | | | | | | | | | | | |
Collapse
|
13
|
Arora RK, Mordan NJ, Spratt DA, Ng YL, Gulabivala K. Bacteria in the cavity-restoration interface after varying periods of clinical service - SEM description of distribution and 16S rRNA gene sequence identification of isolates. Clin Oral Investig 2022; 26:5029-5044. [PMID: 35359188 PMCID: PMC9276561 DOI: 10.1007/s00784-022-04473-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/21/2022] [Indexed: 11/03/2022]
Abstract
OBJECTIVES To use extracted human teeth with amalgam (n = 26) or GIC (n = 3) restorations in service up to 20 years to evaluate microbiota at the cavity/restoration interface by SEM or culture. MATERIALS AND METHODS Extracted teeth with intracoronal restorations (n = 20) of known history (2-20 years) were fixed, split, and prepared for SEM to ascertain the pattern and structure of bacterial aggregates on cavity and restoration surfaces. Another 9 teeth were anaerobically decontaminated, split and sampled (cavity/restorations), and cultured (anaerobically, aerobically); recovered isolates were identified by 16S rRNA gene sequencing. RESULTS SEM showed rods, cocci, and filaments in 11/20 teeth (55%) on cavity and corresponding restoration surfaces; 4/20 (20%) on neither surface; 1/20 (5%) on just cavity; and 4/20 (20%) on just restoration. Microbial growth extended from marginal openings into the deeper interfacial microspace to varying extents but was not always evident. Restoration size or age did not predict bacterial presence. Bacteria-free surfaces (cavity/amalgam) showed possible calcification. Cultivation yielded 160 isolates, mainly Gram-positive (86%) and facultative (81%); and morphotypes of rods (43%), cocci (36%), and cocco-bacilli (18%) belonging to Actinobacteria (45%) and Firmicutes (50%). The most frequent genera were Staphylococcus, Streptococcus, Actinomyces, and Lactobacillus. Biofilms on cavity and restoration appeared independent of each other. CONCLUSIONS Cavity and amalgam surfaces were independently colonised and some not. The penetration of microbiota into marginal gaps varied; resembled root caries and was dominated by Gram-positive species. CLINICAL RELEVANCE Marginal gaps around restorations are unavoidable but are not always colonised by bacteria after long-term clinical service. Calcification of biofilms in the restorative interface may prevent further colonisation. The viable microbiota in the restorative interface resembled root caries and may be subject to ecological fluxes of activity and arrest and therefore preventative management.
Collapse
Affiliation(s)
- Roopinder Kaur Arora
- Unit of Endodontology, Departments of Restorative Dentistry, Microbial Diseases, UCL Eastman Dental Institute, University College London, Bloomsbury Campus, Rockefeller Building, 21 University Street, London, WC1E 6DE, UK
| | - Nicola J Mordan
- Biomaterials and Tissue Engineering, UCL Eastman Dental Institute, University College London, London, UK
| | - David A Spratt
- Unit of Endodontology, Departments of Restorative Dentistry, Microbial Diseases, UCL Eastman Dental Institute, University College London, Bloomsbury Campus, Rockefeller Building, 21 University Street, London, WC1E 6DE, UK
| | - Yuan Ling Ng
- Unit of Endodontology, Departments of Restorative Dentistry, Microbial Diseases, UCL Eastman Dental Institute, University College London, Bloomsbury Campus, Rockefeller Building, 21 University Street, London, WC1E 6DE, UK
| | - Kishor Gulabivala
- Unit of Endodontology, Departments of Restorative Dentistry, Microbial Diseases, UCL Eastman Dental Institute, University College London, Bloomsbury Campus, Rockefeller Building, 21 University Street, London, WC1E 6DE, UK.
| |
Collapse
|
14
|
Cui F, Shen X, Cao B, Ji H, Liu J, Zhuang X, Zeng C, Qu B, Li S, Xu Y, Zhou Q. Bacterial identification and adhesive strength evaluation based on a mannose biosensor with dual-mode detection. Biosens Bioelectron 2022; 203:114044. [PMID: 35123316 DOI: 10.1016/j.bios.2022.114044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 11/23/2022]
Abstract
A biosensor integrated with mannose nano-surface was developed for the identification and adhesive strength evaluation of bacteria. Different bacteria were studied on the designed surface by both electrochemical impedance spectroscopy (EIS) and surface enhanced Raman spectroscopy (SERS). S. typhimurium and E. coli JM109 (type 1 pili) were found to be captured by the mannose nano-surface. SERS spectra were used to identify the species of captured bacteria by combing with partial least squares discriminant analysis (PLS-DA). Meanwhile, binding affinities of the two captured bacteria to mannose nano-surface were obtained by EIS measurements and Frumkin isotherm model analysis, which were 6.859 × 1023 M-1 and 2.054 × 1017 M-1 respectively. A higher binding affinity indicates a stronger adhesive strength. Hence the results show the S. typhimurium has a stronger adhesive strength to mannose. Normalized impedance change (NIC) was proved to have a positive relevant relationship with binding affinities, which could be used as an indicator for the adhesive strength of bacteria. It was demonstrated that 100% accuracy of bacteria species discrimination and good consistency of NIC and adhesive strength for blind samples. The developed biosensor can provide both qualitative and quantitative information of selective recognition between bacteria and mannose.
Collapse
|
15
|
Roux-Dalvai F, Leclercq M, Gotti C, Droit A. DIA Proteomics and Machine Learning for the Fast Identification of Bacterial Species in Biological Samples. Methods Mol Biol 2022; 2456:299-317. [PMID: 35612751 DOI: 10.1007/978-1-0716-2124-0_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Identification of bacterial species in biological samples is essential in many applications. However, the standard methods usually use a time-consuming bacterial culture (24-48 h) and sometimes lack in specificity. To overcome these limitations, we developed a new protocol, combining LC-MS/MS analysis in Data Independent Acquisition mode and machine learning algorithms, enabling the accurate identification of the bacterial species contaminating a sample in a few hours without bacterial culture. In this chapter, we describe the three steps of the protocol (spectral libraries generation, training step, identification step) to generate customized peptide signatures and use them for bacterial identification in biological samples through targeted proteomics analyses and prediction models.
Collapse
Affiliation(s)
- Florence Roux-Dalvai
- Proteomics Platform, CHU de Québec - Université Laval Research Center, Québec City, QC, Canada
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - Mickaël Leclercq
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - Clarisse Gotti
- Proteomics Platform, CHU de Québec - Université Laval Research Center, Québec City, QC, Canada
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - Arnaud Droit
- Proteomics Platform, CHU de Québec - Université Laval Research Center, Québec City, QC, Canada.
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Center, Québec City, QC, Canada.
| |
Collapse
|
16
|
Kashif M, Majeed MI, Nawaz H, Rashid N, Abubakar M, Ahmad S, Ali S, Hyat H, Bashir S, Batool F, Akbar S, Anwar MA. Surface-enhanced Raman spectroscopy for identification of food processing bacteria. Spectrochim Acta A Mol Biomol Spectrosc 2021; 261:119989. [PMID: 34087771 DOI: 10.1016/j.saa.2021.119989] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/16/2021] [Accepted: 05/19/2021] [Indexed: 06/12/2023]
Abstract
Food processing bacteria play important role in providing flavors, ingredients and other beneficial characteristics to the food but at the same time some bacteria are responsible for food spoilage. Therefore, quick and reliable identification of these food processing bacteria is very necessary for the differentiation between different species which may help in the development of more useful food processing methodologies. In this study, analysis of different bacterial species (Lactobacillus fermentum, Fructobacillus fructosus, Pediococcus pentosaceus and Halalkalicoccus jeotgali) was performed with our in-house developed Ag NPs-based surface-enhanced Raman spectroscopy (SERS) method. The SERS spectral data was analyzed by multivariate data analysis techniques including principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA). Bacterial species were differentiated on the basis of SERS spectral features and potential of SERS was compared with the Raman spectroscopy (RS). SERS along with PCA and PLS-DA was found to be an efficient technique for identification and differentiation of food processing bacterial species. Differentiation with accuracy of 99.5% and sensitivity of 99.7% was depicted by PLS-DA model using leave one out cross validation.
Collapse
Affiliation(s)
- Muhammad Kashif
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | | | - Haq Nawaz
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan.
| | - Nosheen Rashid
- Department of Physics, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Abubakar
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Shamsheer Ahmad
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Saqib Ali
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Hamza Hyat
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Saba Bashir
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Fatima Batool
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Saba Akbar
- Department of Chemistry, University of Agriculture, Faisalabad, Pakistan
| | - Munir Ahmad Anwar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| |
Collapse
|
17
|
Choi H, Hwang M, Chatterjee P, Jinadatha C, Navarathna DH. Rare Lelliottia nimipressuralis from a wound infection case report using whole genome sequencing-based bacterial identification. Diagn Microbiol Infect Dis 2021; 101:115538. [PMID: 34619568 DOI: 10.1016/j.diagmicrobio.2021.115538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 11/18/2022]
Abstract
Identification of clinical bacterial isolates is an essential first step to provide guidelines for treatment of pathogenic bacterial infection. Infection occurred in a laceration along the medial aspect of left upper arm of a 71-year-old female. Conventional biochemical testing and MALDI-TOF MS identification failed to correctly identify a bacterial isolate. Using whole genome sequencing, the isolate was identified as Lelliottia nimipressuralis. WGS can overcome the limitations of conventional phenotypic and molecular identification methods and successfully identified a rare pathogen. This case is the first report of a human infection of L. nimipressuralis.
Collapse
Affiliation(s)
- Hosoon Choi
- Department of Research, Central Texas Veterans Health Care System, Temple, TX, USA
| | - Munok Hwang
- Department of Research, Central Texas Veterans Health Care System, Temple, TX, USA
| | - Piyali Chatterjee
- Department of Research, Central Texas Veterans Health Care System, Temple, TX, USA
| | - Chetan Jinadatha
- Department of Medicine, Central Texas Veterans Health Care System, Temple, TX, USA; Department of Medicine, College of Medicine, Texas A&M Health Science Center, Bryan, TX, USA
| | - Dhammika H Navarathna
- Department of Pathology and Laboratory Medicine Services, Central Texas Veterans Health Care System, Temple, TX, USA.
| |
Collapse
|
18
|
Uehara S, Kobayashi M, Kimura K, Suzuki J, Sadamasu K. Rapid identification of histamine-producing bacteria isolated from fish using MALDI-TOF MS. J Food Sci Technol 2021; 58:4055-4061. [PMID: 34471328 PMCID: PMC8357883 DOI: 10.1007/s13197-021-05092-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 02/24/2021] [Accepted: 04/04/2021] [Indexed: 06/13/2023]
Abstract
Histamine-producing bacteria (HPB) produce histamine from histidine contained in food through the action of histidine decarboxylase. To identify HPB isolated from food, it is necessary to detect histamine produced by the bacteria. In this study, we concurrently identified HPB and detected histamine by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. After 24 h of incubation, 30 of 34 bacterial strains were correctly identified. Histamine was detected in all HPB cultured on Niven's medium, and 94% of HPB cultured in histidine broth, except for two strains with low histamine production. This method may greatly simplify the procedure and reduce the time required to identify HPB.
Collapse
Affiliation(s)
- Satomi Uehara
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, 3-24-1, Hyakunin-cho, Shinjuku-ku, Tokyo, 169-0073 Japan
| | - Makiko Kobayashi
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, 3-24-1, Hyakunin-cho, Shinjuku-ku, Tokyo, 169-0073 Japan
| | - Keisuke Kimura
- Department of Food Safety, Tokyo Metropolitan Institute of Public Health, 3-24-1, Hyakunin-cho, Shinjuku-ku, Tokyo, 169-0073 Japan
| | - Jun Suzuki
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, 3-24-1, Hyakunin-cho, Shinjuku-ku, Tokyo, 169-0073 Japan
| | - Kenji Sadamasu
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, 3-24-1, Hyakunin-cho, Shinjuku-ku, Tokyo, 169-0073 Japan
| |
Collapse
|
19
|
Pinar-Méndez A, Fernández S, Baquero D, Vilaró C, Galofré B, González S, Rodrigo-Torres L, Arahal DR, Macián MC, Ruvira MA, Aznar R, Caudet-Segarra L, Sala-Comorera L, Lucena F, Blanch AR, Garcia-Aljaro C. Rapid and improved identification of drinking water bacteria using the Drinking Water Library, a dedicated MALDI-TOF MS database. Water Res 2021; 203:117543. [PMID: 34433109 DOI: 10.1016/j.watres.2021.117543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/23/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
According to the European Directives (UE) 2020/2184 and 2009/54/EC, which establishes the sanitary criteria for water intended for human consumption in Europe, water suitable for human consumption must be free of the bacterial indicators Escherichia coli, Clostridium perfringens and Enterococcus spp. Drinking water is also monitored for heterotrophic bacteria, which are not a human health risk, but can serve as an index of bacteriological water quality. Therefore, a rapid, accurate, and cost-effective method for the identification of these colonies would improve our understanding of the culturable bacteria of drinking water and facilitate the task of water management by treatment facilities. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is potentially such a method, although most of the currently available mass spectral libraries have been developed in a clinical setting and have limited environmental applicability. In this work, a MALDI-TOF MS drinking water library (DWL) was defined and developed by targeting bacteria present in water intended for human consumption. This database, made up of 319 different bacterial strains, can contribute to the routine microbiological control of either treated drinking water or mineral bottled water carried out by water treatment and distribution operators, offering a faster identification rate compared to a clinical sample-based library. The DWL, made up of 96 bacterial genera, 44 of which are not represented in the MALDI-TOF MS bacterial Bruker Daltonics (BDAL) database, was found to significantly improve the identification of bacteria present in drinking water.
Collapse
Affiliation(s)
- Anna Pinar-Méndez
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, General Batet 1-7, Barcelona 08028, Spain; Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain.
| | - Sonia Fernández
- Cetaqua, Water technology center, Cornellà de Llobregat, Spain
| | - David Baquero
- Cetaqua, Water technology center, Cornellà de Llobregat, Spain
| | - Carles Vilaró
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, General Batet 1-7, Barcelona 08028, Spain
| | - Belén Galofré
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, General Batet 1-7, Barcelona 08028, Spain
| | - Susana González
- Cetaqua, Water technology center, Cornellà de Llobregat, Spain
| | - Lidia Rodrigo-Torres
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - David R Arahal
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - M Carmen Macián
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - María A Ruvira
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - Rosa Aznar
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - Laia Caudet-Segarra
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - Laura Sala-Comorera
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - Francisco Lucena
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - Anicet R Blanch
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain.
| |
Collapse
|
20
|
Feng B, Shi L, Zhang H, Shi H, Ding C, Wang P, Yu S. Effective discrimination of Yersinia pestis and Yersinia pseudotuberculosis by MALDI-TOF MS using multivariate analysis. Talanta 2021; 234:122640. [PMID: 34364449 DOI: 10.1016/j.talanta.2021.122640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 01/14/2023]
Abstract
Separating Yersinia pseudotuberculosis and Yersinia pestis is an important issue in plague diagnosis but can be extremely difficult because of the high similarity between the two species. MALDI-TOF MS has grown as a diagnostic tool with great potential in bacterial identification. Its application in this field is largely enhanced by multivariate analysis, especially in extracting subtle spectral differences. In this study, we built a complete MALDI-TOF MS data pipeline and found a Y. pestis-specific biomarker at 3063 Da closely related to Y. pestis plasminogen activation factor. Based on this, we achieved almost perfect separation between Y. pseudotuberculosis and Y. pestis (AUC = 0.999) using a supervised linear discriminant analysis (LDA) model. This is significantly better than the conventionally applied unsupervised spectral similarity comparison methods, such as hierarchical clustering analysis (HCA), which gave a separation accuracy of 75.0%. This new computing method paves the way for automatic differentiation between the two highly similar bacterial species with high separation accuracy.
Collapse
Affiliation(s)
- Bin Feng
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Liyuan Shi
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute for Endemic Disease Control and Prevention (YIEDC), Dali, Yunnan, 671000, China
| | - Haipeng Zhang
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute for Endemic Disease Control and Prevention (YIEDC), Dali, Yunnan, 671000, China
| | - Haimei Shi
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Chuanfan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Peng Wang
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute for Endemic Disease Control and Prevention (YIEDC), Dali, Yunnan, 671000, China.
| | - Shaoning Yu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
| |
Collapse
|
21
|
Talepour N, Hadi M, Nasseri S, Jaafarzadeh Haghighi Fard N, Mesdaghinia A, Borji SH. Isolation, identification and reviewing the health effect of HPC bacteria in household point-of-use (PoU) water treatment devices: a case study, Ahvaz, Iran. J Environ Health Sci Eng 2021; 19:59-69. [PMID: 34150218 PMCID: PMC8172727 DOI: 10.1007/s40201-020-00577-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 10/20/2020] [Indexed: 06/12/2023]
Abstract
In Ahwaz, a city in west southern Iran, the majority of households are using Point of Use (PoU) water treatment units. The heterotrophic plate count (HPC) bacteria were isolated from these units while they were mounted on water distribution system in order to determine the variations in HPC and diversity of the bacterial population using polymerase chain reaction (PCR). Results showed that bacterial population regrowth in PoU units could increase HPC exceeding the limit of the 500 CFU/mL in outlet water. In around 70% of the input water samples, the HPC was less than 500 CFU/ml with a mean of 226.7 (CI 95%: 28.1-425.3). HPC in output treated water samples had an increasing trend from the start of the unit operation with a mean of 2416.4 (CI 95%: 1074.9-3757.9). Out of 49 detected bacterial strains, 20 strains were Gram-negative and 29 Gram-positive. Bacillus was the most frequent genes detected in inlet and outlet water samples. Most of the identified bacterial strains were opportunistic pathogens potentially dangerous for immunocompromised population. HPC population in PoU units significantly can be increased during a one-month period of operation, so replacement of the filters must be done regularly.
Collapse
Affiliation(s)
- Nastaran Talepour
- Department of Environmental Health Engineering, School of Public Health, Ahvaz Jundishapur University of Medical Sciences, PO Box 1579461357, Ahvaz, Iran
| | - Mahdi Hadi
- Center for Water Quality Research (CWQR), Institute for Environmental Research (IER), Tehran University of Medical Sciences, PO Box 1417993361, Tehran, Iran
| | - Simin Nasseri
- Center for Water Quality Research (CWQR), Institute for Environmental Research (IER), Tehran University of Medical Sciences, PO Box 1417993361, Tehran, Iran
- Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, PO Box 1417613151, Tehran, Iran
| | - Neamat Jaafarzadeh Haghighi Fard
- Department of Environmental Health Engineering, School of Public Health, Ahvaz Jundishapur University of Medical Sciences, PO Box 1579461357, Ahvaz, Iran
- Environmental Technologies Research Center, Ahvaz Jundishapur University of Medical Sciences, PO Box 6135715751, Ahvaz, Iran
| | - Alireza Mesdaghinia
- Center for Water Quality Research (CWQR), Institute for Environmental Research (IER), Tehran University of Medical Sciences, PO Box 1417993361, Tehran, Iran
- Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, PO Box 1417613151, Tehran, Iran
| | - Saeedeh Hemmati Borji
- Center for Water Quality Research (CWQR), Institute for Environmental Research (IER), Tehran University of Medical Sciences, PO Box 1417993361, Tehran, Iran
| |
Collapse
|
22
|
Tsuchida S, Umemura H, Murata S, Miyabe A, Satoh M, Matsushita K, Nakayama T, Nomura F. Effect of humidity during sample preparation on bacterial identification using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1176:122780. [PMID: 34052563 DOI: 10.1016/j.jchromb.2021.122780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 01/08/2023]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a highly reliable and efficient technology for the identification of microbial pathogens. We previously found that 40% humidity was the optimal condition for the preparation of samples (co-crystallization of the sample and matrix) for serum peptidomic analysis via MALDI-TOF MS profiling. This optimum temperature was applied to obtain the highest reproducibility and throughput and greatest number of peaks. We therefore hypothesized that humidity control was also essential for MALDI-TOF MS bacterial identification. In this study, we constructed a simple sample preparation device that enables humidity control and used it for co-crystallization of the sample and matrix. Identification scores for five Gram-negative bacteria and six Gram-positive bacteria were determined using the MALDI BioTyper® system at three humidity ranges (10-20%, 30-40%, and 50-60%). As a result, higher identification scores were obtained at 30-40% humidity than at 10-20% or 50-60% humidity. At 30-40% humidity, 517/550 (94.0%) isolates scored greater than 2.0, indicating the success of species-level identification. Similarly, 537/550 (97.6%) isolates scored greater than 1.7, indicating the success of genus-level identification. Thus, 30-40% humidity generated optimal MALDI-TOF MS identification scores and the highest percentage of correct identifications. These results could lead to further improvements in the accuracy of MALDI-TOF MS bacterial identification.
Collapse
|
23
|
Altakhis M, Pillidge CJ, Osborn AM, Torley PJ, Kaur M. Assessment of the potential use of MALDI-TOF MS for the identification of bacteria associated with chilled vacuum-packaged lamb meat. Meat Sci 2021; 177:108508. [PMID: 33798992 DOI: 10.1016/j.meatsci.2021.108508] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/09/2021] [Accepted: 03/19/2021] [Indexed: 10/21/2022]
Abstract
The focus of this study was to compare the effectiveness of MALDI-TOF MS and partial 16S rRNA gene sequencing for the identification of bacteria isolated from VP lamb meat stored chilled at 5 °C for 21 days, at the same time gaining insights into bacterial changes over time. The identity of bacterial isolates on non-selective and selective agars was determined by both methods and results compared. Results showed that total bacterial numbers increased over the 21 days (as expected) with Staphylococcus and Pseudomonas (day 0) being replaced by Carnobacterium, Brochothrix and members of the Enterobacteriaceae family by day 21. A high level of agreement (86-100%) for bacterial isolates' identity at genus level was observed between MALDI-TOF MS and partial 16S rRNA gene-based sequencing for isolates where identification was possible. With its cheaper cost and faster turnaround time, once optimized, MALDI-TOF MS could become a useful alternative to 16S rRNA gene-sequencing for the rapid identification of red meat bacterial isolates.
Collapse
Affiliation(s)
- Mohammed Altakhis
- Biosciences and Food Technology, School of Science, RMIT University, Melbourne, Australia
| | - Christopher J Pillidge
- Biosciences and Food Technology, School of Science, RMIT University, Melbourne, Australia
| | - A Mark Osborn
- Biosciences and Food Technology, School of Science, RMIT University, Melbourne, Australia
| | - Peter J Torley
- Biosciences and Food Technology, School of Science, RMIT University, Melbourne, Australia
| | - Mandeep Kaur
- Biosciences and Food Technology, School of Science, RMIT University, Melbourne, Australia.
| |
Collapse
|
24
|
Malvisi L, Taddei L, Yarraguntla A, Wilkinson TMA, Arora AK. Sputum sample positivity for Haemophilus influenzae or Moraxella catarrhalis in acute exacerbations of chronic obstructive pulmonary disease: evaluation of association with positivity at earlier stable disease timepoints. Respir Res 2021; 22:67. [PMID: 33627095 PMCID: PMC7903661 DOI: 10.1186/s12931-021-01653-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 02/07/2021] [Indexed: 12/04/2022] Open
Abstract
Background Infection with Haemophilus influenzae (Hi) or Moraxella catarrhalis (Mcat) is a risk factor for exacerbation in chronic obstructive pulmonary disease (COPD). The ability to predict Hi- or Mcat-associated exacerbations may be useful for interventions developed to reduce exacerbation frequency. Methods In a COPD observational study, sputum samples were collected at monthly stable-state visits and at exacerbation during two years of follow-up. Bacterial species (Hi, Mcat) were identified by culture and quantitative PCR assay. Post-hoc analyses were conducted to assess: (1) first Hi- or Mcat-positive exacerbations given presence or absence of Hi or Mcat at the screening visit (stable-state timepoint); (2) first Hi- or Mcat-positive exacerbations given presence or absence of Hi or Mcat at stable timepoints within previous 90 days; (3) second Hi- or Mcat-positive exacerbations given presence or absence of Hi or Mcat at stable timepoints within previous 90 days. Percentages and risk ratios (RRs) with 95% confidence intervals were calculated. Results PCR results for analyses 1, 2 and 3 (samples from 84, 88 and 83 subjects, respectively) showed that the risk of an Hi- or Mcat-positive exacerbation is significantly higher if sputum sample was Hi- or Mcat-positive than if Hi- or Mcat-negative at previous stable timepoints (apart from Mcat in analysis 3); RRs ranged from 2.1 to 3.2 for Hi and 1.9 to 2.6 for Mcat.For all analyses, the percentage of Hi- or Mcat-positive exacerbations given previous Hi- or Mcat-positive stable timepoints was higher than the percentage of Hi- or Mcat-positive exacerbations if Hi- or Mcat-negative at previous stable timepoints. Percentage of Hi- or Mcat-positive exacerbations given previous Hi- or Mcat-negative stable timepoints was 26.3%–37.0% for Hi and 17.6%–19.7% for Mcat. Conclusions Presence of Hi or Mcat at a stable timepoint was associated with a higher risk of a subsequent Hi- or Mcat-associated exacerbation compared with earlier absence. However, a large percentage of Hi- or Mcat-associated exacerbations was not associated with Hi/Mcat detection at an earlier timepoint. This suggests that administration of an intervention to reduce these exacerbations should be independent of bacterial presence at baseline. Trial Registrationhttps://clinicaltrials.gov/; NCT01360398, registered May 25, 2011
Collapse
Affiliation(s)
| | | | | | - Tom M A Wilkinson
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK.,Southampton NIHR Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK.,Wessex Investigational Sciences Hub, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | | | | |
Collapse
|
25
|
Xu S, Qiu X, Hou X, Zhou H, Chen D, Wang X, Han L, Li D, Sun L, Ji X, Li M, Zhang J, Li M, Li Z. Direct detection of Corynebacterium striatum, Corynebacterium propinquum, and Corynebacterium simulans in sputum samples by high-resolution melt curve analysis. BMC Infect Dis 2021; 21:21. [PMID: 33413116 PMCID: PMC7788810 DOI: 10.1186/s12879-020-05633-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/19/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pulmonary infections caused by non-diphtheriae corynebacteria are increasing. However, rapid identification of Corynebacterium species poses a challenge due to the low genetic variation within the genus. METHODS Three reference strains and 99 clinical isolates were used in this study. A qPCR followed by high-resolution melting (HRM) targeting ssrA was performed to simultaneously identify C. striatum, C. propinquum and C. simulans. To further evaluate this assay's performance, 88 clinical sputum samples were tested by HRM and the detection results were compared with those of the traditional culture method and multiple cross-displacement amplification (MCDA) assay. RESULTS The melting curve produced by a pair of universal primers generated species-specific HRM curve profiles and could distinguish the three target species from other related bacteria. The limit of detection of HRM assay for DNA from the three purified Corynebacterium species was 100 fg. Compared with the culture method, HRM detected 22 additional positive specimens, representing a 23.9% relative increase in detection rate. The HRM assay had 98.4% (95% confidence interval [CI], 90.5-99.9%) sensitivity and 100% (95% CI, 82.8-100%) specificity. Additionally, 95.5% concordance between HRM and MCDA (κ = 0.89 [95% CI, 0.79-0.99]) was noted. CONCLUSIONS The HRM assay was a simple, rapid, sensitive, and specific diagnostic tool for detecting C. striatum, C. propinquum, and C. simulans, with the potential to contribute to early diagnosis, epidemiological surveillance, and rapid response to outbreak.
Collapse
Affiliation(s)
- Shuai Xu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaotong Qiu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xuexin Hou
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Haijian Zhou
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dongke Chen
- Department, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Xuebing Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lichao Han
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dan Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lina Sun
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xingzhao Ji
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Minghui Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jingshan Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mengtong Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| |
Collapse
|
26
|
Ma Q, Zhang Q, Yuan Y, Yan W, Wang S, Xu J, Zhang J, Wang Y, Li Y. Evaluation of the Autof MS1000 mass spectrometer in the identification of clinical isolates. BMC Microbiol 2020; 20:318. [PMID: 33081722 DOI: 10.1186/s12866-020-02005-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/12/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND To evaluate the accuracy and performance of the Autof MS1000 mass spectrometer in bacteria and yeast identification, 2342 isolates were obtained from microbial cultures of clinical specimens (e.g. blood, cerebrospinal fluid, respiratory tract samples, lumbar puncture fluid, wound samples, stool, and urine) collected in 2019 in Henan Provincial People's Hospital. Repetitive strains from the same patient were excluded. We tested the Autof MS1000 and Bruker Biotyper mass spectrometry systems and the classical biochemical identification system VITEK 2/API 20C AUX. Inconsistencies in strain identification among the three systems were identified by 16S rDNA and gene sequencing. RESULTS At the species level, the Autof MS1000 and Bruker Biotyper systems had isolate identification accuracies of 98.9 and 98.5%, respectively. At the genus level, the Autof MS1000 and Bruker Biotyper systems were 99.7 and 99.4% accurate, respectively. The instruments did not significantly differ in identification accuracy at either taxonomic level. The frequencies of unreliable identification were 1.1% (26/2342) for the Autof MS1000 and 1.5% (34/2342) for the Bruker Biotyper. In vitro experiments demonstrated that the coincidence rate of the Autof MS1000 mass spectrometer in the identification of five types of bacteria was > 93%, the identification error rate was < 3%, and the no identification rate was 0. This indicates that the Autof MS1000 system is acceptable for identification. CONCLUSIONS The Autof MS1000 mass spectrometer can be utilised to identify clinical isolates. However, an upgradation of the database is recommended to correctly identify rare strains.
Collapse
|
27
|
Wong KSK, Dhaliwal S, Bilawka J, Srigley JA, Champagne S, Romney MG, Tilley P, Sadarangani M, Zlosnik JEA, Chilvers MA. Matrix-assisted laser desorption/ionization time-of-flight MS for the accurate identification of Burkholderia cepacia complex and Burkholderia gladioli in the clinical microbiology laboratory. J Med Microbiol 2020; 69:1105-1113. [PMID: 32597748 PMCID: PMC7642978 DOI: 10.1099/jmm.0.001223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 06/09/2020] [Indexed: 12/22/2022] Open
Abstract
Introduction. Burkholderia cepacia complex (Bcc) bacteria, currently consisting of 23 closely related species, and Burkholderia gladioli, can cause serious and difficult-to-treat infections in people with cystic fibrosis. Identifying Burkholderia bacteria to the species level is considered important for understanding epidemiology and infection control, and predicting clinical outcomes. Matrix-assisted laser desorption/ionization time-of-flight MS (MALDI-TOF) is a rapid method recently introduced in clinical laboratories for bacterial species-level identification. However, reports on the ability of MALDI-TOF to accurately identify Bcc to the species level are mixed.Aim. The aim of this project was to evaluate the accuracy of MALDI-TOF using the Biotyper and VITEK MS systems in identifying isolates from 22 different Bcc species and B. gladioli compared to recA gene sequencing, which is considered the current gold standard for Bcc.Methodology. To capture maximum intra-species variation, phylogenetic trees were constructed from concatenated multi-locus sequence typing alleles and clustered with a novel k-medoids approach. One hundred isolates representing 22 Bcc species, plus B. gladioli, were assessed for bacterial identifications using the two MALDI-TOF systems.Results. At the genus level, 100 and 97.0 % of isolates were confidently identified as Burkholderia by the Biotyper and VITEK MS systems, respectively; moreover, 26.0 and 67.0 % of the isolates were correctly identified to the species level, respectively. In many, but not all, cases of species misidentification or failed identification, a representative library for that species was lacking.Conclusion. Currently available MALDI-TOF systems frequently do not accurately identify Bcc bacteria to the species level.
Collapse
Affiliation(s)
- Kendrew S. K. Wong
- Division of Respiratory Medicine, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Suk Dhaliwal
- Microbiology, BC Children’s Hospital, Vancouver, BC, Canada
| | - Jennifer Bilawka
- Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
| | - Jocelyn A. Srigley
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sylvie Champagne
- Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Marc G. Romney
- Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Peter Tilley
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Manish Sadarangani
- Division of Infectious Diseases, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Vaccine Evaluation Centre, BC Children’s Hospital, Vancouver, BC, Canada
| | - James E. A. Zlosnik
- Division of Infectious Diseases, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Mark A. Chilvers
- Division of Respiratory Medicine, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
28
|
Paul B, Kavia Raj K, Murali TS, Satyamoorthy K. Species-specific genomic sequences for classification of bacteria. Comput Biol Med 2020; 123:103874. [PMID: 32658789 DOI: 10.1016/j.compbiomed.2020.103874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/04/2020] [Accepted: 06/20/2020] [Indexed: 02/04/2023]
Abstract
Modern bacterial classification relies on genomic relatedness. Genetic variation in bacterial populations present a big challenge for taxonomic classification and recently several bacterial species have been reclassified based on the intra-species genome comparison. These were facilitated by next generation sequencing technologies and advances in genome comparison approaches which led to the rearrangement of diverse bacterial species and revolution in the microbial classification system. One of the outcome of these studies is the development of suitable DNA barcodes as reliable and cost-effective method for identifying various bacterial genera. Towards refining this further, we have applied a genome comparison approach in 1104 bacterial genome assemblies (excluding plasmids) to identify unique genomic segments among intra-species genome assemblies. Using extensive bioinformatics analysis, we have identified species-specific genomic regions and designed unique primers for 100 different species (belonging to 62 genera) which includes 62 pathogenic and 13 opportunistic pathogenic bacterial species and built a database (http://slsdb.manipal.edu/bact/). These species-specific genomic regions will have a major impact on in silico and molecular methods aimed at bacterial classification and identification. These may also serve as better DNA barcodes than the markers currently used for delineation of bacteria and may also find application in various translational research programs.
Collapse
|
29
|
Talamantes-Becerra B, Carling J, Kilian A, Georges A. Discovery of thermophilic Bacillales using reduced-representation genotyping for identification. BMC Microbiol 2020; 20:114. [PMID: 32404118 PMCID: PMC7222431 DOI: 10.1186/s12866-020-01800-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 04/23/2020] [Indexed: 12/25/2022] Open
Abstract
Background This study demonstrates the use of reduced-representation genotyping to provide preliminary identifications for thermophilic bacterial isolates. The approach combines restriction enzyme digestion and PCR with next-generation sequencing to provide thousands of short-read sequences from across the bacterial genomes. Isolates were obtained from compost, hot water systems, and artesian bores of the Great Artesian Basin. Genomic DNA was double-digested with two combinations of restriction enzymes followed by PCR amplification, using a commercial provider of DArTseq™, Diversity Arrays Technology Pty Ltd. (Canberra, Australia). The resulting fragments which formed a reduced-representation of approximately 2.3% of the genome were sequenced. The sequence tags obtained were aligned against all available RefSeq bacterial genome assemblies by BLASTn to identify the nearest reference genome. Results Based on the preliminary identifications, a total of 99 bacterial isolates were identified to species level, from which 8 isolates were selected for whole-genome sequencing to assess the identification results. Novel species and strains were discovered within this set of isolates. The preliminary identifications obtained by reduced-representation genotyping, as well as identifications obtained by BLASTn alignment of the 16S rRNA gene sequence, were compared with those derived from the whole-genome sequence data, using the same RefSeq sequence database for the three methods. Identifications obtained with reduced-representation sequencing agreed with the identifications provided by whole-genome sequencing in 100% of cases. The identifications produced by BLASTn alignment of 16S rRNA gene sequence to the same database differed from those provided by whole-genome sequencing in 37.5% of cases, and produced ambiguous identifications in 50% of cases. Conclusions Previously, this method has been successfully demonstrated for use in bacterial identification for medical microbiology. This study demonstrates the first successful use of DArTseq™ for preliminary identification of thermophilic bacterial isolates, providing results in complete agreement with those obtained from whole-genome sequencing of the same isolates. The growing database of bacterial genome sequences provides an excellent resource for alignment of reduced-representation sequence data for identification purposes, and as the available sequenced genomes continue to grow, the technique will become more effective.
Collapse
Affiliation(s)
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, Canberra, ACT, 2617, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, Canberra, ACT, 2617, Australia
| | - Arthur Georges
- Institute of Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| |
Collapse
|
30
|
Zargar N, Ashraf H, Marashi SMA, Sabeti M, Aziz A. Identification of microorganisms in irreversible pulpitis and primary endodontic infections with respect to clinical and radiographic findings. Clin Oral Investig 2020; 24:2099-2108. [PMID: 32377864 DOI: 10.1007/s00784-019-03075-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 09/13/2019] [Indexed: 12/18/2022]
Abstract
OBJECTIVES The aim of this study was to evaluate the composition of microbiota of irreversible pulpitis and primary endodontic infections with respect to clinical and radiographic findings by performing cultures and 16s rDNA sequencing in Iranian patients. MATERIAL AND METHODS In this prospective cross-sectional study, samples were collected from 41 root canals for 4 main groups of patients. Bacterial identification was performed by the polymerase chain reaction (PCR) and 16s rDNA sequencing of aerobic and anaerobic cultivable colonies taken from patients' culture plates. Additionally, the presence of 13 bacterial species and 3 nonbacterial species was also explored using PCR and species-specific primers. RESULTS Sixteen microbial species, 1 fungus (Candida albicans), and 1 virus (Herpes simplex virus) were discovered and isolated. Species with the highest prevalence were Dialister invisus (68.3%), Porphyromonas gingivalis (58.8%), Streptococcus salivarius (58.5%), and Treponema denticola (56.1%). Lysinibacillus fusiformis (19.1%) was detected in the root canals for the first time. Candida albicans was seen in 11 cases (26.8%). Herpes simplex virus (HSV) was seen in 4 patients (9.8%). CONCLUSIONS Our results suggest that Gram-negative anaerobic oral bacteria are the majority of the microbes in primary endodontic infections. Various combinations of bacterial species were related to different clinical and radiographic conditions. Lysinibacillus fusiformis was detected for the first time in primary endodontic infections. CLINICAL RELEVANCE The results of this investigation might help clinicians choose to identify suspected endodontic pathogens in the etiology of each form of pulpal and periradicular diseases to determine the best therapeutic measures.
Collapse
Affiliation(s)
- Nazanin Zargar
- Department of Endodontics, School of Dentistry, Shahid Beheshti University of Medical Sciences, Daneshjoo Blv., Daneshgah Square, Chamran Highway, Tehran, 1983963113, Iran
| | - Hengameh Ashraf
- Department of Endodontics, School of Dentistry, Shahid Beheshti University of Medical Sciences, Daneshjoo Blv., Daneshgah Square, Chamran Highway, Tehran, 1983963113, Iran
| | - S M Amin Marashi
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mohammad Sabeti
- UCSF School of Dentistry, 707 Parnassus Ave. Room-D 3226, San Francisco, CA, 94143-0758, USA
| | - Alireza Aziz
- School of Dentistry, Shahid Beheshti University of Medical Sciences, Daneshjoo Blv., Evin Avenue, Chamran Highway, Tehran, 1983963113, Iran.
| |
Collapse
|
31
|
Dussert E, Tourret M, Deracinois B, Duban M, Leclère V, Cudennec B, Ravallec R, Behra-Miellet J. Dataset on phenotypic characterization, on protein and genome analysis of three fluorescent Pseudomonas strains from mid-mountain water. Data Brief 2020; 30:105466. [PMID: 32322618 PMCID: PMC7168345 DOI: 10.1016/j.dib.2020.105466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 03/17/2020] [Indexed: 11/13/2022] Open
Abstract
The identification of non-fermentative Gram negative bacilli from run-off and spring water, including fluorescent Pseudomonas is very complex and investigations are needed to contribute to the systematic of these bacteria. In this dataset, the phenotypical profiles of three strains isolated from Vosges mountains first identified as Pseudomonas fluorescens were determined using APIⓇ 50 CH galleries. Then, the identification of their proteins released directly into water was carried out using tandem/mass spectrometry after separating proteins on native two-dimensional polyacrylamide gels. Finally, genotypic analysis data is presented, that illustrates biodiversity in this fluorescent bacterial group. This data is referred by a research article entitled “Fluorescent Pseudomonas strains from mid-mountain water able to release antioxidant proteins directly into water”.
Collapse
Key Words
- ANI, average nucleotide identity
- Bacterial identification
- Fluorescent Pseudomonas
- Genome sequencing
- MALDI, matrix assisted laser desorption ionization
- MS, mass spectrometry
- MS/MS, tandem mass spectrometry
- MW, molecular weight
- NCBI, National Center for Biotechnology Information
- NR, not reviewed
- Nb, number of experimental peptides recognized
- P., Pseudomonas
- PFF, peptide fragment fingerprinting
- PMF, peptide mass fingerprinting
- Proteomics
- R, reviewed
- Spot no., spot number
- TCS, tetra correlation search
- TOF/TOF, time-of-flight/time-of-flight
- ppm, parts per million
Collapse
Affiliation(s)
- Elodie Dussert
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, F-59000 Lille, France
| | - Mélissa Tourret
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, F-59000 Lille, France
| | - Barbara Deracinois
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, F-59000 Lille, France
| | - Matthieu Duban
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, F-59000 Lille, France
| | - Valérie Leclère
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, F-59000 Lille, France
| | - Benoit Cudennec
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, F-59000 Lille, France
| | - Rozenn Ravallec
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, F-59000 Lille, France
| | - Josette Behra-Miellet
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Côte d'Opale, EA 7394 - ICV - Institut Charles Viollette, F-59000 Lille, France
| |
Collapse
|
32
|
Swanson GM, Moskovtsev S, Librach C, Pilsner JR, Goodrich R, Krawetz SA. What human sperm RNA-Seq tells us about the microbiome. J Assist Reprod Genet 2020; 37:359-368. [PMID: 31902104 PMCID: PMC7056791 DOI: 10.1007/s10815-019-01672-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 12/19/2019] [Indexed: 10/25/2022] Open
Abstract
PURPOSE The study was designed to assess the capacity of human sperm RNA-seq data to gauge the diversity of the associated microbiome within the ejaculate. METHODS Semen samples were collected, and semen parameters evaluated at time of collection. Sperm RNA was isolated and subjected to RNA-seq. Microbial composition was determined by aligning sequencing reads not mapped to the human genome to the NCBI RefSeq bacterial, viral and archaeal genomes following RNA-Seq. Analysis of microbial assignments utilized phyloseq and vegan. RESULTS Microbial composition within each sample was characterized as a function of microbial associated RNAs. Bacteria known to be associated with the male reproductive tract were present at similar levels in all samples representing 11 genera from four phyla with one exception, an outlier. Shannon diversity index (p < 0.001) and beta diversity (unweighted UniFrac distances, p = 9.99e-4; beta dispersion, p = 0.006) indicated the outlier was significantly different from all other samples. The outlier sample exhibited a dramatic increase in Streptococcus. Multiple testing indicated two operational taxonomic units, S. agalactiae and S. dysgalactiae (p = 0.009), were present. CONCLUSION These results provide a first look at the microbiome as a component of human sperm RNA sequencing that has sufficient sensitivity to identify contamination or potential pathogenic bacterial colonization at least among the known contributors.
Collapse
Affiliation(s)
- Grace M Swanson
- Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 275 E. Hancock, Detroit, MI, 48202, USA
| | | | | | - J Richard Pilsner
- Department of Environmental Health Sciences, University of Massachusetts Amherst School of Public Health and Health Sciences, Amherst, MA, 01003, USA
| | - Robert Goodrich
- Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 275 E. Hancock, Detroit, MI, 48202, USA
| | - Stephen A Krawetz
- Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 275 E. Hancock, Detroit, MI, 48202, USA.
| |
Collapse
|
33
|
Colin M, Charpentier E, Klingelschmitt F, Bontemps C, De Champs C, Reffuveille F, Gangloff SC. Specific antibacterial activity of copper alloy touch surfaces in five long-term care facilities for older adults. J Hosp Infect 2019; 104:283-292. [PMID: 31809775 DOI: 10.1016/j.jhin.2019.11.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 11/25/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Pathogens involved in healthcare-associated infections can quickly spread in the environment, particularly to frequently touched surfaces, which can be reservoirs for pathogens. AIM The purpose of this study was to investigate naturally occurring bacterial contamination on touch surfaces in five French long-term care facilities and to compare bacterial populations recovered from copper and control surfaces. METHODS More than 1300 surfaces were sampled. The collected bacteria were identified to obtain a global view of the cultivable bacterial populations colonizing touch surfaces. Haemolytic colonies and putative pathogens were also screened using specific agar plates and then identified with matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. In total, more than 3400 colonies were analysed. FINDINGS Staphylococcus and Micrococcus were the two predominant genera present on touch surfaces, respectively occurring on 51.8% and 48.0% of control surfaces. In these facilities with relatively low bioburden, copper surfaces efficiently reduced the occurrence frequencies of three genera: Staphylococcus, Streptococcus and Roseomonas. Pathogenic species such as Staphylococcus aureus, Enterococcus faecalis and E. faecium were observed in very few samples. In addition, meticillin-resistant S. aureus was observed on five control surfaces and one copper surface. CONCLUSION Contamination of healthcare facilities touch surfaces can be the source for the spread of bacteria through the institution. This in situ study shows that the frequency of the contamination as well as the specific bacterial population bioburden is reduced on copper alloy surfaces.
Collapse
Affiliation(s)
- M Colin
- Université de Reims Champagne-Ardenne, EA 4691 Biomatériaux et Inflammation en site Osseux (BIOS), SFR CAP-Santé, France
| | - E Charpentier
- Université de Reims Champagne-Ardenne, EA 4691 Biomatériaux et Inflammation en site Osseux (BIOS), SFR CAP-Santé, France; Université de Reims Champagne-Ardenne, UFR de Pharmacie, Service de Microbiologie, France
| | - F Klingelschmitt
- Université de Reims Champagne-Ardenne, EA 4691 Biomatériaux et Inflammation en site Osseux (BIOS), SFR CAP-Santé, France
| | - C Bontemps
- Dynamique des génomes et adaptation microbienne, UMR1128, Université de Lorraine, INRA Vandœuvre-lès-Nancy, France
| | - C De Champs
- Université de Reims Champagne-Ardenne, Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Laboratoire de Bactériologie - Virologie - Hygiène hospitalière, CHU Reims, 51100 Reims, France
| | - F Reffuveille
- Université de Reims Champagne-Ardenne, EA 4691 Biomatériaux et Inflammation en site Osseux (BIOS), SFR CAP-Santé, France; Université de Reims Champagne-Ardenne, UFR de Pharmacie, Service de Microbiologie, France
| | - S C Gangloff
- Université de Reims Champagne-Ardenne, EA 4691 Biomatériaux et Inflammation en site Osseux (BIOS), SFR CAP-Santé, France; Université de Reims Champagne-Ardenne, UFR de Pharmacie, Service de Microbiologie, France.
| |
Collapse
|
34
|
Kim D, Ji S, Kim JR, Kim M, Byun JH, Yum JH, Yong D, Lee K. Performance evaluation of a new matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, ASTA MicroIDSys system, in bacterial identification against clinical isolates of anaerobic bacteria. Anaerobe 2019; 61:102131. [PMID: 31778809 DOI: 10.1016/j.anaerobe.2019.102131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 11/15/2019] [Accepted: 11/23/2019] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been introduced for bacterial identification. The ASTA MicroIDSys system (ASTA, Suwon, Korea) is a new MALDI-TOF MS system developed for species identification of microorganisms. We evaluated the performance of MicroIDSys against clinical isolates of anaerobic bacteria. MATERIAL AND METHODS A total of 370 non-duplicated clinical isolates of anaerobic bacteria were tested in this study. Bacterial identification with MicroIDSys was performed with a direct smear method, and measured spectra were analyzed using respective software. The results of MicroIDSys were compared with the results of Bruker Biotyper and 16S rRNA sequencing. RESULTS The overall agreement rates for the 370 clinical isolates (34 genera and 99 species) were 95.4% (353/370) at the genus level and 91.6% (n = 340) at the species level. Only 17 isolates were incorrectly identified at the genus level: five misidentifications and 12 unidentifications. The MicroIDSys system exhibited excellent performance in the identification of clinically relevant bacterial species. Most of the Bacteroides isolates (98.0%, 99/101) and all of the Clostridium difficile (100%, n = 11), Clostridium perfringens (100%, n = 10), Finegoldia magna (100%, n = 11), and Parvimonas micra (100%, n = 10) isolates were correctly identified at the species level. CONCLUSION The MicroIDSys system proved useful in the identification of anaerobic bacteria, especially clinically relevant species. This system could be of use in clinical microbiology laboratories as a primary tool for identifying anaerobic bacteria.
Collapse
Affiliation(s)
- Dokyun Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, College of Medicine, Seoul, South Korea
| | - Seungeun Ji
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, College of Medicine, Seoul, South Korea
| | - Jung Rim Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, College of Medicine, Seoul, South Korea
| | - Myungsook Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, College of Medicine, Seoul, South Korea
| | - Jung-Hyun Byun
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, College of Medicine, Seoul, South Korea
| | - Jong Hwa Yum
- Department of Clinical Laboratory Science, Dong-eui University, Busan, South Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, College of Medicine, Seoul, South Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, College of Medicine, Seoul, South Korea.
| |
Collapse
|
35
|
Tsuchida S, Murata S, Miyabe A, Satoh M, Takiwaki M, Matsushita K, Nomura F. An in-house centrifugation and membrane filtration technique for identifying microorganisms from positive blood culture bottles with high identification rates using matrix-assisted laser desorption ionization-Time-of-flight mass spectrometry: A preliminary report. J Infect Chemother 2019; 26:266-271. [PMID: 31678054 DOI: 10.1016/j.jiac.2019.09.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 09/24/2019] [Accepted: 09/27/2019] [Indexed: 02/06/2023]
Abstract
Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) is one of the most promising technologies for the identification of microbial pathogens directly from positive blood culture bottles. As blood culture bottle medium contains various nonbacterial proteins, including those derived from blood cells, pretreatment to effectively remove host cells is key for successful proteome-based identification of microorganisms. Although the Sepsityper® kit is the most widely used pretreatment protocol, its performance is not satisfactory, particularly for gram-positive isolates. We developed a new in-house protocol, the centrifugation and membrane filtration technique (CMFT), in which vacuum-filtration is coupled with differential centrifugation. We prospectively evaluated the performance of this novel method compared with that of the Sepsityper®. For gram-negative bacterial isolates, the species-level identification rates obtained with the CMFT and the Sepsityper® were comparable (98.8% vs 92.9%). By contrast, for gram-positive isolates, the performance of the CMFT was significantly better than that of the Sepsityper® (P < 0.05). Using our new protocol, 81 (95.3%) isolates were identified with a score >2.0, and 85 (100%) isolates were identified with a score >1.7, versus 46 (54.1%) and 69 (81.2%), respectively, for the Sepsityper®. These results are preliminary, but considering that this novel protocol provides notably high species-level identification rates for gram-positive isolates, it deserves assessment in a larger-scale study with a variety of platforms for MS-based identification of microorganisms.
Collapse
Affiliation(s)
- Sachio Tsuchida
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Syota Murata
- Department of Clinical Laboratory, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Akiko Miyabe
- Department of Clinical Laboratory, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Mamoru Satoh
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Masaki Takiwaki
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Kazuyuki Matsushita
- Department of Clinical Laboratory, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan; Division of Clinical Genetics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Fumio Nomura
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan; Division of Clinical Genetics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan.
| |
Collapse
|
36
|
Zhou J, Zhang L, Chuan H, Sloan A, Tsang R, Cheng K. Mass Spectrometry to Study the Bacterial Proteome from a Single Colony. Methods Mol Biol 2019; 1968:113-21. [PMID: 30929210 DOI: 10.1007/978-1-4939-9199-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Mass spectrometry (MS) has been widely used in recent years for bacterial identification and typing. Single bacterial colonies are regarded as pure cultures of bacteria grown from single cells. In this chapter, we describe a method for identifying bacteria at the species level with 100% accuracy using the proteomes of bacterial cultures from single colonies. In this chapter, six reference strains of gram-negative and gram-positive bacteria are analyzed, producing results of high reproducibility, as examples of bacterial identification through the application of liquid chromatography-tandem mass spectrometry (LC-MS/MS) and a custom database. Details on sample preparation and identification of Streptococcus pneumoniae are also described.
Collapse
|
37
|
Zargar N, Marashi MA, Ashraf H, Hakopian R, Beigi P. Identification of microorganisms in persistent/secondary endodontic infections with respect to clinical and radiographic findings: bacterial culture and molecular detection. Iran J Microbiol 2019; 11:120-128. [PMID: 31341566 PMCID: PMC6635307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
BACKGROUND AND OBJECTIVES Bacterial agents are commonly accepted as the main etiology of endodontic infections. A significant proportion of oral bacteria cannot be cultured using existing methods. Since diversity and abundance of bacterial species are different in different populations, the present study was aimed to identify effective microorganisms in persistent endodontic infections in Iranian patients based on culture and molecular biology methods using sequence analysis of 16S rDNA gene. MATERIALS AND METHODS Thirty patients with previous failure of endodontic treatment were enrolled in the study. After isolation and disinfection of the tooth surrounding area with 3% sodium hypochlorite and 30% hydrogen peroxide, sampling from the root canals was carried out using two sterile Hedstrom files and two sterile paper points, and then the specimens were transferred to the microbiology laboratory in thioglycolate transport medium so that they undergo aerobic-anaerobic culture, PCR, and 16S rDNA gene sequencing. RESULTS Of 30 patients (15 women and 15 men), 15 patients had radiographic lesions smaller than 5 mm and other 15 patients had radiographic lesions larger than 5 mm. The mean age of patients was 40.20 ± 13.76 years. A total of 26 patients were asymptomatic. Only four patients had clinical signs such as pain and percussion sensitivity and Tannerella forsythia was the most common bacterium found in this group of patients. 13 bacterial species were found in 11 different genus, one virus strain and one fungus strain. From 30 studied specimens, Enterococcus faecalis was the most common microorganism with prevalence rate of 63.63%. CONCLUSION This study showed the type and prevalence of effective bacteria in secondary/persistent endodontic infections in Iranian patients. E. faecalis is the most commonly found microorganism in Iranian patients.
Collapse
Affiliation(s)
- Nazanin Zargar
- Iranian Center for Endodontic Research, Research Institute of Dental Sciences, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahmoud Amin Marashi
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Hengameh Ashraf
- Department of Endodontics, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Rene Hakopian
- Iranian Center for Endodontic Research, Research Institute of Dental Sciences, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran,Corresponding author: Rene Hakopian, DDs, Iranian Center for Endodontic Research, Research Institute of Dental Sciences, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran. Tel: +98-21-22403075, Fax: +98-21-22403194,
| | - Peyman Beigi
- Department of Hematology, Faculty of Medicine, Tarbiat Modares University, Tehran, Iran
| |
Collapse
|
38
|
Talamantes-Becerra B, Carling J, Kennedy K, Gahan ME, Georges A. Identification of bacterial isolates from a public hospital in Australia using complexity-reduced genotyping. J Microbiol Methods 2019; 160:11-19. [PMID: 30894330 DOI: 10.1016/j.mimet.2019.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/16/2019] [Accepted: 03/17/2019] [Indexed: 11/25/2022]
Abstract
Bacterial identification methods used in routine identification of pathogens in medical microbiology include a combination approach of biochemical tests, mass spectrometry or molecular biology techniques. Extensive publicly-available databases of DNA sequence data from pathogenic bacteria have been amassed in recent years; this provides an opportunity for using bacterial genome sequencing for identification purposes. Whole genome sequencing is increasing in popularity, although at present it remains a relatively expensive approach to bacterial identification and typing. Complexity-reduced bacterial genome sequencing provides an alternative. We evaluate genomic complexity-reduction using restriction enzymes and sequencing to identify bacterial isolates. A total of 165 bacterial isolates from hospital patients in the Australian Capital Territory, between 2013 and 2015 were used in this study. They were identified and typed by the Microbiology Department of Canberra Public Hospital, and represented 14 bacterial species. DNA extractions from these samples were processed using a combination of the restriction enzymes PstI with MseI, PstI with HpaII and MseI with HpaII. The resulting sequences (length 30-69 bp) were aligned against publicly available bacterial genome and plasmid sequences. Results of the alignment were processed using a bioinformatics pipeline developed for this project, Currito3.1 DNA Fragment Analysis Software. All 165 samples were correctly identified to genus and species by each of the three combinations of restriction enzymes. A further 35 samples typed to the level of strain identified and compared for consistency with MLST typing data and in silico MLST data derived from the nearest sequenced candidate reference. The high level of agreement between bacterial identification using complexity-reduced genome sequencing and standard hospital identifications indicating that this new approach is a viable alternative for identification of bacterial isolates derived from pathology specimens. The effectiveness of species identification and in particular, strain typing, depends on access to a comprehensive and taxonomically accurate bacterial genome sequence database containing relevant bacterial species and strains.
Collapse
Affiliation(s)
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, Canberra, ACT 2617, Australia
| | - Karina Kennedy
- Canberra Health Services, Departments of Microbiology and Infectious Diseases, Canberra Hospital, Yamba Drive, Garran 2605, Australia
| | - Michelle E Gahan
- National Centre for Forensic Studies, University of Canberra, ACT, 2617, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, ACT 2601, Australia
| |
Collapse
|
39
|
Abstract
Matrix-assisted laser desorption time of flight mass spectrometry (MALDI-TOF MS), adapted for use in clinical microbiology laboratories, challenges current standards of microbial detection and identification. This article summarizes the capabilities of MALDI-TOF MS in diagnostic clinical microbiology laboratories and describes the underpinnings of the technology, highlighting topics such as sample preparation, spectral analysis, and accuracy. The use of MALDI-TOF MS in the clinical microbiology laboratory is growing, and, when properly deployed, can accelerate diagnosis and improve patient care.
Collapse
Affiliation(s)
- Donna M Wolk
- Clinical Microbiology, Department of Laboratory Medicine, Diagnostic Medicine Institute, Geisinger Health, 100 North Academy Avenue, Danville, PA 17822-1930, USA.
| | - Andrew E Clark
- Department of Veterinary Science and Microbiology, University of Arizona, Tucson, AZ 85721, USA
| |
Collapse
|
40
|
Pillonetto M, Arend L, Gomes SMT, Oliveira MAA, Timm LN, Martins AF, Barth AL, Mazzetti A, Hersemann L, Smits THM, Mira MT, Rezzonico F. Molecular investigation of isolates from a multistate polymicrobial outbreak associated with contaminated total parenteral nutrition in Brazil. BMC Infect Dis 2018; 18:397. [PMID: 30103698 PMCID: PMC6090600 DOI: 10.1186/s12879-018-3287-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 07/31/2018] [Indexed: 12/14/2022] Open
Abstract
Background Between November 2013 and June 2014, 56 cases of bacteremia (15 deaths) associated with the use of Total Parenteral Nutrition (TPN) and/or calcium gluconate (CG) were reported in four Brazilian states. Methods We analyzed 73 bacterial isolates from four states: 45 from blood, 25 from TPN and three from CG, originally identified as Acinetobacter baumannii, Rhizobium radiobacter, Pantoea sp. or Enterobacteriaceae using molecular methods. Results The first two bacterial species were confirmed while the third group of species could not be identified using standard identification protocols. These isolates were subsequently identified by Multi-Locus Sequence Analysis as Phytobacter diazotrophicus, a species related to strains from similar outbreaks in the United States in the 1970’s. Within each species, TPN and blood isolates proved to be clonal, whereas the R. radiobacter isolates retrieved from CG were found to be unrelated. Conclusion This is the first report of a three-species outbreak caused by TPN contaminated with A. baumannii, R. radiobacter and P. diazotrophicus. The concomitant presence of clonal A. baumannii and P. diazotrophicus isolates in several TPN and blood samples, as well as the case of one patient, where all three different species were isolated simultaneously, suggest that the outbreak may be ascribed to a discrete contamination of TPN. In addition, this study highlights the clinical relevance of P. diazotrophicus, which has been involved in outbreaks in the past, but was often misidentified as P. agglomerans. Electronic supplementary material The online version of this article (10.1186/s12879-018-3287-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Marcelo Pillonetto
- Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, PR, Brazil. .,Central Public Health Laboratory - State of Paraná - LACEN/PR, Molecular Bacteriology Division, São José dos Pinhais, PR, Brazil.
| | - Lavinia Arend
- Central Public Health Laboratory - State of Paraná - LACEN/PR, Molecular Bacteriology Division, São José dos Pinhais, PR, Brazil
| | - Suzie M T Gomes
- Brazilian Health Surveillance Agency - ANVISA, Brasília, DF, Brazil
| | - Marluce A A Oliveira
- Ezequiel Dias Foundation, Central Public Health Laboratory - State of Minas Gerais, Bacteriology Division, Belo Horizonte, MG, Brazil
| | - Loeci N Timm
- Central Public Health Laboratory - State of Rio Grande do Sul, Bacteriology Division, Porto Alegre, RS, Brazil
| | - Andreza F Martins
- Research Laboratory on Bacterial Resistance (LABRESIS), Federal University of Rio Grande do Sul, Hospital de Clínicas, Porto Alegre, RS, Brazil
| | - Afonso L Barth
- Research Laboratory on Bacterial Resistance (LABRESIS), Federal University of Rio Grande do Sul, Hospital de Clínicas, Porto Alegre, RS, Brazil
| | - Alana Mazzetti
- Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, PR, Brazil
| | - Lena Hersemann
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland.,Present Address: Scientific Computing Facility, Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland
| | - Marcelo T Mira
- Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, PR, Brazil
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland
| |
Collapse
|
41
|
Tsuchida S, Murata S, Miyabe A, Satoh M, Takiwaki M, Ashizawa K, Terada T, Ito D, Matsushita K, Nomura F. Application of the biocopolymer preparation system, rapid BACpro® II kit, for mass-spectrometry-based bacterial identification from positive blood culture bottles by the MALDI Biotyper system. J Microbiol Methods 2018; 152:86-91. [PMID: 30075236 DOI: 10.1016/j.mimet.2018.07.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/25/2018] [Accepted: 07/29/2018] [Indexed: 12/20/2022]
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is increasingly used for identification of microorganisms from positive blood cultures. Pretreatments to effectively remove non-bacterial components and selectively collect microorganisms are a prerequisite for successful identification, and a variety of home-brew and commercial protocols have been reported. Although commercially available kits, mainly the Sepsityper Kit, are increasingly used, the identification rates reported often are not satisfactory, particularly for Gram-positive isolates. We recently developed a method to collect bacteria from positive blood culture bottles using a polyallylamine-polystyrene copolymer that has been used in wastewater processing. This pretreatment protocol is now commercially available as the rapid BACpro® II kit (Nittobo Medical Co., Tokyo, Japan). The operation time required for processing using this novel kit is approximately 10 min, and the entire procedure can be completed within a biosafety cabinet. Since the performance of the rapid BACpro® II kit has not been tested using the MALDI Biotyper system, we prospectively evaluated the performance of the rapid BACpro® II kit as compared with the Sepsityper® kit. Performance of the rapid BACpro® II kit was evaluated using a total of 193 monomicrobial cases of positive blood culture. Medium from blood culture bottles was pretreated by the rapid BACpro® II kit or the Sepsityper® Kit, and isolated cells were subjected to direct identification by MS fingerprinting in parallel with conventional subculturing for reference identification. The overall MALDI-TOF MS-based identification rates with >1.7 score and >2.0 score obtained using the rapid BACpro® II kit were 99.5% and 80.8%, respectively, whereas those obtained using the Sepsityper® Kit were 89.1% and 68.4%, respectively (P < 0.05 for >1.7 and P < 0.05 for >2.0 by Pearsons's chi-square). In Gram-positive cases, the rapid BACpro® II kit gave identification rate of 100% with >1.7 score and 69.4% with >2.0 score, whereas there were 84.7% and 56.8%, respectively by the Sepsityper® Kit (P < 0.05 for >1.7). These results are preliminary, but considering that this new kit is easy to perform and the identification rates are promising, the rapid BACpro® II kit deserves assessment in a larger-scale study with a variety of platforms for MS-based bacterial identification.
Collapse
Affiliation(s)
- Sachio Tsuchida
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Syota Murata
- Department of Clinical Laboratory, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Akiko Miyabe
- Department of Clinical Laboratory, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Mamoru Satoh
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Masaki Takiwaki
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | | | | | - Daisuke Ito
- R&D Department, Nittobo Medical Co., Ltd, Japan
| | - Kazuyuki Matsushita
- Department of Clinical Laboratory, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan; Division of Clinical Genetics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Fumio Nomura
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan; Division of Clinical Genetics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan.
| |
Collapse
|
42
|
Santos AS, Ramos RT, Silva A, Hirata R, Mattos-Guaraldi AL, Meyer R, Azevedo V, Felicori L, Pacheco LGC. Searching whole genome sequences for biochemical identification features of emerging and reemerging pathogenic Corynebacterium species. Funct Integr Genomics 2018; 18:593-610. [PMID: 29752561 DOI: 10.1007/s10142-018-0610-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 03/28/2018] [Accepted: 04/16/2018] [Indexed: 12/24/2022]
Abstract
Biochemical tests are traditionally used for bacterial identification at the species level in clinical microbiology laboratories. While biochemical profiles are generally efficient for the identification of the most important corynebacterial pathogen Corynebacterium diphtheriae, their ability to differentiate between biovars of this bacterium is still controversial. Besides, the unambiguous identification of emerging human pathogenic species of the genus Corynebacterium may be hampered by highly variable biochemical profiles commonly reported for these species, including Corynebacterium striatum, Corynebacterium amycolatum, Corynebacterium minutissimum, and Corynebacterium xerosis. In order to identify the genomic basis contributing for the biochemical variabilities observed in phenotypic identification methods of these bacteria, we combined a comprehensive literature review with a bioinformatics approach based on reconstruction of six specific biochemical reactions/pathways in 33 recently released whole genome sequences. We used data retrieved from curated databases (MetaCyc, PathoSystems Resource Integration Center (PATRIC), The SEED, TransportDB, UniProtKB) associated with homology searches by BLAST and profile Hidden Markov Models (HMMs) to detect enzymes participating in the various pathways and performed ab initio protein structure modeling and molecular docking to confirm specific results. We found a differential distribution among the various strains of genes that code for some important enzymes, such as beta-phosphoglucomutase and fructokinase, and also for individual components of carbohydrate transport systems, including the fructose-specific phosphoenolpyruvate-dependent sugar phosphotransferase (PTS) and the ribose-specific ATP-binging cassette (ABC) transporter. Horizontal gene transfer plays a role in the biochemical variability of the isolates, as some genes needed for sucrose fermentation were seen to be present in genomic islands. Noteworthy, using profile HMMs, we identified an enzyme with putative alpha-1,6-glycosidase activity only in some specific strains of C. diphtheriae and this may aid to understanding of the differential abilities to utilize glycogen and starch between the biovars.
Collapse
Affiliation(s)
- André S Santos
- Bioinformatics Post-Graduate Program, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
- Institute of Health Sciences, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - Rommel T Ramos
- Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, PA, Brazil
| | - Artur Silva
- Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, PA, Brazil
| | - Raphael Hirata
- Faculty of Medical Sciences, Rio de Janeiro State University (UERJ), Rio de Janeiro, RJ, Brazil
| | - Ana L Mattos-Guaraldi
- Faculty of Medical Sciences, Rio de Janeiro State University (UERJ), Rio de Janeiro, RJ, Brazil
| | - Roberto Meyer
- Institute of Health Sciences, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - Vasco Azevedo
- Bioinformatics Post-Graduate Program, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Liza Felicori
- Bioinformatics Post-Graduate Program, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Luis G C Pacheco
- Institute of Health Sciences, Federal University of Bahia (UFBA), Salvador, BA, Brazil.
| |
Collapse
|
43
|
Tsuchida S, Murata S, Miyabe A, Satoh M, Takiwaki M, Matsushita K, Nomura F. An improved in-house lysis-filtration protocol for bacterial identification from positive blood culture bottles with high identification rates by MALDI-TOF MS. J Microbiol Methods 2018; 148:40-45. [PMID: 29608928 DOI: 10.1016/j.mimet.2018.03.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 03/26/2018] [Indexed: 01/04/2023]
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is now a well-established method for identification of microorganisms from positive blood cultures. Pretreatments to effectively remove non-bacterial proteins are a prerequisite for successful identification, and a variety of protocols have been reported. Although commercially available kits, mainly the Sepsityper Kit, are increasingly used, the identification rates reported often are not satisfactory, particularly for Gram-positive isolates. We developed a new, in-house lysis-filtration protocol and prospectively evaluated its performance compared to the Sepsityper kit. The in-house protocol consists of three simple steps: lysis by ammonium chloride, aspiration with a syringe fitted with a 0.45-μm membrane, and centrifugation to collect microbes. The novel protocol requires only 20 min. Performance of the in-house protocol was evaluated using a total of 117 monomicrobial cases of positive blood culture. Medium from blood culture bottles was pretreated by the in-house protocol or the commercial kit, and isolated cells were subjected to direct identification by mass spectrometry fingerprinting in parallel with conventional subculturing for reference identification. The overall MALDI-TOF MS-based identification rates with score > 1.7 and > 2.0 obtained using the in-house protocol were 99.2% and 85.5%, respectively, whereas those obtained using the Sepsityper Kit were 85.4% and 61.5%, respectively. For Gram-positive cases, the in-house protocol yielded scores >1.7 and > 2.0 at 98.5% and 76.1%, respectively, whereas the commercial kit yielded these scores at 76.1% and 43.3%, respectively. Although these are preliminary results, these values suggest that this easy lysis-filtration protocol deserves assessment in a larger-scale test.
Collapse
Affiliation(s)
- Sachio Tsuchida
- Division of Clinical Mass Spectrometry, Chiba University Hospital, Chiba, Japan; Department of Clinical Laboratory, Chiba University Hospital, Chiba, Japan
| | - Syota Murata
- Department of Clinical Laboratory, Chiba University Hospital, Chiba, Japan
| | - Akiko Miyabe
- Department of Clinical Laboratory, Chiba University Hospital, Chiba, Japan
| | - Mamoru Satoh
- Division of Clinical Mass Spectrometry, Chiba University Hospital, Chiba, Japan
| | - Masaki Takiwaki
- Division of Clinical Mass Spectrometry, Chiba University Hospital, Chiba, Japan
| | - Kazuyuki Matsushita
- Department of Clinical Laboratory, Chiba University Hospital, Chiba, Japan; Division of Clinical Genetics, Chiba University Hospital, Chiba, Japan
| | - Fumio Nomura
- Division of Clinical Mass Spectrometry, Chiba University Hospital, Chiba, Japan; Division of Clinical Genetics, Chiba University Hospital, Chiba, Japan.
| |
Collapse
|
44
|
Dubourg G, Lamy B, Ruimy R. Rapid phenotypic methods to improve the diagnosis of bacterial bloodstream infections: meeting the challenge to reduce the time to result. Clin Microbiol Infect 2018; 24:935-943. [PMID: 29605563 DOI: 10.1016/j.cmi.2018.03.031] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/17/2018] [Accepted: 03/20/2018] [Indexed: 01/08/2023]
Abstract
BACKGROUND Administration of appropriate antimicrobial therapy is one of the key factors in surviving bloodstream infections. Blood culture is currently the reference standard for diagnosis, but conventional practices have long turnaround times while diagnosis needs to be faster to improve patient care. Phenotypic methods offer an advantage over genotypic methods in that they can identify a wide range of taxa, detect the resistance currently expressed, and resist genetic variability in resistance detection. AIMS We aimed to discuss the wide array of phenotypic methods that have recently been developed to substantially reduce the time to result from identification to antibiotic susceptibility testing. SOURCES A literature review focusing on rapid phenotypic methods for improving the diagnosis of bloodstream infection was the source. CONTENT Rapid phenotypic bacterial identification corresponds to Matrix-assisted laser-desorption/ionization time of flight mass spectrometry (MALDI-TOF), and rapid antimicrobial susceptibility testing methods comprised of numerous different approaches, are considered and critically assessed. Particular attention is also paid to emerging technologies knocking at the door of routine microbiology laboratories. Finally, workflow integration of these methods is considered. IMPLICATIONS The broad panel of phenotypic methods currently available enables healthcare institutions to draw up their own individual approach to improve bloodstream infection diagnosis but requires a thorough evaluation of their workflow integration. Clinical microbiology will probably move towards faster methods while maintaining a complex multi-method approach as there is no all-in-one method.
Collapse
Affiliation(s)
- G Dubourg
- Aix Marseille Université, IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France.
| | - B Lamy
- Laboratoire de Bactériologie, Hôpital L'archet 2, CHU de Nice, Nice, France; INSERM U1065, Centre Méditerranéen de Médecine Moléculaire, Equipe 6, Nice, France; Faculté de Médecine, Université Côte d'Azur, Nice, France
| | - R Ruimy
- Laboratoire de Bactériologie, Hôpital L'archet 2, CHU de Nice, Nice, France; INSERM U1065, Centre Méditerranéen de Médecine Moléculaire, Equipe 6, Nice, France; Faculté de Médecine, Université Côte d'Azur, Nice, France.
| |
Collapse
|
45
|
Bodai Z, Cameron S, Bolt F, Simon D, Schaffer R, Karancsi T, Balog J, Rickards T, Burke A, Hardiman K, Abda J, Rebec M, Takats Z. Effect of Electrode Geometry on the Classification Performance of Rapid Evaporative Ionization Mass Spectrometric (REIMS) Bacterial Identification. J Am Soc Mass Spectrom 2018; 29:26-33. [PMID: 29038998 PMCID: PMC5785610 DOI: 10.1007/s13361-017-1818-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 08/31/2017] [Accepted: 09/17/2017] [Indexed: 06/07/2023]
Abstract
The recently developed automated, high-throughput monopolar REIMS platform is suited for the identification of clinically important microorganisms. Although already comparable to the previously reported bipolar forceps method, optimization of the geometry of monopolar electrodes, at the heart of the system, holds the most scope for further improvements to be made. For this, sharp tip and round shaped electrodes were optimized to maximize species-level classification accuracy. Following optimization of the distance between the sample contact point and tube inlet with the sharp tip electrodes, the overall cross-validation accuracy improved from 77% to 93% in negative and from 33% to 63% in positive ion detection modes, compared with the original 4 mm distance electrode. As an alternative geometry, round tube shaped electrodes were developed. Geometry optimization of these included hole size, number, and position, which were also required to prevent plate pick-up due to vacuum formation. Additional features, namely a metal "X"-shaped insert and a pin in the middle were included to increase the contact surface with a microbial biomass to maximize aerosol production. Following optimization, cross-validation scores showed improvement in classification accuracy from 77% to 93% in negative and from 33% to 91% in positive ion detection modes. Supervised models were also built, and after the leave 20% out cross-validation, the overall classification accuracy was 98.5% in negative and 99% in positive ion detection modes. This suggests that the new generation of monopolar REIMS electrodes could provide substantially improved species level identification accuracies in both polarity detection modes. Graphical abstract.
Collapse
Affiliation(s)
- Zsolt Bodai
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK.
| | - Simon Cameron
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
| | - Frances Bolt
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
| | - Daniel Simon
- Waters Research Center, 7 Zahony Street, Budapest, 1031, Hungary
| | - Richard Schaffer
- Waters Research Center, 7 Zahony Street, Budapest, 1031, Hungary
| | - Tamas Karancsi
- Waters Research Center, 7 Zahony Street, Budapest, 1031, Hungary
| | - Julia Balog
- Waters Research Center, 7 Zahony Street, Budapest, 1031, Hungary
| | - Tony Rickards
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
- Department of Microbiology, Imperial College Healthcare NHS Trust, Charing Cross Hospital, London, W6 8RF, UK
| | - Adam Burke
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
| | - Kate Hardiman
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
| | - Julia Abda
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
| | - Monica Rebec
- Department of Microbiology, Imperial College Healthcare NHS Trust, Charing Cross Hospital, London, W6 8RF, UK
| | - Zoltan Takats
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
| |
Collapse
|
46
|
de Carvalho Filho ÉB, Marson FAL, Levy CE. Challenges in the identification of Chryseobacterium indologenes and Elizabethkingia meningoseptica in cases of nosocomial infections and patients with cystic fibrosis. New Microbes New Infect 2017; 20:27-33. [PMID: 29062487 PMCID: PMC5643076 DOI: 10.1016/j.nmni.2017.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/04/2017] [Accepted: 09/06/2017] [Indexed: 12/30/2022] Open
Abstract
Rare nonfermenting Gram-negative bacilli, such as Chryseobacterium indologenes and Elizabethkingia meningoseptica, have clinical importance in nosocomial infections and cystic fibrosis (CF), and their identification is a challenge to microbiology laboratories. Thus, the objective of this study was to verify the performance of phenotypic and mass spectrometry (matrix-assisted desorption ionization–time of flight mass spectrometry, MALDI-TOF MS) methods to identify C. indologenes and E. meningoseptica. In this context, the results obtained with phenotypic methods—namely manual biochemical and automated VITEK 2 (bioMérieux, Marcy l’Etoile, France) and Phoenix tests (Becton Dickinson (BD), San Diego, CA, USA)—and by MALDI-TOF MS—namely MALDI-TOF VITEK MS (MALDI-MS; bioMérieux) and MALDI-TOF BioTyper (MALDI-BD; BD)—of 22 isolates (blood cultures of patients with nosocomial infection (n = 15) and from patients with CF (n = 7)), initially identified as C. indologenes and E. meningoseptica, were compared. As result, using the manual phenotypic method, it was possible to identify the species level in 18/22; no identification was found in 4/22. There was a low agreement level between manual and VITEK 2 automated phenotypic methods when considering the genus level. The greatest agreement for genus-level identification occurred in MALDI-TOF MS equipment (15/22). When comparing all methods to identify the 22 isolates, there was agreement of 4/22 at the genus level and of 4/22 at the species level. In conclusion, there is low agreement level among identification methods of C. indologenes and E. meningoseptica. Although MALDI-TOF MS equipment shows a higher agreement level among them, results present low levels of confidence.
Collapse
Affiliation(s)
- É B de Carvalho Filho
- Department of Pediatrics, School of Medical Sciences, University of Campinas, São Paulo, Brazil
| | - F A L Marson
- Department of Pediatrics, School of Medical Sciences, University of Campinas, São Paulo, Brazil.,Department of Medical Genetics, School of Medical Sciences, University of Campinas, São Paulo, Brazil
| | - C E Levy
- Department of Clinical Pathology, School of Medical Sciences, University of Campinas, São Paulo, Brazil
| |
Collapse
|
47
|
Santos CS, Ramos JN, Vieira VV, Pinheiro CS, Meyer R, Alcantara-Neves NM, Ramos RT, Silva A, Hirata R, Felicori L, de Alegría Puig CR, Navas J, Azevedo V, Mattos-Guaraldi AL, Pacheco LGC. Efficient differentiation of Corynebacterium striatum, Corynebacterium amycolatum and Corynebacterium xerosis clinical isolates by multiplex PCR using novel species-specific primers. J Microbiol Methods 2017; 142:33-35. [PMID: 28888870 DOI: 10.1016/j.mimet.2017.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 11/28/2022]
Abstract
A multiplex-PCR (mPCR) assay was designed with species-specific primers which generate amplicons of 226bp, 434bp and 106bp for differentiating the species C. striatum, C. amycolatum, and C. xerosis, respectively. mPCR results were 100% in agreement with identifications achieved by 16S rRNA and rpoB gene sequencing and by VITEK-MS.
Collapse
Affiliation(s)
- Carolina S Santos
- Institute of Health Sciences, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - Juliana N Ramos
- National Institute for Quality Control in Health (INCQS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Veronica V Vieira
- Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Carina S Pinheiro
- Institute of Health Sciences, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - Roberto Meyer
- Institute of Health Sciences, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | | | - Rommel T Ramos
- Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, PA, Brazil
| | - Artur Silva
- Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, PA, Brazil
| | - Raphael Hirata
- Faculty of Medical Sciences, Rio de Janeiro State University (UERJ), Rio de Janeiro, RJ, Brazil
| | - Liza Felicori
- Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Carlos Ruiz de Alegría Puig
- Departamento de Biología Molecular, Universidad de Cantabria, Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Jesús Navas
- Departamento de Biología Molecular, Universidad de Cantabria, Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Vasco Azevedo
- Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Ana L Mattos-Guaraldi
- Faculty of Medical Sciences, Rio de Janeiro State University (UERJ), Rio de Janeiro, RJ, Brazil
| | - Luis G C Pacheco
- Institute of Health Sciences, Federal University of Bahia (UFBA), Salvador, BA, Brazil.
| |
Collapse
|
48
|
Wilson DA, Young S, Timm K, Novak-Weekley S, Marlowe EM, Madisen N, Lillie JL, Ledeboer NA, Smith R, Hyke J, Griego-Fullbright C, Jim P, Granato PA, Faron ML, Cumpio J, Buchan BW, Procop GW. Multicenter Evaluation of the Bruker MALDI Biotyper CA System for the Identification of Clinically Important Bacteria and Yeasts. Am J Clin Pathol 2017; 147:623-631. [PMID: 28505220 DOI: 10.1093/ajcp/aqw225] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVES A report on the multicenter evaluation of the Bruker MALDI Biotyper CA System (MBT-CA; Bruker Daltonics, Billerica, MA) for the identification of clinically important bacteria and yeasts. METHODS In total, 4,399 isolates of medically important bacteria and yeasts were assessed in the MBT-CA. These included 2,262 aerobic gram-positive (AGP) bacteria, 792 aerobic gram-negative (AGN) bacteria 530 anaerobic (AnA) bacteria, and 815 yeasts (YSTs). Three processing methods were assesed. RESULTS Overall, 98.4% (4,329/4,399) of all bacterial and yeast isolates were correctly identified to the genus and species/species complex level, and 95.7% of isolates were identified with a high degree of confidence. The percentage correctly identified and the percentage identified correctly with a high level of confidence, respectively, were as follows: AGP bacteria (98.6%/96.5%), AGN bacteria (98.5%/96.8%), AnA bacteria (98.5%/97.4%), and YSTs (97.8%/87.6%). The extended direct transfer method was only minimally superior to the direct transfer method for bacteria (89.9% vs 86.8%, respectively) but significantly superior for yeast isolates (74.0% vs 48.9%, respectively). CONCLUSIONS The Bruker MALDI Biotyper CA System accurately identifies most clinically important bacteria and yeasts and has optional processing methods to improve isolate characterization.
Collapse
Affiliation(s)
| | - Stephen Young
- Tricore Reference Laboratories, Albuquerque, NM
- Department of Pathology, The University of New Mexico Health Sciences Center, Albuquerque
| | - Karen Timm
- Tricore Reference Laboratories, Albuquerque, NM
| | - Susan Novak-Weekley
- Kaiser Permanente Southern California Permanente Medical Group Regional Reference Laboratories, North Hollywood, CA
| | - Elizabeth M Marlowe
- Kaiser Permanente Southern California Permanente Medical Group Regional Reference Laboratories, North Hollywood, CA
| | | | | | - Nathan A Ledeboer
- Wisconsin Diagnostic Laboratory, Milwaukee
- Medical College of Wisconsin, Milwaukee
| | | | - Josh Hyke
- Wisconsin Diagnostic Laboratory, Milwaukee
| | | | | | - Paul A Granato
- Laboratory Alliance of Central New York, Fayetteville
- SUNY Upstate Medical University, Syracuse, NY
| | | | - Joven Cumpio
- Kaiser Permanente Southern California Permanente Medical Group Regional Reference Laboratories, North Hollywood, CA
| | - Blake W Buchan
- Wisconsin Diagnostic Laboratory, Milwaukee
- Medical College of Wisconsin, Milwaukee
| | | |
Collapse
|
49
|
Ashizawa K, Murata S, Terada T, Ito D, Bunya M, Watanabe K, Teruuchi Y, Tsuchida S, Satoh M, Nishimura M, Matsushita K, Sugama Y, Nomura F. Applications of copolymer for rapid identification of bacteria in blood culture broths using matrix-assisted laser desorption ionization time-of-flight mass spectrometry. J Microbiol Methods 2017; 139:54-60. [PMID: 28461023 DOI: 10.1016/j.mimet.2017.04.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 04/27/2017] [Accepted: 04/28/2017] [Indexed: 01/12/2023]
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) can be used to identify pathogens in blood culture samples. However, sample pretreatment is needed for direct identification of microbes in blood culture bottles. Conventional protocols are complex and time-consuming. Therefore, in this study, we developed a method for collecting bacteria using polyallylamine-polystyrene copolymer for application in wastewater treatment technology. Using representative bacterial species Escherichia coli and Staphylococcus capitis, we found that polyallylamine-polystyrene can form visible aggregates with bacteria, which can be identified using MALDI-TOF MS. The processing time of our protocol was as short as 15min. Hemoglobin interference in MALDI spectra analysis was significantly decreased in our method compared with the conventional method. In a preliminary experiment, we evaluated the use of our protocol to identify clinical isolates from blood culture bottles. MALDI-TOF MS-based identification of 17 strains from five bacterial species (E. coli, Klebsiella pneumoniae, Enterococcus faecalis, S. aureus, and S. capitis) collected by our protocol was satisfactory. Prospective large-scale studies are needed to further evaluate the clinical application of this novel and simple method of collecting bacteria in blood culture bottles.
Collapse
Affiliation(s)
- Kazuho Ashizawa
- R&D Department, Nittobo Medical Co., Ltd., 1 Shiojima, Fukuhara, Fukuyama, Koriyama, Fukushima 963-8061, Japan
| | - Syota Murata
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan; Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Takashi Terada
- R&D Department, Nittobo Medical Co., Ltd., 1 Shiojima, Fukuhara, Fukuyama, Koriyama, Fukushima 963-8061, Japan
| | - Daisuke Ito
- R&D Department, Nittobo Medical Co., Ltd., 1 Shiojima, Fukuhara, Fukuyama, Koriyama, Fukushima 963-8061, Japan
| | - Masaru Bunya
- Specialty Chemicals Division, Nittobo Medical Co., Ltd., 1, Shiojima, Fukuhara, Fukuyama, Koriyama, Fukushima 963-8061, Japan
| | - Koji Watanabe
- Specialty Chemicals Division, Nittobo Medical Co., Ltd., 1, Shiojima, Fukuhara, Fukuyama, Koriyama, Fukushima 963-8061, Japan
| | - Yoko Teruuchi
- Specialty Chemicals Division, Nittobo Medical Co., Ltd., 1, Shiojima, Fukuhara, Fukuyama, Koriyama, Fukushima 963-8061, Japan
| | - Sachio Tsuchida
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Mamoru Satoh
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Motoi Nishimura
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan; Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Kazuyuki Matsushita
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Yuji Sugama
- R&D Department, Nittobo Medical Co., Ltd., 1 Shiojima, Fukuhara, Fukuyama, Koriyama, Fukushima 963-8061, Japan.
| | - Fumio Nomura
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| |
Collapse
|
50
|
Barberino MG, Silva MO, Arraes ACP, Correia LC, Mendes AV. Direct identification from positive blood broth culture by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS). Braz J Infect Dis 2017; 21:339-42. [PMID: 28399425 DOI: 10.1016/j.bjid.2017.03.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 11/20/2022] Open
Abstract
Bloodstream infections (BSIs) are among the most concerning bacterial infections. They are one of the leading causes of morbidity and mortality, and occur in 30–70% of critical care patients. The prompt identification of the causative microorganism can help choosing the appropriate antimicrobial therapy that will lead to better clinical outcomes. Blood culture is one of the most relevant tests for microbiological diagnosis of bacterial infections. The introduction of the MALDI-TOF microbiological diagnosis significantly decreased the time of identifying microorganisms. However, it depends on the growth on solid culture medium. In this study, 538 bottles of positive blood cultures were evaluated to test the accuracy of an in house modified protocol. The study sample consisted of 198 Gram-negative and 350 Gram-positive bacteria. In all, 460 (83.94%) species were identified based on the direct plate findings. The protocol allowed the identification of 185/198 (93.43%) of the Gram-negative bacteria, including aerobes, anaerobes, and non-fermenters, and 275/350 (78.85%) of the Gram-positive bacteria. The proposed method has the potential to provide accurate results in comparison to the traditional method with the potential to reduce the turnaround time for the results and optimize antimicrobial therapy in BSI.
Collapse
|