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Yan Y, Xu J, Huang W, Fan Y, Li Z, Tian M, Ma J, Lu X, Liang J. Metagenomic and Culturomics Analysis of Microbial Communities within Surface Sediments and the Prevalence of Antibiotic Resistance Genes in a Pristine River: The Zaqu River in the Lancang River Source Region, China. Microorganisms 2024; 12:911. [PMID: 38792738 PMCID: PMC11124135 DOI: 10.3390/microorganisms12050911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/26/2024] Open
Abstract
Microbial communities inhabiting sedimentary environments in river source regions serve as pivotal indicators of pristine river ecosystems. While the correlation between antibiotic resistome and pathogenicity with core gut bacteria in humans is well established, there exists a significant knowledge gap concerning the interaction of antibiotic resistance genes (ARGs) and human pathogenic bacteria (HPB) with specific microbes in river source basins, often referred to as "terrestrial gut". Understanding the microbial composition, including bacteria and resident genetic elements such as ARGs, HPB, Mobile Genetic Elements (MGEs), and Virulence Factors (VFs), within natural habitats against the backdrop of global change, is imperative. To address this gap, an enrichment-based culturomics complementary along with metagenomics was conducted in this study to characterize the microbial biobank and provide preliminary ecological insights into profiling the dissemination of ARGs in the Lancang River Source Basin. Based on our findings, in the main stream of the Lancang River Source Basin, 674 strains of bacteria, comprising 540 strains under anaerobic conditions and 124 under aerobic conditions, were successfully isolated. Among these, 98 species were identified as known species, while 4 were potential novel species. Of these 98 species, 30 were HPB relevant to human health. Additionally, bacA and bacitracin emerged as the most abundant ARGs and antibiotics in this river, respectively. Furthermore, the risk assessment of ARGs predominantly indicated the lowest risk rank (Rank Ⅳ) in terms of endangering human health. In summary, enrichment-based culturomics proved effective in isolating rare and unknown bacteria, particularly under anaerobic conditions. The emergence of ARGs showed limited correlation with MGEs, indicating minimal threats to human health within the main stream of the Lancang River Source Basin.
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Affiliation(s)
- Yi Yan
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (Y.Y.); (J.X.); (W.H.); (M.T.); (J.M.)
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Jialiang Xu
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (Y.Y.); (J.X.); (W.H.); (M.T.); (J.M.)
| | - Wenmin Huang
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (Y.Y.); (J.X.); (W.H.); (M.T.); (J.M.)
| | - Yufeng Fan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.F.); (Z.L.)
| | - Zhenpeng Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.F.); (Z.L.)
| | - Mingkai Tian
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (Y.Y.); (J.X.); (W.H.); (M.T.); (J.M.)
| | - Jinsheng Ma
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (Y.Y.); (J.X.); (W.H.); (M.T.); (J.M.)
| | - Xin Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.F.); (Z.L.)
| | - Jian Liang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
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Bella Z, Erdelyi E, Szalenko-Tőkés Á, Kiricsi Á, Gaál V, Benedek P, Rovó L, Nagy E. Peritonsillar abscess: an 8-year retrospective, culture based evaluation of 208 cases. J Med Microbiol 2022; 71. [DOI: 10.1099/jmm.0.001576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Peritonsillar abscess (PTA) is a common infection which requires surgical intervention and suitable antibiotic therapy.
Hypotheses/Gap Statement. Beside
Streptococcus pyogenes
and
Fusobacterium necrophorum
several other mostly anaerobic bacteria can be cultured from the properly taken pus samples of PTA, the clinical significance of which is still not fully understood.
Aim. This study focused on the culture-based microbiological evaluation of PTA cases, compared to surgical intervention and empirical antibiotic management.
Methodology. A retrospective analysis of PTA cases was performed between 2012 and 2019. Data about the aerobic and anaerobic culture results of the samples taken during different surgical interventions were summarized and the coverage of the empirically selected antibiotics was evaluated. The patient’s history, the development of complications and the recurrence rate were also evaluated.
Results. The microbiological culture results were available for 208 of 320 patients with clinically diagnosed PTA. Incision and drainage (I and D) and immediate tonsillectomy were the leading surgical interventions. Ninety-five
Fusobacterium
species (including 44
Fusobacterium necrophorum
), 52
Actinomyces
species and 47
Streptococcus pyogenes
were obtained from PTA samples alone or together with polymicrobial flora.
S. pyogenes
(33.7 %, n=28) and
F. necrophorum
(22.9 %, n=19) were the dominating pathogens in the 83 monobacterial PTA samples. In >60 % of the patients polymicrobial infection was demonstrated, involving a great variety of anaerobic bacteria. In 22 out of 42 cases where intravenous cefuroxime was empirically started, the therapy should be changed to properly cover the culture-proven anaerobic flora. There were no serious complications, abscess recurrence was detected in two cases (0.96 %).
Conclusion. PTAs are often polymicrobial infections including a great variety of anaerobes. Targeted antibiotic therapy, in conjunction with adequate surgical drainage eliminating the anaerobic milieu, can accelerate the healing process and radically reduce the complication and recurrence rate.
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Affiliation(s)
- Zsolt Bella
- Department of Oto-Rhino-Laryngology and Head-Neck Surgery, Faculty of Medicine, University of Szeged, Hungary
| | - Eszter Erdelyi
- Department of Oto-Rhino-Laryngology and Head-Neck Surgery, Faculty of Medicine, University of Szeged, Hungary
| | - Ágnes Szalenko-Tőkés
- Department of Oto-Rhino-Laryngology and Head-Neck Surgery, Faculty of Medicine, University of Szeged, Hungary
| | - Ágnes Kiricsi
- Department of Oto-Rhino-Laryngology and Head-Neck Surgery, Faculty of Medicine, University of Szeged, Hungary
| | - Veronika Gaál
- Department of Pediatric-ENT, Faculty of Medicine, University of Pécs, Pécs, Hungary
| | | | - László Rovó
- Department of Oto-Rhino-Laryngology and Head-Neck Surgery, Faculty of Medicine, University of Szeged, Hungary
| | - Elisabeth Nagy
- Department of Medical Microbiology, Faculty of Medicine, University of Szeged, Szeged, Hungary
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Bächli P, Baars S, Simmler A, Zbinden R, Schulthess B. Impact of MALDI-TOF MS identification on anaerobic species and genus diversity in routine diagnostics. Anaerobe 2022; 75:102554. [DOI: 10.1016/j.anaerobe.2022.102554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 02/08/2022] [Accepted: 03/23/2022] [Indexed: 11/30/2022]
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Detection of beta-lactamase production in clinical Prevotella species by MALDI-TOF MS method. Anaerobe 2020; 65:102240. [PMID: 32768494 DOI: 10.1016/j.anaerobe.2020.102240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 11/21/2022]
Abstract
Penicillins, can be used in treatment of infections due to Prevotella species if they are susceptible to penicillin. Early and accurate preliminary detection of β-lactamase-producing isolates is crucial for treatment of infection. The aim of this study was to determine β-lactamase-producing Prevotella species by MALDI-TOF MS and screen them for the presence of cfxA gene, responsible for β-lactamase production. A total of 500 clinically relevant Prevotella isolates, collected from 13 countries for the previous European antibiotic resistance surveillance study, were tested. Susceptibility testing was performed against ampicillin and ampicillin/sulbactam by Etest methodology. EUCAST guidelines were used for susceptibility interpretations; the isolates with MIC value ≤ 0.5 for ampicillin were considered susceptible and >2 resistant. All Prevotella isolates, were tested for detection of β-lactamase activity by MALDI-TOF MS (Vitek® MS Research Use Only) system and the presence of the cfxA gene by PCR method. The susceptibility levels of the isolates to ampicillin/sulbactam and ampicillin were 99.6% and 43.4%, respectively. A total 59% of isolates presented β-lactamase activity and 60.8% were cfxA gene positive. Both these tests were positive for isolates in the resistant category. Additionally, >95% of the isolates (n = 65) which ampicillin MIC values ranged from >0.5 μg/mL to 2 μg/ml displayed β-lactamase activity. We also found that the MALDI-TOF MS-based β-lactamase assay delivers results in 2 h. We found a high concordance between the MALDI-TOF MS β-lactamase results in terms of cfxA β-lactamase gene presence. MALDI-TOF MS may serve as a simple and efficient alternative method of the existing phenotypic and PCR-based methods.
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Lefever S, Van Den Bossche D, Van Moerkercke W, D’Hondt M, Alegret Pampols MDC, Struyve M, De Bel A, Boudewijns M. Ruminococcus gnavus bacteremia, an uncommon presentation of a common member of the human gut microbiota: case report and literature review. Acta Clin Belg 2019; 74:435-438. [PMID: 31658898 DOI: 10.1080/17843286.2018.1541045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Case report: We present a case of a 66-year-old female diagnosed with R. gnavus bacteremia associated with fecal peritonits secondary to small-bowel herniation and perforation. Identification as R. gnavus was delayed because of absence of this species in the MALDI-TOF MS database (Vitek MS, bioMérieux). Identification was provided by 16S rRNA gene sequencing. Review: R. gnavus, a Gram-positive, strictly anaerobic bacterium, is a member of the human gut microbiota. Dysbiosis in the gut microbiota, with increased amounts of R. gnavus, has been described in inflammatory bowel disease. R. gnavus has only been reported occasionally as the cause of infections. Hence the potential pathogenicity is not yet fully recognized, and data regarding the antimicrobial susceptibility profile are rare. Identification of anaerobic bacteria such as R. gnavus is greatly accelerated as a result of the introduction of MALDI-TOF MS. However, as illustrated in this case report, an extensive and up-to-date MALDI-TOF MS database is necessary for providing an accurate identification.
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Affiliation(s)
- Stefanie Lefever
- Department of Microbiology, AZ Groeninge, Kortrijk, Belgium
- Department of Laboratory Medicine, University Hospital Leuven and KU Leuven, Leuven, Belgium
| | - Dorien Van Den Bossche
- Department of Microbiology, AZ Groeninge, Kortrijk, Belgium
- Department of Laboratory Medicine, University Hospital Leuven and KU Leuven, Leuven, Belgium
| | - Wouter Van Moerkercke
- Department of Gastroenterology, AZ Groeninge, Kortrijk, Belgium
- Department of Gastroenterology, University Hospital Leuven, Leuven, Belgium
| | - Mathieu D’Hondt
- Department of Abdominal Surgery, AZ Groeninge, Kortrijk, Belgium
| | | | - Mathieu Struyve
- Department of Gastroenterology, University Hospital Leuven, Leuven, Belgium
- Department of Gastroenterology, Hospital Oost-Limburg (ZOL), Genk, Belgium
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Kostrzewa M, Nagy E, Schröttner P, Pranada AB. How MALDI-TOF mass spectrometry can aid the diagnosis of hard-to-identify pathogenic bacteria - the rare and the unknown. Expert Rev Mol Diagn 2019; 19:667-682. [PMID: 31303071 DOI: 10.1080/14737159.2019.1643238] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Ten years after its introduction into clinical microbiology, MALDI-TOF mass spectrometry has become the standard routine identification tool for bacteria in most laboratories. The technology has accelerated analyses and improved the quality of results. The greatest significance has been observed for bacteria that were challenging to be identified by traditional methods. Areas covered: We searched in existing literature (Pubmed) for reports how MALDI-TOF MS has contributed to identification of rare and unknown bacteria from different groups. We describe how this has improved the diagnostics in different groups of bacteria. Reference patterns for strains which yet cannot be assigned to a known species even enable the search for related bacteria in studies as well as in routine diagnostics. MALDI-TOF MS can help to discover and investigate new species and their clinical relevance. It is a powerful tool in the elucidation of the bacterial composition of complex microbiota in culturomics studies. Expert opinion: MALDI-TOF MS has improved the diagnosis of bacterial infections. It also enables knowledge generation for prospective diagnostics. The term 'hard-to-identify' might only be rarely attributed to bacteria in the future. Novel applications are being developed, e.g. subspecies differentiation, typing, and antibiotic resistance testing which may further contribute to improved microbial diagnostics.
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Affiliation(s)
- Markus Kostrzewa
- Bioanalytical Development, Bruker Daltonik GmbH , Bremen , Germany
| | - Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged , Szeged , Hungary
| | - Percy Schröttner
- Institut für Medizinische Mikrobiologie und Hygiene, Technische Universität Dresden , Dresden , Germany
| | - Arthur B Pranada
- Department of Medical Microbiology, MVZ Dr. Eberhard & Partner Dortmund (ÜBAG) , Dortmund , Germany
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Wang Y, Chen XF, Xie XL, Xiao M, Yang Y, Zhang G, Zhang JJ, Duan SM, Zhang Q, Zhang P, Tsui C, Xu YC. Evaluation of VITEK MS, Clin-ToF-II MS, Autof MS 1000 and VITEK 2 ANC card for identification of Bacteroides fragilis group isolates and antimicrobial susceptibilities of these isolates in a Chinese university hospital. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2019; 52:456-464. [PMID: 30772212 DOI: 10.1016/j.jmii.2018.12.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 12/18/2018] [Accepted: 12/25/2018] [Indexed: 11/19/2022]
Abstract
BACKGROUND AND PURPOSE Bacteroides fragilis group isolates are most frequently isolated anaerobic pathogens. This study aimed to evaluate the accuracy of VITEK MS, Clin-ToF-II MS, Autof MS 1000 and VITEK 2 ANC card on the identification of clinical B. fragilis group isolates, as well as to determine their antimicrobial susceptibilities. METHODS A total of 138 isolates of B. fragilis group isolates were identified with the three MALDI-TOF MS systems and VITEK 2 ANC cards. 16S rRNA gene sequencing was used as the reference identification method for comparison. Antimicrobial susceptibilities were determined by agar dilution method to 19 antimicrobial agents recommended by Clinical and Laboratory Standards Institute (CLSI). RESULTS Hundred thirty three isolates of Bacteroides spp. and 5 isolates of Parabacteroides spp. were identified by 16S rRNA sequencing. The rates of accurate identification at species level of VITEK MS, Clin-ToF-II MS, Autof MS 1000 and VITEK 2 ANC card were 94.2%, 94.2%, 98.6% and 94.9%, respectively, while that at genus level were 99.3%, 100%, 100% and 97.8%, respectively. Metronidazole and chloramphenicol were the most susceptible agents (99.3% and 92.8%, respectively), followed by meropenem, ertapenem, imipenem and piperacillin/tazobactam to which the susceptible rates ranged from 76.8% to 79.0%. The susceptible rates to carbapenems decreased 12.4-15.3% from 2010-2013 to 2014-2017. CONCLUSION All the four systems provided high accurate rate on the identification of B. fragilis group isolates. Metronidazole showed highest activity against these isolates. Attention should be paid to the higher resistant rates to carbapenems, clindamycin, moxifloxacin and tigecycline than the other countries.
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Affiliation(s)
- Yao Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xin-Fei Chen
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiu-Li Xie
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Yang Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Ge Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Jing-Jia Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Si-Meng Duan
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Qian Zhang
- Department of Clinical Laboratory, Qinghai Provincial People's Hospital, Xining, China
| | - Peng Zhang
- Department of Clinical Laboratory, Dalian Third People's Hospital, Dalian, China
| | - Clement Tsui
- Department of Pathology, Sidra Medicine, Doha, Qatar; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Ying-Chun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China.
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Nagy E, Schuetz A. Advancing MALDI-TOF MS applications in anaerobic bacteriology. Anaerobe 2018; 54:189-190. [PMID: 30541685 DOI: 10.1016/j.anaerobe.2018.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary.
| | - Audrey Schuetz
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA.
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Chong YK, Ho CC, Leung SY, Lau SK, Woo PC. Clinical Mass Spectrometry in the Bioinformatics Era: A Hitchhiker's Guide. Comput Struct Biotechnol J 2018; 16:316-334. [PMID: 30237866 PMCID: PMC6138949 DOI: 10.1016/j.csbj.2018.08.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 08/20/2018] [Accepted: 08/21/2018] [Indexed: 02/06/2023] Open
Abstract
Mass spectrometry (MS) is a sensitive, specific and versatile analytical technique in the clinical laboratory that has recently undergone rapid development. From initial use in metabolic profiling, it has matured into applications including clinical toxicology assays, target hormone and metabolite quantitation, and more recently, rapid microbial identification and antimicrobial resistance detection by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). In this mini-review, we first succinctly outline the basics of clinical mass spectrometry. Examples of hard ionization (electron ionization) and soft ionization (electrospray ionization, MALDI) are presented to demonstrate their clinical applications. Next, a conceptual discourse on mass selection and determination is presented: quadrupole mass filter, time-of-flight mass spectrometer and the Orbitrap; and MS/MS (tandem-in-space, tandem-in-time and data acquisition), illustrated with clinical examples. Current applications in (1) bacterial and fungal identification, antimicrobial susceptibility testing and phylogenetic classification, (2) general unknown urine toxicology screening and expanded new-born metabolic screening and (3) clinical metabolic profiling by gas chromatography are outlined. Finally, major limitations of MS-based techniques, including the technical challenges of matrix effect and isobaric interference; and novel challenges in the post-genomic era, such as protein molecular variants, are critically discussed from the perspective of service laboratories. Computer technology and structural biology have played important roles in the maturation of this field. MS-based techniques have the potential to replace current analytical techniques, and existing expertise and instrument will undergo rapid evolution. Significant automation and adaptation to regulatory requirements are underway. Mass spectrometry is unleashing its potentials in clinical laboratories.
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Affiliation(s)
- Yeow-Kuan Chong
- Hospital Authority Toxicology Reference Laboratory, Department of Pathology, Princess Margaret Hospital (PMH), Kowloon, Hong Kong
- Chemical Pathology and Medical Genetics, Department of Pathology, Princess Margaret Hospital (PMH), Kowloon, Hong Kong
| | - Chi-Chun Ho
- Division of Chemical Pathology, Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital (PYNEH), Hong Kong
- Division of Clinical Biochemistry, Department of Pathology, Queen Mary Hospital (QMH), Hong Kong
- Centre for Genomic Sciences, The University of Hong Kong, Hong Kong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Shui-Yee Leung
- Department of Ocean Science, School of Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Susanna K.P. Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong
| | - Patrick C.Y. Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong
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Ulger Toprak N, Alida C M V, Urban E, Wybo I, Justesen US, Jean-Pierre H, Morris T, Akgul O, Kulekci G, Soyletir G, Nagy E. Performance of mass spectrometric identification of clinical Prevotella species using the VITEK MS system: A prospective multi-center study. Anaerobe 2018; 54:205-209. [PMID: 29880448 DOI: 10.1016/j.anaerobe.2018.05.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 05/15/2018] [Accepted: 05/29/2018] [Indexed: 12/12/2022]
Abstract
Prevotella species, members of the human microbiota, can cause opportunistic infections. Rapid and accurate identification of Prevotella isolates plays a critical role in successful treatment, especially since the antibiotic susceptibility profile differs between species. Studies, mostly carried out using the Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) Biotyper system, showed that MALDI-TOF MS is an accurate, rapid and satisfactory method for the identification of clinically important anaerobes. In this multi-center study, we assessed the performance of the MALDI-TOF MS VITEK MS system for the identification of clinical Prevotella isolates. A total of 508 Prevotella isolates, representing 19 different species, collected from 11 European countries, Kuwait and Turkey between January 2014 and April 2016, were identified using VITEK MS (v3.0). The reliability of the identification was assessed by 16S rRNA gene sequencing. Using VITEK MS, 422 (83.1%) of the 508 isolates were identified on the species level, 459 (90.4%) on the genus level. A total of 49 (9.6%) isolates were not identified correctly. 16S rRNA gene sequencing results showed that this was partly due to the fact that several species were not represented in the database. However, some species that were represented in the database were also not identified. Five Prevotella strains were misidentified at the genus level, 2 of these strains belonged to a species not represented in the database. In general, the VITEK MS offers a reliable and rapid identification of Prevotella species, however the databases needs to be expanded.
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Affiliation(s)
- Nurver Ulger Toprak
- Marmara University School of Medicine, Department of Microbiology, Istanbul, Turkey.
| | - Veloo Alida C M
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, the Netherlands
| | - Edit Urban
- Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
| | - Ingrid Wybo
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - Ulrik S Justesen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Helene Jean-Pierre
- Centre Hospitalier Universitaire de Montpellier, Laboratoire de Bactériologie, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Trefor Morris
- UK Anaerobe Reference Unit, Public Health Wales Microbiology, Cardiff, UK
| | - Oncu Akgul
- Marmara University School of Medicine, Department of Microbiology, Istanbul, Turkey
| | - Guven Kulekci
- Istanbul University, Faculty of Dentistry, Department of Microbiology, Istanbul, Turkey
| | - Guner Soyletir
- Marmara University School of Medicine, Department of Microbiology, Istanbul, Turkey
| | - Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
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Jeverica S, Nagy E, Mueller-Premru M, Papst L. Sample preparation method influences direct identification of anaerobic bacteria from positive blood culture bottles using MALDI-TOF MS. Anaerobe 2018; 54:231-235. [PMID: 29861277 DOI: 10.1016/j.anaerobe.2018.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/09/2018] [Accepted: 05/14/2018] [Indexed: 02/08/2023]
Abstract
Rapid detection and identification of anaerobic bacteria from blood is important to adjust antimicrobial therapy by including antibiotics with activity against anaerobic bacteria. Limited data is available about direct identification of anaerobes from positive blood culture bottles using MALDI-TOF mass spectrometry (MS). In this study, we evaluated the performance of two sample preparation protocols for direct identification of anaerobes from positive blood culture bottles, the MALDI Sepsityper kit (Sepsityper) and the in-house saponin (saponin) method. Additionally, we compared two blood culture bottle types designed to support the growth of anaerobic bacteria, the BacT/ALERT-FN Plus (FN Plus) and the BACTEC-Lytic (Lytic), and their influence on direct identification. A selection of 30 anaerobe strains belonging to 22 different anaerobic species (11 reference strains and 19 clinical isolates) were inoculated to 2 blood culture bottle types in duplicate. In total, 120 bottles were inoculated and 99.2% (n = 119) signalled growth within 5 days of incubation. The Sepsityper method correctly identified 56.3% (n = 67) of anaerobes, while the saponin method correctly identified 84.9% (n = 101) of anaerobes with at least log(score) ≥1.6 (low confidence correct identification), (p < 0.001). Gram negative anaerobes were better identified with the saponin method (100% vs. 46.5%; p < 0.001), while Gram positive anaerobes were better identified with the Sepsityper method (70.8% vs. 62.5%; p = 0.454). Average log(score) values among only those isolates that were correctly identified simultaneously by both sample preparation methods were 2.119 and 2.029 in favour of the Sepsityper method, (p = 0.019). The inoculated bottle type didn't influence the performance of the two sample preparation methods. We confirmed that direct identification from positive blood culture bottles with MALDI-TOF MS is reliable for anaerobic bacteria. However, the results are influenced by the sample preparation method used.
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Affiliation(s)
- Samo Jeverica
- Institute of Microbiology and Immunology, Medical Faculty, University of Ljubljana, Ljubljana, Slovenia.
| | - Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
| | - Manica Mueller-Premru
- Institute of Microbiology and Immunology, Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Lea Papst
- Clinic for Infectious Diseases and Febrile Illnesses, University Medical Centre Ljubljana, Ljubljana, Slovenia
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Kierzkowska M, Pędzisz P, Babiak I, Janowicz J, Kulig M, Majewska A, Sawicka-Grzelak A, Młynarczyk G. Difficulties in identifying the bacterial species from the genus Clostridium in a case of injury-related osteitis. Folia Microbiol (Praha) 2018. [PMID: 29524152 DOI: 10.1007/s12223-018-0597-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Most Clostridium species are part of saprophytic microflora in humans and animals; however, some are well-known human pathogens. We presented the challenges in identifying the Clostridium species isolated from a patient with an infected open dislocation of the proximal interphalangeal joint of the fourth digit of the right hand. The clinical materials were intraoperative samples collected from a patient diagnosed with an injury-related infection, with soft tissue loss and tendon sheath involvement. The available biochemical, molecular, and genetic techniques were used in identifying the isolated bacteria. The isolated bacterium was shown to have low biochemical activity; hence, it was not definitively identified via biochemical tests Api 20A or Rapid 32A. Vitek 2 and mass spectrometry methods were equally inconclusive. Clostridium tetani infection was strongly suspected based on the bacterium's morphology and the appearance of its colonies on solid media. It was only via the 16S rRNA sequencing method, which is non-routine and unavailable in most clinical laboratories, that this pathogen was excluded. Despite appropriate pre-laboratory procedures, which are critical for obtaining reliable test results, the routine methods of anaerobic bacterium identification are not always useful in diagnostics. Diagnostic difficulties occur in the case of environment-derived bacteria of low or not fully understood biological activity, which are absent from databases of automatic bacterial identification systems.
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Affiliation(s)
- Marta Kierzkowska
- Chair and Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego 5 Str, 02-004, Warsaw, Poland
| | - Piotr Pędzisz
- Department of Orthopedics and Traumatology, Medical University of Warsaw, Lindleya 4 Str, 02-005, Warsaw, Poland
| | - Ireneusz Babiak
- Department of Orthopedics and Traumatology, Medical University of Warsaw, Lindleya 4 Str, 02-005, Warsaw, Poland
| | - Jakub Janowicz
- Department of Orthopedics and Traumatology, Medical University of Warsaw, Lindleya 4 Str, 02-005, Warsaw, Poland
| | - Mateusz Kulig
- Department of Orthopedics and Traumatology, Medical University of Warsaw, Lindleya 4 Str, 02-005, Warsaw, Poland
| | - Anna Majewska
- Chair and Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego 5 Str, 02-004, Warsaw, Poland.
| | - Anna Sawicka-Grzelak
- Chair and Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego 5 Str, 02-004, Warsaw, Poland
| | - Grażyna Młynarczyk
- Chair and Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego 5 Str, 02-004, Warsaw, Poland
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How to isolate, identify and determine antimicrobial susceptibility of anaerobic bacteria in routine laboratories. Clin Microbiol Infect 2018; 24:1139-1148. [PMID: 29458156 DOI: 10.1016/j.cmi.2018.02.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/09/2018] [Accepted: 02/11/2018] [Indexed: 02/04/2023]
Abstract
BACKGROUND There has been increased interest in the study of anaerobic bacteria that cause human infection during the past decade. Many new genera and species have been described using 16S rRNA gene sequencing of clinical isolates obtained from different infection sites with commercially available special culture media to support the growth of anaerobes. Several systems, such as anaerobic pouches, boxes, jars and chambers provide suitable anaerobic culture conditions to isolate even strict anaerobic bacteria successfully from clinical specimens. Beside the classical, time-consuming identification methods and automated biochemical tests, the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry has revolutionized identification of even unusual and slow-growing anaerobes directly from culture plates, providing the possibility of providing timely information about anaerobic infections. AIMS The aim of this review article is to present methods for routine laboratories, which carry out anaerobic diagnostics on different levels. SOURCES Relevant data from the literature mostly published during the last 7 years are encompassed and discussed. CONTENT The review involves topics on the anaerobes that are members of the commensal microbiota and their role causing infection, the key requirements for collection and transport of specimens, processing of specimens in the laboratory, incubation techniques, identification and antimicrobial susceptibility testing of anaerobic bacteria. Advantages, drawbacks and specific benefits of the methods are highlighted. IMPLICATIONS The present review aims to update and improve anaerobic microbiology in laboratories with optimal conditions as well as encourage its routine implementation in laboratories with restricted resources.
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Grégory D, Chaudet H, Lagier JC, Raoult D. How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota. Expert Rev Proteomics 2018; 15:217-229. [PMID: 29336192 DOI: 10.1080/14789450.2018.1429271] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Describing the human hut gut microbiota is one the most exciting challenges of the 21st century. Currently, high-throughput sequencing methods are considered as the gold standard for this purpose, however, they suffer from several drawbacks, including their inability to detect minority populations. The advent of mass-spectrometric (MS) approaches to identify cultured bacteria in clinical microbiology enabled the creation of the culturomics approach, which aims to establish a comprehensive repertoire of cultured prokaryotes from human specimens using extensive culture conditions. Areas covered: This review first underlines how mass spectrometric approaches have revolutionized clinical microbiology. It then highlights the contribution of MS-based methods to culturomics studies, paying particular attention to the extension of the human gut microbiota repertoire through the discovery of new bacterial species. Expert commentary: MS-based approaches have enabled cultivation methods to be resuscitated to study the human gut microbiota and thus to fill in the blanks left by high-throughput sequencing methods in terms of culturing minority populations. Continued efforts to recover new taxa using culture methods, combined with their rapid implementation in genomic databases, would allow for an exhaustive analysis of the gut microbiota through the use of a comprehensive approach.
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Affiliation(s)
- Dubourg Grégory
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Hervé Chaudet
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Jean-Christophe Lagier
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Didier Raoult
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
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New Technologies for the Diagnosis of Infection. DIAGNOSTIC PATHOLOGY OF INFECTIOUS DISEASE 2018. [PMCID: PMC7152403 DOI: 10.1016/b978-0-323-44585-6.00006-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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16
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Performance of MALDI-TOF MS for identification of oral Prevotella species. Anaerobe 2017; 47:89-93. [DOI: 10.1016/j.anaerobe.2017.04.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/17/2017] [Accepted: 04/20/2017] [Indexed: 01/26/2023]
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Jeverica S, Kolenc U, Mueller-Premru M, Papst L. Evaluation of the routine antimicrobial susceptibility testing results of clinically significant anaerobic bacteria in a Slovenian tertiary-care hospital in 2015. Anaerobe 2017; 47:64-69. [PMID: 28433670 DOI: 10.1016/j.anaerobe.2017.04.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 04/14/2017] [Accepted: 04/15/2017] [Indexed: 11/30/2022]
Abstract
The aim of our study was to determined antimicrobial susceptibility profiles of 2673 clinically significant anaerobic bacteria belonging to the major genera, isolated in 2015 in a large tertiary-care hospital in Slovenia. The species identification was performed by MALDI-TOF mass spectrometry. Antimicrobial susceptibility was determined immediately at the isolation of the strains against: penicillin, co-amoxiclav, imipenem, clindamycin and metronidazole, using gradient diffusion methodology and EUCAST breakpoints. The most frequent anaerobes were Bacteroides fragilis group with 31% (n = 817), Gram positive anaerobic cocci (GPACs) with 22% (n = 589), Prevotella with 14% (n = 313) and Propionibacterium with 8% (n = 225). Metronidazole has retained full activity (100%) against all groups of anaerobic bacteria intrinsically susceptible to it. Co-amoxiclav and imipenem were active against most tested anaerobes with zero or low resistance rates. However, observed resistance to co-amoxiclav (8%) and imipenem (1%) is worrying especially among B. fragilis group isolates. High overall resistance (23%) to clindamycin was detected in our study and was highest among the genera Prevotella, Bacteroides, Parabacteroides, GPACs and Clostridium. Routine testing of antimicrobial susceptibility of clinically relevant anaerobic bacteria is feasible and provides good surveillance data.
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Affiliation(s)
- Samo Jeverica
- Institute of Microbiology and Immunology, Medical Faculty, University of Ljubljana, Ljubljana, Slovenia.
| | - Urša Kolenc
- Institute of Microbiology and Immunology, Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Manica Mueller-Premru
- Institute of Microbiology and Immunology, Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Lea Papst
- Department of Infectious Diseases, University Medical Centre Ljubljana, Ljubljana, Slovenia
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Jin P, Wang K, Huang C, Nice EC. Mining the fecal proteome: from biomarkers to personalised medicine. Expert Rev Proteomics 2017; 14:445-459. [PMID: 28361558 DOI: 10.1080/14789450.2017.1314786] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Fecal proteomics has gained increased prominence in recent years. It can provide insights into the diagnosis and surveillance of many bowel diseases by both identifying potential biomarkers in stool samples and helping identify disease-related pathways. Fecal proteomics has already shown its potential for the discovery and validation of biomarkers for colorectal cancer screening, and the analysis of fecal microbiota by MALDI-MS for the diagnosis of a range of bowel diseases is gaining clinical acceptance. Areas covered: Based on a comprehensive analysis of the current literature, we introduce the range of sensitive and specific proteomics methods which comprise the current 'Proteomics Toolbox', explain how the integration of fecal proteomics with data processing/bioinformatics has been used for the identification of potential biomarkers for both CRC and other gut-related pathologies and analysis of the fecal microbiome, outline some of the current fecal assays in current clinical practice and introduce the concept of personalised medicine which these technologies will help inform. Expert commentary: Integration of fecal proteomics with other proteomics and genomics strategies as well as bioinformatics is paving the way towards personalised medicine, which will bring with it improved global healthcare.
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Affiliation(s)
- Ping Jin
- a Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology , the Affiliated Hospital of Hainan Medical College , Haikou , China.,b State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Kui Wang
- b State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Canhua Huang
- a Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology , the Affiliated Hospital of Hainan Medical College , Haikou , China.,b State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Edouard C Nice
- b State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,c Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia
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Xiao Z, Luo Y, Ye L, Wang R, Zhang Y, Zhao Q, Guo L, Ma Y, Cui S. Evaluation of VITEK matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of anaerobes. Microbiol Immunol 2017; 60:477-82. [PMID: 27278253 DOI: 10.1111/1348-0421.12393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 05/21/2016] [Accepted: 05/31/2016] [Indexed: 12/11/2022]
Abstract
Rapid and adequate identification of anaerobic bacterial species still presents a challenge for most diagnostic laboratories, hindering the selection of appropriate therapy. In this study, the identification capacity of 16S rRNA sequence analysis, VITEK 2 (BioMérieux, Lyon, France) compact analysis and VITEK MS-mediated identification for anaerobic bacterial species was compared. Eighty-five anaerobic bacterial isolates from 11 provinces in China belonging to 14 genera were identified by these three methods. Differences in identification between these three methods were compared. Consistent identification results were obtained for 54 (54/85, 63.5%) isolates by all three methods, the most discordant results being concentrated in Clostridium XI (n = 8) and Bacteroides fragilis (n = 9) clusters. Using the VITEK MS system, 74 (74/90, 82.2%) isolates were identified as single species consistent with 16S rRNA sequence analysis, which was significantly better than the results obtained with VITEK 2 Compact (P < 0.01). Misidentifications by the Vitek 2 Compact and Vitek MS systems were mainly observed in the Clostridium XI (n = 8)and B. fragilis clusters (n = 9). VITEK MS identified anaerobic bacteria even after they had been exposed to oxygen for a week. Identification by the Vitek MS system was more consistent with 16S rRNA sequence analysis than identification by Vitek 2 Compact. Continuous expansion of the VITEK MS database with rare described anaerobic species is warranted to improve both the efficiency and accuracy of VITEK MS identification in routine diagnostic microbiology.
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Affiliation(s)
- Zheng Xiao
- Department of Microbiology, General Hospital of PLA, 28 Fuxing Road, Haidian District, Beijing, China
| | - Yanping Luo
- Department of Microbiology, General Hospital of PLA, 28 Fuxing Road, Haidian District, Beijing, China
| | - Liyan Ye
- Department of Microbiology, General Hospital of PLA, 28 Fuxing Road, Haidian District, Beijing, China
| | - Rui Wang
- Department of Microbiology, General Hospital of PLA, 28 Fuxing Road, Haidian District, Beijing, China
| | - Ying Zhang
- Department of Microbiology, General Hospital of PLA, 28 Fuxing Road, Haidian District, Beijing, China
| | - Qiang Zhao
- Department of Microbiology, General Hospital of PLA, 28 Fuxing Road, Haidian District, Beijing, China
| | - Ling Guo
- Department of Microbiology, General Hospital of PLA, 28 Fuxing Road, Haidian District, Beijing, China
| | - Yanning Ma
- Department of Microbiology, General Hospital of PLA, 28 Fuxing Road, Haidian District, Beijing, China
| | - Shenghui Cui
- Department of Food Science, National Institutes for Food and Drug Control, 2 Tiantan Xili, Dongcheng District, Beijing, China
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Al-Hatmi AMS, Normand AC, van Diepeningen AD, Hendrickx M, de Hoog GS, Piarroux R. Rapid identification of clinical members of Fusarium fujikuroi complex using MALDI-TOF MS. Future Microbiol 2015; 10:1939-52. [DOI: 10.2217/fmb.15.108] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Aim: To develop the matrix-assisted laser desorption ionization mass spectrometry (MALDI-TOF MS) method for identification of Fusarium species within Fusarium fujikuroi complex for use in clinical microbiology laboratories. Materials & methods: A total of 24 reference and 60 clinical and environmental isolates belonging to the F. fujikuroi complex were subjected to MALDI-TOF MS identification. Protein extracts of Fusarium isolates were obtained using formic acid extraction. Multilocus sequence analysis was used as a gold standard. Results: The MALDI-TOF MS Biotyper correctly identified 93.6% of the strains down to the species level, while the remaining isolates (6.4%) were identified at the genus level when using scores of ≥ 2.0 as cut-off values. Correct identification was obtained despite large intraspecific heterogeneities in MALDI-TOF spectra. Conclusion: MALDI-TOF MS is a rapid identification tool for the recognition of species within F. fujikuroi complex, provided a database is available.
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Affiliation(s)
- Abdullah MS Al-Hatmi
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
- Institute of Biodiversity & Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- Directorate General of Health Services, Ministry of Health, Ibri Hospital, Ibri, Oman
| | - Anne-Cécile Normand
- Laboratoire de Parasitologie-Mycologie, CHU Timone, Université de la Méditerranée, Marseille, France
| | | | - Marijke Hendrickx
- BCCM/IHEM: Scientific Institute of Public Health, Mycology & Aerobiology Section, Bruxelles, Belgium
| | - G Sybren de Hoog
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
- Institute of Biodiversity & Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- Peking University Health Science Center, Research Center for Medical Mycology, Beijing, China
- Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
- King Abdulaziz University, Jeddah, Saudi Arabia
| | - Renaud Piarroux
- Laboratoire de Parasitologie-Mycologie, CHU Timone, Université de la Méditerranée, Marseille, France
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Almuhayawi M, Altun O, Abdulmajeed AD, Ullberg M, Özenci V. The Performance of the Four Anaerobic Blood Culture Bottles BacT/ALERT-FN, -FN Plus, BACTEC-Plus and -Lytic in Detection of Anaerobic Bacteria and Identification by Direct MALDI-TOF MS. PLoS One 2015; 10:e0142398. [PMID: 26554930 PMCID: PMC4640713 DOI: 10.1371/journal.pone.0142398] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/21/2015] [Indexed: 11/18/2022] Open
Abstract
Detection and identification of anaerobic bacteria in blood cultures (BC) is a well-recognized challenge in clinical microbiology. We studied 100 clinical anaerobic BC isolates to evaluate the performance of BacT/ALERT-FN, -FN Plus (BioMérieux), BACTEC-Plus and -Lytic (Becton Dickinson BioSciences) BC bottles in detection and time to detection (TTD) of anaerobic bacteria. BACTEC Lytic had higher detection rate (94/100, 94%) than BacT/ALERT FN Plus (80/100, 80%) (p<0.01) in the studied material. There was no significant difference in detection of anaerobic bacteria among the remaining bottle types. The 67 anaerobic bacteria that signalled positive in all four bottle types were analyzed to compare the time to detection (TTD) and isolates were directly identified by MALDI-TOF MS. There was a significant difference in TTD among the four bottle types (p<0.0001). The shortest median TTD was 18 h in BACTEC Lytic followed by BacT/ALERT FN (23.5 h), BACTEC Plus (27 h) and finally BacT/ALERT FN Plus (38 h) bottles. In contrast, MALDI-TOF MS performed similarly in all bottle types with accurate identification in 51/67 (76%) BacT/ALERT FN, 51/67 (76%) BacT/ALERT FN Plus, 53/67 (79%) BACTEC Plus and 50/67 (75%) BACTEC Lytic bottles. In conclusion, BACTEC Lytic bottles have significantly better detection rates and shorter TTD compared to the three other bottle types. The anaerobic BC bottles are equally suitable for direct MALDI-TOF MS for rapid and reliable identification of common anaerobic bacteria. Further clinical studies are warranted to investigate the performance of anaerobic BC bottles in detection of anaerobic bacteria and identification by direct MALDI-TOF MS.
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Affiliation(s)
- Mohammed Almuhayawi
- Division of Clinical Microbiology F 72, Karolinska Institutet, Karolinska University Hospital, Huddinge, SE 141 86, Stockholm, Sweden
- Department of Microbiology, King Abdul-Aziz University, Jeddah, Saudi Arabia
| | - Osman Altun
- Division of Clinical Microbiology F 72, Karolinska Institutet, Karolinska University Hospital, Huddinge, SE 141 86, Stockholm, Sweden
| | - Adam Dilshad Abdulmajeed
- Division of Clinical Microbiology F 72, Karolinska Institutet, Karolinska University Hospital, Huddinge, SE 141 86, Stockholm, Sweden
| | - Måns Ullberg
- Division of Clinical Microbiology F 72, Karolinska Institutet, Karolinska University Hospital, Huddinge, SE 141 86, Stockholm, Sweden
| | - Volkan Özenci
- Division of Clinical Microbiology F 72, Karolinska Institutet, Karolinska University Hospital, Huddinge, SE 141 86, Stockholm, Sweden
- * E-mail:
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Influence of microbiome species in hard-to-heal wounds on disease severity and treatment duration. Braz J Infect Dis 2015; 19:604-13. [PMID: 26518264 PMCID: PMC9425364 DOI: 10.1016/j.bjid.2015.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 08/04/2015] [Accepted: 08/08/2015] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Infections, mostly those associated with colonization of wound by different pathogenic microorganisms, are one of the most serious health complications during a medical treatment. Therefore, this study is focused on the isolation, characterization, and identification of microorganisms prevalent in superficial wounds of patients (n=50) presenting with bacterial infection. METHODS After successful cultivation, bacteria were processed and analyzed. Initially the identification of the strains was performed through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry based on comparison of protein profiles (2-30kDa) with database. Subsequently, bacterial strains from infected wounds were identified by both matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and sequencing of 16S rRNA gene 108. RESULTS The most prevalent species was Staphylococcus aureus (70%), and out of those 11% turned out to be methicillin-resistant (mecA positive). Identified strains were compared with patients' diagnoses using the method of artificial neuronal network to assess the association between severity of infection and wound microbiome species composition. Artificial neuronal network was subsequently used to predict patients' prognosis (n=9) with 85% success. CONCLUSIONS In all of 50 patients tested bacterial infections were identified. Based on the proposed artificial neuronal network we were able to predict the severity of the infection and length of the treatment.
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Pailhoriès H, Daure S, Eveillard M, Joly-Guillou ML, Kempf M. Using Vitek MALDI-TOF mass spectrometry to identify species belonging to the Acinetobacter calcoaceticus–Acinetobacter baumannii complex: a relevant alternative to molecular biology? Diagn Microbiol Infect Dis 2015. [DOI: 10.1016/j.diagmicrobio.2015.06.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Frey KG, Bishop-Lilly KA. Next-Generation Sequencing for Pathogen Detection and Identification. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Lee W, Kim M, Yong D, Jeong SH, Lee K, Chong Y. Evaluation of VITEK mass spectrometry (MS), a matrix-assisted laser desorption ionization time-of-flight MS system for identification of anaerobic bacteria. Ann Lab Med 2014; 35:69-75. [PMID: 25553283 PMCID: PMC4272968 DOI: 10.3343/alm.2015.35.1.69] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 05/26/2014] [Accepted: 10/02/2014] [Indexed: 11/19/2022] Open
Abstract
Background By conventional methods, the identification of anaerobic bacteria is more time consuming and requires more expertise than the identification of aerobic bacteria. Although the matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems are relatively less studied, they have been reported to be a promising method for the identification of anaerobes. We evaluated the performance of the VITEK MS in vitro diagnostic (IVD; 1.1 database; bioMérieux, France) in the identification of anaerobes. Methods We used 274 anaerobic bacteria isolated from various clinical specimens. The results for the identification of the bacteria by VITEK MS were compared to those obtained by phenotypic methods and 16S rRNA gene sequencing. Results Among the 249 isolates included in the IVD database, the VITEK MS correctly identified 209 (83.9%) isolates to the species level and an additional 18 (7.2%) at the genus level. In particular, the VITEK MS correctly identified clinically relevant and frequently isolated anaerobic bacteria to the species level. The remaining 22 isolates (8.8%) were either not identified or misidentified. The VITEK MS could not identify the 25 isolates absent from the IVD database to the species level. Conclusions The VITEK MS showed reliable identifications for clinically relevant anaerobic bacteria.
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Affiliation(s)
- Wonmok Lee
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Myungsook Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Yunsop Chong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
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