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Litterio M, Castello L, Venuta ME, Abel S, Fernández-Canigia L, Legaria MC, Rollet R, Vaustat D, Azula N, Fox B, Otero S, Maldonado ML, Mangieri NA, Rossetti MA, Predari SC, Cejas D, Barberis C. Comparison of two MALDI-TOF MS systems for the identification of clinically relevant anaerobic bacteria in Argentina. Rev Argent Microbiol 2024; 56:33-61. [PMID: 38368217 DOI: 10.1016/j.ram.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 10/02/2023] [Accepted: 12/05/2023] [Indexed: 02/19/2024] Open
Abstract
The aim of this study was to compare the performance of two MALDI-TOF MS systems in the identification of clinically relevant strict anaerobic bacteria. The 16S rRNA gene sequencing was the gold standard method when discrepancies or inconsistencies were observed between platforms. A total of 333 isolates were recovered from clinical samples of different centers in Buenos Aires City between 2016 and 2021. The isolates were identified in duplicate using two MALDI-TOF MS systems, BD Bruker Biotyper (Bruker Daltonics, Bremen, Germany) and Vitek MS (bioMèrieux, Marcy-l'Etoile, France). Using the Vitek MS system, the identification of anaerobic isolates yielded the following percentages: 65.5% (n: 218) at the species or species-complex level, 71.2% (n: 237) at the genus level, 29.4% (n: 98) with no identification and 5.1% (n: 17) with misidentification. Using the Bruker Biotyper system, the identification rates were as follows: 85.3% (n: 284) at the species or species-complex level, 89.7% (n: 299) at the genus level, 14.1% (n: 47) with no identification and 0.6% (n: 2) with misidentification. Differences in the performance of both methods were statistically significant (p-values <0.0001). In conclusion, MALDI-TOF MS systems speed up microbial identification and are particularly effective for slow-growing microorganisms, such as anaerobic bacteria, which are difficult to identify by traditional methods. In this study, the Bruker system showed greater accuracy than the Vitek system. In order to be truly effective, it is essential to update the databases of both systems by increasing the number of each main spectrum profile within the platforms.
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Affiliation(s)
- Mirta Litterio
- Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Liliana Castello
- Universidad de Buenos Aires, Instituto de Investigaciones Médicas Alfredo Lanari, Departamento de Microbiología, Buenos Aires, Argentina
| | - María Elena Venuta
- Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Sofía Abel
- Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | | | - María Cristina Legaria
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Buenos Aires, Argentina
| | - Raquel Rollet
- Hospital de Enfermedades Infecciosas Dr. Francisco Javier Muñiz, Buenos Aires, Argentina
| | - Daniela Vaustat
- Hospital de Enfermedades Infecciosas Dr. Francisco Javier Muñiz, Buenos Aires, Argentina
| | - Natalia Azula
- Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno (CEMIC), Buenos Aires, Argentina
| | | | - Silvina Otero
- Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | | | - Natalia Alejandra Mangieri
- Universidad de Buenos Aires, Instituto de Investigaciones Médicas Alfredo Lanari, Departamento de Microbiología, Buenos Aires, Argentina
| | - María Adelaida Rossetti
- Hospital Interzonal de Agudos Presidente Perón, Avellaneda, Provincia de Buenos Aires, Argentina
| | - Silvia Carla Predari
- Universidad de Buenos Aires, Instituto de Investigaciones Médicas Alfredo Lanari, Departamento de Microbiología, Buenos Aires, Argentina
| | - Daniela Cejas
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina; CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Buenos Aires, Argentina
| | - Claudia Barberis
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Buenos Aires, Argentina.
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Cobo F, Pérez-Carrasco V, Martín-Hita L, García-Salcedo JA, Navarro-Marí JM. Comparative evaluation of MALDI-TOF MS and 16S rRNA gene sequencing for the identification of clinically relevant anaerobic bacteria: critical evaluation of discrepant results. Anaerobe 2023; 82:102754. [PMID: 37321445 DOI: 10.1016/j.anaerobe.2023.102754] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/17/2023]
Abstract
OBJECTIVES The main study objective was to evaluate the correlation between matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing results for the identification of anaerobes. METHODS A retrospective study was conducted of all anaerobic bacteria isolated from clinically significant specimens. MALDI-TOF (Bruker Byotyper) and 16S rRNA gene sequencing were performed in all strains. Identifications were considered correct when the concordance with gene sequencing was ≥99%. RESULTS The study included 364 isolates of anaerobic bacteria: 201 (55.2%) Gram-negative and 163 (44.8%) Gram-positive, mostly belonging to the genus Bacteroides. Isolates were largely obtained from blood cultures (128/35.4%) and intra-abdominal samples (116/32.1%). Overall, 87.3% of isolates were identified at species level using the version 9 database (89.5% of Gram-negative and 84.6% of Gram-positive anaerobic bacteria). All isolates belonging to the species B. fragilis sensu stricto were correctly identified by MALDI-TOF MS, but five cases of Phocaeicola (Bacteroides) dorei were misidentified as Phocaeicola (Bacteroides) vulgatus; all Prevotella isolates were correctly identified at the genus level, and most were correctly identified at the species level. Among Gram-positive anaerobes, 12 Anaerococcus species were not identified by MALDI-TOF MS, while six cases identified as Peptoniphilus indolicus were found to belong to other genera/species. CONCLUSIONS MALDI-TOF is a reliable technique for identifying most anaerobic bacteria, although the database needs frequent updating to identify rare, infrequent, and newly discovered species.
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Affiliation(s)
- Fernando Cobo
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain.
| | - Virginia Pérez-Carrasco
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
| | - Lina Martín-Hita
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
| | - José Antonio García-Salcedo
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
| | - José María Navarro-Marí
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
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Toyoshima H, Tanigawa M, Ishiguro C, Tanaka H, Nakanishi Y, Sakabe S. Vertebral osteomyelitis caused by Fusobacterium nucleatum with an associated asymptomatic liver abscess in an immunocompetent adult: a case report and literature review. IDCases 2023; 32:e01754. [PMID: 37096206 PMCID: PMC10121789 DOI: 10.1016/j.idcr.2023.e01754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 03/31/2023] Open
Abstract
Fusobacterium nucleatum rarely causes vertebral osteomyelitis or liver abscesses, and no reports exist of it concurrently causing vertebral osteomyelitis and pyogenic liver abscess. A 58-year-old woman with a history of periodontitis presented with worsening lumbago, left lower leg pain, numbness, and fever for a week. Physical examination indicated knocking pain at the L2-L3 levels with a psoas sign on the left side. A magnetic resonance image showed L2-S1 vertebral osteomyelitis and intervertebral discitis, with a left psoas major muscle abscess. Vertebral osteomyelitis caused by Staphylococcus aureus was suspected; blood cultures were obtained, and intravenous cefazolin was administered. Computed tomography, which was performed to detect disseminated foci, revealed a multilocular liver abscess. On day 4 of incubation, the anaerobic blood culture bottles were positive for characteristic filamentous gram-negative rods. The empiric antimicrobial therapy was changed to ampicillin/sulbactam. The isolate was identified as F. nucleatum based on 16S rRNA gene sequencing. The liver abscess was drained on day 12. Based on the antimicrobial susceptibility test results, the patient was treated with intravenous ampicillin/sulbactam for 4 weeks followed by oral amoxicillin/clavulanate for an additional 8 weeks and remained disease-free at the 1-year follow-up. Clinicians should consider F. nucleatum as the causative organism for vertebral osteomyelitis presenting with asymptomatic pyogenic liver abscess. The gold standard for identifying and diagnosing F. nucleatum infections is 16S rRNA gene sequencing, and gram staining helps determine appropriate antimicrobials.
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Church DL, Griener T, Gregson D. Multi-year comparison of VITEK® MS and 16S rRNA gene sequencing performance for the identification of rarely encountered anaerobes causing invasive human infections in a large Canadian region: can our laboratory abandon 16S rRNA gene sequencing? Anaerobe 2022; 78:102640. [PMID: 36126828 DOI: 10.1016/j.anaerobe.2022.102640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/13/2022] [Accepted: 09/07/2022] [Indexed: 11/01/2022]
Abstract
BACKGROUND Our large regional laboratory routinely provides a definitive identification (ID) for 800-1,200 anaerobic bacteria per annum that cause invasive human infections. An increasing number of isolates (i.e., 10-13%) recovered from clinical specimens from these cases were more unusual or rarely isolated genera and/or species (i.e., ≤5 individual cases/annum). METHODS VITEK® MS (MALDI-TOF MS)is done initially on all anaerobic bacteria, but rare isolates undergo in-house PCR/sequencing when proteomics provides a wrong ID or no results despite repeat testing. A clinical microbiologist in consultation with the Infectious Diseases service approves molecular analyses. This multi-year comparison (2014-19) of the performance of MALDI-TOF MS and 16S rRNA gene sequencing using the IDNS Smart Gene bacterial dataset shows both method's abilities to provide a genus-level and/or species-level ID for rare isolates. RESULTS 489 rare anaerobes were recovered from a variety of clinical specimens: 57% blood cultures, 19% other sterile fluids, 14% sterile tissues, 8% deep wounds/abscesses, and 2% prosthetic implants. 16S rRNA gene sequencing gave an accurate genus-vs. species level ID for 487/489 (99.6%) and 401/489 (82.0%) of isolates respectively. Accurate genus-vs species-level ID were obtained by MALDI-TOF MS for 269/489 (53.4%) and 187/489 (37.3%) of isolates respectively. MALDI-TOF MS gave wrong or no results for 35.1% of Gram-negative anaerobic cocci (GNAC), 62% of Gram-negative anaerobic bacilli (GNAB), 30.8% of Gram-positive anaerobic cocci (GPAC) and 46.3% of Gram-positive anaerobic bacilli (GPAB). Neither method gave an ID for one GNAB and one GPAC isolate. MALDI-TOF MS genus-level ID of GNAC and genus/species-level ID of GPAB improved during the study but its performance remained stable for genus- or species-level ID of other organism groups. CONCLUSIONS MALDI-TOF MS provides accurate ID for most common anaerobes, but molecular analyses need to be available for rare isolates. Large complex laboratories should have a workflow for sending rare isolates for 16S rRNA gene sequencing in invasive cases where a definitive ID is clinically required.
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Affiliation(s)
- D L Church
- Department of Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Department of Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Calgary Laboratory Services (now Alberta Precision Laboratories), Research Rd NW, Calgary Alberta T2L 2K8, 9-3535, Canada.
| | - T Griener
- Department of Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Calgary Laboratory Services (now Alberta Precision Laboratories), Research Rd NW, Calgary Alberta T2L 2K8, 9-3535, Canada
| | - D Gregson
- Department of Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Department of Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Calgary Laboratory Services (now Alberta Precision Laboratories), Research Rd NW, Calgary Alberta T2L 2K8, 9-3535, Canada
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Olcu M, Atalay MA, Percin Renders D. Development of multiplex PCR panel for detection of anaerobic bacteria in clinical samples. Anaerobe 2022; 76:102611. [PMID: 35820595 DOI: 10.1016/j.anaerobe.2022.102611] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/11/2022] [Accepted: 07/06/2022] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Although anaerobic bacteria are important agents of a wide variety of serious infections, they are overlooked often in the etiology of infection due to difficulties in isolation and detection. The aim of this study was to develop a new multiplex PCR panel that could detect Bacteroides, Fusobacterium, Prevotella, Veillonella, Clostridium, Peptostreptococcus, and Actinomyces bacteria, which are the most frequently isolated from anaerobic infections, at the genus level. METHOD Aerobic and anaerobic cultures were performed on 46 clinical specimens, with suspicion of anaerobic infection and were sent to the laboratory. DNA isolation was performed with the same samples and anaerobic bacteria were detected by the multiplex PCR test developed in the study. RESULT The analytical sensitivity of the multiplex PCR assay was found to be 1-103 CFU/ml, depending on the bacterial species. In this study, anaerobic growth was observed in eight (17.4%) of 46 clinical samples. The multiplex PCR test detected 35 anaerobic bacteria from 20 (43.5%) of 46 clinical samples. The most common anaerobes isolated from clinical specimens by the multiplex PCR assay were Prevotella spp. (37.1%) and Fusobacterium spp. (22.9%) while Clostridium spp. (14.3%), Peptostreptococcus spp. (11.4%), Bacteroides spp. (8.6%), and Veillonella spp. (5.7%) followed these genera. CONCLUSION As a result, it was concluded that the multiplex PCR panel developed in this study eliminates problems in the detection of anaerobes based on culture, provides more accurate detection of anaerobic bacteria from clinical specimens, takes a shorter time, and allows more accurate infection treatment.
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Affiliation(s)
- Mehmet Olcu
- Medical Laboratory Program, Department of Medical Services and Techniques, Vocational School of Health Services, Aksaray University, Aksaray, Turkey.
| | - Mustafa Altay Atalay
- Department of Medical Microbiology, School of Medicine, Erciyes University, Kayseri, Turkey
| | - Duygu Percin Renders
- Department of Medical Microbiology, School of Medicine, Kutahya Health Sciences University, Kutahya, Turkey
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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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Amiri R, Norouzbabaei Z, Kalali N, Ghourchian S, Yaseri M, Abdollahi A, Douraghi M. Identification of enterotoxigenic Bacteroides fragilis in patients with diarrhea: A study targeting 16S rRNA, gyrB and nanH genes. Anaerobe 2022; 75:102546. [DOI: 10.1016/j.anaerobe.2022.102546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 11/25/2022]
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Wolf EA, Rettig HC, Lupatsii M, Schlüter B, Schäfer K, Friedrich D, Graspeuntner S, Rupp J. Culturomics Approaches Expand the Diagnostic Accuracy for Sexually Transmitted Infections. Int J Mol Sci 2021; 22:ijms221910815. [PMID: 34639153 PMCID: PMC8509341 DOI: 10.3390/ijms221910815] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/26/2021] [Accepted: 10/01/2021] [Indexed: 02/07/2023] Open
Abstract
Sexually transmitted infections (STIs) are a major health concern with clinical manifestations being acknowledged to cause severe reproductive impairment. Research in infectious diseases has been centered around the known major pathogens for decades. However, we have just begun to understand that the microbiota of the female genital tract is of particular importance for disease initiation, infection progression, and pathological outcome. Thus, we are now aware that many poorly described, partially not yet known, or cultured bacteria may pave the way for an infection and/or contribute to disease severity. While sequencing-based methods are an important step in diagnosing STIs, culture-based methods are still the gold-standard method in diagnostic routine, providing the opportunity to distinguish phenotypic traits of bacteria. However, current diagnostic culture routines suffer from several limitations reducing the content of information about vaginal microbiota. A detailed characterization of microbiota-associated factors is needed to assess the impact of single-bacterial isolates from the vaginal community on vaginal health and the containment of STIs. Here we provide current concepts to enable modern culture routines and create new ideas to improve diagnostic approaches with a conjunct usage of bioinformatics. We aim to enable scientists and physicians alike to overcome long-accepted limitations in culturing bacteria of interest to the human health. Eventually, this may improve the quality of culture-based diagnostics, facilitate a research interface, and lead to a broader understanding of the role of vaginal microbiota in reproductive health and STIs.
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Affiliation(s)
- Ellinor Anna Wolf
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Hannah Clara Rettig
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Mariia Lupatsii
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Britta Schlüter
- Department of Gynecology and Obstetrics, University Medical Center Schleswig-Holstein, 23538 Lübeck, Germany;
| | - Kathrin Schäfer
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Dirk Friedrich
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23538 Lübeck, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23538 Lübeck, Germany
- Correspondence:
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Wang J, Guo R, Ma W, Dong X, Yan S, Xie W. Eggerthella lenta Bacteremia in a Middle-Aged Healthy Man with Acute Hepatic Abscess: Case Report and Literature Review, 1970-2020. Infect Drug Resist 2021; 14:3307-3318. [PMID: 34434054 PMCID: PMC8382309 DOI: 10.2147/idr.s321282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/23/2021] [Indexed: 12/14/2022] Open
Abstract
Eggerthella lenta (E. lenta) is a rare but significant human emerging pathogen. Infections caused by it are rare and little-known, both on clinical and therapeutical aspects, in spite of new emergence of bacteria isolation and identification techniques. In this article, we report a case involving a previously healthy 52-year-old man suffering from a newly diagnosed hepatic abscess who developed E. lenta bacteremia, which was treated successfully using empirical therapy with ertapenem and teicoplanin. To the best of our knowledge, this is the first documented report of E. lenta bacteremia related specifically to liver abscess. Cases related to this bacterial species are infrequent and sporadic; thus, we reviewed English literature on E. lenta infection in PubMed/MEDLINE in the last 50 years. A total of 31 sporadic cases were identified. The majority of patients were male (71%), had an average age of 54.3 years and presented predisposing conditions, such as digestive system trouble (45.2%), immunocompromised state (25.8%) or risk factors (22.6%). Two of the cases had more than one predisposing factors. Fever was common (93.5%). Average days to diagnosis of them were 6.8 days. MALDI-TOF MS is emerging as a fast and useful tool in the identification of it. Teicoplanin, vancomycin, amoxicillin-clavulanate, metronidazole, clindamycin, cefoxitin, chloramphenicol, and carbapenems appear to be the most used antibiotic treatment options. The purpose of this review is to increase awareness about the clinical infections caused by E. lenta.
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Affiliation(s)
- Jiazheng Wang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, People's Republic of China
| | - Rui Guo
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, People's Republic of China
| | - Wanshan Ma
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, People's Republic of China
| | - Xiutao Dong
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, People's Republic of China
| | - Shaofeng Yan
- Department of Neurosurgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Neurosurgery, Jinan, People's Republic of China
| | - Wenyan Xie
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, People's Republic of China
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Innovative and Highly Sensitive Detection of Clostridium perfringens Enterotoxin Based on Receptor Interaction and Monoclonal Antibodies. Toxins (Basel) 2021; 13:toxins13040266. [PMID: 33917845 PMCID: PMC8068247 DOI: 10.3390/toxins13040266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/03/2021] [Accepted: 04/06/2021] [Indexed: 11/16/2022] Open
Abstract
Clostridium perfringens enterotoxin (CPE) regularly causes food poisoning and antibiotic-associated diarrhea; therefore, reliable toxin detection is crucial. To this aim, we explored stationary and mobile strategies to detect CPE either exclusively by monoclonal antibodies (mAbs) or, alternatively, by toxin-enrichment via the cellular receptor of CPE, claudin-4, and mAb detection. Among the newly generated mAbs, we identified nine CPE-specific mAbs targeting five distinct epitopes, among them mAbs recognizing CPE bound to claudin-4 or neutralizing CPE activity in vitro. In surface plasmon resonance experiments, all mAbs and claudin-4 revealed excellent affinities towards CPE, ranging from 0.05 to 2.3 nM. Integrated into sandwich enzyme-linked immunosorbent assays (ELISAs), the most sensitive mAb/mAb and claudin-4/mAb combinations achieved similar detection limits of 0.3 pg/mL and 1.0 pg/mL, respectively, specifically detecting recombinant CPE from spiked feces and native CPE from 30 different C. perfringens culture supernatants. The implementation of mAb- and receptor-based ELISAs into a mobile detection platform enabled the fast detection of CPE, which will be helpful in clinical laboratories to diagnose diarrhea of assumed bacterial origin. In conclusion, we successfully employed an endogenous receptor and novel high affinity mAbs for highly sensitive and specific CPE-detection. These tools will be useful for both basic and applied research.
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Gunalan A, Biswas R, Sridharan B, Elamurugan TP. Pathogenic potential of Parabacteroides distasonis revealed in a splenic abscess case: a truth unfolded. BMJ Case Rep 2020; 13:13/12/e236701. [PMID: 33318274 PMCID: PMC7737074 DOI: 10.1136/bcr-2020-236701] [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] [Indexed: 12/15/2022] Open
Abstract
Splenic abscess is a rare entity, however if unrecognised or left untreated, it is invariably fatal. We herein report a case of splenic abscess in a 40-year-old man presenting with fever, left-sided abdominal pain, altered sensorium and vomiting. On clinical examination, hepatosplenomegaly was noted and the ultrasound of the abdomen showed multiple hypoechoic regions in the upper pole of spleen, and the diagnosis of splenic abscess was made. The patient received antimicrobial therapy and underwent an open splenectomy with full recovery. Pus aspirated from the splenic abscess grew an unusual organism named Parabacteroides distasonis In the literature, there are only a few recorded cases of P. distasonis causing splenic abscess. Through this case report, we would like to emphasise the pathogenic role of P. distasonis in causing clinical disease, as this organism is typically known to constitute a part of the normal flora.
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Affiliation(s)
- Anitha Gunalan
- Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Rakhi Biswas
- Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Balamurugan Sridharan
- General Surgery, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
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Wang M, Zhang M, Xu H. First report of bacteremia caused by Eggerthia catenaformis in a patient with gastric malignancy in China. Anaerobe 2020; 64:102218. [DOI: 10.1016/j.anaerobe.2020.102218] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/21/2020] [Accepted: 05/25/2020] [Indexed: 01/08/2023]
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Puerperal Sepsis Caused by Clostridium Innocuum in a Patient with Placenta Accreta and Literature Review. MATERNAL-FETAL MEDICINE 2020. [DOI: 10.1097/fm9.0000000000000027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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14
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Toprak NU, Veloo ACM, Urban E, Wybo I, Jean-Pierre H, Morris T, Justesen US, Tripkovic V, Jeverica S, Soyletir G, Nagy E. Comparing identification of clinically relevant Prevotella species by VITEK MS and MALDI biotyper. Acta Microbiol Immunol Hung 2019; 67:6-13. [PMID: 31813262 DOI: 10.1556/030.66.2019.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 08/12/2019] [Indexed: 11/19/2022]
Abstract
In this multicenter study, we aimed to evaluate the performance of MALDI Biotyper and VITEK MS, for identification of Prevotella species. Three hundred and fourteen clinical isolates, collected in eight European countries between January 2014 and April 2016, were identified at the collecting sites by MALDI Biotyper (versions 3.0 and 3.1) and then reidentified by VITEK MS (version 3.0) in the central laboratory. 16S rRNA gene sequencing was used as a standard method. According to sequence analysis, the 314 Prevotella strains belonged to 19 species. MALDI Biotyper correctly identified 281 (89.5%) isolates to the species level and 33 (10.5%) only at the genus level. VITEK MS correctly identified 253 (80.6%) isolates at the species level and 276 (87.9%) isolates at the genus level. Thirty-three isolates belonging to P. bergensis, P. conceptionensis, P. corporis, P. histicola, and P. nanciensis, unavailable in the VITEK MS 3.0 database, were resulted in genus level or no identification. Six Prevotella strains, belonged to P. veroralis, P. timonensis, and P. conceptionensis not represented in the MALDI Biotyper system database, were misidentified at the genus level. In conclusion, both VITEK MS and MALDI Biotyper provided reliable and rapid identification. However, the permanent extension of the databases is needed.
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Affiliation(s)
- Nurver Ulger Toprak
- Department of Medical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Alida C. M. Veloo
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, 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
| | - Helene Jean-Pierre
- Laboratoire de Bactériologie, Hôpital Arnaud de Villeneuve, Centre Hospitalier Régional Universitaire de Montpellier, Montpellier, France
| | - Trefor Morris
- UK Anaerobe Reference Unit, Public Health Wales Microbiology, Cardiff, UK
| | - Ulrik Stenz Justesen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Vesna Tripkovic
- Department of Clinical and Molecular Microbiology, University Hospital Center, Zagreb, Croatia
| | - Samo Jeverica
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Guner Soyletir
- Department of Medical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
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15
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Li Y, Shan M, Zhu Z, Mao X, Yan M, Chen Y, Zhu Q, Li H, Gu B. Application of MALDI-TOF MS to rapid identification of anaerobic bacteria. BMC Infect Dis 2019; 19:941. [PMID: 31699042 PMCID: PMC6836477 DOI: 10.1186/s12879-019-4584-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 10/21/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been rapidly developed and widely used as an analytical technique in clinical laboratories with high accuracy in microorganism identification. OBJECTIVE To validate the efficacy of MALDI-TOF MS in identification of clinical pathogenic anaerobes. METHODS Twenty-eight studies covering 6685 strains of anaerobic bacteria were included in this meta-analysis. Fixed-effects models based on the P-value and the I-squared were used for meta-analysis to consider the possibility of heterogeneity between studies. Statistical analyses were performed by using STATA 12.0. RESULTS The identification accuracy of MALDI-TOF MS was 84% for species (I2 = 98.0%, P < 0.1), and 92% for genus (I2 = 96.6%, P < 0.1). Thereinto, the identification accuracy of Bacteroides was the highest at 96% with a 95% CI of 95-97%, followed by Lactobacillus spp., Parabacteroides spp., Clostridium spp., Propionibacterium spp., Prevotella spp., Veillonella spp. and Peptostreptococcus spp., and their correct identification rates were all above 90%, while the accuracy of rare anaerobic bacteria was relatively low. Meanwhile, the overall capabilities of two MALDI-TOF MS systems were different. The identification accuracy rate was 90% for VITEK MS vs. 86% for MALDI biotyper system. CONCLUSIONS Our research showed that MALDI-TOF-MS was satisfactory in genus identification of clinical pathogenic anaerobic bacteria. However, this method still suffers from different drawbacks in precise identification of rare anaerobe and species levels of common anaerobic bacteria.
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Affiliation(s)
- Ying Li
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Mingzhu Shan
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Zuobin Zhu
- Department of Genetics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Xuhua Mao
- Department of Clinical Laboratory, Yixing People's Hospital, Wuxi, 214200, China
| | - Mingju Yan
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Ying Chen
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Qiuju Zhu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, 221004, China
| | - Hongchun Li
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China.,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Bing Gu
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China. .,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China.
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16
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Evaluation of the Vitek MS and the MALDI Biotyper systems for the identification of less commonly isolated but clinically relevant anaerobes and facultative anaerobes. Anaerobe 2018; 54:210-216. [DOI: 10.1016/j.anaerobe.2018.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/25/2018] [Accepted: 05/28/2018] [Indexed: 12/11/2022]
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17
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Sárvári KP, Sóki J, Iván M, Miszti C, Latkóczy K, Melegh SZ, Urbán E. MALDI-TOF MS versus 16S rRNA sequencing: Minor discrepancy between tools in identification of Bacteroides isolates. Acta Microbiol Immunol Hung 2018; 65:173-181. [PMID: 28889758 DOI: 10.1556/030.64.2017.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Members of the genus Bacteroides are important components of the normal microbiota of gastrointestinal tract; however, as opportunistic pathogens are also associated with severe or even life-threatening infections with significant mortality. Various species within Bacteroides fragilis group are phenotypically very similar; thus, their identifications with traditional-automated biochemical methods are frequently inaccurate. The identification of the newly discovered or reclassified bacteria can be doubtful because of the lack of biochemical profile in the database of these tests. The aim of this study was to determine the accuracy of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) method by testing of 400 Hungarian Bacteroides clinical isolates. Inaccurate identification results with MALDI-TOF MS were confirmed by 16S rRNA gene sequencing and findings were compared with traditional-automated biochemical test rapid ID 32A method as well.
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Affiliation(s)
| | - József Sóki
- 1 Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
| | - Miklós Iván
- 2 Institute of Laboratory Medicine, Semmelweis University, Budapest, Hungary
| | - Cecilia Miszti
- 3 Institute of Medical Microbiology, University of Debrecen, Debrecen, Hungary
| | | | - Szilvia Zsóka Melegh
- 5 Institute of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary
| | - Edit Urbán
- 1 Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
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18
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Park KG, Kim SH, Choi JT, Kim S, Kim YK, Yu YB. An Evaluation of Vitek MS System for Rapid Identification of Bacterial Species in Positive Blood Culture. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2017. [DOI: 10.15324/kjcls.2017.49.4.407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Kang-Gyun Park
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sang-Ha Kim
- Department of Laboratory Medicine, Konyang University Hospital, Daejeon, Korea
| | - Jong-Tae Choi
- Department of Biomedical Laboratory Science, Kyungdong University, Gangwondo, Korea
| | - Sunghyun Kim
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, Korea
| | - Young-Kwon Kim
- Department of Biomedical Laboratory Science, College of Medical Sciences, Konyang University, Daejeon, Korea
| | - Young-Bin Yu
- Department of Biomedical Laboratory Science, College of Medical Sciences, Konyang University, Daejeon, Korea
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19
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A case of severe empyema with acute respiratory distress syndrome caused by Slackia exigua requiring veno-venous extracorporeal membrane oxygenation. Anaerobe 2017; 48:7-11. [DOI: 10.1016/j.anaerobe.2017.06.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 06/20/2017] [Accepted: 06/27/2017] [Indexed: 11/19/2022]
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20
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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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21
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Yunoki T, Matsumura Y, Yamamoto M, Tanaka M, Hamano K, Nakano S, Noguchi T, Nagao M, Ichiyama S. Genetic identification and antimicrobial susceptibility of clinically isolated anaerobic bacteria: A prospective multicenter surveillance study in Japan. Anaerobe 2017; 48:215-223. [PMID: 28935196 DOI: 10.1016/j.anaerobe.2017.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 09/12/2017] [Accepted: 09/15/2017] [Indexed: 12/23/2022]
Abstract
This prospective multicenter surveillance study was designed to provide antimicrobial susceptibility profiles of clinical anaerobic bacteria with genetic species identification in Japan. In 2014, a total of 526 non-duplicate clinical anaerobic isolates were collected from 11 acute-care hospitals in the Kyoto and Shiga regions of Japan. Genetic identification was performed using 16S rRNA sequencing. Minimum inhibitory concentrations were determined in the central laboratory and were interpreted using the CLSI criteria. Genetic analysis provided species-level identification for 496 isolates (83 species in 40 genera) and genus-level identification for 21 isolates (13 genera). Among these 517 isolates, the most frequent anaerobes were Bacteroides spp. (n = 207), Prevotella spp. (n = 43), Clostridium spp. (n = 40), and Peptoniphilus spp. (n = 40). B. fragilis was the most common species (n = 107) and showed 91.6%-97.2% susceptibility to β-lactam/β-lactamase inhibitor combinations (BLBLIs; ampicillin-sulbactam, amoxicillin-clavulanate, and piperacillin-tazobactam) and carbapenems (imipenem and meropenem) as well as 100% susceptibility to metronidazole. Gram-negative anaerobes were highly susceptible to metronidazole (99.0%) followed by BLBLIs and carbapenems (>90% each). BLBLIs or carbapenems also retained activity against Gram-positive anaerobes (99.5%-100%) except Clostridioides difficile. All isolates were susceptible to combinations of metronidazole with BLBLIs or carbapenems. Thus, BLBLIs or carbapenems are first choices for empirical therapy of anaerobic infections in Japan, and these antimicrobials in combination with metronidazole should be reserved for very severe infections and targeted therapy.
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Affiliation(s)
- Tomoyuki Yunoki
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto 6068507, Japan; Department of Clinical Laboratory, Kyoto University Hospital, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto 6068507, Japan
| | - Yasufumi Matsumura
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto 6068507, Japan; Department of Clinical Laboratory, Kyoto University Hospital, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto 6068507, Japan.
| | - Masaki Yamamoto
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto 6068507, Japan; Department of Clinical Laboratory, Kyoto University Hospital, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto 6068507, Japan
| | - Michio Tanaka
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto 6068507, Japan
| | - Kyoko Hamano
- Department of Clinical Laboratory, Kyoto University Hospital, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto 6068507, Japan
| | - Satoshi Nakano
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto 6068507, Japan; Department of Clinical Laboratory, Kyoto University Hospital, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto 6068507, Japan
| | - Taro Noguchi
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto 6068507, Japan
| | - Miki Nagao
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto 6068507, Japan; Department of Clinical Laboratory, Kyoto University Hospital, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto 6068507, Japan
| | - Satoshi Ichiyama
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto 6068507, Japan; Department of Clinical Laboratory, Kyoto University Hospital, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto 6068507, Japan
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22
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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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23
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Abstract
Clostridium difficile infections (CDIs) have emerged as one of the principal threats to the health of hospitalized and immunocompromised patients. The importance of C difficile colonization is increasingly recognized not only as a source for false-positive clinical testing but also as a source of new infections within hospitals and other health care environments. In the last five years, several new treatment strategies that capitalize on the increasing understanding of the altered microbiome and host defenses in patients with CDI have completed clinical trials, including fecal microbiota transplantation. This article highlights the changing epidemiology, laboratory diagnostics, pathogenesis, and treatment of CDI.
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24
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Jo SJ, Park KG, Han K, Park DJ, Park YJ. Direct Identification and Antimicrobial Susceptibility Testing of Bacteria From Positive Blood Culture Bottles by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry and the Vitek 2 System. Ann Lab Med 2017; 36:117-23. [PMID: 26709258 PMCID: PMC4713844 DOI: 10.3343/alm.2016.36.2.117] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 08/27/2015] [Accepted: 11/16/2015] [Indexed: 12/02/2022] Open
Abstract
Background We evaluated the reliability and accuracy of the combined use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) bacterial identification and Vitek 2 antimicrobial susceptibility testing (AST) for bacteria from positive blood culture bottles. Methods Direct identification and AST were performed in parallel to the standard methods in monomicrobial positive blood culture bottles. In total, 254 isolates grown on aerobic and/or anaerobic bottles were identified with MALDI-TOF Vitek MS (bioMérieux, France), and 1,978 microorganism/antimicrobial agent combinations were assessed. For isolates from anaerobic bottles, an aliquot of the culture broth was centrifuged, washed, and filtered through a nylon mesh. For isolates from aerobic/pediatric bottles, a lysis step using 9.26% ammonium chloride solution and 2% saponin solution was included. Results The overall correct identification rate was 81.8% (208/254) and that for gram-positive/gram-negative isolates was 73.9%/92.6%, respectively, and it was 81.8%, 87.6%, and 57.9% for isolates from aerobic, anaerobic, and pediatric bottles, respectively. Identification was not possible in 45 cases, and most of these isolates were streptococci (N=14) and coagulase-negative staphylococci (N=11). Misidentification occurred only in one case. Compared with standard methods, direct AST showed 97.9% (1,936/1,978) agreement with very major error of 0.25%, major error of 0.05%, and minor error of 1.8%. Conclusions This simple and cost-effective sample preparation method gives reliable results for the direct identification and AST of bacteria. For the identification of streptococci and coagulase-negative staphylococci, the method should be further improved.
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Affiliation(s)
- Sung Jin Jo
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kang Gyun Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kyungja Han
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Dong Jin Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yeon-Joon Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.
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25
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Brook I. Anaerobic Bacteria. Infect Dis (Lond) 2017. [DOI: 10.1016/b978-0-7020-6285-8.00184-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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26
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Rodríguez-Sánchez B, Alcalá L, Marín M, Ruiz A, Alonso E, Bouza E. Evaluation of MALDI-TOF MS (Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry) for routine identification of anaerobic bacteria. Anaerobe 2016; 42:101-107. [PMID: 27702604 DOI: 10.1016/j.anaerobe.2016.09.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 08/30/2016] [Accepted: 09/30/2016] [Indexed: 12/22/2022]
Abstract
Information regarding the use of MALDI-TOF MS as an alternative to conventional laboratory methods for the rapid and reliable identification of bacterial isolates is still limited. In this study, MALDI-TOF MS was evaluated on 295 anaerobic isolates previously identified by 16S rRNA gene sequencing and with biochemical tests (Rapid ID 32A system, BioMérieux). In total, 85.8% of the isolates were identified by MALDI-TOF MS at the species level vs 49.8% using the Rapid ID 32A system (p < 0.0001). None of the isolates was discordantly identified at the genus level using MALDI-TOF MS and only 9 of them could not be identified using the method. Thus, our results show that MALDI-TOF MS is a robust and reliable tool for the identification of anaerobic isolates in the microbiology laboratory. Its implementation will reduce the turnaround time for a final identification and the number of isolates that require 16S rRNA sequencing.
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Affiliation(s)
- Belén Rodríguez-Sánchez
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.
| | - Luis Alcalá
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Mercedes Marín
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058), Madrid, Spain
| | - Adrián Ruiz
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Elena Alonso
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Emilio Bouza
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058), Madrid, Spain; Medicine Department, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
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27
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Abstract
Alteration in the host microbiome at skin and mucosal surfaces plays a role in the function of the immune system, and may predispose immunocompromised patients to infection. Because obligate anaerobes are the predominant type of bacteria present in humans at skin and mucosal surfaces, immunocompromised patients are at increased risk for serious invasive infection due to anaerobes. Laboratory approaches to the diagnosis of anaerobe infections that occur due to pyogenic, polymicrobial, or toxin-producing organisms are described. The clinical interpretation and limitations of anaerobe recovery from specimens, anaerobe-identification procedures, and antibiotic-susceptibility testing are outlined. Bacteriotherapy following analysis of disruption of the host microbiome has been effective for treatment of refractory or recurrent Clostridium difficile infection, and may become feasible for other conditions in the future.
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Affiliation(s)
- Deirdre L Church
- Departments of Pathology & Laboratory Medicine and Medicine, University of Calgary, and Division of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada T2N 1N4
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28
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Shields MV, Abdullah L, Namdari S. The challenge of Propionibacterium acnes and revision shoulder arthroplasty: a review of current diagnostic options. J Shoulder Elbow Surg 2016; 25:1034-40. [PMID: 27038565 DOI: 10.1016/j.jse.2016.01.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/19/2015] [Accepted: 01/07/2016] [Indexed: 02/01/2023]
Abstract
BACKGROUND Propionibacterium acnes is the most common cause of infection after shoulder arthroplasty. Whereas there are several methods that can aid in the diagnosis of P. acnes infection, there is not a single "gold standard" because of the difficulties inherent in identifying this bacterium. We present an evidence-based discussion of the demographic, clinical, and radiographic predictors of P. acnes infection and review the current options for diagnosis. METHODS This review was written after a comprehensive analysis of the current literature related to shoulder periprosthetic joint infection and P. acnes identification. RESULTS AND CONCLUSIONS Of the techniques reviewed, α-defensin had the highest sensitivity in detecting P. acnes infection (63%). C-reactive protein level and erythrocyte sedimentation rate were often normal in cases of infection. Whereas P. acnes can be challenging to successfully diagnose, there are several options that are considered preferable because of their higher sensitivities and specificities. The current gold standard is intraoperative culture, but major advances in molecular techniques may provide future improvements in diagnostic accuracy.
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Affiliation(s)
- Margaret V Shields
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Leath Abdullah
- Drexel University College of Medicine, Philadelphia, PA, USA
| | - Surena Namdari
- Rothman Institute Department of Orthopaedics, Thomas Jefferson University Hospital, Philadelphia, PA, USA.
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Kostrzewa M, Nagy E. How MALDI-TOF mass spectrometry can aid diagnosis of hard-to-identify pathogenic bacteria. Expert Rev Mol Diagn 2016; 16:509-11. [DOI: 10.1586/14737159.2016.1157019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | - Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
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Brook I. Spectrum and treatment of anaerobic infections. J Infect Chemother 2015; 22:1-13. [PMID: 26620376 DOI: 10.1016/j.jiac.2015.10.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/05/2015] [Accepted: 10/25/2015] [Indexed: 02/07/2023]
Abstract
Anaerobes are the most predominant components of the normal human skin and mucous membranes bacterial flora, and are a frequent cause of endogenous bacterial infections. Anaerobic infections can occur in all body locations: the central nervous system, oral cavity, head and neck, chest, abdomen, pelvis, skin, and soft tissues. Treatment of anaerobic infection is complicated by their slow growth in culture, by their polymicrobial nature and by their growing resistance to antimicrobials. Antimicrobial therapy is frequently the only form of therapy needed, whereas in others it is an important adjunct to drainage and surgery. Because anaerobes generally are isolated mixed with aerobes, the antimicrobial chosen should provide for adequate coverage of both. The most effective antimicrobials against anaerobes are: metronidazole, the carbapenems (imipenem, meropenem, doripenem, ertapenem), chloramphenicol, the combinations of a penicillin and a beta-lactamase inhibitors (ampicillin or ticarcillin plus clavulanate, amoxicillin plus sulbactam, piperacillin plus tazobactam), tigecycline, cefoxitin and clindamycin.
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Affiliation(s)
- Itzhak Brook
- Department of Pediatrics, Georgetown, University School of Medicine, Washington DC, USA.
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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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32
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Kiyosuke M, Kibe Y, Oho M, Kusaba K, Shimono N, Hotta T, Kang D, Shoubuike T, Miyamoto H. Comparison of two types of matrix-assisted laser desorption/ionization time-of-flight mass spectrometer for the identification and typing of Clostridium difficile. J Med Microbiol 2015; 64:1144-1150. [DOI: 10.1099/jmm.0.000136] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Makiko Kiyosuke
- Division of Microbiology, Department of Pathology and Microbiology, Faculty of Medicine, Saga University, Saga, Japan
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka, Japan
- Center for the Study of Global Infection, Kyushu University Hospital, Fukuoka, Japan
| | - Yasushi Kibe
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Megumi Oho
- Department of Laboratory Medicine, Saga University Hospital, Saga, Japan
| | - Koji Kusaba
- Department of Laboratory Medicine, Saga University Hospital, Saga, Japan
| | - Nobuyuki Shimono
- Center for the Study of Global Infection, Kyushu University Hospital, Fukuoka, Japan
| | - Taeko Hotta
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Takeo Shoubuike
- Division of Microbiology, Department of Pathology and Microbiology, Faculty of Medicine, Saga University, Saga, Japan
| | - Hiroshi Miyamoto
- Division of Microbiology, Department of Pathology and Microbiology, Faculty of Medicine, Saga University, Saga, Japan
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Handal N, Bakken Jørgensen S, Smith Tunsjø H, Johnsen BO, Leegaard TM. Anaerobic blood culture isolates in a Norwegian university hospital: identification by MALDI-TOF MS vs 16S rRNA sequencing and antimicrobial susceptibility profiles. APMIS 2015; 123:749-58. [DOI: 10.1111/apm.12410] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 05/12/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Nina Handal
- Department of Microbiology and Infection Control; Akershus University Hospital; Lørenskog Norway
| | - Silje Bakken Jørgensen
- Department of Microbiology and Infection Control; Akershus University Hospital; Lørenskog Norway
| | - Hege Smith Tunsjø
- Department of Multidisciplinary Laboratory Medicine and Medical Biochemistry; Unit of Gene Technology; Akershus University Hospital; Lørenskog Norway
| | - Bjørn Odd Johnsen
- Department of Microbiology and Infection Control; Akershus University Hospital; Lørenskog Norway
| | - Truls Michael Leegaard
- Department of Microbiology and Infection Control; Akershus University Hospital; Lørenskog Norway
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Use of MALDI-TOF MS for Identification of Nontuberculous Mycobacterium Species Isolated from Clinical Specimens. BIOMED RESEARCH INTERNATIONAL 2015; 2015:854078. [PMID: 26106617 PMCID: PMC4463989 DOI: 10.1155/2015/854078] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 10/18/2014] [Accepted: 10/19/2014] [Indexed: 11/30/2022]
Abstract
The aim of this study was to compare the results obtained for identification by MALDI-TOF of nontuberculous mycobacteria (NTM) isolated in clinical samples with those obtained by GenoType Mycobacterium CM/AS (common mycobacteria/additional species). A total of 66 Mycobacterium isolates from various clinical specimens (mainly respiratory) were tested in this study. They were identified using MALDI-TOF Bruker from strains isolated in Lowenstein, following the recommended protocol of heat inactivation and extraction, and were simultaneously analyzed through hybridization by GenoType Mycobacterium from liquid culture MGIT. Our results showed that identification by MALDI-TOF was correct in 98.4% (65/66) of NTM isolated in our clinical practice (M. avium, M. intracellulare, M. abscessus, M. chelonae, M. fortuitum, M. mucogenicum, M. kansasii, and M. scrofulaceum). MALDI-TOF was found to be an accurate, rapid, and cost-effective system for identification of mycobacteria species.
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Comparing the identification of Clostridium spp. by two Matrix-Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF) mass spectrometry platforms to 16S rRNA PCR sequencing as a reference standard: A detailed analysis of age of culture and sample preparation. Anaerobe 2014; 30:85-9. [DOI: 10.1016/j.anaerobe.2014.09.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 07/31/2014] [Accepted: 09/07/2014] [Indexed: 11/30/2022]
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36
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Gilligan PH. Contemporary approaches for the laboratory diagnosis of Clostridium difficile infections. SEMINARS IN COLON AND RECTAL SURGERY 2014. [DOI: 10.1053/j.scrs.2014.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Krutova M, Matejkova J, Nyc O. C. difficile ribotype 027 or 176? Folia Microbiol (Praha) 2014; 59:523-6. [PMID: 24970104 DOI: 10.1007/s12223-014-0323-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 05/13/2014] [Indexed: 12/18/2022]
Abstract
Clostridium difficile is a major nosocomial pathogen of present times. The analysis of 624 C. difficile strains from 11 hospitals in the Czech Republic in 2013 revealed that 40% of isolates belonged to ribotype 176. These results suggest that the incidence of CDI (C. difficile infection) in the Czech Republic has increased probably in connection with C. difficile ribotype 176. The molecular systems Xpert C. difficile Epi assay (Cepheid Inc., Sunnyvale, CA) diagnoses toxigenic strains and supports C. difficile ribotype 027 determination based on three specific target places in the toxigenic C. difficile genome. Twenty-nine strains cultivated from stool specimens were evaluated by the Xpert systems as presumed C. difficile PCR ribotype 027 were confirmed as a C. difficile ribotype 176 based on ribotyping. A further 120 C. difficile strains of ribotype 176 were examined for the presence of genes tcdB, cdtB and deletion in position 117 in the tcdC gene. Our experience shows that due to the correspondence of the target places, C. difficile ribotype 176 may be interpreted as ribotype 027 by Xpert C. difficile Epi assay (Cepheid Inc., Sunnyvale, CA). Further molecular analysis as ribotyping based on capillary electrophoresis is needed to differentiate between C. difficile ribotypes 027 and 176 for appropriate epidemiological situation control on local and national levels.
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Affiliation(s)
- Marcela Krutova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, V Uvalu 84, 150 06, Prague 5, Czech Republic,
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38
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Moore JL, Caprioli RM, Skaar EP. Advanced mass spectrometry technologies for the study of microbial pathogenesis. Curr Opin Microbiol 2014; 19:45-51. [PMID: 24997399 PMCID: PMC4125470 DOI: 10.1016/j.mib.2014.05.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/12/2014] [Accepted: 05/28/2014] [Indexed: 02/08/2023]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) has been successfully applied to the field of microbial pathogenesis with promising results, principally in diagnostic microbiology to rapidly identify bacteria based on the molecular profiles of small cell populations. Direct profiling of molecules from serum and tissue samples by MALDI MS provides a means to study the pathogen-host interaction and to discover potential markers of infection. Systematic molecular profiling across tissue sections represents a new imaging modality, enabling regiospecific molecular measurements to be made in situ, in both two-dimensional and three-dimensional analyses. Herein, we briefly summarize work that employs MALDI MS to study the pathogenesis of microbial infection.
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Affiliation(s)
- Jessica L Moore
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, United States
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, United States.
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States.
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Li Y, Gu B, Liu G, Xia W, Fan K, Mei Y, Huang P, Pan S. MALDI-TOF MS versus VITEK 2 ANC card for identification of anaerobic bacteria. J Thorac Dis 2014; 6:517-23. [PMID: 24822113 DOI: 10.3978/j.issn.2072-1439.2014.02.15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 02/26/2014] [Indexed: 12/29/2022]
Abstract
BACKGROUND Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an accurate, rapid and inexpensive technique that has initiated a revolution in the clinical microbiology laboratory for identification of pathogens. The Vitek 2 anaerobe and Corynebacterium (ANC) identification card is a newly developed method for identification of corynebacteria and anaerobic species. The aim of this study was to evaluate the effectiveness of the ANC card and MALDI-TOF MS techniques for identification of clinical anaerobic isolates. METHODS Five reference strains and a total of 50 anaerobic bacteria clinical isolates comprising ten different genera and 14 species were identified and analyzed by the ANC card together with Vitek 2 identification system and Vitek MS together with version 2.0 database respectively. 16S rRNA gene sequencing was used as reference method for accuracy in the identification. RESULTS Vitek 2 ANC card and Vitek MS provided comparable results at species level for the five reference strains. Of 50 clinical strains, the Vitek MS provided identification for 46 strains (92%) to the species level, 47 (94%) to genus level, one (2%) low discrimination, two (4%) no identification and one (2%) misidentification. The Vitek 2 ANC card provided identification for 43 strains (86%) correct to the species level, 47 (94%) correct to the genus level, three (6%) low discrimination, three (6%) no identification and one (2%) misidentification. CONCLUSIONS Both Vitek MS and Vitek 2 ANC card can be used for accurate routine clinical anaerobe identification. Comparing to the Vitek 2 ANC card, Vitek MS is easier, faster and more economic for each test. The databases currently available for both systems should be updated and further developed to enhance performance.
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Affiliation(s)
- Yang Li
- 1 Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Bing Gu
- 1 Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Genyan Liu
- 1 Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Wenying Xia
- 1 Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Kun Fan
- 1 Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Yaning Mei
- 1 Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Peijun Huang
- 1 Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Shiyang Pan
- 1 Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
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Hartmann EM, Durighello E, Pible O, Nogales B, Beltrametti F, Bosch R, Christie-Oleza JA, Armengaud J. Proteomics meets blue biotechnology: a wealth of novelties and opportunities. Mar Genomics 2014; 17:35-42. [PMID: 24780860 DOI: 10.1016/j.margen.2014.04.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 04/11/2014] [Accepted: 04/12/2014] [Indexed: 10/25/2022]
Abstract
Blue biotechnology, in which aquatic environments provide the inspiration for various products such as food additives, aquaculture, biosensors, green chemistry, bioenergy, and pharmaceuticals, holds enormous promise. Large-scale efforts to sequence aquatic genomes and metagenomes, as well as campaigns to isolate new organisms and culture-based screenings, are helping to push the boundaries of known organisms. Mass spectrometry-based proteomics can complement 16S gene sequencing in the effort to discover new organisms of potential relevance to blue biotechnology by facilitating the rapid screening of microbial isolates and by providing in depth profiles of the proteomes and metaproteomes of marine organisms, both model cultivable isolates and, more recently, exotic non-cultivable species and communities. Proteomics has already contributed to blue biotechnology by identifying aquatic proteins with potential applications to food fermentation, the textile industry, and biomedical drug development. In this review, we discuss historical developments in blue biotechnology, the current limitations to the known marine biosphere, and the ways in which mass spectrometry can expand that knowledge. We further speculate about directions that research in blue biotechnology will take given current and near-future technological advancements in mass spectrometry.
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Affiliation(s)
- Erica M Hartmann
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Emie Durighello
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Olivier Pible
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Balbina Nogales
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | | | - Rafael Bosch
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Joseph A Christie-Oleza
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV47AL, United Kingdom
| | - Jean Armengaud
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France.
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Lee HJ, Hong SK, Choi WS, Kim EC. The first case of Eggerthella lenta bacteremia in Korea. Ann Lab Med 2014; 34:177-9. [PMID: 24624360 PMCID: PMC3948837 DOI: 10.3343/alm.2014.34.2.177] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 10/08/2013] [Accepted: 12/26/2013] [Indexed: 11/27/2022] Open
Affiliation(s)
- Hwa Jeen Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sung Kuk Hong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Woo Suk Choi
- Department of Urology, Seoul National University Hospital, Seoul, Korea
| | - Eui-Chong Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
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42
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Nagy E. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: a new possibility for the identification and typing of anaerobic bacteria. Future Microbiol 2014; 9:217-33. [DOI: 10.2217/fmb.13.150] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
ABSTRACT: Anaerobic bacteria predominate in the normal flora of humans and are important, often life-threatening pathogens in mixed infections originating from the indigenous microbiota. The isolation and identification of anaerobes by phenotypic and DNA-based molecular methods at a species level is time-consuming and laborious. Following the successful adaptation of the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the routine laboratory identification of bacteria, the extensive development of a database has been initiated to use this method for the identification of anaerobic bacteria. Not only frequently isolated anaerobic species, but also newly recognized and taxonomically rearranged genera and species can be identified using direct smear samples or whole-cell protein extraction, and even phylogenetically closely related species can be identified correctly by means of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Typing of anaerobic bacteria on a subspecies level, determination of antibiotic resistance and direct identification of blood culture isolates will revolutionize anaerobe bacteriology in the near future.
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Affiliation(s)
- Elizabeth Nagy
- Institute of Clinical Microbiology, University of Szeged, 6701 Szeged, PO Box 427, Hungary
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Abstract
Clostridium difficile has re-emerged as a major hospital-acquired infection since 2001. Despite development of polymerase chain reaction-based testing, no single clinical diagnostic test has emerged with sufficient sensitivity, specificity, and turnaround time to be entirely reliable for disease diagnosis. The importance of C difficile acquired outside the hospital environment remains an unknown factor and awaits further epidemiologic investigation. This article discusses the changing epidemiology, clinical presentation, and pathogenesis of C difficile infection and highlights the ongoing challenges of laboratory diagnosis, treatment, and disease relapse.
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