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Sumiyoshi S, Aoki K, Motobayashi H, Yogo A, Tochitani K. Contamination rate of rare bacterial species detected by MALDI-TOFMS: a retrospective cohort study. Diagn Microbiol Infect Dis 2024; 108:116110. [PMID: 37924747 DOI: 10.1016/j.diagmicrobio.2023.116110] [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: 08/18/2023] [Revised: 10/07/2023] [Accepted: 10/12/2023] [Indexed: 11/06/2023]
Abstract
When rare bacterial species are identified in blood cultures, determining the clinical significance is sometimes difficult. This study aimed to analyze the clinical significance of rare bacterial species detected in blood cultures using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOFMS) by comparing their contamination rates with those of common species. We retrospectively analyzed medical records of adult patients with positive blood cultures at Kyoto City Hospital from 2014 to 2022. Rare species were defined by low detection rates and few PubMed reports. Of 4880 microorganisms identified from 3441 individuals, 1150 (23.6%) were classified as contamination. Meanwhile, 24 rare microorganisms were identified, of which 14 (58.3%) were classified as contamination, which was significantly higher than common species (odds ratio 4.56, 95% confidence Interval 1.88-11.50, P < 0.001). These findings may help in determining the clinical significance of rare bacterial species in blood cultures with few reported cases.
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Affiliation(s)
- Shougen Sumiyoshi
- Department of Infection Control and Prevention, Osaka University, Osaka, Japan.
| | - Kazuaki Aoki
- Department of General Internal Medicine, Kameda Medical Center, Chiba, Japan
| | | | - Aoi Yogo
- Division of Infectious Diseases, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
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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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Nishio M, Morioka H, Takai S, Osada Y, Seki Y, Osugi T, Oba A, Miyaki Y. Bacteraemia and obstructive pyelonephritis caused by Bifidobacterium breve in an elderly woman: a case report and literature review. Access Microbiol 2023; 5:000574.v3. [PMID: 37970080 PMCID: PMC10634491 DOI: 10.1099/acmi.0.000574.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 07/19/2023] [Indexed: 11/17/2023] Open
Abstract
Bifidobacterium spp. are non-spore-forming Gram-positive anaerobes that are indigenous to the human gastrointestinal tract and vagina. They are believed to be non-pathogenic organisms for humans and thus are widely used as probiotics. An 83-year-old woman taking cephalexin for 4 days was diagnosed with obstructive pyelonephritis. Y-branched Gram-positive rods were found in both anaerobic and aerobic blood culture bottles, and in an anaerobic urine culture. Bifidobacterium breve was finally identified. Ceftriaxone and metronidazole were administered to the patient, and she was discharged after intermittent catheterization for dysuria. Urinary tract infection caused by Bifidobacterium spp. is believed to be rare, but it can develop in patients with underlying urological conditions. Recognition of the characteristic morphology and conducting anaerobic urine culture may help in identifying more cases of Bifidobacterium urinary tract infections.
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Affiliation(s)
- Mitsuru Nishio
- Department of Clinical Laboratory, Komaki City Hospital, Komaki, Aichi, Japan
- Infection Control Team, Komaki City Hospital, Komaki, Aichi, Japan
| | - Hiroshi Morioka
- Infection Control Team, Komaki City Hospital, Komaki, Aichi, Japan
- Department of Infectious Diseases, Nagoya University Hospital, Nagoya, Aichi, Japan
| | - Shun Takai
- Department of Urology, Komaki City Hospital, Komaki, Aichi, Japan
| | - Yukari Osada
- Department of Medical Technique, Nagoya University Hospital, Nagoya, Aichi, Japan
| | - Yoshie Seki
- Department of Clinical Laboratory, Komaki City Hospital, Komaki, Aichi, Japan
| | - Takato Osugi
- Department of Clinical Laboratory, Komaki City Hospital, Komaki, Aichi, Japan
| | - Airi Oba
- Department of Clinical Laboratory, Komaki City Hospital, Komaki, Aichi, Japan
| | - Yuki Miyaki
- Department of Clinical Laboratory, Komaki City Hospital, Komaki, Aichi, Japan
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Miyazaki AN, Salles MJC, Gonçalves GV, Conte LHG, de Oliveira TG, Santili ABN, Kurihara MNL, Santos INM, da Silva LA. Detection of Cutibacterium acnes in Tissue Samples from Clean Primary Shoulder Surgeries - Part II. Rev Bras Ortop 2023; 58:257-264. [PMID: 37252300 PMCID: PMC10212644 DOI: 10.1055/s-0042-1757306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 08/17/2022] [Indexed: 05/31/2023] Open
Abstract
Objective Research and identification of Cutibacterium acnes ( C. acnes ) and other microorganisms in deep tissue samples collected in clean shoulder surgeries of patients who did not undergo any previous invasive joint procedure and who had no clinical history of infection. Methods We analyzed the results of cultures of intraoperative deep tissue samples from 84 patients submitted to primary clean shoulder surgery. Tubes containing culture medium were used for storage and transport of anaerobic agents, prolonged incubation time, and mass spectrometer for diagnosis of bacterial agents. Results Bacteria growth was evidenced in 34 patients (40.4%) of the 84 included in the study. Of these, 23 had growth of C. acnes in at least one sample of deep tissue collected, corresponding to 27.3% of the total patients. The second most common agent was Staphylococcus epidermidis , present in 7.2% of the total individuals included. We showed a higher relationship between sample positivity and males, a lower mean age, absence of diabetes mellitus, ASA I score, and antibiotic prophylaxis in anesthetic induction with cefuroxime. Conclusions A high percentage of isolates of different bacteria was found in shoulder tissue samples of patients undergoing clean and primary surgeries, who had no history of previous infection. Identification of C. acnes was high (27.6%), and Staphylococcus epidermidis was the second most frequent agent (7.2%).
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Affiliation(s)
- Alberto Naoki Miyazaki
- Hospital Alemão Oswaldo Cruz em São Paulo, São Paulo, SP, Brasil
- Departamento de Ortopedia e Traumatologia da Faculdade de Ciências Médicas da Santa Casa de São Paulo, São Paulo, SP, Brasil
| | - Mauro José Costa Salles
- Disciplina de Doenças Infecciosas e Parasitárias da Universidade Federal de São Paulo, São Paulo, Brasil
- Disciplina de Infectologia da Faculdade de Ciências Médicas da Santa Casa de São Paulo, São Paulo, SP, Brasil
| | - Guilherme Vieira Gonçalves
- Grupo de Cirurgia do Ombro da Faculdade de Ciências Médicas da Santa Casa de São Paulo, São Paulo, SP, Brasil
| | - Luiz Henrique Gallego Conte
- Grupo de Cirurgia do Ombro da Faculdade de Ciências Médicas da Santa Casa de São Paulo, São Paulo, SP, Brasil
| | | | | | - Mariana Neri Lucas Kurihara
- Disciplina de Infectologia do Departamento de Medicina da Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, Brasil
| | - Ingrid Nayara Marcelino Santos
- Disciplina de Infectologia do Departamento de Medicina da Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, Brasil
| | - Luciana Andrade da Silva
- Grupo de Cirurgia do Ombro da Faculdade de Ciências Médicas da Santa Casa de São Paulo, São Paulo, SP, Brasil
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Ji C, Xu F, Wang Y, Qin Y. Peptoniphilus indolicus infection in a pregnant woman: a case report. Curr Med Res Opin 2022; 38:1439-1442. [PMID: 35481409 DOI: 10.1080/03007995.2022.2072091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Peptoniphilus indolicus belongs is a gram-positive anaerobic coccus (GPAC), which can cause bacterial vaginitis. However, only a few studies have reported severe infection of P. indolicus. This study presented the first case of severe infection of P. indolicus during pregnancy. It aimed to help to fill the gap in the literature, find out the factors that accelerate infection and discuss the significance of the GPAC test. CASE PRESENTATION A 35-year-old woman was admitted due to unbearable abdominal pain with dilation of the cervical opening at 22+ weeks of gestation. A blood test revealed electrolyte disturbance and hypoproteinemia. A day before admission, the patient developed pain in the lower abdomen accompanied by yellow-green vaginal discharge. Two hours after admission, the patient suddenly presented with hyperpyrexia and chills. Timely and adequate antibiotic and cooling treatments were administered. After 14 h, the patient again developed chills that lasted for approximately 20 min, accompanied by uterine contractions and membrane rupture. After 3 h, she had a miscarriage and rapidly developed septic shock. She was transferred to the intensive care unit for further infection control, shock correction, and circulatory stabilization. The cultures of blood, secretion specimen, and amniotic fluid indicated P. indolicus infection using a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, an advanced tool for bacterial species identification. CONCLUSIONS P. indolicus is an opportunistic pathogen in pregnant women. Poor physical conditions and pregnancy may accelerate disease progression and lead to severe inflammation.
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Affiliation(s)
- Chao Ji
- Department of Obstetrics, Qingdao Municipal Hospital, Qingdao, China
| | - Fengsen Xu
- Department of Obstetrics, Qingdao Municipal Hospital, Qingdao, China
| | - Yujie Wang
- Department of Laboratory Medicine, Qingdao Municipal Hospital, Qingdao, China
| | - Yichen Qin
- Department of Gynecology, The Third People's Hospital of Qingdao, Qingdao, China
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Costescu Strachinaru DI, Gallez JL, Daras S, Paridaens MS, Engel H, François PM, Rose T, Vanbrabant P, Soentjens P. A case of Flavonifractor plautii blood stream infection in a severe burn patient and a review of the literature. Acta Clin Belg 2022; 77:693-697. [PMID: 34151750 DOI: 10.1080/17843286.2021.1944584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
BACKGROUND Flavonifractor plautii is a strictly anaerobic rod shaped bacterium belonging to the family of Clostridiales. It is a commensal of the human intestinal microbiota which was seldom isolated from clinical samples, therefore clinical data are scarce. To date, only four cases of F. plautii infections were described, all occurring in immunosuppressed patients. CASE PRESENTATION We report a case where F. plautii was isolated from the blood culture of a severe burn victim and identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. DISCUSSION To the best of our knowledge, this is the first case of F. plautii blood stream infection described in a burn patient.
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Affiliation(s)
| | - Jean-Luc Gallez
- Department of Microbiology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Sonia Daras
- Department of Microbiology, Queen Astrid Military Hospital, Brussels, Belgium
| | | | - Harald Engel
- Burn Unit, Queen Astrid Military Hospital, Brussels, Belgium
| | | | - Thomas Rose
- Burn Unit, Queen Astrid Military Hospital, Brussels, Belgium
| | - Peter Vanbrabant
- Center for Infectious Diseases, Queen Astrid Military Hospital, Brussels, Belgium
| | - Patrick Soentjens
- Center for Infectious Diseases, Queen Astrid Military Hospital, Brussels, Belgium
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Costescu Strachinaru DI, Gallez JL, Paridaens MS, Djebara S, Soete O, Soentjens P. A case of Escherichia coli and Peptoniphilus species mixed osteomyelitis successfully identified by MALDI TOF-MS with a review of the literature. Acta Clin Belg 2022; 77:126-129. [PMID: 32552621 DOI: 10.1080/17843286.2020.1783908] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
BACKGROUND Peptoniphilus species are Gram-positive anaerobic cocci that are commensals of the human vagina and gut. METHODS AND RESULTS We describe a case of mixed Escherichia coli and Peptoniphilus spp. osteomyelitis identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry as Peptoniphilus harei and present a short literature review. CONCLUSION To our knowledge, only six cases of P. harei osteomyelitis have been reported to date.
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Affiliation(s)
| | - Jean-Luc Gallez
- Department of Microbiology, Queen Astrid Military Hospital, Brussels, Belgium
| | | | - Sarah Djebara
- Center for Infectious Diseases, Queen Astrid Military Hospital, Brussels, Belgium
| | - Olivier Soete
- Burn Unit, Queen Astrid Military Hospital, Brussels, Belgium
| | - Patrick Soentjens
- Center for Infectious Diseases, Queen Astrid Military Hospital, Brussels, Belgium
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Moore NFE, Batten TJ, Hutton CEJ, White WJ, Smith CD. The management of the shoulder skin microbiome ( Cutibacterium acnes) in the context of shoulder surgery: a review of the current literature. Shoulder Elbow 2021; 13:592-599. [PMID: 34804207 PMCID: PMC8600668 DOI: 10.1177/1758573220945226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/02/2020] [Accepted: 07/04/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND This review aims to establish current knowledge of the shoulder skin microbiome and how to manage the bacteria that reside within it. METHODS A review was undertaken of the current literature through OvidSP. All abstracts were reviewed by three independent researchers. RESULTS Thirty-five studies met the inclusion criteria. With forward referencing an additional 14 were included. None commented on organisms specific to the shoulder microbiome other than Cutibacterium acnes. Therefore, this review is focussed on the current knowledge of C. acnes. DISCUSSION C. acnes is a skin commensal within the pilo-sebaceous glands reported to be the primary pathogen in up to 86% of shoulder joint infections. Pre-operative culture of unprepared skin can be indicative of underlying joint infection in shoulder arthroplasty revision. Intra-articular biopsies may have a high false positive due to skin contamination. Correlating the number of positive samples and certain associated signs can give a greater than 90% probability of a true infection. Standard surgical skin preparation, peri-surgical intravenous antibiotics and oral pre-operative antibiotics do not reduce bacterial load within the skin. However, topical benzoyl peroxide and clindamycin have both demonstrated significantly reduced bacteria load. Phylogenetically there are six main types. Patients may have more than one phenotype present during infection.
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Affiliation(s)
| | - Timothy J Batten
- Timothy J Batten, Department of Trauma and
Orthopaedic Surgery, Princess Elizabeth Orthopaedic Centre, Royal Devon and
Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK.
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Eggerthella lenta bacteremia successfully treated with ceftizoxime: case report and review of the literature. Eur J Med Res 2021; 26:111. [PMID: 34544476 PMCID: PMC8454090 DOI: 10.1186/s40001-021-00582-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 09/09/2021] [Indexed: 11/17/2022] Open
Abstract
Eggerthella lenta is a normal human microflora that is anaerobic, non-sporulating, and Gram positive. However, an increasing number of studies have shown that it could also be an important pathogen for humans, even causing life-threatening infection under certain conditions. However, understanding its pathogenic mechanism and treatment options still need to be improved; more clinical data are needed to explore it further. In this article, we report a case of ceftizoxime-cured E. lenta bacteremia and review the recent literature to provide more clinical data for the diagnosis of E. lenta bacteremia. Our report suggests that the frequency of E. lenta bacteremia is increased in patients with hematologic or solid organ cancer, diabetes mellitus and also in those with appendicitis.
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Direct Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Testing from Positive Blood Cultures for Rapid Identification of Bloodstream Infection-Causing Anaerobic Bacteria. J Clin Microbiol 2021; 59:e0052121. [PMID: 33883181 DOI: 10.1128/jcm.00521-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Ray S, Narayanan A, Giske CG, Neogi U, Sönnerborg A, Nowak P. Altered Gut Microbiome under Antiretroviral Therapy: Impact of Efavirenz and Zidovudine. ACS Infect Dis 2021; 7:1104-1115. [PMID: 33346662 PMCID: PMC8154435 DOI: 10.1021/acsinfecdis.0c00536] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Millions
of individuals currently living with HIV globally are
receiving antiretroviral therapy (ART) that suppresses viral replication
and improves host immune responses. The involvement of gut microbiome
during HIV infection has been studied, exposing correlation with immune
status and inflammation. However, the direct effect of ART on gut
commensals of HIV-infected individuals has been mostly overlooked
in microbiome studies. We used 16S rRNA sequencing (Illumina MiSeq)
for determining the microbiota composition of stool samples from 16
viremic patients before and one year after ART. We also tested the
direct effect of 15 antiretrovirals against four gut microbes, namely, Escherichia coli, Enterococcus faecalis, Bacteroides, and Prevotella to assess their in vitro antibacterial effect. 16S rRNA analysis of fecal samples showed
that effective ART for one year does not restore the microbiome diversity
in HIV-infected patients. A significant reduction in α-diversity
was observed in patients under non-nucleoside reverse transcriptase
inhibitors; (NNRTI; 2 NRTI+NNRTI; NRTIs are nucleoside reverse transcriptase
inhibitors) as compared to ritonavir-boosted protease inhibitors (PI/r;
2 NRTI+PI/r). Prevotella (P = 0.00001) showed a significantly decreased abundance in patients
after ART (n = 16). We also found the direct effect
of antivirals on gut microbes, where zidovudine (ZDV) and efavirenz
(EFV) showed in vitro antimicrobial activity against Bacteroides fragilis and Prevotella. EFV also inhibited the growth of E. faecalis. Therefore, we observed that ART does not reverse the HIV-induced
gut microbiome dysbiosis and might aggravate those microbiota alterations
due to the antibacterial effect of certain antiretrovirals (like EFV,
ZDV). Our results imply that restructuring the microbiota could be
a potential therapeutic target in HIV-1 patients under ART.
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Affiliation(s)
- Shilpa Ray
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, Stockholm 141 52 Sweden
- The Laboratory for Molecular Infection Medicine Sweden MIMS, Umeå University, Umeå 901 87, Sweden
| | - Aswathy Narayanan
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, Stockholm 141 52 Sweden
| | - Christian G. Giske
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, Stockholm 141 52 Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Solna, Stockholm 171 76,Sweden
| | - Ujjwal Neogi
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, Stockholm 141 52 Sweden
| | - Anders Sönnerborg
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, Stockholm 141 52 Sweden
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska University Hospital, Huddinge, Stockholm 141 86, Sweden
| | - Piotr Nowak
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, Stockholm 141 52 Sweden
- The Laboratory for Molecular Infection Medicine Sweden MIMS, Umeå University, Umeå 901 87, Sweden
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska University Hospital, Huddinge, Stockholm 141 86, Sweden
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Declerck B, Van der Beken Y, De Geyter D, Piérard D, Wybo I. Antimicrobial susceptibility testing of Eggerthella lenta blood culture isolates at a university hospital in Belgium from 2004 to 2018. Anaerobe 2021; 69:102348. [PMID: 33596468 DOI: 10.1016/j.anaerobe.2021.102348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/04/2021] [Accepted: 02/06/2021] [Indexed: 10/22/2022]
Abstract
OBJECTIVES Eggerthella lenta is a Gram-positive anaerobic bacillus that is an important cause of bloodstream infections. This study aims to test the susceptibility of Eggerthella lenta blood culture isolates to commonly used antibiotics for the empirical treatment of anaerobic infections. METHODS In total, 49 positive blood cultures for Eggerthella lenta were retrospectively included from patients hospitalised at the Universitair Ziekenhuis Brussel, Belgium, between 2004 and 2018. Identification was done by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system. Antimicrobial susceptibility testing was performed using the reference agar dilution method according to Clinical and Laboratory Standards Institute (CLSI) guidelines with Brucella agar supplemented with 5 μg/mL hemin, 1 μg/mL vitamin K1 and 5% laked sheep blood. The minimal inhibitory concentrations were interpreted using the EUCAST breakpoints. Clinical characteristics were collected by reviewing the patient's medical records. RESULTS All isolates were susceptible to amoxicillin-clavulanate, metronidazole and meropenem. Eighty-eight % of them were susceptible to clindamycin and 94% (20% S, 74% I) were susceptible to piperacillin-tazobactam. The mean age of the patients was 64 (±20) and they showed a 30-day mortality of 27%. The source of infection was in 65.3% of the cases abdominal, 20.4% were sacral pressure ulcers and 14.3% were unknown causes. While all isolates were fully susceptible at standard dosing regimen to amoxicillin-clavulanate, most were only susceptible at increased exposure or resistant to piperacillin-tazobactam. CONCLUSIONS Our results suggest to be careful with the use of piperacillin-tazobactam and clindamycin in the empirical treatment of Eggerthella lenta infections.
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Affiliation(s)
- Baptist Declerck
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Brussels, Belgium.
| | | | - Deborah De Geyter
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Denis Piérard
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Ingrid Wybo
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Brussels, Belgium
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Gajdács M, Urbán E. The Pathogenic Role of Actinomyces spp. and Related Organisms in Genitourinary Infections: Discoveries in the New, Modern Diagnostic Era. Antibiotics (Basel) 2020; 9:E524. [PMID: 32824418 PMCID: PMC7459602 DOI: 10.3390/antibiotics9080524] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 08/14/2020] [Accepted: 08/15/2020] [Indexed: 12/16/2022] Open
Abstract
Actinomycosis is a chronic, suppurative, granulomatous infectious disease, caused by different species of Actinomyces bacteria. To date, 26 validly published Actinomyces species have been described as part of a normal human microbiota or from human clinical specimens. Due to the rapid spread of new, modern diagnostic procedures, 13 of 26 of these species have been described in this century and the Actinomycetaceae family has undergone several taxonomic revisions, including the introduction of many novel species termed Actinomyces-like organisms (ALOs). There is scarce data available on the role of these novel bacterial species in various infectious processes in human medicine. The aim of this review is to provide a comprehensive overview of Actinomyces and closely related organisms involved in human diseases-with a special focus on newly described species-in particular their role in genitourinary tract infections in females and males.
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Affiliation(s)
- Márió Gajdács
- Department of Pharmacodynamics and Biopharmacy, Faculty of Pharmacy, University of Szeged, 6720 Szeged, Hungary;
- Institute of Medical Microbiology, Faculty of Medicine, Semmelweis University, 1089 Budapest, Hungary
| | - Edit Urbán
- Institute of Translational Medicine, Faculty of Medicine, University of Pécs, 7624 Pécs, Hungary
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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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15
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Wang W, Liu W, Chu W. Isolation and preliminary screening of potentially probiotic Weissella confusa strains from healthy human feces by culturomics. Microb Pathog 2020; 147:104356. [PMID: 32610159 DOI: 10.1016/j.micpath.2020.104356] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 12/11/2022]
Abstract
PURPOSE The objective of this study was to isolate and identify strains of bacteria from feces of healthy human and screen potential probiotic candidate by using culturomics method combined with the matrix-assisted laser desorption/ionization-time of flight mass spectrum (MALDI-TOF MS) and 16S rRNA gene sequencing. METHODS AND RESULTS 31 strains were isolated and purified from human feces by culturomics method, and identified by MALDI-TOF MS and 16S rRNA gene sequencing. Then the obtained strains were tested for haemolytic activity, antibiotic susceptibility, acid and bile salts tolerance, antimicrobial activity, morphological and physiological characteristics. Three potential probiotic candidate strains named YM5Y, YM5S1 and YM5S2 were selected and identified as Weissella confusa. CONCLUSION Our results suggest the culturomics approach could be used to isolate and screen human fecal strains which could eventually be used for the development of novel probiotics. In addition, the isolated strains of W. confusa can act as potential probiotics and should be explored further for their potential application.
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Affiliation(s)
- Wenqian Wang
- Department of Pharmaceutical Microbiology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China
| | - Wugao Liu
- Lishui People's Hospital, The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, China
| | - Weihua Chu
- Department of Pharmaceutical Microbiology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China.
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16
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GAJDÁCS MÁRIÓ, URBÁN EDIT. Relevance of anaerobic bacteremia in adult patients: A never-ending story? Eur J Microbiol Immunol (Bp) 2020; 10:64-75. [PMID: 32590337 PMCID: PMC7391379 DOI: 10.1556/1886.2020.00009] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/19/2020] [Indexed: 11/30/2022] Open
Abstract
Obligate anaerobic bacteria are considered important constituents of the microbiota of humans; in addition, they are also important etiological agents in some focal or invasive infections and bacteremia with a high level of mortality. Conflicting data have accumulated over the last decades regarding the extent in which these pathogens play an intrinsic role in bloodstream infections. Clinical characteristics of anaerobic bloodstream infections do not differ from bacteremia caused by other pathogens, but due to their longer generation time and rigorous growth requirements, it usually takes longer to establish the etiological diagnosis. The introduction of matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) has represented a technological revolution in microbiological diagnostics, which has allowed for the fast, accurate and reliable identification of anaerobic bacteria at a low sample cost. The purpose of this review article is to summarize the currently available literature data on the prevalence of anaerobic bacteremia in adults for physicians and clinical microbiologists and to shed some light on the complexity of this topic nowadays.
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Affiliation(s)
- MÁRIÓ GAJDÁCS
- Department of Pharmacodynamics and Biopharmacy, Faculty of Pharmacy, University of Szeged, Eötvös utca 6., Szeged, 6720, Hungary
| | - EDIT URBÁN
- Department of Public Health, Faculty of Medicine, University of Szeged, Dóm tér 10., Szeged, 6720, Hungary
- Institute for Translational Medicine, Medical School, University of Pécs, Szigeti út 12., Pécs, 7624, Hungary
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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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MacLean SBM, Phadnis J, Ling CM, Bain GI. Application of dermal chlorhexidine antisepsis is ineffective at reducing Proprionibacterium acnes colonization in shoulder surgery. Shoulder Elbow 2019; 11:98-105. [PMID: 30936948 PMCID: PMC6434954 DOI: 10.1177/1758573218755570] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/07/2017] [Accepted: 12/11/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Chlorhexidine as a skin surface antiseptic has been shown to be ineffective with respect to reducing Proprionibacterium acnes colonization within the dermis. The purpose of the present study was to determine whether the application of aqueous chlorhexidine solution to the dermal layer decreased P. acnes colonization during open shoulder surgery. METHODS The present study enrolled 50 patients who were undergoing open shoulder surgery. Patients received standard antimicrobial preparation. Three dermal swabs were taken from each patient: swab 1 following skin incision; swab taken 2 minutes to 5 minutes post-application of aqueous chlorhexidine to the dermis; and swab 3 taken 60 minutes post-application. RESULTS Mean age was 57.5 years (22 males, 28 females). There were 21 patients (42%) with P. acnes present on any dermal swab. There were significantly more P. acnes positive cultures identified at swab 3 compared to swab 1 (p = 0.043). In nine patients with positive P. acnes at cultures swab 1, eight also isolated P. acnes after at swabs 2 or 3. Males were significantly more likely to have P. acnes on any swab (p < 0.001). Positive P. acnes cultures were significantly more common in patients ≤50 years (p < .001). None of the patients had any clinical signs of infection at a minimum of 1 year following surgery. CONCLUSIONS Dermal application of aqueous chlorhexidine during open shoulder surgery fails to eradicate or reduce P. acnes on deep cultures.
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Affiliation(s)
- Simon B. M. MacLean
- Department of Orthopaedics and Trauma, Flinders University, Adelaide, SA, Australia,Simon B. M. MacLean, Unit 6, 57 Lambert St, Kangaroo Point, Queensland 4169, Australia.
| | - Joideep Phadnis
- Department of Trauma and Orthopaedics, Brighton and Sussex University Hospitals, Brighton, UK
| | - Chi M. Ling
- Department of Orthopaedics and Trauma, Flinders University, Adelaide, SA, Australia
| | - Gregory I. Bain
- Department of Orthopaedics and Trauma, Flinders University, Adelaide, SA, Australia
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Zamora-Cintas M, Marín M, Quiroga L, Martínez A, Fernández-Chico MA, Bouza E, Rodríguez-Sánchez B, Alcalá L. Identification of Porphyromonas isolates from clinical origin using MALDI-TOF Mass Spectrometry. Anaerobe 2018; 54:197-200. [PMID: 30541687 DOI: 10.1016/j.anaerobe.2018.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/13/2018] [Accepted: 06/30/2018] [Indexed: 11/25/2022]
Abstract
Despite the wide implementation of MALDI-TOF MS for the rapid and reliable identification of most microorganisms, some taxonomic groups such as the Porphyromonas genus remain largely untested. In this study we evaluated the performance of MALDI-TOF MS on this genus using a collection of 39 isolates sent for routine identification to our institution over a 16-year period. All of them were identified by DNA-sequencing analysis of the 16S rRNA gene plus the hsp60 gene when the previous one did not yield species-level assignment. MALDI-TOF MS provided correct identification at least at the genus level of 21/39 isolates (53.9%). Twelve isolates were correctly identified at the species level with a score value ≥ 2.0 and 9 more with score values < 2.0 and ≥ 1.7. The species most represented in the database (P. gingivalis and P. somerae) lay within this category. However, the species poorly represented in this database (P. asaccharolytica and P. uenonis) were mostly identified with lower scores (1.35-1.67) or remained unidentified by MALDI-TOF MS. The addition of two P. asaccharolytica reference spectra to our in-house library allowed 72.9% of genus-level identifications with 17/37 isolates (45.9%) identified with score values ≥ 2.0. Our results showed a high level of correlation between MALDI-TOF MS and DNA-based identification for Porphyromonas spp. strains at the species level, even with score values < 2.0. The reliability provided by MALDI-TOF MS increased when the database was fed with spectra from the species poorly represented in the commercial database.
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Affiliation(s)
- Maribel Zamora-Cintas
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria 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; Medicine Department, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain.
| | - Lidia Quiroga
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Andrea Martínez
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - María Antonia Fernández-Chico
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Emilio Bouza
- Medicine Department, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Belén Rodríguez-Sánchez
- 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.
| | - Luis Alcalá
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
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20
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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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Boisrenoult P. Cutibacterium acnes prosthetic joint infection: Diagnosis and treatment. Orthop Traumatol Surg Res 2018; 104:S19-S24. [PMID: 29203432 DOI: 10.1016/j.otsr.2017.05.030] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/17/2017] [Accepted: 05/17/2017] [Indexed: 02/02/2023]
Abstract
Cutibacterium acnes is a commensal skin bacterium, regularly implicated in prosthetic joint infection, particularly of the shoulder. Diagnosis has been improved by progress in bacteriological techniques: longer culture time, liquid medium culture, MALDI-TOF mass spectrography, and universal 16S rRNA PCR, associated by some authors to sonication of ablated implants. C. acnes pathogenicity involves many virulence factors, notably including biofilm formation. C. acnes may lead to infection that is clinically evident or, frequently, relatively asymptomatic. C. acnes is an anaerobic Gram-positive bacterium, susceptible to many antibiotics that are regularly used in bone and joint infection: beta-lactams, quinolone, rifampicin and clindamycin. It shows increasing resistance to clindamycin and natural resistance to metronidazole. Treatment is medical and surgical, associating synovectomy or complete 1- or 2-step revision depending on time to treatment, and antibiotic therapy. Antibiotic therapy is typically for three months with an initial 2-6 weeks' intravenous phase. Prognosis is generally favorable with well-conducted treatment. Late discovery of positive samples after apparently aseptic implant change is an at-risk situation, usually managed by antibiotic therapy, but with late initiation and hence increased risk of failure. Adverse secondary progression requires repeat revision under good conditions.
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Affiliation(s)
- P Boisrenoult
- Service d'orthopédie traumatologie, centre hospitalier de Versailles, 177, rue de Versailles, 78150 Le-Chesnay, France.
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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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Gajdács M, Spengler G, Urbán E. Identification and Antimicrobial Susceptibility Testing of Anaerobic Bacteria: Rubik's Cube of Clinical Microbiology? Antibiotics (Basel) 2017; 6:E25. [PMID: 29112122 PMCID: PMC5745468 DOI: 10.3390/antibiotics6040025] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 10/30/2017] [Accepted: 11/03/2017] [Indexed: 12/26/2022] Open
Abstract
Anaerobic bacteria have pivotal roles in the microbiota of humans and they are significant infectious agents involved in many pathological processes, both in immunocompetent and immunocompromised individuals. Their isolation, cultivation and correct identification differs significantly from the workup of aerobic species, although the use of new technologies (e.g., matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, whole genome sequencing) changed anaerobic diagnostics dramatically. In the past, antimicrobial susceptibility of these microorganisms showed predictable patterns and empirical therapy could be safely administered but recently a steady and clear increase in the resistance for several important drugs (β-lactams, clindamycin) has been observed worldwide. For this reason, antimicrobial susceptibility testing of anaerobic isolates for surveillance purposes or otherwise is of paramount importance but the availability of these testing methods is usually limited. In this present review, our aim was to give an overview of the methods currently available for the identification (using phenotypic characteristics, biochemical testing, gas-liquid chromatography, MALDI-TOF MS and WGS) and antimicrobial susceptibility testing (agar dilution, broth microdilution, disk diffusion, gradient tests, automated systems, phenotypic and molecular resistance detection techniques) of anaerobes, when should these methods be used and what are the recent developments in resistance patterns of anaerobic bacteria.
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Affiliation(s)
- Márió Gajdács
- Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary.
| | - Gabriella Spengler
- Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary.
| | - Edit Urbán
- Institute of Clinical Microbiology, Faculty of Medicine, University of Szeged, 6725 Szeged, Hungary.
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Veloo ACM, Jean-Pierre H, Justesen US, Morris T, Urban E, Wybo I, Shah HN, Friedrich AW, Morris T, Shah HN, Jean-Pierre H, Justesen US, Nagy E, Urban E, Kostrzewa M, Veloo A, Friedrich AW. A multi-center ring trial for the identification of anaerobic bacteria using MALDI-TOF MS. Anaerobe 2017; 48:94-97. [PMID: 28797803 DOI: 10.1016/j.anaerobe.2017.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 11/15/2022]
Abstract
Inter-laboratory reproducibility of Matrix Assisted Laser Desorption Time-of-Flight Mass Spectrometry (MALDI-TOF MS) of anaerobic bacteria has not been shown before. Therefore, ten anonymized anaerobic strains were sent to seven participating laboratories, an initiative of the European Network for the Rapid Identification of Anaerobes (ENRIA). On arrival the strains were cultured and identified using MALDI-TOF MS. The spectra derived were compared with two different Biotyper MALDI-TOF MS databases, the db5627 and the db6903. The results obtained using the db5627 shows a reasonable variation between the different laboratories. However, when a more optimized database is used, the variation is less pronounced. In this study we show that an optimized database not only results in a higher number of strains which can be identified using MALDI-TOF MS, but also corrects for differences in performance between laboratories.
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Affiliation(s)
- A C M Veloo
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands.
| | - H Jean-Pierre
- Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France; Université Montpellier 1, UMR5119 ECOSYM, Equipe Pathogènes Hydriques Santé Environnements, UMR 5569 Hydrosciences, UFR Pharmacie, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France
| | - U S Justesen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - T Morris
- UK Anaerobe Reference Unit, Public Health Wales Microbiology, Cardiff, UK
| | - E Urban
- Institute of Clinical Microbiology, University of Szeged, Hungary
| | - I Wybo
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - H N Shah
- Department of Natural Sciences, Middlesex University, London NW4 4BT, UK
| | - A W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands
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First report on sepsis caused by Porphyromonas pogonae. Anaerobe 2017; 44:96-98. [DOI: 10.1016/j.anaerobe.2017.02.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/10/2017] [Accepted: 02/20/2017] [Indexed: 11/20/2022]
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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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Veloo ACM, de Vries ED, Jean-Pierre H, Justesen US, Morris T, Urban E, Wybo I, van Winkelhoff AJ. The optimization and validation of the Biotyper MALDI-TOF MS database for the identification of Gram-positive anaerobic cocci. Clin Microbiol Infect 2016; 22:793-798. [PMID: 27404365 DOI: 10.1016/j.cmi.2016.06.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/13/2016] [Accepted: 06/22/2016] [Indexed: 11/29/2022]
Abstract
Gram-positive anaerobic cocci (GPAC) account for 24%-31% of the anaerobic bacteria isolated from human clinical specimens. At present, GPAC are under-represented in the Biotyper MALDI-TOF MS database. Profiles of new species have yet to be added. We present the optimization of the matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) database for the identification of GPAC. Main spectral profiles (MSPs) were created for 108 clinical GPAC isolates. Identity was confirmed using 16S rRNA gene sequencing. Species identification was considered to be reliable if the sequence similarity with its closest relative was ≥98.7%. The optimized database was validated using 140 clinical isolates. The 16S rRNA sequencing identity was compared with the MALDI-TOF MS result. MSPs were added from 17 species that were not yet represented in the MALDI-TOF MS database or were under-represented (fewer than five MSPs). This resulted in an increase from 53.6% (75/140) to 82.1% (115/140) of GPAC isolates that could be identified at the species level using MALDI-TOF MS. An improved log score was obtained for 51.4% (72/140) of the strains. For strains with a sequence similarity <98.7% with their closest relative (n = 5) or with an inconclusive sequence identity (n = 4), no identification was obtained by MALDI-TOF MS or in the latter case an identity with one of its relatives. For some species the MSP of the type strain was not part of the confined cluster of the corresponding clinical isolates. Also, not all species formed a homogeneous cluster. It emphasizes the necessity of adding sufficient MSPs of human clinical isolates.
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Affiliation(s)
- A C M Veloo
- Department of Medical Microbiology, University of Groningen, University Medical Centre Groningen, The Netherlands.
| | - E D de Vries
- Department of Medical Microbiology, University of Groningen, University Medical Centre Groningen, The Netherlands
| | - H Jean-Pierre
- Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, Montpellier, France; Université Montpellier 1, UMR5119 ECOSYM, Equipe Pathogènes Hydriques Santé Environnements, UMR 5569 Hydrosciences, UFR Pharmacie, Montpellier, France
| | - U S Justesen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - T Morris
- UK Anaerobe Reference Unit, Public Health Wales Microbiology, Cardiff, UK
| | - E Urban
- Institute of Clinical Microbiology, University of Szeged, Hungary
| | - I Wybo
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - A J van Winkelhoff
- Department of Medical Microbiology, University of Groningen, University Medical Centre Groningen, The Netherlands; Department of Dentistry and Oral Hygiene, University of Groningen, University Medical Centre Groningen, The Netherlands
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29
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MALDI-TOF MS is more accurate than VITEK II ANC card and API Rapid ID 32 A system for the identification of Clostridium species. Anaerobe 2016; 40:73-5. [PMID: 27296834 DOI: 10.1016/j.anaerobe.2016.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 06/02/2016] [Accepted: 06/09/2016] [Indexed: 11/20/2022]
Abstract
All 50 Clostridium difficile strains were definitely identified by Vitek2 system, Rapid ID 32A system, and MALDI-TOF.
For 18 non-difficile Clostridium strains, the identification results were correct in 2, 0, and 17 strains by Vitek2, Rapid ID 32A, and MALDI-TOF, respectively [corrected].
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30
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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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31
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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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32
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Liderot K, Ratcliffe P, Lüthje P, Thidholm E, Özenci V. Microbiological diagnosis of Eggerthella lenta blood culture isolates in a Swedish tertiary hospital: Rapid identification and antimicrobial susceptibility profile. Anaerobe 2015; 38:21-24. [PMID: 26612006 DOI: 10.1016/j.anaerobe.2015.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 11/10/2015] [Accepted: 11/16/2015] [Indexed: 10/22/2022]
Abstract
Eggerthella lenta is a Gram-positive anaerobic bacillus. Improved diagnostics and increased awareness of rare pathogens have revealed its potential to cause serious invasive infections. In this study, 18 clinical E. lenta isolates derived from positive blood cultures were included. Underlying problems of the patients were in the majority of cases related to the gastrointestinal tract. The performance of two MALDI-TOF MS systems, i.e. Bruker and Vitek MS, in identification of E. lenta was analyzed. In addition, the minimal inhibitory concentrations for clinically relevant antimicrobial agents were determined by routine procedures using E-test. 17 of the 18 E. lenta isolates investigated in this study were correctly identified to species level by the Bruker MS system, while the Vitek MS system identified all 18 isolates. Antimicrobial sensitivity towards the tested agents was in general good. However, high resistance rates were observed for penicillin G and piperacillin-tazobactam based on EUCAST breakpoints.
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Affiliation(s)
- Karin Liderot
- Division of Clinical Microbiology, Karolinska Institutet and Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Paul Ratcliffe
- Division of Clinical Microbiology, Karolinska Institutet and Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Petra Lüthje
- Division of Clinical Microbiology, Karolinska Institutet and Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Ellinor Thidholm
- Division of Clinical Microbiology, Karolinska Institutet and Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Volkan Özenci
- Division of Clinical Microbiology, Karolinska Institutet and Karolinska University Hospital, Huddinge, Stockholm, Sweden.
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33
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The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev 2015; 28:237-64. [PMID: 25567229 DOI: 10.1128/cmr.00014-14] [Citation(s) in RCA: 507] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a "dark matter" of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the "great plate count anomaly," which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.
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34
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The aerobic activity of metronidazole against anaerobic bacteria. Int J Antimicrob Agents 2015; 45:537-40. [DOI: 10.1016/j.ijantimicag.2014.12.032] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 12/29/2014] [Indexed: 11/18/2022]
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35
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Veloo A, van Winkelhoff A. Antibiotic susceptibility profiles of anaerobic pathogens in The Netherlands. Anaerobe 2015; 31:19-24. [DOI: 10.1016/j.anaerobe.2014.08.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/21/2014] [Accepted: 08/23/2014] [Indexed: 10/24/2022]
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36
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Bourassa L, Butler-Wu SM. MALDI-TOF Mass Spectrometry for Microorganism Identification. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.07.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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37
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Abstract
Abstract
BACKGROUND
First introduced into clinical microbiology laboratories in Europe, MALDI-TOF MS is being rapidly embraced by laboratories around the globe. Although it has multiple applications, its widespread adoption in clinical microbiology relates to its use as an inexpensive, easy, fast, and accurate method for identification of grown bacteria and fungi based on automated analysis of the mass distribution of bacterial proteins.
CONTENT
This review provides a historical perspective on this new technology. Modern applications in the clinical microbiology laboratory are reviewed with a focus on the most recent publications in the field. Identification of aerobic and anaerobic bacteria, mycobacteria, and fungi are discussed, as are applications for testing urine and positive blood culture bottles. The strengths and limitations of MALDI-TOF MS applications in clinical microbiology are also addressed.
SUMMARY
MALDI-TOF MS is a tool for rapid, accurate, and cost-effective identification of cultured bacteria and fungi in clinical microbiology. The technology is automated, high throughput, and applicable to a broad range of common as well as esoteric bacteria and fungi. MALDI-TOF MS is an incontrovertibly beneficial technology for the clinical microbiology laboratory.
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Affiliation(s)
- Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, and
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN
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38
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Clinical and microbiological characteristics of Eggerthella lenta bacteremia. J Clin Microbiol 2014; 53:626-35. [PMID: 25520446 DOI: 10.1128/jcm.02926-14] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Eggerthella lenta is an emerging pathogen that has been underrecognized due to historical difficulties with phenotypic identification. Until now, its pathogenicity, antimicrobial susceptibility profile, and optimal treatment have been poorly characterized. In this article, we report the largest cohort of patients with E. lenta bacteremia to date and describe in detail their clinical features, microbiologic characteristics, treatment, and outcomes. We identified 33 patients; the median age was 68 years, and there was no gender predominance. Twenty-seven patients (82%) had serious intra-abdominal pathology, often requiring a medical procedure. Of those who received antibiotics (28/33, 85%), the median duration of treatment was 21.5 days. Mortality from all causes was 6% at 7 days, 12% at 30 days, and 33% at 1 year. Of 26 isolates available for further testing, all were identified as E. lenta by both commercially available matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems, and none were found to harbor a vanA or vanB gene. Of 23 isolates which underwent susceptibility testing, all were susceptible to amoxicillin-clavulanate, cefoxitin, metronidazole, piperacillin-tazobactam, ertapenem, and meropenem, 91% were susceptible to clindamycin, 74% were susceptible to moxifloxacin, and 39% were susceptible to penicillin.
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39
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Peel TN, Cole NC, Dylla BL, Patel R. Matrix-assisted laser desorption ionization time of flight mass spectrometry and diagnostic testing for prosthetic joint infection in the clinical microbiology laboratory. Diagn Microbiol Infect Dis 2014; 81:163-8. [PMID: 25533615 DOI: 10.1016/j.diagmicrobio.2014.11.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 11/13/2014] [Accepted: 11/24/2014] [Indexed: 11/18/2022]
Abstract
Identification of pathogen(s) associated with prosthetic joint infection (PJI) is critical for patient management. Historically, many laboratories have not routinely identified organisms such as coagulase-negative staphylococci to the species level. The advent of matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) has enhanced clinical laboratory capacity for accurate species-level identification. The aim of this study was to describe the species-level identification of microorganisms isolated from periprosthetic tissue and fluid specimens using MALDI-TOF MS alongside other rapid identification tests in a clinical microbiology laboratory. Results of rapid identification of bacteria isolated from periprosthetic joint fluid and/or tissue specimens were correlated with clinical findings at Mayo Clinic, Rochester, Minnesota, between May 2012 and May 2013. There were 178 PJI and 82 aseptic failure (AF) cases analyzed, yielding 770 organisms (median, 3/subject; range, 1-19/subject). MALDI-TOF MS was employed for the identification of 455 organisms (59%) in 197 subjects (123 PJIs and 74 AFs), with 89% identified to the species level using this technique. Gram-positive bacteria accounted for 68% and 93% of isolates in PJI and AF, respectively. However, the profile of species associated with infection compared to specimen contamination differed. Staphylococcus aureus and Staphylococcus caprae were always associated with infection, Staphylococcus epidermidis and Staphylococcus lugdunensis were equally likely to be a pathogen or a contaminant, whereas the other coagulase-negative staphylococci were more frequently contaminants. Most streptococcal and Corynebacterium isolates were pathogens. The likelihood that an organism was a pathogen or contaminant differed with the prosthetic joint location, particularly in the case of Propionibacterium acnes. MALDI-TOF MS is a valuable tool for the identification of bacteria isolated from patients with prosthetic joints, providing species-level identification that may inform culture interpretation of pathogens versus contaminants.
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Affiliation(s)
- Trisha N Peel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA; Department of Surgery, St Vincent's Hospital Melbourne, University of Melbourne, Melbourne, VIC, Australia.
| | - Nicolynn C Cole
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Brenda L Dylla
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA; Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN, USA.
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40
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Nagy E, Ábrók M, Bartha N, Bereczki L, Juhász E, Kardos G, Kristóf K, Miszti C, Urbán E. Special application of matrix-assisted laser desorption ionization time-of-flight mass spectrometry in clinical microbiological diagnostics. Orv Hetil 2014; 155:1495-503. [DOI: 10.1556/oh.2014.29985] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry as a new possibility for rapid identification of bacteria and fungi revolutionized the clinical microbiological diagnostics. It has an extreme importance in the routine microbiological laboratories, as identification of the pathogenic species rapidly will influence antibiotic selection before the final determination of antibiotic resistance of the isolate. The classical methods for identification of bacteria or fungi, based on biochemical tests, are influenced by many environmental factors. The matrix-assisted laser desorption ionization time-of-flight mass spectrometry is a rapid method which is able to identify a great variety of the isolated bacteria and fungi based on the composition of conserved ribosomal proteins. Recently several other applications of the method have also been investigated such as direct identification of pathogens from the positive blood cultures. There are possibilities to identify bacteria from the urine samples in urinary tract infection or from other sterile body fluids. Using selective enrichment broth Salmonella sp from the stool samples can be identified more rapidly, too. The extended spectrum beta-lactamase or carbapenemase production of the isolated bacteria can be also detected by this method helping the antibiotic selection in some cases. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry based methods are suitable to investigate changes in deoxyribonucleic acid or ribonucleic acid, to carry out rapid antibiotic resistance determination or other proteomic analysis. The aim of this paper is to give an overview about present possibilities of using this technique in the clinical microbiological routine procedures. Orv. Hetil., 2014, 155(38), 1495–1503.
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Affiliation(s)
- Erzsébet Nagy
- Szegedi Tudományegyetem, Általános Orvostudományi Kar Klinikai Mikrobiológiai Diagnosztikai Intézet Szeged Pf. 427 6701
| | - Marianna Ábrók
- Szegedi Tudományegyetem, Általános Orvostudományi Kar Klinikai Mikrobiológiai Diagnosztikai Intézet Szeged Pf. 427 6701
| | - Noémi Bartha
- Szegedi Tudományegyetem, Általános Orvostudományi Kar Klinikai Mikrobiológiai Diagnosztikai Intézet Szeged Pf. 427 6701
| | - László Bereczki
- Szegedi Tudományegyetem, Általános Orvostudományi Kar Klinikai Mikrobiológiai Diagnosztikai Intézet Szeged Pf. 427 6701
| | - Emese Juhász
- Semmelweis Egyetem, Általános Orvostudományi Kar Laboratóriumi Medicina Intézet, Klinikai Mikrobiológiai Diagnosztikai Laboratórium Budapest
| | - Gábor Kardos
- Debreceni Egyetem, Általános Orvostudományi Kar Orvosi Mikrobiológiai Intézet Debrecen
| | - Katalin Kristóf
- Semmelweis Egyetem, Általános Orvostudományi Kar Laboratóriumi Medicina Intézet, Klinikai Mikrobiológiai Diagnosztikai Laboratórium Budapest
| | - Cecilia Miszti
- Debreceni Egyetem, Általános Orvostudományi Kar Orvosi Mikrobiológiai Intézet Debrecen
| | - Edit Urbán
- Szegedi Tudományegyetem, Általános Orvostudományi Kar Klinikai Mikrobiológiai Diagnosztikai Intézet Szeged Pf. 427 6701
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41
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Angelakis E, Raoult D. Methods for the discovery of emerging pathogens. Microb Pathog 2014; 77:114-8. [PMID: 25014736 PMCID: PMC7127287 DOI: 10.1016/j.micpath.2014.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 06/23/2014] [Indexed: 01/18/2023]
Abstract
Recently, there has been a steady increase in the number of recognized pathogenic microorganisms, specifically bacteria. The development of genetic technologies, MALDI-TOF mass spectrometry and new culturing techniques has significantly widened the repertoire of known microorganisms and therefore pathogenic microorganisms. The repertoire of infectious agents has been studied in various environments including water, soil, pets, livestock, wildlife and arthropods. Using different methods, many known pathogens can be identified in these samples; therefore, the impact of emergent pathogens on humans can be examined and novel pathogens can be identified. In this special issue, we discuss the identification of emerging pathogens in the environment and animals.
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Affiliation(s)
- Emmanouil Angelakis
- URMITE CNRS-IRD 198 UMR 6236, Université de la Méditerranée, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille, France.
| | - Didier Raoult
- URMITE CNRS-IRD 198 UMR 6236, Université de la Méditerranée, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille, France
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42
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Suwantarat N, Romagnoli M, Wakefield T, Carroll KC. Ventriculoperitoneal shunt infection caused by Bifidobacterium breve. Anaerobe 2014; 28:1-3. [PMID: 24755114 DOI: 10.1016/j.anaerobe.2014.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/02/2014] [Accepted: 04/05/2014] [Indexed: 12/20/2022]
Abstract
Bifidobacterium breve is a rare cause of human infections. Previously, bacteremia and meningitis caused by this organism linked to probiotic use have been reported in a neonate. We report the first case of a ventriculoperitoneal shunt infection caused by B. breve in an adult without a history of probiotic use.
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Affiliation(s)
- Nuntra Suwantarat
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Mark Romagnoli
- Microbiology Laboratory, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Teresa Wakefield
- Microbiology Laboratory, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Microbiology Laboratory, Johns Hopkins Hospital, Baltimore, MD, USA
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43
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O'Connor C, Fitzgibbon M, Powell J, Barron D, O'Mahony J, Power L, O'Connell NH, Dunne C. A commentary on the role of molecular technology and automation in clinical diagnostics. Bioengineered 2014; 5:155-60. [PMID: 24658184 DOI: 10.4161/bioe.28599] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Historically, the identification of bacterial or yeast isolates has been based on phenotypic characteristics such as growth on defined media, colony morphology, Gram stain, and various biochemical reactions, with significant delay in diagnosis. Clinical microbiology as a medical specialty has embraced advances in molecular technology for rapid species identification with broad-range 16S rDNA polymerase chain reaction (PCR) and matrix-assisted laser desorption and/or ionization time of flight (MALDI-TOF) mass spectrometry demonstrated as accurate, rapid, and cost-effective methods for the identification of most, but not all, bacteria and yeasts. Protracted conventional incubation times previously necessary to identify certain species have been mitigated, affording patients quicker diagnosis with associated reduction in exposure to empiric broad-spectrum antimicrobial therapy and shortened hospital stay. This short commentary details such molecular advances and their implications in the clinical microbiology setting.
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Affiliation(s)
- Ciara O'Connor
- Department of Clinical Microbiology; University Hospital Limerick; Limerick, Ireland; Centre for Interventions in Infection, Inflammation, and Immunity (4i) and Graduate Entry Medical School; University of Limerick; Limerick, Ireland
| | - Marie Fitzgibbon
- Department of Clinical Microbiology; University Hospital Limerick; Limerick, Ireland
| | - James Powell
- Department of Clinical Microbiology; University Hospital Limerick; Limerick, Ireland
| | - Denis Barron
- Department of Clinical Microbiology; University Hospital Limerick; Limerick, Ireland
| | | | - Lorraine Power
- Department of Clinical Microbiology; University Hospital Limerick; Limerick, Ireland
| | - Nuala H O'Connell
- Department of Clinical Microbiology; University Hospital Limerick; Limerick, Ireland; Centre for Interventions in Infection, Inflammation, and Immunity (4i) and Graduate Entry Medical School; University of Limerick; Limerick, Ireland
| | - Colum Dunne
- Centre for Interventions in Infection, Inflammation, and Immunity (4i) and Graduate Entry Medical School; University of Limerick; Limerick, Ireland
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44
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Dec M, Urban-Chmiel R, Gnat S, Puchalski A, Wernicki A. Identification of Lactobacillus strains of goose origin using MALDI-TOF mass spectrometry and 16S-23S rDNA intergenic spacer PCR analysis. Res Microbiol 2014; 165:190-201. [PMID: 24607713 DOI: 10.1016/j.resmic.2014.02.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 02/15/2014] [Indexed: 11/18/2022]
Abstract
The objective of our study was to identify Lactobacillus sp. strains of goose origin using MALDI-TOF mass spectrometry, ITS-PCR and ITS-PCR/RFLP. All three techniques proved to be valuable tools for identification of avian lactobacilli and produced comparable classification results. Lactobacillus strains were isolated from 100% of geese aged 3 weeks to 4 years, but from only 25% of chicks aged 1-10 days. Among the 104 strains isolated, we distinguished 14 Lactobacillus species. The dominant species was Lactobacillus salivarius (35.6%), followed by Lactobacillus johnsonii (18.3%), Lactobacillus ingluviei (11.5%) and Lactobacillus agilis (7.7%). The intact-cell MALDI-TOF mass spectrometry enabled rapid species identification of the lactobacilli with minimal pretreatment. However, it produced more than one identification result for 11.5% examined strains (mainly of the species L. johnsonii). ITS-PCR distinguished 12 genotypes among the isolates, but was not able to differentiate closely related strains, i.e. between Lactobacillus amylovorus and Lactobacillus kitasatonis and between Lactobacillus paracasei, Lactobacillus rhamnosus and Lactobacillus zeae. These species were differentiated by ITS-PCR/RFLP using the restriction enzymes TaqI and MseI. The results obtained indicate that ITS-PCR and ITS-PCR/RFLP assays could be used not only for interspecific, but also for intraspecific, typing.
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Affiliation(s)
- Marta Dec
- Sub-Department of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences, Akademicka 12, 20-033 Lublin, Poland.
| | - Renata Urban-Chmiel
- Sub-Department of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences, Akademicka 12, 20-033 Lublin, Poland.
| | - Sebastian Gnat
- Sub-Department of Veterinary Microbiology, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences, Akademicka 12, 20-033 Lublin, Poland.
| | - Andrzej Puchalski
- Sub-Department of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences, Akademicka 12, 20-033 Lublin, Poland.
| | - Andrzej Wernicki
- Sub-Department of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences, Akademicka 12, 20-033 Lublin, Poland.
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45
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Walter G, Vernier M, Pinelli PO, Million M, Coulange M, Seng P, Stein A. Bone and joint infections due to anaerobic bacteria: an analysis of 61 cases and review of the literature. Eur J Clin Microbiol Infect Dis 2014; 33:1355-64. [DOI: 10.1007/s10096-014-2073-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 01/28/2014] [Indexed: 11/30/2022]
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46
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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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47
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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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48
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Charnot-Katsikas A, Tesic V, Boonlayangoor S, Bethel C, Frank KM. Prospective evaluation of the VITEK MS for the routine identification of bacteria and yeast in the clinical microbiology laboratory: assessment of accuracy of identification and turnaround time. J Med Microbiol 2013; 63:235-241. [PMID: 24227878 DOI: 10.1099/jmm.0.063636-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This study assessed the accuracy of bacterial and yeast identification using the VITEK MS, and the time to reporting of isolates before and after its implementation in routine clinical practice. Three hundred and sixty-two isolates of bacteria and yeast, consisting of a variety of clinical isolates and American Type Culture Collection strains, were tested. Results were compared with reference identifications from the VITEK 2 system and with 16S rRNA sequence analysis. The VITEK MS provided an acceptable identification to species level for 283 (78 %) isolates. Considering organisms for which genus-level identification is acceptable for routine clinical care, 315 isolates (87 %) had an acceptable identification. Six isolates (2 %) were identified incorrectly, five of which were Shigella species. Finally, the time for reporting the identifications was decreased significantly after implementation of the VITEK MS for a total mean reduction in time of 10.52 h (P<0.0001). Overall, accuracy of the VITEK MS was comparable or superior to that from the VITEK 2. The findings were also comparable to other studies examining the accuracy of the VITEK MS, although differences exist, depending on the diversity of species represented as well as on the versions of the databases used. The VITEK MS can be incorporated effectively into routine use in a clinical microbiology laboratory and future expansion of the database should provide improved accuracy for the identification of micro-organisms.
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Affiliation(s)
- Angella Charnot-Katsikas
- Department of Pathology, University of Chicago Medicine, 5841 S. Maryland Avenue, Chicago, IL 60637, USA
| | - Vera Tesic
- Department of Pathology, University of Chicago Medicine, 5841 S. Maryland Avenue, Chicago, IL 60637, USA
| | - Sue Boonlayangoor
- Department of Pathology, University of Chicago Medicine, 5841 S. Maryland Avenue, Chicago, IL 60637, USA
| | - Cindy Bethel
- Department of Pathology, University of Chicago Medicine, 5841 S. Maryland Avenue, Chicago, IL 60637, USA
| | - Karen M Frank
- Department of Pathology, University of Chicago Medicine, 5841 S. Maryland Avenue, Chicago, IL 60637, USA
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