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Romero LC, Silva LP, Teixeira NB, de Camargo KV, Del Masso Pereira MA, Corrente JE, Pereira VC, Ribeiro de Souza da Cunha MDL. Staphylococcus capitis Bloodstream Isolates: Investigation of Clonal Relationship, Resistance Profile, Virulence and Biofilm Formation. Antibiotics (Basel) 2024; 13:147. [PMID: 38391533 PMCID: PMC10885910 DOI: 10.3390/antibiotics13020147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
Staphylococcus capitis has been recognized as a relevant opportunistic pathogen, particularly its persistence in neonatal ICUs around the world. Therefore, the aim of this study was to describe the epidemiological profile of clinical isolates of S. capitis and to characterize the factors involved in the persistence and pathogenesis of these strains isolated from blood cultures collected in a hospital in the interior of the state of São Paulo, Brazil. A total of 141 S. capitis strains were submitted to detection of the mecA gene and SCCmec typing by multiplex PCR. Genes involved in biofilm production and genes encoding enterotoxins and hemolysins were detected by conventional PCR. Biofilm formation was evaluated by the polystyrene plate adherence test and phenotypic resistance was investigated by the disk diffusion method. Finally, pulsed-field gel electrophoresis (PFGE) was used to analyze the clonal relationship between isolates. The mecA gene was detected in 99 (70.2%) isolates, with this percentage reaching 100% in the neonatal ICU. SCCmec type III was the most prevalent type, detected in 31 (31.3%) isolates and co-occurrence of SCCmec was also observed. In vitro biofilm formation was detected in 46 (32.6%) isolates but was not correlated with the presence of the ica operon genes. Furthermore, biofilm production in ICU isolates was favored by hyperosmotic conditions, which are common in ICUs because of the frequent parenteral nutrition. Analysis of the clonal relationship between the isolates investigated in the present study confirms a homogeneous profile of S. capitis and the persistence of clones that are prevalent in the neonatal ICU and disseminated across the hospital. This study highlights the adaptation of isolates to specific hospital environments and their high clonality.
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Affiliation(s)
- Letícia Calixto Romero
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-691, Brazil
| | - Lucas Porangaba Silva
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-691, Brazil
| | - Nathalia Bibiana Teixeira
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-691, Brazil
| | - Karen Vilegas de Camargo
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-691, Brazil
| | | | - José Eduardo Corrente
- Department of Biostatistics, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-900, Brazil
| | - Valéria Cataneli Pereira
- Microbiology Laboratory, Universidade do Oeste Paulista (UNOESTE), Presidente Prudente 18618-970, Brazil
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Khongsri U, Chongrattanameteekul P, Chantarachart S, Photichai K, Chanayat N, Varinrak T, Mektrirat R, Srifawattana N. Comparative Susceptibility of Pathogenic Methicillin-Resistant and Methicillin-Susceptible Staphylococcus pseudintermedius to Empirical Cotrimazole for Canine Pyoderma. Life (Basel) 2023; 13:life13051210. [PMID: 37240855 DOI: 10.3390/life13051210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/09/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
The prevalence of methicillin-resistant Staphylococcus pseudintermedius (MRSP) that causes pyoderma has been gradually shifting, according to many surveillance studies, with annual changes. The empirical cotrimazole regimen remains interesting, but research on cotrimazole susceptibility to MRSP is limited. The objective of this study was to evaluate the susceptibility of cotrimazole to canine pyoderma MRSP isolates. Sixty isolates of S. pseudintermedius were identified as 16 MRSP and 44 methicillin-susceptible S. pseudintermedius (MSSP) using an oxacillin disk diffusion test and VITEK 2 system with VITEK GP card. Using the VITEK 2 system with a VITEK AST-GP81 card, the susceptibility rates of MRSP (15.00%) and MSSP (35.00%) to cotrimazole was observed. The median MIC of cotrimazole on MSSP (median, ≤10; IQR, 10-320) was lower than that of MRSP (median, ≥320; IQR, 10-320) (p = 0.5889, Mann-Whitney test). Percent attainment of PK/PD targets in MRSP (q 12 h, 43.75; q 8 h, 43.75) were lower than that of MSSP (q 12 h, 52.27; q 8 h, 52.27) (p = 0.7710). These findings show the moderately phenotypic cotrimazole susceptibilities of both MRSP and MSSP. Further study is required to develop clinical trials examining the use of cotrimazole in dogs with pyoderma.
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Affiliation(s)
- Usasom Khongsri
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
- Small Animal Hospital, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Peerawit Chongrattanameteekul
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Sineenart Chantarachart
- Small Animal Hospital, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Kornravee Photichai
- Center of Veterinary Diagnosis and Technology Transfer, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Nittaya Chanayat
- Center of Veterinary Diagnosis and Technology Transfer, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Thanya Varinrak
- Center of Veterinary Diagnosis and Technology Transfer, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Raktham Mektrirat
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
- Epidemiological and Innovative Research Group for Infectious Diseases, Chiang Mai University, Chiang Mai 50200, Thailand
- Research Center for Pharmaceutical Nanotechnology, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nuttawan Srifawattana
- Small Animal Hospital, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
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Characterization and validation of an alternative reference bacterium Korean Pharmacopoeia Staphylococcus aureus strain. J Microbiol 2022; 60:187-191. [PMID: 34994956 PMCID: PMC8739380 DOI: 10.1007/s12275-022-1335-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/04/2021] [Accepted: 11/26/2021] [Indexed: 11/03/2022]
Abstract
The National Culture Collection of Pathogens (NCCP) is a microbial resource bank in Korea that collects pathogen resources causing infectious disease in human and distributes them for research and education. The NCCP bank attempts to discover strains with various characteristics and specific purposes to provide diverse resources to researchers. Staphylococcus aureus American Type Culture Collection (ATCC) 6538P is used as a reference strain in the microbial assay for antibiotics in the Korean and in the United States Pharmacopoeias. We aimed to analyze domestically isolated microbial resources from the NCCP to replace the S. aureus reference strain. Staphylococcus aureus strains were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and the VITEK-2 system and characterized by multilocus sequence typing, 16S rRNA sequencing, and antibiotic susceptibility testing. Several candidate strains had similar characteristics as the reference strain. Among them, the nucleotide sequence of the 16S rRNA region of NCCP 16830 was 100% identical to that of the reference strain; it was sensitive to six types of antibiotics and showed results most similar to the reference strain. A validity evaluation was conducted using the cylinder-plate method. NCCP 16830 presented valid results and had the same performance as ATCC 6538P; therefore, it was selected as an alternative candidate strain.
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Kim MH, Baek KO, Park GG, Jang JY, Lee JH. A Study on Concentration, Identification, and Reduction of Airborne Microorganisms in the Military Working Dog Clinic. Saf Health Work 2020; 11:517-525. [PMID: 33329919 PMCID: PMC7728695 DOI: 10.1016/j.shaw.2020.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/16/2020] [Accepted: 09/01/2020] [Indexed: 12/03/2022] Open
Abstract
Background The study was planned to show the status of indoor microorganisms and the status of the reduction device in the military dog clinic. Methods Airborne microbes were analyzed according to the number of daily patient canines. For identification of bacteria, sampled bacteria was identified using VITEK®2 and molecular method. The status of indoor microorganisms according to the operation of the ventilation system was analyzed. Results Airborne bacteria and fungi concentrations were 1000.6 ± 800.7 CFU/m3 and 324.7 ± 245.8 CFU/m3. In the analysis using automated identification system, based on fluorescence biochemical test, VITEK®2, mainly human pathogenic bacteria were identified. The three most frequently isolated genera were Kocuria (26.6%), Staphylococcus (24.48%), and Granulicatella (12.7%). The results analyzed by molecular method were detected in the order of Kocuria (22.6%), followed by Macrococcus (18.1%), Glutamicibacter (11.1%), and so on. When the ventilation system was operated appropriately, the airborne bacteria and fungi level were significantly decreased. Conclusion Airborne bacteria in the clinic tend to increase with the number of canines. Human pathogenic bacteria were mainly detected in VITEK®2, and relatively various bacteria were detected in molecular analysis. A decrease in the level of bacteria and fungi was observed with proper operation of the ventilation system.
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Affiliation(s)
- Min-Ho Kim
- Department of Work Environment Monitoring, Armed Forces Medical Research Institute, 90, Jaun-ro, Yuseong-gu, Daejeon, Republic of Korea.,Department of Environmental Engineering, Chungnam National University of Engineering, 99, Daehak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Ki-Ook Baek
- Department of Work Environment Monitoring, Armed Forces Medical Research Institute, 90, Jaun-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Gyeong-Gook Park
- Department of Research of Infectious Disease, Armed Forces Medical Research Institute, 90, Jaun-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Je-Youn Jang
- Department of Veterinary Medicine, Armed Forces Medical Research Institute, 90, Jaun-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jin-Hong Lee
- Department of Environmental Engineering, Chungnam National University of Engineering, 99, Daehak-ro, Yuseong-gu, Daejeon, Republic of Korea
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Vermassen A, Talon R, Andant C, Provot C, Desvaux M, Leroy S. Cell-Wall Hydrolases as Antimicrobials against Staphylococcus Species: Focus on Sle1. Microorganisms 2019; 7:microorganisms7110559. [PMID: 31726796 PMCID: PMC6921076 DOI: 10.3390/microorganisms7110559] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 12/29/2022] Open
Abstract
Some staphylococcal species are opportunistic pathogens of humans and/or animals with Staphylococcus epidermidis as one of the most important. It causes a broad spectrum of diseases in humans and animals. This species is able to form biofilms and has developed antibiotic resistance, which has motivated research on new antibacterial agents. Cell-wall hydrolases (CWHs) can constitute a potential alternative. Following a hijacking strategy, we inventoried the CWHs of S. epidermidis. The lytic potential of representative CWHs that could be turned against staphylococci was explored by turbidity assays which revealed that cell wall glycosidases were not efficient, while cell wall amidases and cell wall peptidases were able to lyse S. epidermidis. Sle1, which is encoded by chromosomal gene and composed of three anchoring LysM domains and a C-terminal CHAP (cysteine, histidine-dependent amidohydrolase/peptidase) domain, was one of the most active CWHs. The phylogeny of Sle1 revealed seven clusters mostly identified among staphylococci. Sle1 was able to lyse several staphylococcal species, including Staphylococcus aureus, both in planktonic and sessile forms, but not Micrococcus.
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Affiliation(s)
- Aurore Vermassen
- Université Clermont-Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France; (A.V.); (R.T.); (C.A.); (M.D.)
| | - Régine Talon
- Université Clermont-Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France; (A.V.); (R.T.); (C.A.); (M.D.)
| | - Carine Andant
- Université Clermont-Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France; (A.V.); (R.T.); (C.A.); (M.D.)
| | - Christian Provot
- BioFilm Control, Biopôle Clermont Limagne, F-63360 Saint-Beauzire, France;
| | - Mickaël Desvaux
- Université Clermont-Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France; (A.V.); (R.T.); (C.A.); (M.D.)
| | - Sabine Leroy
- Université Clermont-Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France; (A.V.); (R.T.); (C.A.); (M.D.)
- Correspondence:
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Gaio V, Lima CA, Oliveira F, França Â, Cerca N. Carvacrol is highly disruptive against coagulase-negative staphylococci in in vitro biofilms. Future Microbiol 2017; 12:1487-1496. [PMID: 29168651 DOI: 10.2217/fmb-2017-0122] [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] [Indexed: 11/21/2022] Open
Abstract
AIM To evaluate the antimicrobial activity of carvacrol against stationary-phase planktonic and biofilm cells of coagulase-negative staphylococci and comparison to traditional antistaphylococcal antibiotics. MATERIALS & METHODS The antimicrobial effect of carvacrol and antibiotics against planktonic and biofilm cells were assessed through quantification of the number of culturable and/or viable cells. Confocal laser scanning microscopy was used to evaluate the effect of carvacrol on the biofilm structure. RESULTS A concentration of 4 mM of carvacrol demonstrated a potent antimicrobial effect, vastly superior than ciprofloxacin, rifampicin, gentamicin and vancomycin, both in planktonic and biofilm cells. CONCLUSION Carvacrol is a potential antimicrobial agent, which applicability for the prevention and/or treatment of coagulase-negative staphylococci biofilm-associated infections is worthwhile investigating in more detail.
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Affiliation(s)
- Vânia Gaio
- CEB-LIBRO - Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Cláudia Afonso Lima
- CEB-LIBRO - Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Fernando Oliveira
- CEB-LIBRO - Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Ângela França
- CEB-LIBRO - Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Nuno Cerca
- CEB-LIBRO - Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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Rapid identification of staphylococci by Raman spectroscopy. Sci Rep 2017; 7:14846. [PMID: 29093473 PMCID: PMC5665888 DOI: 10.1038/s41598-017-13940-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 10/03/2017] [Indexed: 12/25/2022] Open
Abstract
Clinical treatment of the infections caused by various staphylococcal species differ depending on the actual cause of infection. Therefore, it is necessary to develop a fast and reliable method for identification of staphylococci. Raman spectroscopy is an optical method used in multiple scientific fields. Recent studies showed that the method has a potential for use in microbiological research, too. Our work here shows a possibility to identify staphylococci by Raman spectroscopy. We present a method that enables almost 100% successful identification of 16 of the clinically most important staphylococcal species directly from bacterial colonies grown on a Mueller-Hinton agar plate. We obtained characteristic Raman spectra of 277 staphylococcal strains belonging to 16 species from a 24-hour culture of each strain grown on the Mueller-Hinton agar plate using the Raman instrument. The results show that it is possible to distinguish among the tested species using Raman spectroscopy and therefore it has a great potential for use in routine clinical diagnostics.
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Pathogenic features of clinically significant coagulase-negative staphylococci in hospital and community infections in Benin. Int J Med Microbiol 2016; 307:75-82. [PMID: 27876296 DOI: 10.1016/j.ijmm.2016.11.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/14/2016] [Accepted: 11/08/2016] [Indexed: 11/21/2022] Open
Abstract
In West Africa, very little consideration has been given to coagulase negative Staphylococci (CNS). Herein, we describe the features contributing to the pathogenicity of 99 clinically-significant independent CNS isolates associated with infections encountered at the National Teaching Hospital Center of Cotonou (Benin). The pathogenic potentials of nosocomial strains were compared with community strains. S. haemolyticus (44%), S. epidermidis (22%) and S. hominis (7%) were the most frequently isolated while bacteremia (66.7%) and urinary tract infections (24.2%) were the most commonly encountered infections. Most strains were resistant to multiple antibiotics, including penicillin (92%), fosfomycin (81%), methicillin (74%) and trimethoprim-sulfamethoxazole (72%). The most frequently isolated species were also the most frequently resistant to methicillin: S. hominis (100%), S. haemolyticus (93%) and S. epidermidis (67%). Screening of toxic functions or toxin presence revealed hemolytic potential in 25% of strains in over 50% of human erythrocytes in 1h. Twenty-six percent of strains exhibited protease activity with low (5%), moderate (10%) and high activity (11%), while 25% of strains displayed esterase activity. Three percent of strain supernatants were able to lyse 100% of human polymorphonuclear cells after 30min. Polymerase chain reaction and latex agglutination methods revealed staphylococcal enterotoxin C gene expression in 9% of S. epidermidis. A majority of hospital-associated CNS strains (68%) had at least one important virulence feature, compared with only 32% for community-acquired strains. The present investigation confirms that these microorganisms can be virulent, at least in some individual cases, possibly through genetic transfer from S. aureus.
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Monteiro ACM, Fortaleza CMCB, Ferreira AM, Cavalcante RDS, Mondelli AL, Bagagli E, da Cunha MDLRDS. Comparison of methods for the identification of microorganisms isolated from blood cultures. Ann Clin Microbiol Antimicrob 2016; 15:45. [PMID: 27496125 PMCID: PMC4974807 DOI: 10.1186/s12941-016-0158-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/14/2016] [Indexed: 11/12/2022] Open
Abstract
Background Bloodstream infections are responsible for thousands of deaths each year. The rapid identification of the microorganisms causing these infections permits correct therapeutic management that will improve the prognosis of the patient. In an attempt to reduce the time spent on this step, microorganism identification devices have been developed, including the VITEK® 2 system, which is currently used in routine clinical microbiology laboratories. Methods This study evaluated the accuracy of the VITEK® 2 system in the identification of 400 microorganisms isolated from blood cultures and compared the results to those obtained with conventional phenotypic and genotypic methods. In parallel to the phenotypic identification methods, the DNA of these microorganisms was extracted directly from the blood culture bottles for genotypic identification by the polymerase chain reaction (PCR) and DNA sequencing. Results The automated VITEK® 2 system correctly identified 94.7 % (379/400) of the isolates. The YST and GN cards resulted in 100 % correct identifications of yeasts (15/15) and Gram-negative bacilli (165/165), respectively. The GP card correctly identified 92.6 % (199/215) of Gram-positive cocci, while the ANC card was unable to correctly identify any Gram-positive bacilli (0/5). Conclusions The performance of the VITEK® 2 system was considered acceptable and statistical analysis showed that the system is a suitable option for routine clinical microbiology laboratories to identify different microorganisms.
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Affiliation(s)
- Aydir Cecília Marinho Monteiro
- Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil
| | - Carlos Magno Castelo Branco Fortaleza
- Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil
| | - Adriano Martison Ferreira
- Laboratório de Análises Clínicas do Hospital das Clínicas de Botucatu, Faculdade de Medicina de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil
| | - Ricardo de Souza Cavalcante
- Comissão de Controle de Infecção Relacionada à Assistência à Saúde, Hospital das Clínicas, Faculdade de Medicina de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil
| | - Alessandro Lia Mondelli
- Departamento de Clínica Médica, Faculdade de Medicina de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil
| | - Eduardo Bagagli
- Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil
| | - Maria de Lourdes Ribeiro de Souza da Cunha
- Departamento de Microbiologia e Imunologia, Instituto de Biociências de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil. .,Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, UNESP-Univ. Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, CEP: 18618-970, Brazil.
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Detection of methicillin-resistant coagulase-negative staphylococci by the Vitek 2 system. J Clin Microbiol 2014; 52:3196-9. [PMID: 24951799 DOI: 10.1128/jcm.01162-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The accurate performance of the Vitek 2 GP67 card for detecting methicillin-resistant coagulase-negative staphylococci (CoNS) is not known. We prospectively determined the ability of the Vitek 2 GP67 card to accurately detect methicillin-resistant CoNS, with mecA PCR results used as the gold standard for a 4-month period in 2012. Included in the study were 240 consecutively collected nonduplicate CoNS isolates. Cefoxitin susceptibility by disk diffusion testing was determined for all isolates. We found that the three tested systems, Vitek 2 oxacillin and cefoxitin testing and cefoxitin disk susceptibility testing, lacked specificity and, in some cases, sensitivity for detecting methicillin resistance. The Vitek 2 oxacillin and cefoxitin tests had very major error rates of 4% and 8%, respectively, and major error rates of 38% and 26%, respectively. Disk cefoxitin testing gave the best performance, with very major and major error rates of 2% and 24%, respectively. The test performances were species dependent, with the greatest errors found for Staphylococcus saprophyticus. While the 2014 CLSI guidelines recommend reporting isolates that test resistant by the oxacillin MIC or cefoxitin disk test as oxacillin resistant, following such guidelines produces erroneous results, depending on the test method and bacterial species tested. Vitek 2 cefoxitin testing is not an adequate substitute for cefoxitin disk testing. For critical-source isolates, mecA PCR, rather than Vitek 2 or cefoxitin disk testing, is required for optimal antimicrobial therapy.
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De Bel A, Van Hoorde K, Wybo I, Vandoorslaer K, Echahidi F, De Brandt E, Schumann P, Ieven M, Soetens O, Piérard D, Vandamme P. Staphylococcus
jettensis sp. nov., a coagulase-negative staphylococcal species isolated from human clinical specimens. Int J Syst Evol Microbiol 2013; 63:3250-3256. [DOI: 10.1099/ijs.0.044438-0] [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
Eight coagulase-negative, novobiocin-susceptible staphylococcal strains were isolated from human clinical specimens at two different Belgian medical facilities. All strains were non-motile, Gram-stain-positive, catalase-positive cocci. DNA G+C content, peptidoglycan type, menaquinone pattern, the presence of teichoic acid and cellular fatty acid composition were in agreement with the characteristics of species of the genus
Staphylococcus
. Sequencing of the 16S rRNA gene and four housekeeping genes (dnaJ, tuf, gap and rpoB) demonstrated that these strains constitute a separate taxon within the genus
Staphylococcus
. Less than 41 % DNA–DNA hybridization with the most closely related species of the genus
Staphylococcus
(
Staphylococcus haemolyticus
,
Staphylococcus hominis
and
Staphlococcus lugdunensis
) was observed. Key biochemical characteristics that allowed these bacteria to be distinguished from their nearest phylogenetic neighbours are arginine dihydrolase positivity, ornithine decarboxylase negativity and inability to produce acid aerobically from d-mannose, α-lactose and turanose. Acid is produced aerobically from trehalose. Based on these results, a novel species of the genus
Staphylococcus
is described and named
Staphylococcus
jettensis sp. nov. The type strain is SEQ110T ( = LMG 26879T = CCUG 62657T = DSM 26618T).
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Affiliation(s)
- Annelies De Bel
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Koenraad Van Hoorde
- Faculty of Applied Bioscience Engineering, University College Ghent, Valentin Vaerwyckweg 1, 9000 Ghent, Belgium
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Ingrid Wybo
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Kristof Vandoorslaer
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Fedoua Echahidi
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Evie De Brandt
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Peter Schumann
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, 38124 Braunschweig, Germany
| | - Margareta Ieven
- Laboratory of Microbiology, Universitair Ziekenhuis Antwerpen, Wilrijkstraat 10, 2650 Edegem, Belgium
| | - Oriane Soetens
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Denis Piérard
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
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Comparison of the epidemiological behavior of mastitis pathogens by applying time-series analysis in results of milk samples submitted for microbiological examination. Vet Res Commun 2013; 37:259-67. [PMID: 23779256 DOI: 10.1007/s11259-013-9570-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2013] [Indexed: 10/26/2022]
Abstract
The objective of this study is to examine and compare the trends of mastitis pathogens in quarter milk samples (n = 240,232) submitted for microbiological examination at the Milk Analysis Laboratory (L.I.G.A.L.) at Galicia, Spain from June 2005 to September 2011. Autoregressive Integrated Moving Average (ARIMA) models and multivariate statistical techniques such as Cluster Analysis were used in order to detect seasonal trends and similarities between the series trends and to classify mastitis pathogens into relatively homogeneous groups. The decrease of bulk milk somatic cell counts achieved by the mastitis control program, developed in recent years in this region, is the result of the decrease in IMI caused by a limited number of mastitis pathogens. The obtained results reflect a greater complexity in the behavior of mastitis pathogens, unlike the traditional classification into contagious or environmental. Staphylococcus aureus showed a trend similar to Streptococcus dysgalactiae, a mastitis pathogen can behave in both a contagious and an environmental manner. Among the traditionally considered environmental mastitis pathogens, Strep. uberis showed a different behavior to Escherichia coli and Klebsiella pneumoniae. Coagulase-negative staphylococci (CNS) species and Streptococcus other than Strep. agalactiae showed differences in the trend model. Time-series analysis and multivariate statistical techniques, such as Cluster Analysis, could be powerful tools to assess the isolation trend of mastitis pathogens because of their ability to cope with stochastic dependence of consecutive data. Furthermore, they could be used to identify the epidemiological behavior of mastitis pathogens using the results of milk samples submitted for routine microbiological examination, by classifying them into relatively homogeneous groups.
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Kilic A, Basustaoglu AC. Double triplex real-time PCR assay for simultaneous detection of Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus hominis, and Staphylococcus haemolyticus and determination of their methicillin resistance directly from positive blood culture bottles. Res Microbiol 2011; 162:1060-6. [PMID: 21925597 DOI: 10.1016/j.resmic.2011.07.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 07/28/2011] [Indexed: 10/17/2022]
Abstract
We developed and validated here a double triplex real-time PCR assay to simultaneously detect and identify Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus hominis, Staphylococcus haemolyticus and their methicillin resistance in a single reaction directly from Gram-positive cocci-in-clusters (GPCs)-positive blood culture bottles. From August 15, 2009 through February 15, 2010, 238 GPC-positive samples were collected and identified by conventional methods as 11 methicillin-resistant S. aureus (MRSA), 28 methicillin-susceptible S. aureus (MSSA), 176 MR coagulase-negative staphylococci (MRCoNS), 21 MSCoNS and two Enterococcus faecalis. The double triplex real-time PCR assay was targeted and detected tuf, nuc and mecA genes in the first tube and atlE, gap and mvaA genes in the second tube which could be run simultaneously. The detection limit of the assay was found at 10(3) CFU/ml for the atleE gene, 10(4) CFU/ml for the mva gene and 10(5) CFU/ml for gap, nuc, mecA and tuf genes based on seeding experiments. All Staphylococcus species except two S. epidermidis were correctly identified by the assay. The double triplex real-time PCR assay quickly and accurately detects S. aureus, S. epidermidis, S. hominis and S. haemolyticus and their methicillin resistance in a single reaction directly from positive blood culture bottles within 83 min.
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Affiliation(s)
- Abdullah Kilic
- Department of Microbiology and Clinical Microbiology, Gulhane Military Medical Academy and School of Medicine, 06018 Ankara, Turkey.
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Phoenix 100 versus Vitek 2 in the identification of gram-positive and gram-negative bacteria: a comprehensive meta-analysis. J Clin Microbiol 2011; 49:3284-91. [PMID: 21752980 DOI: 10.1128/jcm.00182-11] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Phoenix 100 and Vitek 2 (operating with the current colorimetric cards) are commonly used in hospital laboratories for rapid identification of microorganisms. The present meta-analysis aims to evaluate and compare their performance on Gram-positive and Gram-negative bacteria. The MEDLINE database was searched up to October 2010 for the retrieval of relevant articles. Pooled correct identification rates were derived from random-effects models, using the arcsine transformation. Separate analyses were conducted at the genus and species levels; subanalyses and meta-regression were undertaken to reveal meaningful system- and study-related modifiers. A total of 29 (6,635 isolates) and 19 (4,363 isolates) articles were eligible for Phoenix and colorimetric Vitek 2, respectively. No significant differences were observed between Phoenix and Vitek 2 either at the genus (97.70% versus 97.59%, P = 0.919) or the species (92.51% versus 88.77%, P = 0.149) level. Studies conducted with conventional comparator methods tended to report significantly better results compared to those using molecular reference techniques. Speciation of Staphylococcus aureus was significantly more accurate in comparison to coagulase-negative staphylococci by both Phoenix (99.78% versus 88.42%, P < 0.00001) and Vitek 2 (98.22% versus 91.89%, P = 0.043). Vitek 2 also reached higher correct identification rates for Gram-negative fermenters versus nonfermenters at the genus (99.60% versus 95.90%, P = 0.004) and the species (97.42% versus 84.85%, P = 0.003) level. In conclusion, the accuracy of both systems seems modified by underlying sample- and comparator method-related parameters. Future simultaneous assessment of the instruments against molecular comparator procedures may facilitate interpretation of the current observations.
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Chatzigeorgiou KS, Siafakas N, Petinaki E, Argyropoulou A, Tarpatzi A, Bobola M, Paniara O, Velegraki A, Zerva L. Identification of staphylococci by Phoenix: validation of a new protocol and comparison with Vitek 2. Diagn Microbiol Infect Dis 2011; 68:375-81. [PMID: 21094424 DOI: 10.1016/j.diagmicrobio.2010.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 08/09/2010] [Accepted: 08/13/2010] [Indexed: 11/19/2022]
Abstract
Because of their frequent isolation in the routine laboratory and their increasing clinical significance, fast and accurate species identification of staphylococci may be required; this can only be achieved by automated systems. A total of 147 clinical isolates (52 Staphylococcus aureus, 50 Staphylococcus epidermidis, and 45 other coagulase-negative staphylococci [CoNS]) were first identified by molecular methodology and then comparatively tested by Vitek 2 (new colorimetric identification card) and Phoenix using the novel 0.25 McFarland and the standard 0.50 McFarland inoculum protocols. All S. aureus isolates were accurately identified. Vitek 2 identified correctly all S. epidermidis and 93.3% of the other CoNS, whereas the respective rates were 86% and 82.2% for Phoenix's standard and 92% and 82.2% for the novel protocol. It appears that both systems provide excellent identification of S. aureus, but Vitek 2 recognizes CoNS species more accurately than Phoenix. The 0.25 McFarland protocol does not improve system performance.
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Quan F, Liu G, Wang L, Wang X. Investigation of pulmonary infection pathogens in neurological intensive care unit. Ther Clin Risk Manag 2011; 7:21-5. [PMID: 21339939 PMCID: PMC3039010 DOI: 10.2147/tcrm.s15730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Indexed: 12/21/2022] Open
Abstract
Purpose: The purpose of this study is to investigate the distribution and antimicrobial susceptibility of pathogenic bacteria in inpatients with pulmonary infection in the neurological intensive care unit (NICU). Methods: A total of 947 sputum specimens of 428 inpatients from May 2007 to May 2008 in the NICU were enrolled in the study, and bacterial identification and antibiotic susceptibility tests were analyzed using a VITEK 2 system. Results: A total of 400 positive bacterial strains were separated from 947 sputum specimens, with Gram-negative bacteria accounting for 69.0% of the total strains collected. The most common strain of Gram-negative bacteria was Klebsiella pneumoniae (20.5%). Gram-positive bacteria accounted for 10.0% of the total strains, with the most common strain being Staphylococcus aureus (2.5%). Fungal species accounted for 21.0% of the total strains, and the most common strain collected was Candida albicans (12.25%). Imipenem was the most effective antibiotic against Gram-positive and Gram-negative bacteria. The drug resistance rate of Gram-positive bacteria to penicillin G was 100%, and the Gram-positive bacteria were 100% sensitive to teicoplanin, vancomycin, and linezolid. Conclusions: Gram-negative bacterial infections account for the majority of pulmonary infections in the NICU, with fungal infections being the second most common infection type observed. In addition, fungal infections seem to be related to mortality in the NICU.
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Affiliation(s)
- Fengying Quan
- Department of Neurology, The First Affiliated Hospital of Chongqing, Medical University, Chongqing, China
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Hung KH, Yan JJ, Lu YC, Chen HM, Wu JJ. Evaluation of discrepancies between oxacillin and cefoxitin susceptibility in coagulase-negative staphylococci. Eur J Clin Microbiol Infect Dis 2011; 30:785-8. [DOI: 10.1007/s10096-011-1156-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 12/22/2010] [Accepted: 12/25/2010] [Indexed: 10/18/2022]
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Species identification of staphylococci by amplification and sequencing of the tuf gene compared to the gap gene and by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Eur J Clin Microbiol Infect Dis 2010; 30:343-54. [PMID: 20967479 DOI: 10.1007/s10096-010-1091-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Accepted: 10/01/2010] [Indexed: 10/18/2022]
Abstract
Staphylococcal species, notably, coagulase-negative staphylococci (CoNS), are frequently misidentified using phenotypic methods. The partial nucleotide sequences of the tuf and gap genes were determined in 47 reference strains to assess their suitability, practicability, and discriminatory power as target molecules for staphylococcal identification. The partial tuf gene sequence was selected and further assessed with a collection of 186 strains, including 35 species and subspecies. Then, to evaluate the efficacy of this genotyping method versus the technology of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS), the 186 strains were identified using MALDI-TOF-MS (Axima® Shimadzu) coupled to the SARAMIS® database (AnagnosTec). The French National Reference Center for Staphylococci identification method was used as a reference. One hundred and eighty-four strains (98.9%) were correctly identified by tuf gene sequencing. Only one strain was misidentified and one was unidentified. MALDI-TOF-MS identified correctly 138 isolates (74.2%). Four strains were misidentified, 39 were unidentified, five were identified at the group (hominis/warneri) level, and one strain was identified at the genus level. These results confirm the value of MALDI-TOF-MS identification for common species in clinical laboratory practice and the value of the partial tuf gene sequence for the identification of all staphylococcal species as required in a reference laboratory.
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Spohr M, Rau J, Friedrich A, Klittich G, Fetsch A, Guerra B, Hammerl JA, Tenhagen BA. Methicillin-resistant Staphylococcus aureus (MRSA) in three dairy herds in southwest Germany. Zoonoses Public Health 2010; 58:252-61. [PMID: 20630047 DOI: 10.1111/j.1863-2378.2010.01344.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The objective of this study was to analyse the occurrence of methicillin-resistant Staphylococcus aureus (MRSA) in three dairy herds in the southwest of Germany that had experienced individual cases of clinical and subclinical mastitis associated with MRSA. The herds were identified by the detection of MRSA during routine resistance testing of mastitis pathogens. All quarters of all cows in the herds that were positive on California Mastitis Test were sampled for bacteriological analysis on two occasions. Bulk tank milk samples were also tested. Furthermore, nasal swabs were collected from people working on the farms and from cattle. Environmental samples were collected from associated pig holdings. Isolates were characterized using spa-typing and testing for antimicrobial resistance. Our results revealed a substantial spread of MRSA in the three dairy herds. In the first of the two investigations carried out on all cows in the three herds, milk samples of 5.1-16.7% of dairy cows were found positive for MRSA. The respective proportions in the second herd level investigation were 1.4-10.0%. Quarters harbouring MRSA had higher somatic cell counts than quarters that were negative on culture. Methicillin-resistant Staphylococcus aureus were also detected in nasal swabs of staff (7/9), cows (7/15) and calves (4/7), bulk tank milk samples (3/3) and environmental samples from pig premises (4/5) on the farm. Herds B and C had no contact to herd A. However, in all three herds MRSA of spa-type t011 were detected in milk samples. Results show that MRSA of spa-type t011 is a problem in dairy farms that needs urgent attention.
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Affiliation(s)
- M Spohr
- Tierseuchenkasse Baden-Württemberg, Eutergesundheitsdienst, Fellbach, Germany
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Dubois D, Leyssene D, Chacornac JP, Kostrzewa M, Schmit PO, Talon R, Bonnet R, Delmas J. Identification of a variety of Staphylococcus species by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2010; 48:941-5. [PMID: 20032251 PMCID: PMC2832446 DOI: 10.1128/jcm.00413-09] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Revised: 08/05/2009] [Accepted: 12/11/2009] [Indexed: 11/20/2022] Open
Abstract
Whole-cell fingerprinting by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) in combination with a dedicated bioinformatic software tool (MALDI Biotyper 2.0) was used to identify 152 staphylococcal strains corresponding to 22 staphylococcal species. Spectra of the 152 isolates, previously identified at the species level using a sodA gene-based oligonucleotide array, were analyzed against the main spectra of 3,030 microorganisms. A total of 151 strains out of 152 (99.3%) were correctly identified at the species level; only one strain was identified at the genus level. The MALDI-TOF MS method revealed different clonal lineages of Staphylococcus epidermidis that were of either human or environmental origin, which suggests that the MALDI-TOF MS method could be useful in the profiling of staphylococcal strains. The topology of the dendrogram generated by the MALDI Biotyper 2.0 software from the spectra of 120 Staphylococcus reference strains (representing 36 species) was in general agreement with that inferred from the 16S rRNA gene-based analysis. Our findings indicate that the MALDI-TOF MS technology, associated with a broad-spectrum reference database, is an effective tool for the swift and reliable identification of Staphylococci.
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Affiliation(s)
- Damien Dubois
- CHU Clermont-Ferrand, Centre de Biologie, Laboratoire de Bactériologie Clinique, Clermont-Ferrand F-63003, France, Université d'Auvergne Clermont-1, Faculté de Médecine, Laboratoire de Bactériologie, JE2526, USC-INRA 2018, Clermont-Ferrand F-63001, France, INRA, Centre de Clermont-Ferrand-Theix, UR 454, Microbiologie, 63122 Saint-Genes Champanelle, France, Bruker Daltonik GmbH, Leipzig, Germany, Bruker Daltonique, Wissembourg, France
| | - David Leyssene
- CHU Clermont-Ferrand, Centre de Biologie, Laboratoire de Bactériologie Clinique, Clermont-Ferrand F-63003, France, Université d'Auvergne Clermont-1, Faculté de Médecine, Laboratoire de Bactériologie, JE2526, USC-INRA 2018, Clermont-Ferrand F-63001, France, INRA, Centre de Clermont-Ferrand-Theix, UR 454, Microbiologie, 63122 Saint-Genes Champanelle, France, Bruker Daltonik GmbH, Leipzig, Germany, Bruker Daltonique, Wissembourg, France
| | - Jean Paul Chacornac
- CHU Clermont-Ferrand, Centre de Biologie, Laboratoire de Bactériologie Clinique, Clermont-Ferrand F-63003, France, Université d'Auvergne Clermont-1, Faculté de Médecine, Laboratoire de Bactériologie, JE2526, USC-INRA 2018, Clermont-Ferrand F-63001, France, INRA, Centre de Clermont-Ferrand-Theix, UR 454, Microbiologie, 63122 Saint-Genes Champanelle, France, Bruker Daltonik GmbH, Leipzig, Germany, Bruker Daltonique, Wissembourg, France
| | - Markus Kostrzewa
- CHU Clermont-Ferrand, Centre de Biologie, Laboratoire de Bactériologie Clinique, Clermont-Ferrand F-63003, France, Université d'Auvergne Clermont-1, Faculté de Médecine, Laboratoire de Bactériologie, JE2526, USC-INRA 2018, Clermont-Ferrand F-63001, France, INRA, Centre de Clermont-Ferrand-Theix, UR 454, Microbiologie, 63122 Saint-Genes Champanelle, France, Bruker Daltonik GmbH, Leipzig, Germany, Bruker Daltonique, Wissembourg, France
| | - Pierre Olivier Schmit
- CHU Clermont-Ferrand, Centre de Biologie, Laboratoire de Bactériologie Clinique, Clermont-Ferrand F-63003, France, Université d'Auvergne Clermont-1, Faculté de Médecine, Laboratoire de Bactériologie, JE2526, USC-INRA 2018, Clermont-Ferrand F-63001, France, INRA, Centre de Clermont-Ferrand-Theix, UR 454, Microbiologie, 63122 Saint-Genes Champanelle, France, Bruker Daltonik GmbH, Leipzig, Germany, Bruker Daltonique, Wissembourg, France
| | - Régine Talon
- CHU Clermont-Ferrand, Centre de Biologie, Laboratoire de Bactériologie Clinique, Clermont-Ferrand F-63003, France, Université d'Auvergne Clermont-1, Faculté de Médecine, Laboratoire de Bactériologie, JE2526, USC-INRA 2018, Clermont-Ferrand F-63001, France, INRA, Centre de Clermont-Ferrand-Theix, UR 454, Microbiologie, 63122 Saint-Genes Champanelle, France, Bruker Daltonik GmbH, Leipzig, Germany, Bruker Daltonique, Wissembourg, France
| | - Richard Bonnet
- CHU Clermont-Ferrand, Centre de Biologie, Laboratoire de Bactériologie Clinique, Clermont-Ferrand F-63003, France, Université d'Auvergne Clermont-1, Faculté de Médecine, Laboratoire de Bactériologie, JE2526, USC-INRA 2018, Clermont-Ferrand F-63001, France, INRA, Centre de Clermont-Ferrand-Theix, UR 454, Microbiologie, 63122 Saint-Genes Champanelle, France, Bruker Daltonik GmbH, Leipzig, Germany, Bruker Daltonique, Wissembourg, France
| | - Julien Delmas
- CHU Clermont-Ferrand, Centre de Biologie, Laboratoire de Bactériologie Clinique, Clermont-Ferrand F-63003, France, Université d'Auvergne Clermont-1, Faculté de Médecine, Laboratoire de Bactériologie, JE2526, USC-INRA 2018, Clermont-Ferrand F-63001, France, INRA, Centre de Clermont-Ferrand-Theix, UR 454, Microbiologie, 63122 Saint-Genes Champanelle, France, Bruker Daltonik GmbH, Leipzig, Germany, Bruker Daltonique, Wissembourg, France
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Diversity of Staphylococcus species strains based on partial kat (catalase) gene sequences and design of a PCR-restriction fragment length polymorphism assay for identification and differentiation of coagulase-positive species (S. aureus, S. delphini, S. hyicus, S. intermedius, S. pseudintermedius, and S. schleiferi subsp. coagulans). J Clin Microbiol 2009; 48:192-201. [PMID: 19889901 DOI: 10.1128/jcm.00542-09] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
A set of degenerate PCR primers was designed and used to amplify and sequence about 75% of the catalase (kat) gene from each of 49 staphylococcal strains. In some strains of Staphylococcus xylosus, S. saprophyticus, and S. equorum, two catalase genes, katA and katB, were found. A phylogenetic tree was generated and showed diversities among 66 partial (about 900-bp) staphylococcal kat nucleotide sequences (including 17 sequences found in GenBank) representing 26 different species. The topology of this tree showed a distribution of staphylococcal species similar, but not identical, to those reported previously based on 16S rRNA, hsp60, sodA, rpoB, tuf, and gap genes. The kat gene sequences were less conserved than those of 16S rRNA, rpoB, hsp60, and tuf genes and slightly more conserved than those of the gap gene. Therefore, kat gene sequence analysis may provide an additional marker for inferring phylogenetic relationships of staphylococci. Moreover, the discrete nucleotide polymorphism revealed in this gene could be exploited for rapid, low-cost identification of staphylococcal species through PCR-restriction fragment length polymorphism (RFLP) analysis. In this study, a PCR-RFLP assay performed by using only the TaqI restriction enzyme was successfully developed for rapid unequivocal identification/differentiation, at species and subspecies levels, of coagulase-positive staphylococci (CPS). The assay was validated by testing the DNA from 100 staphylococcal strains, including reference and wild CPS strains isolated from different environments. This reliable, rapid, and low-cost approach (requiring about 6 h from DNA isolation to the achievement of results and <5 Euros for each strain tested) allowed unambiguous identification of all the strains assayed, including the newly described S. delphini and S. pseudintermedius CPS species.
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Dupont C, Sivadon-Tardy V, Bille E, Dauphin B, Beretti JL, Alvarez AS, Degand N, Ferroni A, Rottman M, Herrmann JL, Nassif X, Ronco E, Carbonnelle E. Identification of clinical coagulase-negative staphylococci, isolated in microbiology laboratories, by matrix-assisted laser desorption/ionization-time of flight mass spectrometry and two automated systems. Clin Microbiol Infect 2009; 16:998-1004. [PMID: 19732092 DOI: 10.1111/j.1469-0691.2009.03036.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A study was performed to compare matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS), linked to a recently engineered microbial identification database, and two rapid identification (ID) automated systems, BD Phoenix (Becton Dickinson Diagnostic Systems, France) and VITEK-2 (bioMérieux, Marcy L'Etoile, France), for the ID of coagulase-negative staphylococci (CoNS). Two hundred and thirty-four clinical isolates of CoNS representing 20 species were analyzed. All CoNS isolates were characterized by sodA gene sequencing, allowing interpretation of the ID results obtained using the respective database of each apparatus. Overall correct ID results were obtained in 93.2%, 75.6% and 75.2% of the cases with the MALDI-TOF-MS, Phoenix and VITEK-2 systems, respectively. Mis-ID and absence of results occurred in 1.7% and 5.1% of the cases with MALDI-TOF-MS, in 23.1% and 1.3% with the Phoenix, and in 13.7% and 0.9% with the VITEK-2 systems, respectively. In addition, with the latter automate, 10.3% of the IDs were proposed with remote possibility. When excluding the CoNS species not included in the databases of at least one of the three systems, the final percentage of correct results, Mis-ID and absence of ID were 97.4%, 1.3% and 1.3% with MALDI-TOF-MS, 79%, 21% and 0% with the Phoenix, and 78.6%, 10.3% and 0.9% with the VITEK-2 system, respectively. The present study demonstrates the robustness and high sensitivity of our microbial identification database used with MALDI-TOF-MS technology. This approach represents a powerful tool for the fast ID of clinical CoNS isolates.
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Affiliation(s)
- C Dupont
- Hopital Raymond Poincaré, Garches, France
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Orenga S, James AL, Manafi M, Perry JD, Pincus DH. Enzymatic substrates in microbiology. J Microbiol Methods 2009; 79:139-55. [PMID: 19679151 DOI: 10.1016/j.mimet.2009.08.001] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 07/24/2009] [Accepted: 08/03/2009] [Indexed: 11/15/2022]
Abstract
Enzymatic substrates are powerful tools in biochemistry. They are widely used in microbiology to study metabolic pathways, to monitor metabolism and to detect, enumerate and identify microorganisms. Synthetic enzymatic substrates have been customized for various microbial assays, to detect an expanding range of both new enzymatic activities and target microorganisms. Recent developments in synthetic enzymatic substrates with new spectral, chemical and biochemical properties allow improved detection, enumeration and identification of food-borne microorganisms, clinical pathogens and multi-resistant bacteria in various sample types. In the past 20 years, the range of synthetic enzymatic substrates used in microbiology has been markedly extended supporting the development of new multi-test systems (e.g., Microscan, Vitek 2, Phoenix) and chromogenic culture media. The use of such substrates enables an improvement in time to detection and specificity over conventional tests that employ natural substrates. In the era of intense developments in molecular biology, phenotypic tests involving enzymatic substrates remain useful to analyse both simple and complex samples. Such tests are applicable to diagnostic and research laboratories all over the world.
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Affiliation(s)
- Sylvain Orenga
- Research & Development Microbiology, bioMérieux, 3 route de Port Michaud, La Balme-les-Grottes, France.
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Kim M, Heo SR, Choi SH, Kwon H, Park JS, Seong MW, Lee DH, Park KU, Song J, Kim EC. Comparison of the MicroScan, VITEK 2, and Crystal GP with 16S rRNA sequencing and MicroSeq 500 v2.0 analysis for coagulase-negative Staphylococci. BMC Microbiol 2008; 8:233. [PMID: 19105808 PMCID: PMC2633347 DOI: 10.1186/1471-2180-8-233] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Accepted: 12/23/2008] [Indexed: 11/10/2022] Open
Abstract
Background Three phenotypic identification systems (MicroScan, VITEK 2, and Crystal GP) were evaluated for their accuracy to identify coagulase-negative staphylococci (CNS). A total of 120 clinical isolates confirmed to be CNS via 16S rRNA sequencing and analysis with the MicroSeq 500 v2.0 database were assessed. Results The MicroScan, VITEK 2, and Crystal GP systems correctly identified 82.5%, 87.5%, and 67.5% of the isolates, respectively. Misidentification was the main problem in MicroScan (10.8%) and Crystal GP (23.3%) systems, whereas the main problem of VITEK 2 was low-level discrimination (7.5%). Conclusion None of the 3 phenotypic systems tested could accurately and reliably identify CNS at the species level. Further verifications such as biochemical testing or 16S rRNA sequencing together with analysis using a comparable database might be helpful in this regard.
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Affiliation(s)
- Miyoung Kim
- Department of Laboratory Medicine, Seoul National University Hospital, 101 Daehang-no, Jongno-gu, Seoul, South Korea.
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Identification of coagulase-negative Staphylococci by using the BD phoenix system in the low-inoculum mode. J Clin Microbiol 2008; 46:3826-8. [PMID: 18784315 DOI: 10.1128/jcm.00877-08] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The new "low-inoculum" mode of the Phoenix system was evaluated to identify clinical coagulase-negative staphylococci. API ID32 Staph panels were used as comparators, and discrepancies were resolved by 16S rRNA and tuf gene analysis. The system correctly identified 90.5% of isolates, with a mean time of 10.2 h. Accuracy was satisfactory for Staphylococcus epidermidis, S. saprophyticus, and S. haemolyticus.
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