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Kos A, Papić B, Golob M, Avberšek J, Kušar D, Ledina T, Đorđević J, Bulajić S. Genomic Insights into Methicillin-Resistant Staphylococci and Mammaliicocci from Bulk Tank Milk of Dairy Farms in Serbia. Antibiotics (Basel) 2023; 12:1529. [PMID: 37887230 PMCID: PMC10604148 DOI: 10.3390/antibiotics12101529] [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: 09/15/2023] [Revised: 09/29/2023] [Accepted: 10/07/2023] [Indexed: 10/28/2023] Open
Abstract
The potential risk to human and animal health provides a rationale for research on methicillin-resistant staphylococci (MRS) and mammaliicocci (MRM) in dairy herds. Here, we aimed to estimate their occurrence in the bulk tank milk (BTM) samples collected in 2019-2021 from 283 bovine dairy farms in the Belgrade district. We used whole-genome sequencing to characterize the obtained isolates and assess their genetic relatedness. A total of 70 MRS/MRM were recovered, most frequently Staphylococcus haemolyticus and Mammaliicoccus sciuri. Five clusters of 2-4 genetically related isolates were identified and epidemiological data indicated transmission through, e.g., farm visits by personnel or milk collection trucks. Most MRSA isolates belonged to the typical livestock-associated lineage ST398-t034. One MRSA isolate (ST152-t355) harbored the PVL-encoding genes. Since MRS/MRM isolates obtained in this study frequently harbored genes conferring multidrug resistance (MDR), this argues for their role as reservoirs for the spread of antimicrobial resistance genes. The pipeline milking system and total bacterial count >100,000 CFU/mL were significantly associated with higher occurrences of MRS/MRM. Our study confirms that BTM can be a zoonotic source of MRS, including MDR strains. This highlights the urgent need for good agricultural practices and the continuous monitoring of MRS/MRM in dairy farms.
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Affiliation(s)
- Andrea Kos
- Directorate for National Reference Laboratories, Ministry of Agriculture, Forestry and Water Management, Batajnički drum 7, 11186 Belgrade, Serbia;
| | - Bojan Papić
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia; (B.P.); (M.G.); (J.A.); (D.K.)
| | - Majda Golob
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia; (B.P.); (M.G.); (J.A.); (D.K.)
| | - Jana Avberšek
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia; (B.P.); (M.G.); (J.A.); (D.K.)
| | - Darja Kušar
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia; (B.P.); (M.G.); (J.A.); (D.K.)
| | - Tijana Ledina
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, University of Belgrade, Bulevar Oslobođenja 18, 11000 Belgrade, Serbia; (T.L.); (J.Đ.)
| | - Jasna Đorđević
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, University of Belgrade, Bulevar Oslobođenja 18, 11000 Belgrade, Serbia; (T.L.); (J.Đ.)
| | - Snežana Bulajić
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, University of Belgrade, Bulevar Oslobođenja 18, 11000 Belgrade, Serbia; (T.L.); (J.Đ.)
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Elbehiry A, Marzouk E, Moussa I, Anagreyyah S, AlGhamdi A, Alqarni A, Aljohani A, Hemeg HA, Almuzaini AM, Alzaben F, Abalkhail A, Alsubki RA, Najdi A, Algohani N, Abead B, Gazzaz B, Abu-Okail A. Using Protein Fingerprinting for Identifying and Discriminating Methicillin Resistant Staphylococcus aureus Isolates from Inpatient and Outpatient Clinics. Diagnostics (Basel) 2023; 13:2825. [PMID: 37685363 PMCID: PMC10486511 DOI: 10.3390/diagnostics13172825] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
In hospitals and other clinical settings, Methicillin-resistant Staphylococcus aureus (MRSA) is a particularly dangerous pathogen that can cause serious or even fatal infections. Thus, the detection and differentiation of MRSA has become an urgent matter in order to provide appropriate treatment and timely intervention in infection control. To ensure this, laboratories must have access to the most up-to-date testing methods and technology available. This study was conducted to determine whether protein fingerprinting technology could be used to identify and distinguish MRSA recovered from both inpatients and outpatients. A total of 326 S. aureus isolates were obtained from 2800 in- and outpatient samples collected from King Faisal Specialist Hospital and Research Centre in Riyadh, Saudi Arabia, from October 2018 to March 2021. For the phenotypic identification of 326 probable S. aureus cultures, microscopic analysis, Gram staining, a tube coagulase test, a Staph ID 32 API system, and a Vitek 2 Compact system were used. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), referred to as protein fingerprinting, was performed on each bacterial isolate to determine its proteomic composition. As part of the analysis, Principal Component Analysis (PCA) and a single-peak analysis of MALDI-TOF MS software were also used to distinguish between Methicillin-sensitive Staphylococcus aureus (MSSA) and MRSA. According to the results, S. aureus isolates constituted 326 out of 2800 (11.64%) based on the culture technique. The Staph ID 32 API system and Vitek 2 Compact System were able to correctly identify 262 (80.7%) and 281 (86.2%) S. aureus strains, respectively. Based on the Oxacillin Disc Diffusion Method, 197 (62.23%) of 326 isolates of S. aureus exhibited a cefoxitin inhibition zone of less than 21 mm and an oxacillin inhibition zone of less than 10 mm, and were classified as MRSA under Clinical Laboratory Standards Institute guidelines. MALDI-TOF MS was able to correctly identify 100% of all S. aureus isolates with a score value equal to or greater than 2.00. In addition, a close relationship was found between S. aureus isolates and higher peak intensities in the mass ranges of 3990 Da, 4120 Da, and 5850 Da, which were found in MRSA isolates but absent in MSSA isolates. Therefore, protein fingerprinting has the potential to be used in clinical settings to rapidly detect and differentiate MRSA isolates, allowing for more targeted treatments and improved patient outcomes.
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Affiliation(s)
- Ayman Elbehiry
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32511, Egypt
| | - Eman Marzouk
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Ihab Moussa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Sulaiman Anagreyyah
- Family Medicine Department, King Fahad Armed Forces Hospital, Jeddah 23311, Saudi Arabia
| | - Abdulaziz AlGhamdi
- Medical Director Office, North Area Armed Forces Hospital, King Khalid Military City 39747, Saudi Arabia
| | - Ali Alqarni
- Respiratory Therapy Department, Armed Forces Hospital Dhahran, Dhahran 34641, Saudi Arabia
| | - Ahmed Aljohani
- Patient Affairs Department, Sharourah Armed Forces Hospital, Sharourah 68372, Saudi Arabia
| | - Hassan A. Hemeg
- Department of Medical Technology/Microbiology, College of Applied Medical Science, Taibah University, Madina 30001, Saudi Arabia
| | - Abdulaziz M. Almuzaini
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52571, Saudi Arabia
| | - Feras Alzaben
- Department of Food Service, King Fahad Armed Forces Hospital, Jeddah 23311, Saudi Arabia
| | - Adil Abalkhail
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Roua A. Alsubki
- Department of Clinical Laboratory Science, College of Applied Medical Science, King Saud University, Riyadh 11433, Saudi Arabia
| | - Ali Najdi
- Northern Area Armed Forces Hospital, King Khalid Military City 39748, Saudi Arabia
| | - Nawaf Algohani
- Consultant Forensic Medicine, Forensic Medicine Center, Madina 42319, Saudi Arabia
| | - Banan Abead
- Support Service Department, King Fahad Armed Forces Hospital, Jeddah 23311, Saudi Arabia;
| | - Bassam Gazzaz
- Patient Affairs Department, King Fahad Armed Forces Hospital, Jeddah 23311, Saudi Arabia
| | - Akram Abu-Okail
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52571, Saudi Arabia
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Jenkins CL, Bean HD. Current Limitations of Staph Infection Diagnostics, and the Role for VOCs in Achieving Culture-Independent Detection. Pathogens 2023; 12:pathogens12020181. [PMID: 36839453 PMCID: PMC9963134 DOI: 10.3390/pathogens12020181] [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: 08/01/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Staphylococci are broadly adaptable and their ability to grow in unique environments has been widely established, but the most common and clinically relevant staphylococcal niche is the skin and mucous membranes of mammals and birds. S. aureus causes severe infections in mammalian tissues and organs, with high morbidities, mortalities, and treatment costs. S. epidermidis is an important human commensal but is also capable of deadly infections. Gold-standard diagnostic methods for staph infections currently rely upon retrieval and characterization of the infectious agent through various culture-based methods. Yet, obtaining a viable bacterial sample for in vitro identification of infection etiology remains a significant barrier in clinical diagnostics. The development of volatile organic compound (VOC) profiles for the detection and identification of pathogens is an area of intensive research, with significant efforts toward establishing breath tests for infections. This review describes the limitations of existing infection diagnostics, reviews the principles and advantages of VOC-based diagnostics, summarizes the analytical tools for VOC discovery and clinical detection, and highlights examples of how VOC biomarkers have been applied to diagnosing human and animal staph infections.
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Affiliation(s)
- Carrie L. Jenkins
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA
| | - Heather D. Bean
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Tempe, AZ 85287, USA
- Correspondence:
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Chiquet C, Bron AM, Lundström M, Maurin M. Acute postoperative endophthalmitis: Microbiology from the laboratory to the bedside. Surv Ophthalmol 2022; 67:1698-1710. [PMID: 35843367 DOI: 10.1016/j.survophthal.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 11/26/2022]
Abstract
Postoperative endophthalmitis is a dreaded complication of intraocular surgery. Acute presentations need prompt management and good knowledge of differential diagnoses. In the last 10 years, progress in direct microbial detection and identification from intraocular samples included the use of blood culture systems and, more recently, matrix-assisted laser desorption ionization time-of-flight mass spectrometry, improving the rate of bacterial identification. Whatever the method used, diagnostic sensitivity is better for vitreous samples than for aqueous humor samples. Besides, molecular biology techniques have further improved the identification rate of infectious agents in intraocular samples. They also provide faster results compared to culture-based techniques. Quantitative real-time PCR (qPCR) can also determine the bacterial load in intraocular samples. Several studies have shown that intraocular bacterial loads in endophthalmitis patients are usually high, which helps differentiating infection from contamination. The prognostic value of qPCR remains to be validated. Whole genome DNA sequencing technologies facilitate direct and sequencing of single DNA molecules. They have the potential to increase the rate of microbiological identification. Some antibiotic resistance markers (e.g., methicillin resistance in staphylococci and vancomycin resistance in enterococci) may be detected earlier using molecular techniques (usually real-time PCR tests). Early determination of the involved microorganism and their antibiotic resistances can help establishing an earlier therapeutic strategy.
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Affiliation(s)
- Christophe Chiquet
- Department of Ophthalmology, University Hospital of Grenoble, France; Grenoble Alpes University, Grenoble, France; HP2 Laboratory, INSERM U1042, University Grenoble Alpes, Grenoble, France.
| | - Alain M Bron
- Department of Ophthalmology, University Hospital, Dijon, France; Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRAE, Université Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Mats Lundström
- Department of Clinical Sciences, Ophthalmology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Max Maurin
- Laboratoire de Bactériologie, Institut de Biologie et Pathologie, CHU, Grenoble, Alpes; University Grenoble Alpes, CNRS, Grenoble, INP; CHU Grenoble Alpes, TIMC-IMAG, 38000, Grenoble, France
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Iversen S, Johannesen TB, Ingham AC, Edslev SM, Tevell S, Månsson E, Nilsdotter-Augustinsson Å, Söderquist B, Stegger M, Andersen PS. Alteration of Bacterial Communities in Anterior Nares and Skin Sites of Patients Undergoing Arthroplasty Surgery: Analysis by 16S rRNA and Staphylococcal-Specific tuf Gene Sequencing. Microorganisms 2020; 8:E1977. [PMID: 33322779 PMCID: PMC7763315 DOI: 10.3390/microorganisms8121977] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 12/24/2022] Open
Abstract
The aim was to study alterations of bacterial communities in patients undergoing hip or knee arthroplasty to assess the impact of chlorhexidine gluconate soap decolonisation and systemic antibiotic prophylaxis. A Swedish multicentre, prospective collection of samples obtained from elective arthroplasty patients (n = 83) by swabbing anterior nares, skin sites in the groin and the site of planned surgery, before and after arthroplasty surgery, was analysed by 16S rRNA (V3-V4) gene sequencing and a complementary targeted tuf gene sequencing approach to comprehensively characterise alterations in staphylococcal communities. Significant reductions in alpha diversity was detected for both bacterial (p = 0.04) and staphylococcal (p = 0.03) groin communities after arthroplasty surgery with significant reductions in relative Corynebacterium (p = 0.001) abundance and Staphylococcus hominis (p = 0.01) relative staphylococcal abundance. In nares, significant reductions occurred for Staphylococcus hominis (p = 0.02), Staphylococcus haemolyticus (p = 0.02), and Staphylococcus pasteuri (p = 0.003) relative to other staphylococci. Staphylococcus aureus colonised 35% of anterior nares before and 26% after arthroplasty surgery. Staphylococcus epidermidis was the most abundant staphylococcal species at all sampling sites. No bacterial genus or staphylococcal species increased significantly after arthroplasty surgery. Application of a targeted tuf gene sequencing approach provided auxiliary staphylococcal community profiles and allowed species-level characterisation directly from low biomass clinical samples.
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Affiliation(s)
- Søren Iversen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark; (T.B.J.); (A.C.I.); (S.M.E.); (M.S.); (P.S.A.)
| | - Thor Bech Johannesen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark; (T.B.J.); (A.C.I.); (S.M.E.); (M.S.); (P.S.A.)
| | - Anna Cäcilia Ingham
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark; (T.B.J.); (A.C.I.); (S.M.E.); (M.S.); (P.S.A.)
| | - Sofie Marie Edslev
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark; (T.B.J.); (A.C.I.); (S.M.E.); (M.S.); (P.S.A.)
| | - Staffan Tevell
- Department of Infectious Diseases and Centre for Clinical Research and Education, County Council of Värmland, SE-651 82 Karlstad, Sweden;
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden; (E.M.); (B.S.)
| | - Emeli Månsson
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden; (E.M.); (B.S.)
- Centre for Clinical Research, Hospital Västmanland, Uppsala University, Region Västmanland, SE‐721 89 Västerås, Sweden
| | - Åsa Nilsdotter-Augustinsson
- Department of Infectious Diseases and Department of Clinical and Biomedical Sciences, Linköping University, SE-581 83 Norrköping, Sweden;
| | - Bo Söderquist
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden; (E.M.); (B.S.)
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark; (T.B.J.); (A.C.I.); (S.M.E.); (M.S.); (P.S.A.)
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden; (E.M.); (B.S.)
| | - Paal Skytt Andersen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark; (T.B.J.); (A.C.I.); (S.M.E.); (M.S.); (P.S.A.)
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Freitas Ribeiro L, Akira Sato R, de Souza Pollo A, Marques Rossi GA, do Amaral LA. Occurrence of Methicillin-Resistant Staphylococcus spp. on Brazilian Dairy Farms that Produce Unpasteurized Cheese. Toxins (Basel) 2020; 12:toxins12120779. [PMID: 33302353 PMCID: PMC7762534 DOI: 10.3390/toxins12120779] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/26/2020] [Accepted: 09/04/2020] [Indexed: 02/06/2023] Open
Abstract
Methicillin-resistant Staphylococcus spp. (MRS) have been identified in several foods, including dairy products. Studies are needed about their occurrence and genetic diversity in the dairy production chain in order to gain a better understanding of their epidemiology and control. This study therefore focuses on isolating and characterizing MRS strains detected in milk used in the production of Brazilian artisanal unpasteurized cheeses. To this end, samples were collected from bovine feces, the hands of milkmen, milking buckets, sieves, unpasteurized milk, whey, water, artisanal unpasteurized cheeses, cheese processing surfaces, cheese handlers, cheese trays, cheese molds, and skimmers at five dairy farms located in the state of São Paulo, Brazil. Colonies suggestive of Staphylococcus spp. were subjected to multiplex PCR to confirm the presence of Staphylococcus aureus and to detect the mecA gene. Sixteen isolates containing mecA gene were detected in samples from unpasteurized cheese and from cheese handlers. None of these isolates were positive to enterotoxin genes. These 16 isolates were subjected to antimicrobial susceptibility tests, which revealed they were resistant to oxacillin, penicillin, and cefepime. Using gene sequencing, the MRS isolates were identified as S. haemolyticus, S. hominis, and S. epidermidis. Furthermore, isolates from cheese handlers’ hands and artisanal unpasteurized cheese presented high genetic similarity by random amplified polymorphic DNA (RAPD-PCR) analysis, which indicates cross contamination during cheese production. Thus, we found that people directly involved in milking and cheese processing activities at small dairy farms are a potential source of contamination of MRS strains in unpasteurized milk and cheese, representing a risk to public health.
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Evaluation of the Autof MS1000 mass spectrometer in the identification of clinical isolates. BMC Microbiol 2020; 20:318. [PMID: 33081722 PMCID: PMC7576717 DOI: 10.1186/s12866-020-02005-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/12/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND To evaluate the accuracy and performance of the Autof MS1000 mass spectrometer in bacteria and yeast identification, 2342 isolates were obtained from microbial cultures of clinical specimens (e.g. blood, cerebrospinal fluid, respiratory tract samples, lumbar puncture fluid, wound samples, stool, and urine) collected in 2019 in Henan Provincial People's Hospital. Repetitive strains from the same patient were excluded. We tested the Autof MS1000 and Bruker Biotyper mass spectrometry systems and the classical biochemical identification system VITEK 2/API 20C AUX. Inconsistencies in strain identification among the three systems were identified by 16S rDNA and gene sequencing. RESULTS At the species level, the Autof MS1000 and Bruker Biotyper systems had isolate identification accuracies of 98.9 and 98.5%, respectively. At the genus level, the Autof MS1000 and Bruker Biotyper systems were 99.7 and 99.4% accurate, respectively. The instruments did not significantly differ in identification accuracy at either taxonomic level. The frequencies of unreliable identification were 1.1% (26/2342) for the Autof MS1000 and 1.5% (34/2342) for the Bruker Biotyper. In vitro experiments demonstrated that the coincidence rate of the Autof MS1000 mass spectrometer in the identification of five types of bacteria was > 93%, the identification error rate was < 3%, and the no identification rate was 0. This indicates that the Autof MS1000 system is acceptable for identification. CONCLUSIONS The Autof MS1000 mass spectrometer can be utilised to identify clinical isolates. However, an upgradation of the database is recommended to correctly identify rare strains.
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Conesa A, Dieser S, Barberis C, Bonetto C, Lasagno M, Vay C, Odierno L, Porporatto C, Raspanti C. Differentiation of non-aureus staphylococci species isolated from bovine mastitis by PCR-RFLP of groEL and gap genes in comparison to MALDI-TOF mass spectrometry. Microb Pathog 2020; 149:104489. [PMID: 32910983 DOI: 10.1016/j.micpath.2020.104489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 10/23/2022]
Abstract
Intramammary infections (IMI) cause serious economic losses for farmers and the dairy industry. Cases of subclinical mastitis are commonly the result of infection by minor pathogens such as non-aureus staphylococci (NAS), so their correct identification is important for appropriate therapeutic intervention and management. The aim of this study was to assess the reliability of PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) of the groEL and gap genes to discriminate between bovine-associated NAS species, using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) as the reference method. MALDI-TOF MS was able to correctly identify 112 NAS isolates from bovine IMI at species level out of a total of 115 (97.4%). These results were considered definitive and thus compared with those from the PCR-RFLP analyses. Only 50% (56/112) of the samples classified through groEL PCR-RFLP matched the molecular identity determined by MALDI-TOF MS, whereas coincidence rose to 96.4% (108/112) when comparing results from gap PCR-RFLP and the spectral analysis. This study demonstrates that gap PCR-RFLP is a useful and reliable tool for the identification of NAS species isolated from bovine mastitis.
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Affiliation(s)
- Agustín Conesa
- Instituto Académico Pedagógico de Ciencias Básicas y Aplicadas (IAPCByA), Universidad Nacional de Villa María, Arturo Jauretche 1555, X5900KBJ, Villa María, Córdoba, Argentina
| | - Silvana Dieser
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales. Universidad Nacional de Río Cuarto, Ruta 36 km 601, X5806JRA, Río Cuarto, Córdoba, Argentina
| | - Claudia Barberis
- Instituto de Fisiopatología y Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 954, C1113AAD, Caba, Argentina
| | - Cesar Bonetto
- Instituto Académico Pedagógico de Ciencias Básicas y Aplicadas (IAPCByA), Universidad Nacional de Villa María, Arturo Jauretche 1555, X5900KBJ, Villa María, Córdoba, Argentina
| | - Mirta Lasagno
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales. Universidad Nacional de Río Cuarto, Ruta 36 km 601, X5806JRA, Río Cuarto, Córdoba, Argentina
| | - Carlos Vay
- Instituto de Fisiopatología y Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 954, C1113AAD, Caba, Argentina
| | - Liliana Odierno
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales. Universidad Nacional de Río Cuarto, Ruta 36 km 601, X5806JRA, Río Cuarto, Córdoba, Argentina
| | - Carina Porporatto
- Instituto Académico Pedagógico de Ciencias Básicas y Aplicadas (IAPCByA), Universidad Nacional de Villa María, Arturo Jauretche 1555, X5900KBJ, Villa María, Córdoba, Argentina
| | - Claudia Raspanti
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales. Universidad Nacional de Río Cuarto, Ruta 36 km 601, X5806JRA, Río Cuarto, Córdoba, Argentina.
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Grimshaw SG, Smith AM, Arnold DS, Xu E, Hoptroff M, Murphy B. The diversity and abundance of fungi and bacteria on the healthy and dandruff affected human scalp. PLoS One 2019; 14:e0225796. [PMID: 31851674 PMCID: PMC6919596 DOI: 10.1371/journal.pone.0225796] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/12/2019] [Indexed: 12/22/2022] Open
Abstract
Dandruff is a skin condition that affects the scalp of up to half the world's population, it is characterised by an itchy, flaky scalp and is associated with colonisation of the skin by Malassezia spp. Management of this condition is typically via antifungal therapies, however the precise role of microbes in the aggravation of the condition are incompletely characterised. Here, a combination of 454 sequencing and qPCR techniques were used to compare the scalp microbiota of dandruff and non-dandruff affected Chinese subjects. Based on 454 sequencing of the scalp microbiome, the two most abundant bacterial genera found on the scalp surface were Cutibacterium (formerly Propionibacterium) and Staphylococcus, while Malassezia was the main fungal inhabitant. Quantitative PCR (qPCR) analysis of four scalp taxa (M. restricta, M. globosa, C. acnes and Staphylococcus spp.) believed to represent the bulk of the overall population was additionally carried out. Metataxonomic and qPCR analyses were performed on healthy and lesional buffer scrub samples to facilitate assessment of whether the scalp condition is associated with differential microbial communities on the sampled skin. Dandruff was associated with greater frequencies of M. restricta and Staphylococcus spp. compared with the healthy population (p<0.05). Analysis also revealed the presence of an unclassified fungal taxon that could represent a novel Malassezia species.
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Affiliation(s)
- Sally G. Grimshaw
- Unilever Research & Development, Port Sunlight, England, United Kingdom
| | - Adrian M. Smith
- Unilever Research & Development, Colworth, England, United Kingdom
| | - David S. Arnold
- Unilever Research & Development, Port Sunlight, England, United Kingdom
| | - Elaine Xu
- Unilever Research & Development, Shanghai, China
| | - Michael Hoptroff
- Unilever Research & Development, Port Sunlight, England, United Kingdom
| | - Barry Murphy
- Unilever Research & Development, Port Sunlight, England, United Kingdom
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Kosecka-Strojek M, Sabat AJ, Akkerboom V, Becker K, van Zanten E, Wisselink G, Miedzobrodzki J, Kooistra-Smid AMDM, Friedrich AW. Development and Validation of a Reference Data Set for Assigning Staphylococcus Species Based on Next-Generation Sequencing of the 16S-23S rRNA Region. Front Cell Infect Microbiol 2019; 9:278. [PMID: 31456949 PMCID: PMC6698797 DOI: 10.3389/fcimb.2019.00278] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/22/2019] [Indexed: 11/13/2022] Open
Abstract
Many members of the Staphylococcus genus are clinically relevant opportunistic pathogens that warrant accurate and rapid identification for targeted therapy. The aim of this study was to develop a careful assignment scheme for staphylococcal species based on next-generation sequencing (NGS) of the 16S-23S rRNA region. All reference staphylococcal strains were identified at the species level using Sanger sequencing of the 16S rRNA, sodA, tuf, and rpoB genes and NGS of the 16S-23S rRNA region. To broaden the database, an additional 100 staphylococcal strains, including 29 species, were identified by routine diagnostic methods, 16S rRNA Sanger sequencing and NGS of the 16S-23S rRNA region. The results enabled development of reference sequences encompassing the 16S-23S rRNA region for 50 species (including one newly proposed species) and 6 subspecies of the Staphylococcus genus. This study showed sodA and rpoB targets were the most discriminative but NGS of the 16S-23S rRNA region was more discriminative than tuf gene sequencing and much more discriminative than 16S rRNA gene sequencing. Almost all Staphylococcus species could be distinguished when the max score was 99.0% or higher and the sequence similarity between the best and second best species was equal to or >0.2% (min. 9 nucleotides). This study allowed development of reference sequences for 21 staphylococcal species and enrichment for 29 species for which sequences were publicly available. We confirmed the usefulness of NGS of the 16S-23S rRNA region by identifying the whole species content in 45 clinical samples and comparing the results to those obtained using routine diagnostic methods. Based on the developed reference database, all staphylococcal species can be reliably detected based on the 16S-23S rRNA sequences in samples composed of both single species and more complex polymicrobial communities. This study will be useful for introduction of a novel diagnostic tool, which undoubtedly is an improvement for reliable species identification in polymicrobial samples. The introduction of this new method is hindered by a lack of reference sequences for the 16S-23S rRNA region for many bacterial species. The results will allow identification of all Staphylococcus species, which are clinically relevant pathogens.
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Affiliation(s)
- Maja Kosecka-Strojek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.,Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Artur J Sabat
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Viktoria Akkerboom
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Karsten Becker
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Evert van Zanten
- Certe, Department of Medical Microbiology, Groningen, Netherlands
| | - Guido Wisselink
- Certe, Department of Medical Microbiology, Groningen, Netherlands
| | - Jacek Miedzobrodzki
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Anna M D Mirjam Kooistra-Smid
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Certe, Department of Medical Microbiology, Groningen, Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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11
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Ruiz-Ripa L, Gómez P, Alonso CA, Camacho MC, de la Puente J, Fernández-Fernández R, Ramiro Y, Quevedo MA, Blanco JM, Zarazaga M, Höfle U, Torres C. Detection of MRSA of Lineages CC130-mecC and CC398-mecA and Staphylococcus delphini-lnu(A) in Magpies and Cinereous Vultures in Spain. MICROBIAL ECOLOGY 2019; 78:409-415. [PMID: 30694341 DOI: 10.1007/s00248-019-01328-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/15/2019] [Indexed: 06/09/2023]
Abstract
The aim of this study was to determine the carriage rate of coagulase-positive staphylococci (CoPS) in wild birds and to characterize recovered isolates. Tracheal samples from 324 wild birds, obtained in different Spanish regions during 2015-2016, were screened for CoPS carriage. The antimicrobial resistance profile and the virulence gene content were investigated. Molecular typing was performed by spa, agr, MLST, SCCmec, and S. delphini group classification. CoPS were recovered from 26 samples of wild birds (8.3%), and 27 isolates were further characterized. Two CoPS species were detected: S. aureus (n = 15; eight cinereous vultures and seven magpies) and S. delphini (n = 12; 11 cinereous vultures and one red kite). Thirteen S. aureus were methicillin-resistant (MRSA) and the remaining two strains were methicillin-susceptible (MSSA). Twelve MRSA were mecC-positive, typed as t843-ST1583/ST1945/ST1581/ST1571 (n = 11) and t1535-ST1945 (n = 1) (all of clonal-complex CC130); they were susceptible to the non-β-lactams tested. The remaining MRSA strain carried the mecA gene, was typed as t011-ST398-CC398-agrI-SCCmec-V, and showed a multiresistance phenotype. MSSA isolates were ascribed to lineages ST97-CC97 and ST425-CC425. All S. aureus lacked the studied virulence genes (lukS/F-PV, tst, eta, etb, and etd), and the IEC type E (with scn and sak genes) was detected in four mecC-positive and one MSSA isolates. S. delphini strains were methicillin-susceptible but showed resistance to at least one of the antimicrobials tested, with high penicillin (75%, with blaZ gene) and tetracycline [58%, with tet(K)± tet(L)] resistance rates. All S. delphini isolates presented the virulence genes lukS-I, siet, and se-int, and four carried the clindamycin-resistance lnu(A) gene.
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Affiliation(s)
- Laura Ruiz-Ripa
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Madre de Dios 51, 26006, Logroño, Spain
| | - Paula Gómez
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Madre de Dios 51, 26006, Logroño, Spain
| | - Carla Andrea Alonso
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Madre de Dios 51, 26006, Logroño, Spain
| | - Maria Cruz Camacho
- Grupo SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Javier de la Puente
- SEO/BirdLife, Bird Monitoring Unit, Madrid, Spain
- Parque Nacional de la Sierra de Guadarrama, Centro de Investigación, Seguimiento y Evaluación, Rascafría, Madrid, Spain
| | - Rosa Fernández-Fernández
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Madre de Dios 51, 26006, Logroño, Spain
| | - Yolanda Ramiro
- Grupo SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | | | | | - Myriam Zarazaga
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Madre de Dios 51, 26006, Logroño, Spain
| | - Ursula Höfle
- Grupo SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Carmen Torres
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Madre de Dios 51, 26006, Logroño, Spain.
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12
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Hosseinzadeh S, Dastmalchi Saei H. Staphylococcal species associated with bovine mastitis in the North West of Iran: Emerging of coagulase-negative staphylococci. Int J Vet Sci Med 2019. [DOI: 10.1016/j.ijvsm.2014.02.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Somayyeh Hosseinzadeh
- Department of Microbiology, Faculty of Veterinary Medicine, Urmia University, P.O. Box 1177, Urmia, Iran
| | - Habib Dastmalchi Saei
- Department of Microbiology, Faculty of Veterinary Medicine, Urmia University, P.O. Box 1177, Urmia, Iran
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13
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Pérez-Sancho M, Vela AI, Horcajo P, Ugarte-Ruiz M, Domínguez L, Fernández-Garayzábal JF, de la Fuente R. Rapid differentiation of Staphylococcus aureus subspecies based on MALDI-TOF MS profiles. J Vet Diagn Invest 2018; 30:813-820. [PMID: 30280650 DOI: 10.1177/1040638718805537] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Staphylococcus aureus encompasses 2 subspecies ( aureus and anaerobius) with significant differences in their epidemiology and pathogenicity. We evaluated the suitability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the rapid identification of both subspecies using a panel of 52 S. aureus isolates (30 subsp. anaerobius and 22 subsp. aureus) recovered from different origins, countries, and years. The on-board library identification system correctly identified 42 of 52 (81%) S. aureus isolates at the species level with score values >2.0. Limited performance was observed for differentiation of S. aureus subspecies (particularly subsp. anaerobius). Visual inspection of MALDI-TOF MS profiles identified 5 subspecies-specific mass peaks ( m/ z 3430 and 6861 in S. aureus subsp. anaerobius, and m/ z 4046, 6890, and 8093 in S. aureus subsp. aureus) with 100% sensitivity and specificity values, which is potentially useful for differentiating these subspecies. The suitability of 3 models, Genetic Analysis (GA), Quick Classifier (QC), and Supervised Neural Network, for automatic identification of both subspecies was evaluated using the Recognition Capability (RC) and Cross Validation (CV) values provided by the on-board ClinProTools software. The GA and QC models reached RC and CV values of 100%. Both models were externally validated using a panel of 26 S. aureus isolates of both subspecies, with both models correctly classifying all isolates of both subspecies. MALDI-TOF MS coupled with ClinProTools software represents a rapid and simple approach for S. aureus subspecies discrimination.
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Affiliation(s)
- Marta Pérez-Sancho
- VISAVET Health Surveillance Centre (Pérez-Sancho, Vela, Ugarte-Ruiz, Fernández-Garayzábal, Domínguez), Complutense University, Madrid, Spain.,Animal Health Department, Veterinary Faculty (Vela, Horcajo, Fernández-Garayzábal, Domínguez, de la Fuente), Complutense University, Madrid, Spain
| | - Ana I Vela
- VISAVET Health Surveillance Centre (Pérez-Sancho, Vela, Ugarte-Ruiz, Fernández-Garayzábal, Domínguez), Complutense University, Madrid, Spain.,Animal Health Department, Veterinary Faculty (Vela, Horcajo, Fernández-Garayzábal, Domínguez, de la Fuente), Complutense University, Madrid, Spain
| | - Pilar Horcajo
- VISAVET Health Surveillance Centre (Pérez-Sancho, Vela, Ugarte-Ruiz, Fernández-Garayzábal, Domínguez), Complutense University, Madrid, Spain.,Animal Health Department, Veterinary Faculty (Vela, Horcajo, Fernández-Garayzábal, Domínguez, de la Fuente), Complutense University, Madrid, Spain
| | - María Ugarte-Ruiz
- VISAVET Health Surveillance Centre (Pérez-Sancho, Vela, Ugarte-Ruiz, Fernández-Garayzábal, Domínguez), Complutense University, Madrid, Spain.,Animal Health Department, Veterinary Faculty (Vela, Horcajo, Fernández-Garayzábal, Domínguez, de la Fuente), Complutense University, Madrid, Spain
| | - Lucas Domínguez
- VISAVET Health Surveillance Centre (Pérez-Sancho, Vela, Ugarte-Ruiz, Fernández-Garayzábal, Domínguez), Complutense University, Madrid, Spain.,Animal Health Department, Veterinary Faculty (Vela, Horcajo, Fernández-Garayzábal, Domínguez, de la Fuente), Complutense University, Madrid, Spain
| | - José F Fernández-Garayzábal
- VISAVET Health Surveillance Centre (Pérez-Sancho, Vela, Ugarte-Ruiz, Fernández-Garayzábal, Domínguez), Complutense University, Madrid, Spain.,Animal Health Department, Veterinary Faculty (Vela, Horcajo, Fernández-Garayzábal, Domínguez, de la Fuente), Complutense University, Madrid, Spain
| | - Ricardo de la Fuente
- VISAVET Health Surveillance Centre (Pérez-Sancho, Vela, Ugarte-Ruiz, Fernández-Garayzábal, Domínguez), Complutense University, Madrid, Spain.,Animal Health Department, Veterinary Faculty (Vela, Horcajo, Fernández-Garayzábal, Domínguez, de la Fuente), Complutense University, Madrid, Spain
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14
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Khosravi AD, Roointan M, Abbasi Montazeri E, Aslani S, Hashemzadeh M, Taheri Soodejani M. Application of tuf gene sequence analysis for the identification of species of coagulase-negative staphylococci in clinical samples and evaluation of their antimicrobial resistance pattern. Infect Drug Resist 2018; 11:1275-1282. [PMID: 30197525 PMCID: PMC6112803 DOI: 10.2147/idr.s172144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Introduction Coagulase-negative staphylococci (CoNS) are normal inhabitants of human skin and mucous membranes. However, CoNS represent one of the major nosocomial pathogens, especially in immunocompromised patients. The increasing incidence of CoNS and mainly methicillin-resistant strains underlines the need for an accurate identification of Staphylococcus isolates at the species level. Analysis of the tuf gene proved to be an accurate tool for the species identification of CoNS. The aims of this study were to identify the CoNS species by tuf gene-based polymerase chain reaction method and sequencing, and to determine the frequency of CoNS clinical isolates resistant to methicillin (MRCoNS) and other antibiotics. Methods A total of 200 staphylococci isolates were collected from various clinical samples. Phenotyping methods were used for initial identification followed by polymerase chain reaction amplification of tuf gene with subsequent sequencing. The phylogenetic relationships among species were analyzed using the neighbor-joining method based on the partial gene sequence of tuf. Microbroth dilution test was used for screening methicillin resistance, and disk diffusion susceptibility testing was performed for evaluation of antibiotic resistance among the isolates. Results In the present study, 125 isolates were identified as CoNS; among them, Staphylococcus epidermidis 54(43.2%) and Staphylococcus haemolyticus 50 (40.0%) were demonstrated as the most prevalent species. Resistance to methicillin was detected in 54.4% of the CoNS based on microbroth dilution method. In disk diffusion susceptibility testing, the greatest resistance of CoNS was demonstrated for cefoxitin (65.4%), cotrimethoxazole (54.4%), and clindamycin (49.6%), while daptomycin (87.2%) and linezolid (83.2%) showed the greatest effectiveness for CoNS isolates. Conclusion Our results confirmed the predominance of S. epidermidis and S. haemolyticus among CoNS isolates. The high prevalence of MRCoNS strains is a serious concern and strongly suggests the need for control program measures in our hospitals in order to reduce MRCoNS infections, especially in immunocompromised patients.
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Affiliation(s)
- Azar Dokht Khosravi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,
| | - Mitra Roointan
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,
| | - Effat Abbasi Montazeri
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,
| | - Sajad Aslani
- Department of Microbiology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran.,Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Hashemzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,
| | - Moslem Taheri Soodejani
- Department of Biostatistics and Epidemiology, School of Health, Kerman University of Medical Sciences, Kerman, Iran
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15
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Chiquet C, Musson C, Aptel F, Boisset S, Maurin M. Genetic and Phenotypic Traits of Staphylococcus Epidermidis Strains Causing Postcataract Endophthalmitis Compared to Commensal Conjunctival Flora. Am J Ophthalmol 2018; 191:76-82. [PMID: 29654738 DOI: 10.1016/j.ajo.2018.03.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 03/28/2018] [Accepted: 03/30/2018] [Indexed: 11/29/2022]
Abstract
PURPOSE The aim of this study was to compare the virulence and antibiotic resistance traits of Staphylococcus epidermidis strains causing acute postcataract endophthalmitis to those isolated from the conjunctiva of uninfected control patients. DESIGN Case-control study. METHODS We isolated an S epidermidis strain from each of the 22 endophthalmitis patients, and from 43 of the 72 controls. Species identification was confirmed using both Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and tuf gene amplification and sequencing. Antibiotic susceptibilities were evaluated using the AST-P631 card and the Vitek II automated system. The S epidermidis strains were tested for the presence of 7 virulence genes (icaA, icaB, icaC, icaD, atlE, aap, and capA), the insertion sequence IS256, and the mecA gene. RESULTS The S epidermidis strains from the endophthalmitis patients displayed higher prevalence rates for aap, atlE, and mecA gene carriage compared to those of the control group (77% vs 42%, P = .007; 100% vs 79%, P = .02; and 54% vs 11%, P < .001, respectively). They also harbored the combination of the mecA and icaA genes more frequently compared to the control group (13% vs 2%, P = .01). They were significantly more resistant than control strains to methicillin, fluoroquinolones, and the aminoglycosides. CONCLUSIONS A higher capacity of adhesion to the intraocular lens and formation of biofilms as well as greater resistance to antibiotics were found in S epidermidis strains causing postcataract endophthalmitis. The usefulness of such virulence and antibiotic resistance markers warrants further evaluation for prevention, treatment, and prognostic evaluation of S epidermidis endophthalmitis.
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Affiliation(s)
- Christophe Chiquet
- Grenoble Alpes University, Grenoble, France; Department of Ophthalmology, Grenoble Alpes University Hospital, Grenoble, France; Department of Microbiology, Grenoble Alpes University Hospital, Grenoble, France.
| | - Cécile Musson
- Grenoble Alpes University, Grenoble, France; Department of Ophthalmology, Grenoble Alpes University Hospital, Grenoble, France
| | - Florent Aptel
- Grenoble Alpes University, Grenoble, France; Department of Ophthalmology, Grenoble Alpes University Hospital, Grenoble, France
| | - Sandrine Boisset
- Department of Microbiology, Grenoble Alpes University Hospital, Grenoble, France
| | - Max Maurin
- Department of Microbiology, Grenoble Alpes University Hospital, Grenoble, France
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16
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El-Bouri K, Johnston S, Rees E, Thomas I, Bome-Mannathoko N, Jones C, Reid M, Ben-Ismaeil B, Davies AP, Harris LG, Mack D. Comparison of bacterial identification by MALDI-TOF mass spectrometry and conventional diagnostic microbiology methods: agreement, speed and cost implications. Br J Biomed Sci 2018. [DOI: 10.1080/09674845.2012.12002436] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- K. El-Bouri
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
| | - S. Johnston
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
| | - E. Rees
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
| | - I. Thomas
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
| | - N. Bome-Mannathoko
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
| | - C. Jones
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
| | - M. Reid
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
| | - B. Ben-Ismaeil
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
| | - A. P. Davies
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
| | - L. G. Harris
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
| | - D. Mack
- Public Health Wales Microbiology Laboratory ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, United Kingdom
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, United Kingdom
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17
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Kim J, Hong J, Lim JA, Heu S, Roh E. Improved multiplex PCR primers for rapid identification of coagulase-negative staphylococci. Arch Microbiol 2017; 200:73-83. [PMID: 28795230 PMCID: PMC5758691 DOI: 10.1007/s00203-017-1415-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 07/13/2017] [Accepted: 07/25/2017] [Indexed: 11/04/2022]
Abstract
Coagulase-negative staphylococci (CNS) are opportunistic pathogens that are currently emerging as causative agents of human disease. Though CNS are widespread in the clinic and food, their precise identification at species level is important. Here, using 16S rRNA sequencing, 55 staphylococcal isolates were identified as S. capitis, S. caprae, S. epidermidis, S. haemolyticus, S. pasteuri, S. saprophyticus, S. warneri, and S. xylosus. Although 16S rRNA sequencing is universally accepted as a standard for bacterial identification, the method did not effectively discriminate closely related species, and additional DNA sequencing was required. The divergence of the sodA gene sequence is higher than that of 16S rRNA. To devise a rapid and accurate identification method, sodA-specific primers were designed to demonstrate that species-specific multiplex polymerase chain reaction (PCR) can be used for the identification of CNS species. The accuracy of this method was higher than that of phenotypic identification; the method is simple and less time-consuming than 16S rRNA sequencing. Of the 55 CNS isolates, 92.72% were resistant to at least one antibiotic, and 60% were resistant to three or more antibiotics. CNS isolates produced diverse virulence-associated enzymes, including hemolysin (produced by 69.09% of the isolates), protease (65.45%), lipase (54.54%), lecithinase (36.36%), and DNase (29.09%); all isolates could form a biofilm. Because of the increasing pathogenic significance of CNS, the efficient multiplex PCR detection method developed in this study may contribute to studies for human health.
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Affiliation(s)
- Jonguk Kim
- Microbial Safety Team, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jisoo Hong
- Microbial Safety Team, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jeong-A Lim
- Microbial Safety Team, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Sunggi Heu
- Crop Cultivation and Environment Research Division, National Institute of Crop Science, Rural Development Administration, Suwon, 16613, Republic of Korea
| | - Eunjung Roh
- Microbial Safety Team, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea.
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18
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McMurray CL, Hardy KJ, Calus ST, Loman NJ, Hawkey PM. Staphylococcal species heterogeneity in the nasal microbiome following antibiotic prophylaxis revealed by tuf gene deep sequencing. MICROBIOME 2016; 4:63. [PMID: 27912796 PMCID: PMC5134057 DOI: 10.1186/s40168-016-0210-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/22/2016] [Indexed: 05/10/2023]
Abstract
BACKGROUND Staphylococci are a major constituent of the nasal microbiome and a frequent cause of hospital-acquired infection. Antibiotic surgical prophylaxis is administered prior to surgery to reduce a patient's risk of postoperative infection. The impact of surgical prophylaxis on the nasal staphylococcal microbiome is largely unknown. Here, we report the species present in the nasal staphylococcal microbiome and the impact of surgical prophylaxis revealed by a novel culture independent technique. Daily nasal samples from 18 hospitalised patients, six of whom received no antibiotics and 12 of whom received antibiotic surgical prophylaxis (flucloxacillin and gentamicin or teicoplanin +/- gentamicin), were analysed by tuf gene fragment amplicon sequencing. RESULTS On admission to hospital, the species diversity of the nasal staphylococcal microbiome varied from patient to patient ranging from 4 to 10 species. Administration of surgical prophylaxis did not substantially alter the diversity of the staphylococcal species present in the nose; however, surgical prophylaxis did impact on the relative abundance of the staphylococcal species present. The dominant staphylococcal species present in all patients on admission was Staphylococcus epidermidis, and antibiotic administration resulted in an increase in species relative abundance. Following surgical prophylaxis, a reduction in the abundance of Staphylococcus aureus was observed in carriers, but not a complete eradication. CONCLUSIONS Utilising the tuf gene fragment has enabled a detailed study of the staphylococcal microbiome in the nose and highlights that although there is no change in the heterogeneity of species present, there are changes in abundance. The sensitivity of the methodology has revealed that the abundance of S. aureus is reduced to a low level by surgical prophylaxis and therefore reduces the potential risk of infection following surgery but also highlights that S. aureus does persist.
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Affiliation(s)
- Claire L McMurray
- Heart of England NHS Foundation Trust, Birmingham Heartlands Hospital, Bordesley Green East, Birmingham, B9 5SS, UK.
- Institute of Microbiology and Infection, School of Immunity and Infection, The College of Medical and Dental Sciences, The University of Birmingham, Birmingham, B15 2TT, UK.
| | - Katherine J Hardy
- Public Health England Birmingham Laboratory, Birmingham Heartlands Hospital, Bordesley Green East, Birmingham, B9 5SS, UK
- Institute of Microbiology and Infection, School of Immunity and Infection, The College of Medical and Dental Sciences, The University of Birmingham, Birmingham, B15 2TT, UK
| | - Szymon T Calus
- Institute of Microbiology and Infection, School of Immunity and Infection, The College of Medical and Dental Sciences, The University of Birmingham, Birmingham, B15 2TT, UK
- Present address: Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, School of Immunity and Infection, The College of Medical and Dental Sciences, The University of Birmingham, Birmingham, B15 2TT, UK
| | - Peter M Hawkey
- Public Health England Birmingham Laboratory, Birmingham Heartlands Hospital, Bordesley Green East, Birmingham, B9 5SS, UK
- Institute of Microbiology and Infection, School of Immunity and Infection, The College of Medical and Dental Sciences, The University of Birmingham, Birmingham, B15 2TT, UK
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19
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Švec P, Petráš P, Pantůček R, Doškař J, Sedláček I. High intraspecies heterogeneity within Staphylococcus sciuri and rejection of its classification into S. sciuri subsp. sciuri, S. sciuri subsp. carnaticus and S. sciuri subsp. rodentium. Int J Syst Evol Microbiol 2016; 66:5181-5186. [DOI: 10.1099/ijsem.0.001493] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Pavel Švec
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, Bld. A25, 625 00 Brno, Czech Republic
| | - Petr Petráš
- Reference Laboratory for Staphylococci, National Institute of Public Health, Šrobárova 48, 100 42 Prague 10, Czech Republic
| | - Roman Pantůček
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Jiří Doškař
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 5, Bld. A25, 625 00 Brno, Czech Republic
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20
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Han HW, Chang HC, Chang TC. Identification of Staphylococcus spp. and detection of mecA by an oligonucleotide array. Diagn Microbiol Infect Dis 2016; 86:23-9. [PMID: 27342780 DOI: 10.1016/j.diagmicrobio.2016.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 05/31/2016] [Accepted: 06/01/2016] [Indexed: 01/15/2023]
Abstract
Phenotypic identification of coagulase-negative staphylococci (CoNS) is difficult and many staphylococcal species carry mecA. This study developed an array that was able to detect mecA and identify 30 staphylococcal species by targeting the internal transcribed spacer regions. A total of 129 target reference strains (30 species) and 434 clinical isolates of staphylococci were analyzed. Gene sequencing of 16S rRNA, gap or tuf genes was the reference method for species identification. All reference strains (100%) were correctly identified, while the identification rates of clinical isolates of S. aureus and CoNS were 98.9% and 98%, respectively. The sensitivity and specificity for mecA detection were 99% and 100%, respectively, in S. aureus isolates, and both values were 100% in isolates of CoNS. The assay takes 6 h from a purified culture isolate, and so far it has not been performed directly on patient samples.
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Affiliation(s)
- Huan Wen Han
- Institute of Biomedical Engineering, College of Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Hsien Chang Chang
- Institute of Biomedical Engineering, College of Engineering, National Cheng Kung University, Tainan, Taiwan; Medical Device Innovation Center, National Cheng Kung University, Tainan, Taiwan.
| | - Tsung Chain Chang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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21
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Ben Said M, Hays S, Bonfils M, Jourdes E, Rasigade JP, Laurent F, Picaud JC. Late-onset sepsis due to Staphylococcus capitis 'neonatalis' in low-birthweight infants: a new entity? J Hosp Infect 2016; 94:95-8. [PMID: 27424947 DOI: 10.1016/j.jhin.2016.06.008] [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: 02/25/2016] [Accepted: 06/10/2016] [Indexed: 10/21/2022]
Abstract
During hospitalization, sepsis occurs in one of every five very-low-birthweight infants. The emergence of Staphylococcus capitis (SC)-related sepsis in preterm infants was observed recently. This study aimed to evaluate the clinical severity of SC-related sepsis in preterm infants. Of the 105 infants who presented with sepsis related to coagulase-negative staphylococci, 74 were SC. Severe morbidity was more common in the SC group (55.4%) than in the non-SC coagulase-negative staphylococci group (32.0%) (P=0.03). Multi-variate analysis identified SC-related sepsis as an independent risk factor for severe morbidity.
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Affiliation(s)
- M Ben Said
- Neonatology, University Hospital Croix Rousse, Hospices Civils de Lyon, Lyon, France; Faculty of Medicine of Tunis, University of Tunis El-Manar, Tunis, Tunisia
| | - S Hays
- Neonatology, University Hospital Croix Rousse, Hospices Civils de Lyon, Lyon, France; Rhone-Alpes Human Nutrition Research Centre, Pierre Bénite, France
| | - M Bonfils
- Neonatology, University Hospital Croix Rousse, Hospices Civils de Lyon, Lyon, France
| | - E Jourdes
- Neonatology, University Hospital Croix Rousse, Hospices Civils de Lyon, Lyon, France
| | - J-P Rasigade
- Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France; Department of Bacteriology - National Reference Centre for Staphylococci, Hospices Civils de Lyon, Lyon, France
| | - F Laurent
- Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France; Department of Bacteriology - National Reference Centre for Staphylococci, Hospices Civils de Lyon, Lyon, France
| | - J-C Picaud
- Neonatology, University Hospital Croix Rousse, Hospices Civils de Lyon, Lyon, France; Rhone-Alpes Human Nutrition Research Centre, Pierre Bénite, France; Lyon-Sud Charles Merieux Medical School, Claude Bernard University Lyon 1, Pierre Bénite, France.
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22
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Kleinschmidt S, Huygens F, Faoagali J, Rathnayake IU, Hafner LM. Staphylococcus epidermidis as a cause of bacteremia. Future Microbiol 2015; 10:1859-79. [DOI: 10.2217/fmb.15.98] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Staphylococcus epidermidis is a biofilm-producing commensal organism found ubiquitously on human skin and mucous membranes, as well as on animals and in the environment. Biofilm formation enables this organism to evade the host immune system. Colonization of percutaneous devices or implanted medical devices allows bacteria access to the bloodstream. Isolation of this organism from blood cultures may represent either contamination during the blood collection procedure or true bacteremia. S. epidermidis bloodstream infections may be indolent compared with other bacteria. Isolation of S. epidermidis from a blood culture may present a management quandary for clinicians. Over-treatment may lead to patient harm and increases in healthcare costs. There are numerous reports indicating the difficulty of predicting clinical infection in patients with positive blood cultures with this organism. No reliable phenotypic or genotypic algorithms currently exist to predict the pathogenicity of a S. epidermidis bloodstream infection. This review will discuss the latest advances in identification methods, global population structure, pathogenicity, biofilm formation, antimicrobial resistance and clinical significance of the detection of S. epidermidis in blood cultures. Previous studies that have attempted to discriminate between invasive and contaminating strains of S. epidermidis in blood cultures will be analyzed.
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Affiliation(s)
- Sharon Kleinschmidt
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Microbiology Department, Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Flavia Huygens
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Joan Faoagali
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Irani U Rathnayake
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Louise M Hafner
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
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23
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Han HW, Chang HC, Hunag AH, Chang TC. Optimization of the score cutoff value for routine identification of Staphylococcus species by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. Diagn Microbiol Infect Dis 2015; 83:349-54. [PMID: 26423657 DOI: 10.1016/j.diagmicrobio.2015.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 07/07/2015] [Accepted: 08/04/2015] [Indexed: 10/23/2022]
Abstract
Staphylococcus species are important pathogens. We evaluated 2 score cutoffs (2.0 and 1.7) and the replicate number (a single or a duplicate test) on the identification of staphylococci using the Bruker matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS). A collection of 440 clinical isolates (11 species) and 144 reference strains (36 species) was evaluated. For clinical isolates using a cutoff of 2.0 and duplicate tests, the rates of species, genus, and unreliable identifications were 93.4%, 5.7%, and 0.9% respectively, while the respective values were 99.3%, 0.2%, and 0.5% when the cutoff was 1.7. The species identification rates were significantly higher (P<0.01) when a cutoff of 1.7 or a duplicate test was used. Similar results were obtained for reference strains. In conclusion, a cutoff of 1.7 and duplicate tests are recommended for identification of staphylococci using MALDI-TOF MS.
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Affiliation(s)
- Huan Wen Han
- Institute of Biomedical Engineering, College of Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Hsien Chang Chang
- Institute of Biomedical Engineering, College of Engineering, National Cheng Kung University, Tainan, Taiwan; Medical Device Innovation Center, National Cheng Kung University, Tainan, Taiwan
| | - Ay Huei Hunag
- Division of Clinical Microbiology, Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Tsung Chain Chang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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24
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Ugwu CC, Gomez-Sanz E, Agbo IC, Torres C, Chah KF. Characterization of mannitol-fermenting methicillin-resistant staphylococci isolated from pigs in Nigeria. Braz J Microbiol 2015; 46:885-92. [PMID: 26413075 PMCID: PMC4568864 DOI: 10.1590/s1517-838246320140644] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 02/02/2015] [Indexed: 11/22/2022] Open
Abstract
This study was conducted to determine the species distribution, antimicrobial resistance pheno- and genotypes and virulence traits of mannitol-positive methicillin-resistant staphylococci (MRS) isolated from pigs in Nsukka agricultural zone, Nigeria. Twenty mannitol-positive methicillin-resistant coagulase-negative staphylococcal (MRCoNS) strains harboring the mecA gene were detected among the 64 Staphylococcus isolates from 291 pigs. A total of 4 species were identified among the MRCoNS isolates, namely, Staphylococcus sciuri (10 strains), Staphylococcus lentus (6 strains), Staphylococcus cohnii (3 strains) and Staphylococcus haemolyticus (one strain). All MRCoNS isolates were multidrug-resistant. In addition to β-lactams, the strains were resistant to fusidic acid (85%), tetracycline (75%), streptomycin (65%), ciprofloxacin (65%), and trimethoprim/sulphamethoxazole (60%). In addition to the mecA and blaZ genes, other antimicrobial resistance genes detected were tet(K), tet(M), tet(L), erm(B), erm(C), aacA-aphD, aphA3, str, dfrK, dfrG, cat pC221, and cat pC223. Thirteen isolates were found to be ciprofloxacin-resistant, and all harbored a Ser84Leu mutation within the QRDR of the GyrA protein, with 3 isolates showing 2 extra substitutions, Ser98Ile and Arg100Lys (one strain) and Glu88Asp and Asp96Thr (2 strains). A phylogenetic tree of the QRDR nucleotide sequences in the gyrA gene revealed a high nucleotide diversity, with several major clusters not associated with the bacterial species. Our study highlights the possibility of transfer of mecA and other antimicrobial resistance genes from MRCoNS to pathogenic bacteria, which is a serious public health and veterinary concern.
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Affiliation(s)
- Clifford C Ugwu
- Department of Animal Science and Technology, Federal University of Technology, Owerri, Nigeria
| | - Elena Gomez-Sanz
- Biochemistry and Molecular Biology Laboratory, Department of Food and Agriculture, University of La Rioja, Logrono, Spain
| | - Ifeoma C Agbo
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Nigeria
| | - Carmen Torres
- Biochemistry and Molecular Biology Laboratory, Department of Food and Agriculture, University of La Rioja, Logrono, Spain
| | - Kennedy F Chah
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Nigeria
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25
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Chiquet C, Maurin M, Altayrac J, Aptel F, Boisset S, Vandenesch F, Cornut P, Romanet J, Gain P, Carricajo A. Correlation between clinical data and antibiotic resistance in coagulase-negative Staphylococcus species isolated from 68 patients with acute post-cataract endophthalmitis. Clin Microbiol Infect 2015; 21:592.e1-8. [DOI: 10.1016/j.cmi.2015.01.028] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 01/26/2015] [Indexed: 11/30/2022]
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26
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Švec P, Bel AD, Sedláček I, Petráš P, Gelbíčová T, Černohlávková J, Mašlanˇová I, Cnockaert M, Varbanovová I, Echahidi F, Vandamme P, Pantu Ček R. Staphylococcus petrasii subsp. pragensis subsp. nov., occurring in human clinical material. Int J Syst Evol Microbiol 2015; 65:2071-2077. [PMID: 25829332 DOI: 10.1099/ijs.0.000220] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seven coagulase-negative, oxidase-negative and novobiocin-susceptible staphylococci assigned tentatively as Staphylococcus petrasii were investigated in this study in order to elucidate their taxonomic position. All strains were initially shown to form a genetically homogeneous group separated from remaining species of the genus Staphylococcus by using a repetitive sequence-based PCR fingerprinting with the (GTG)5 primer. Phylogenetic analysis based on 16S rRNA gene, hsp60, rpoB, dnaJ, gap and tuf sequences showed that the group is closely related to Staphylococcus petrasii but separated from the three hitherto known subspecies, S. petrasii subsp. petrasii, S. petrasii subsp. croceilyticus and S. petrasii subsp. jettensis. Further investigation using automated ribotyping, MALDI-TOF mass spectrometry, fatty acid methyl ester analysis, DNA-DNA hybridization and extensive biotyping confirmed that the analysed group represents a novel subspecies within S. petrasii, for which the name Staphylococcus petrasii subsp. pragensis subsp. nov. is proposed. The type strain is NRL/St 12/356(T) ( = CCM 8529(T) = LMG 28327(T)).
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Affiliation(s)
- Pavel Švec
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Bld. A25, 625 00 Brno, Czech Republic
| | - Annelies De Bel
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Ivo Sedláček
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Bld. A25, 625 00 Brno, Czech Republic
| | - Petr Petráš
- Reference Laboratory for Staphylococci, National Institute of Public Health, Šrobárova 48, 100 42 Prague 10, Czech Republic
| | - Tereza Gelbíčová
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Bld. A25, 625 00 Brno, Czech Republic
| | - Jitka Černohlávková
- Czech Collection of Microorganisms, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, Bld. A25, 625 00 Brno, Czech Republic
| | - Ivana Mašlanˇová
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlárˇská 2, 611 37 Brno, Czech Republic
| | - Margo Cnockaert
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Ivana Varbanovová
- Reference Laboratory for Staphylococci, National Institute of Public Health, Šrobárova 48, 100 42 Prague 10, Czech Republic
| | - Fedoua Echahidi
- 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
| | - Roman Pantu Ček
- Division of Genetics and Molecular Biology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlárˇská 2, 611 37 Brno, Czech Republic
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27
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Caspar Y, Jeanty M, Blu J, Burchak O, Le Pihive E, Maigre L, Schneider D, Jolivalt C, Paris JM, Hequet A, Minassian F, Denis JN, Maurin M. Novel synthetic bis-indolic derivatives with antistaphylococcal activity, including against MRSA and VISA strains. J Antimicrob Chemother 2015; 70:1727-37. [PMID: 25691323 DOI: 10.1093/jac/dkv015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 01/07/2015] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES We report the synthesis, antibacterial activity and toxicity of 24 bis-indolic derivatives obtained during the development of new ways of synthesis of marine bis-indole alkaloids from the spongotine, topsentin and hamacanthin classes. METHODS Innovative ways of synthesis and further structural optimizations led to bis-indoles presenting either the 1-(1H-indol-3'-yl)-1,2-diaminoethane unit or the 1-(1H-indol-3-yl)ethanamine unit. MIC determination was performed for reference and clinical strains of Staphylococcus aureus and CoNS species. MBC, time-kill kinetics, solubility, hydrophobicity index, plasma protein-binding and cytotoxicity assays were performed for lead compounds. Inhibition of the S. aureus NorA efflux pump was also tested for bis-indoles with no antistaphylococcal activity. RESULTS Lead compounds were active against both S. aureus and CoNS species, with MICs between 1 and 4 mg/L. Importantly, the same MICs were found for MRSA and vancomycin-intermediate S. aureus strains. Early concentration-dependent bactericidal activity was observed for lead derivatives. Compounds with no intrinsic antibacterial activity could inhibit the S. aureus NorA efflux pump, which is involved in resistance to fluoroquinolones. At 0.5 mg/L, the most effective compound led to an 8-fold reduction of the ciprofloxacin MIC for the SA-1199B S. aureus strain, which overexpresses NorA. However, the bis-indole compounds displayed a high hydrophobicity index and high plasma protein binding, which significantly reduced antibacterial activity. CONCLUSIONS We have synthesized and characterized novel bis-indole derivatives as promising candidates for the development of new antistaphylococcal treatments, with preserved activity against MDR S. aureus strains.
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Affiliation(s)
- Yvan Caspar
- Laboratoire de bactériologie, Centre Hospitalier Universitaire de Grenoble, CS10217, 38043 Grenoble cedex 9, France Université Grenoble Alpes, CNRS, LAPM, F-38000 Grenoble, France
| | - Matthieu Jeanty
- Université Grenoble Alpes, CNRS, DCM, F-38000 Grenoble, France
| | - Jérôme Blu
- Université Grenoble Alpes, CNRS, DCM, F-38000 Grenoble, France
| | - Olga Burchak
- Université Grenoble Alpes, CNRS, DCM, F-38000 Grenoble, France
| | | | - Laure Maigre
- Université Grenoble Alpes, CNRS, LAPM, F-38000 Grenoble, France
| | | | - Claude Jolivalt
- Chimie ParisTech, Laboratoire Charles Friedel, 75005 Paris, France
| | - Jean-Marc Paris
- Chimie ParisTech, Laboratoire Charles Friedel, 75005 Paris, France
| | - Arnaud Hequet
- Chimie ParisTech, Laboratoire Charles Friedel, 75005 Paris, France
| | | | - Jean-Noël Denis
- Université Grenoble Alpes, CNRS, DCM, F-38000 Grenoble, France
| | - Max Maurin
- Laboratoire de bactériologie, Centre Hospitalier Universitaire de Grenoble, CS10217, 38043 Grenoble cedex 9, France Université Grenoble Alpes, CNRS, LAPM, F-38000 Grenoble, France
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28
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Valour F, Rasigade JP, Trouillet-Assant S, Gagnaire J, Bouaziz A, Karsenty J, Lacour C, Bes M, Lustig S, Bénet T, Chidiac C, Etienne J, Vandenesch F, Ferry T, Laurent F. Delta-toxin production deficiency in Staphylococcus aureus: a diagnostic marker of bone and joint infection chronicity linked with osteoblast invasion and biofilm formation. Clin Microbiol Infect 2015; 21:568.e1-11. [PMID: 25677632 DOI: 10.1016/j.cmi.2015.01.026] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 01/21/2015] [Accepted: 01/24/2015] [Indexed: 11/29/2022]
Abstract
Biofilm formation, intra-osteoblastic persistence, small-colony variants (SCVs) and the dysregulation of agr, the major virulence regulon, are possibly involved in staphylococcal bone and joint infection (BJI) pathogenesis. We aimed to investigate the contributions of these mechanisms among a collection of 95 Staphylococcus aureus clinical isolates from 64 acute (67.4%) and 31 chronic (32.6%) first episodes of BJI. The included isolates were compared for internalization rate, cell damage and SCV intracellular emergence using an ex vivo model of human osteoblast infection. Biofilm formation was assessed in a microbead immobilization assay (BioFilm Ring test). Virulence gene profiles were assessed by DNA microarray. Seventeen different clonal complexes were identified among the screened collection. The staphylococcal internalization rate in osteoblasts was significantly higher for chronic than acute BJI isolates, regardless of the genetic background. Conversely, no differences regarding cytotoxicity, SCV emergence, biofilm formation and virulence gene distribution were observed. Additionally, agr dysfunction, detected by the lack of delta-toxin production using whole-cell matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) analysis (n = 15; 15.8%), was significantly associated with BJI chronicity, osteoblast invasion and biofilm formation. These findings provide new insights into MSSA BJI pathogenesis, suggesting the correlation between chronicity and staphylococcal osteoblast invasion. This adaptive mechanism, along with biofilm formation, is associated with agr dysfunction, which can be routinely assessed by delta-toxin detection using MALDI-TOF spectrum analysis, possibly providing clinicians with a diagnostic marker of BJI chronicity at the time of diagnosis.
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Affiliation(s)
- F Valour
- Department of Infectious Diseases, Hospices Civils de Lyon, France; Department of Microbiology, French National Reference Centre for Staphylococci, Hospices Civils de Lyon, France; INSERM U1111, International Centre for Infectiology Research, France; Claude Bernard Lyon 1 University, France.
| | - J-P Rasigade
- Department of Microbiology, French National Reference Centre for Staphylococci, Hospices Civils de Lyon, France; INSERM U1111, International Centre for Infectiology Research, France; Claude Bernard Lyon 1 University, France
| | | | - J Gagnaire
- Department of Microbiology, French National Reference Centre for Staphylococci, Hospices Civils de Lyon, France
| | - A Bouaziz
- Department of Infectious Diseases, Hospices Civils de Lyon, France
| | - J Karsenty
- Department of Infectious Diseases, Hospices Civils de Lyon, France
| | - C Lacour
- Department of Microbiology, French National Reference Centre for Staphylococci, Hospices Civils de Lyon, France
| | - M Bes
- Department of Microbiology, French National Reference Centre for Staphylococci, Hospices Civils de Lyon, France; INSERM U1111, International Centre for Infectiology Research, France
| | - S Lustig
- INSERM U1111, International Centre for Infectiology Research, France; Claude Bernard Lyon 1 University, France; Orthopaedic Surgery department, Hospices Civils de Lyon, France
| | - T Bénet
- Department of Infection Control and Epidemiology, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France
| | - C Chidiac
- Department of Infectious Diseases, Hospices Civils de Lyon, France; INSERM U1111, International Centre for Infectiology Research, France; Claude Bernard Lyon 1 University, France
| | - J Etienne
- Department of Microbiology, French National Reference Centre for Staphylococci, Hospices Civils de Lyon, France; INSERM U1111, International Centre for Infectiology Research, France; Claude Bernard Lyon 1 University, France
| | - F Vandenesch
- Department of Microbiology, French National Reference Centre for Staphylococci, Hospices Civils de Lyon, France; INSERM U1111, International Centre for Infectiology Research, France; Claude Bernard Lyon 1 University, France
| | - T Ferry
- Department of Infectious Diseases, Hospices Civils de Lyon, France; INSERM U1111, International Centre for Infectiology Research, France; Claude Bernard Lyon 1 University, France
| | - F Laurent
- Department of Microbiology, French National Reference Centre for Staphylococci, Hospices Civils de Lyon, France; INSERM U1111, International Centre for Infectiology Research, France; Claude Bernard Lyon 1 University, France
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29
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Vanderhaeghen W, Piepers S, Leroy F, Van Coillie E, Haesebrouck F, De Vliegher S. Identification, typing, ecology and epidemiology of coagulase negative staphylococci associated with ruminants. Vet J 2014; 203:44-51. [PMID: 25467994 DOI: 10.1016/j.tvjl.2014.11.001] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 10/28/2014] [Accepted: 11/03/2014] [Indexed: 11/29/2022]
Abstract
Since phenotypic methods to identify coagulase negative staphylococci (CNS) from the milk of ruminants often yield unreliable results, methods for molecular identification based on gene sequencing or fingerprinting techniques have been developed. In addition to culture-based detection of isolates, culture-independent methods may be of interest. On the basis of molecular studies, the five CNS species commonly causing intramammary infections (IMI) are Staphylococcus chromogenes, Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus simulans and Staphylococcus xylosus. Current knowledge suggests that S. chromogenes is a bovine-adapted species, with most cases of IMI due to this bacterium being opportunistic. S. haemolyticus also appears to be an opportunistic pathogen, but this bacterium occupies a variety of habitats, the importance of which as a source of IMI remains to be elucidated. S. xylosus appears to be a versatile species, but little is known of its epidemiology. S. epidermidis is considered to be a human-adapted species and most cases of IMI appear to arise from human sources, but the organism is capable of residing in other habitats. S. simulans typically causes contagious IMI, but opportunistic cases also occur and the ecology of this bacterium requires further study. Further studies of the ecology and epidemiology of CNS as a cause of IMI in cattle are required, along with careful attention to classification of these bacteria and the diseases they cause.
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Affiliation(s)
- Wannes Vanderhaeghen
- M-team and Mastitis and Milk Quality Research Unit, Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
| | - Sofie Piepers
- M-team and Mastitis and Milk Quality Research Unit, Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Frédéric Leroy
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Els Van Coillie
- Technology and Food Science Unit, Institute for Agricultural and Fisheries Research (ILVO), Brusselsesteenweg 370, 9090 Melle, Belgium
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Sarne De Vliegher
- M-team and Mastitis and Milk Quality Research Unit, Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
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The ecological importance of the Staphylococcus sciuri species group as a reservoir for resistance and virulence genes. Vet Microbiol 2014; 171:342-56. [DOI: 10.1016/j.vetmic.2014.02.005] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/30/2014] [Accepted: 02/01/2014] [Indexed: 11/18/2022]
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Roberts AL. Identification of Staphylococcus epidermidis in the clinical microbiology laboratory by molecular methods. Methods Mol Biol 2014; 1106:33-53. [PMID: 24222453 DOI: 10.1007/978-1-62703-736-5_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Biochemical assays for the phenotypic identification of coagulase-negative staphylococci in the clinical microbiology laboratory have been well described in previous publications (Becker and Von Eiff Manual of Clinical Microbiology, ASM Press, Washington, pp. 308-330, 2011; Kloos and Wolfshohl J Clin Microbiol 16:509-516, 1982). This discussion focuses on identification of Staphylococcus epidermidis through molecular and proteomic methods. Molecular assays have been shown to be more discriminatory between the coagulase-negative staphylococcal species than are phenotypic assays (Zadoks and Watts Vet Microbiol 134:20-28, 2009; Sheraba et al. BMC Res Notes 3:278, 2010; Patteet et al. Eur J Clin Microbiol Infect Dis 31:747-751, 2012). The molecular and proteomic methods that have shown the greatest utilization potential within the clinical laboratory are as follows: PCR amplification and sequencing of discriminatory genes, real-time polymerase chain reaction with species-specific probes in conjunction with a melt-curve analysis, fluorescence in situ hybridization, and matrix-assisted laser desorption-ionization time-of-flight mass spectrometry.
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Affiliation(s)
- Amity L Roberts
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
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Chah KF, Gómez-Sanz E, Nwanta JA, Asadu B, Agbo IC, Lozano C, Zarazaga M, Torres C. Methicillin-resistant coagulase-negative staphylococci from healthy dogs in Nsukka, Nigeria. Braz J Microbiol 2014; 45:215-20. [PMID: 24948934 PMCID: PMC4059299 DOI: 10.1590/s1517-83822014005000034] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 04/01/2013] [Indexed: 01/24/2023] Open
Abstract
The occurrence, resistance phenotype and molecular mechanisms of resistance of methicillin-resistant staphylococci from groin swabs of 109 clinically healthy dogs in Nsukka, Nigeria were investigated. The groin swab samples were cultured on mannitol salt agar supplemented with 10 μg of cloxacillin. Sixteen methicillin-resistant coagulase negative staphylococci (MRCoNS), all harbouring the mecA gene were isolated from 14 (12.8%) of the 109 dogs studied. The MRCoNS isolated were: S. sciuri subspecies rodentium, S. lentus, S. haemolyticus, and S. simulans with S. sciuri subspecies rodentium (62.5%) being the predominant species. Thirteen (81.3%) of the MRCoNS were resistant to tetracycline while 12 (75%) and 10 (62.5%) were resistant to kanamycin and trimthoprim-sulphamethoxazole respectively. None of the isolates was resistant to fusidic acid, linezolid and vancomycin. Thirteen (81.3%) of the MRCoNS were multi-drug resistance (MDR). Other antimicrobial genes detected were: blaZ, tet(K), tet(M), tet(L), erm(B), lnu(A), aacA-aphD, aphA3, str, dfr(G), catpC221, and catpC223. Methicillin-resistant staphylococci are common colonizers of healthy dogs in Nigeria with a major species detected being S. sciuri subsp. rodentium.
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Affiliation(s)
- Kennedy F Chah
- Department of Veterinary Pathology and Microbiology University of Nigeria Nsukka
| | - Elena Gómez-Sanz
- Biochemistry and Molecular Biology University of La Rioja Logroño Spain
| | - John A Nwanta
- Department of Veterinary Public Health and Preventive Medicine University of Nigeria Nsukka
| | - Brendan Asadu
- Department of Veterinary Public Health and Preventive Medicine University of Nigeria Nsukka
| | - Ifeoma C Agbo
- Department of Veterinary Pathology and Microbiology University of Nigeria Nsukka
| | - Carmen Lozano
- Biochemistry and Molecular Biology University of La Rioja Logroño Spain
| | - Myriam Zarazaga
- Biochemistry and Molecular Biology University of La Rioja Logroño Spain
| | - Carmen Torres
- Biochemistry and Molecular Biology University of La Rioja Logroño Spain
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Filleron A, Simon M, Hantova S, Jacquot A, Cambonie G, Marchandin H, Jumas-Bilak E. tuf-PCR-temporal temperature gradient gel electrophoresis for molecular detection and identification of staphylococci: Application to breast milk and neonate gut microbiota. J Microbiol Methods 2014; 98:67-75. [DOI: 10.1016/j.mimet.2013.12.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 12/29/2013] [Accepted: 12/30/2013] [Indexed: 11/30/2022]
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Schmidt VM, Williams NJ, Pinchbeck G, Corless CE, Shaw S, McEwan N, Dawson S, Nuttall T. Antimicrobial resistance and characterisation of staphylococci isolated from healthy Labrador retrievers in the United Kingdom. BMC Vet Res 2014; 10:17. [PMID: 24423104 PMCID: PMC3896740 DOI: 10.1186/1746-6148-10-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 01/06/2014] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Coagulase-positive (CoPS) and coagulase-negative (CoNS) staphylococci are normal commensals of the skin and mucosa, but are also opportunist pathogens. Meticillin-resistant (MR) and multidrug-resistant (MDR) isolates are increasing in human and veterinary healthcare. Healthy humans and other animals harbour a variety of staphylococci, including MR-CoPS and MR-CoNS. The main aims of the study were to characterise the population and antimicrobial resistance profiles of staphylococci from healthy non-vet visiting and non-antimicrobial treated Labrador retrievers in the UK. RESULTS Nasal and perineal samples were collected from 73 Labrador retrievers; staphylococci isolated and identified using phenotypic and biochemical methods. They were also confirmed by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF-MS), PCR of the nuc gene and PCR and sequencing of the tuf gene. Disc diffusion and minimum inhibitory concentration (MIC) susceptibility tests were determined for a range of antimicrobials. In total, 102 CoPS (S. pseudintermedius n = 91, S. aureus n = 11) and 334 CoNS isolates were detected from 99% of dogs in this study. In 52% of dogs CoNS only were detected, with both CoNS and CoPS detected in 43% dogs and CoPS only detected in 4% of dogs. Antimicrobial resistance was not common among CoPS, but at least one MDR-CoNS isolate was detected in 34% of dogs. MR-CoNS were detected from 42% of dogs but no MR-CoPS were isolated. S. epidermidis (52% of dogs) was the most common CoNS found followed by S. warneri (30%) and S. equorum (27%), with another 15 CoNS species isolated from ≤ 15% of dogs. S. pseudintermedius and S. aureus were detected in 44% and 8% of dogs respectively. CONCLUSIONS MR- and MDR-CoPS were rare. However a high prevalence of MR- and MDR-CoNS were found in these dogs, even though they had no prior antimicrobial treatment or admission to veterinary premises. These findings are of concern due to the potential for opportunistic infections, zoonotic transmission and transmission of antimicrobial resistant determinants from these bacteria to coagulase positive staphylococci.
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Affiliation(s)
- Vanessa M Schmidt
- Department of Infection Biology, The University of Liverpool, Leahurst Campus, Neston, UK
- The University of Liverpool School of Veterinary Science, Leahurst Campus, Chester High Road, Neston, Wirral CH64 7TE, UK
| | - Nicola J Williams
- Department of Epidemiology and Population Health, The University of Liverpool, Leahurst Campus, Neston, UK
| | - Gina Pinchbeck
- Department of Epidemiology and Population Health, The University of Liverpool, Leahurst Campus, Neston, UK
| | - Caroline E Corless
- Infection and Immunity, Royal Liverpool University Hospital, Liverpool, UK
| | | | - Neil McEwan
- Department of Infection Biology, The University of Liverpool, Leahurst Campus, Neston, UK
- The University of Liverpool School of Veterinary Science, Leahurst Campus, Chester High Road, Neston, Wirral CH64 7TE, UK
| | - Susan Dawson
- Department of Epidemiology and Population Health, The University of Liverpool, Leahurst Campus, Neston, UK
| | - Tim Nuttall
- The Royal (Dick) School of Veterinary Studies, Easter Bush Campus, University of Edinburgh, Midlothian, UK
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Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology. Clin Microbiol Rev 2014; 26:547-603. [PMID: 23824373 DOI: 10.1128/cmr.00072-12] [Citation(s) in RCA: 524] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the "nuts and bolts" of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care.
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Valour F, Trouillet-Assant S, Rasigade JP, Lustig S, Chanard E, Meugnier H, Tigaud S, Vandenesch F, Etienne J, Ferry T, Laurent F. Staphylococcus epidermidis in orthopedic device infections: the role of bacterial internalization in human osteoblasts and biofilm formation. PLoS One 2013; 8:e67240. [PMID: 23840636 PMCID: PMC3696042 DOI: 10.1371/journal.pone.0067240] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 05/15/2013] [Indexed: 11/19/2022] Open
Abstract
Background Staphylococcus epidermidis orthopedic device infections are caused by direct inoculation of commensal flora during surgery and remain rare, although S. epidermidis carriage is likely universal. We wondered whether S. epidermidis orthopedic device infection strains might constitute a sub-population of commensal isolates with specific virulence ability. Biofilm formation and invasion of osteoblasts by S. aureus contribute to bone and joint infection recurrence by protecting bacteria from the host-immune system and most antibiotics. We aimed to determine whether S. epidermidis orthopedic device infection isolates could be distinguished from commensal strains by their ability to invade osteoblasts and form biofilms. Materials and Methods Orthopedic device infection S. epidermidis strains (n = 15) were compared to nasal carriage isolates (n = 22). Osteoblast invasion was evaluated in an ex vivo infection model using MG63 osteoblastic cells co-cultured for 2 hours with bacteria. Adhesion of S. epidermidis to osteoblasts was explored by a flow cytometric approach, and internalized bacteria were quantified by plating cell lysates after selective killing of extra-cellular bacteria with gentamicin. Early and mature biofilm formations were evaluated by a crystal violet microtitration plate assay and the Biofilm Ring Test method. Results No difference was observed between commensal and infective strains in their ability to invade osteoblasts (internalization rate 308+/−631 and 347+/−431 CFU/well, respectively). This low internalization rate correlated with a low ability to adhere to osteoblasts. No difference was observed for biofilm formation between the two groups. Conclusion Osteoblast invasion and biofilm formation levels failed to distinguish S. epidermidis orthopedic device infection strains from commensal isolates. This study provides the first assessment of the interaction between S. epidermidis strains isolated from orthopedic device infections and osteoblasts, and suggests that bone cell invasion is not a major pathophysiological mechanism in S. epidermidis orthopedic device infections, contrary to what is observed for S. aureus.
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Affiliation(s)
- Florent Valour
- INSERM U1111, International Center for Research in Infectiology, Lyon, France.
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Geraghty L, Booth M, Rowan N, Fogarty A. Investigations on the efficacy of routinely used phenotypic methods compared to genotypic approaches for the identification of staphylococcal species isolated from companion animals in Irish veterinary hospitals. Ir Vet J 2013; 66:7. [PMID: 23635328 PMCID: PMC3649918 DOI: 10.1186/2046-0481-66-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Accepted: 04/02/2013] [Indexed: 11/17/2022] Open
Abstract
Background Identification of Staphylococci to species level in veterinary microbiology is important to inform therapeutic intervention and management. We report on the efficacy of three routinely used commercial phenotypic methods for staphylococcal species identification, namely API Staph 32 (bioMérieux), RapID (Remel) and Staph-Zym (Rosco Diagnostica) compared to genotyping as a reference method to identify 52 staphylococcal clinical isolates (23 coagulase positive; 29 coagulase negative) from companion animals in Irish veterinary hospitals. Results Genotyping of a 412 bp fragment of the staphylococcal tuf gene and coagulase testing were carried out on all 52 veterinary samples along with 7 reference strains. In addition, genotyping of the staphylococcal rpoB gene, as well as PCR-RFLP of the pta gene, were performed to definitively identify members of the Staphylococcus intermedius group (SIG). The API Staph 32 correctly identified all S. aureus isolates (11/11), 83% (10/12) of the SIG species, and 66% (19/29) of the coagulase negative species. RapID and Staph-Zym correctly identified 61% (14/23) and 0% (0/23) respectively of the coagulase-positives, and 10% (3/29) and 3% (1/29) respectively of the coagulase-negative species. Conclusions Commercially available phenotypic species identification tests are inadequate for the correct identification of both coagulase negative and coagulase positive staphylococcal species from companion animals. Genotyping using the tuf gene sequence is superior to phenotyping for identification of staphylococcal species of animal origin. However, use of PCR-RFLP of pta gene or rpoB sequencing is recommended as a confirmatory method for discriminating between SIG isolates.
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Affiliation(s)
- Lisa Geraghty
- Biosciences Research Institute, Athlone Institute of Technology, Dublin Rd., Athlone, Co. Westmeath, Ireland ; Department of Life and Physical Science, School of Science, Athlone Institute of Technology, Dublin Rd., Athlone, Ireland
| | - Mary Booth
- Biosciences Research Institute, Athlone Institute of Technology, Dublin Rd., Athlone, Co. Westmeath, Ireland ; Department of Life and Physical Science, School of Science, Athlone Institute of Technology, Dublin Rd., Athlone, Ireland
| | - Neil Rowan
- Biosciences Research Institute, Athlone Institute of Technology, Dublin Rd., Athlone, Co. Westmeath, Ireland
| | - Andrew Fogarty
- Biosciences Research Institute, Athlone Institute of Technology, Dublin Rd., Athlone, Co. Westmeath, Ireland ; Department of Life and Physical Science, School of Science, Athlone Institute of Technology, Dublin Rd., Athlone, Ireland
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Comparison of the accuracy of matrix-assisted laser desorption ionization-time of flight mass spectrometry with that of other commercial identification systems for identifying Staphylococcus saprophyticus in urine. J Clin Microbiol 2013; 51:1563-6. [PMID: 23390286 DOI: 10.1128/jcm.00261-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Among 30 urinary isolates of Staphylococcus saprophyticus identified by sequencing methods, the rate of accurate identification was 100% for Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), 86.7% for the Phoenix PID and Vitek 2 GP systems, 93.3% for the MicroScan GP33 system, and 46.7% for the BBL CHROMagar Orientation system.
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Böhme K, Morandi S, Cremonesi P, Fernández No IC, Barros-Velázquez J, Castiglioni B, Brasca M, Cañas B, Calo-Mata P. Characterization of Staphylococcus aureus strains isolated from Italian dairy products by MALDI-TOF mass fingerprinting. Electrophoresis 2012; 33:2355-64. [PMID: 22887156 DOI: 10.1002/elps.201100480] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Staphylococcus aureus is a known pathogen, causing serious food-borne intoxications due to the production of enterotoxins, being otherwise a major cause of mastitis. In this sense, the detection of S. aureus is an important issue for the food industry to avoid health hazards and economic losses. The present work applied MALDI-TOF MS for the classification of 40 S. aureus strains, 36 isolated from Italian dairy products and four from human samples. All isolated strains were clearly identified as S. aureus by their spectral fingerprints. The peak masses m/z 3444, 5031, and 6887 were determined to be specific biomarkers for S. aureus. Furthermore, clustering of the peak mass lists was successfully applied as a typing method, resulting in eight groups of strains. This is the first time that a detailed spectral comparison was carried out and characteristic peak masses were determined for every spectral group. Three strains exhibited a peak at m/z 6917 instead of m/z 6887, which was related to four polymorphisms in their 16S rRNA sequences. However, the grouping obtained by MALDI-TOF MS fingerprinting could not be related to toxin production or to the origin of the strains.
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Affiliation(s)
- Karola Böhme
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Lugo, Spain
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Temporal trends in infective endocarditis in the context of prophylaxis guideline modifications: three successive population-based surveys. J Am Coll Cardiol 2012; 59:1968-76. [PMID: 22624837 DOI: 10.1016/j.jacc.2012.02.029] [Citation(s) in RCA: 257] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 02/10/2012] [Accepted: 02/14/2012] [Indexed: 12/21/2022]
Abstract
OBJECTIVES The goal of this study was to evaluate temporal trends in infective endocarditis (IE) incidence and clinical characteristics after 2002 French IE prophylaxis guideline modifications. BACKGROUND There are limited data on changes in the epidemiology of IE since recent guidelines recommended restricting the indications of antibiotic prophylaxis of IE. METHODS Three 1-year population-based surveys were conducted in 1991, 1999, and 2008 in 3 French regions totaling 11 million inhabitants age ≥20 years. We prospectively collected IE cases from all medical centers and analyzed age- and sex-standardized IE annual incidence trends. RESULTS Overall, 993 expert-validated IE cases were analyzed (323 in 1991; 331 in 1999; and 339 in 2008). IE incidence remained stable over time (95% confidence intervals given in parentheses/brackets): 35 (31 to 39), 33 (30 to 37), and 32 (28 to 35) cases per million in 1991, 1999, and 2008, respectively. Oral streptococci IE incidence did not increase either in the whole patient population (8.1 [6.4 to 10.1], 6.3 [4.8 to 8.1], and 6.3 [4.9 to 8.0] in 1991, 1999, and 2008, respectively) or in patients with pre-existing native valve disease. The increased incidence of Staphylococcus aureus IE (5.2 [3.9 to 6.8], 6.8 [5.3 to 8.6], and 8.2 [6.6 to 10.2]) was not significant in the whole patient population (p = 0.228) but was significant in the subgroup of patients without previously known native valve disease (1.6 [0.9 to 2.7], 3.7 [2.6 to 5.1], and 4.1 [3.0 to 5.6]; p = 0.012). CONCLUSIONS Scaling down antibiotic prophylaxis indications was not associated with an increased incidence of oral streptococcal IE. A focus on avoidance of S. aureus bacteremia in all patients, including those with no previously known valve disease, will be required to improve IE prevention.
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Gagnaire J, Dauwalder O, Boisset S, Khau D, Freydière AM, Ader F, Bes M, Lina G, Tristan A, Reverdy ME, Marchand A, Geissmann T, Benito Y, Durand G, Charrier JP, Etienne J, Welker M, Van Belkum A, Vandenesch F. Detection of Staphylococcus aureus delta-toxin production by whole-cell MALDI-TOF mass spectrometry. PLoS One 2012; 7:e40660. [PMID: 22792394 PMCID: PMC3391297 DOI: 10.1371/journal.pone.0040660] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 06/11/2012] [Indexed: 12/18/2022] Open
Abstract
The aim of the present study was to detect the Staphylococcus aureus delta-toxin using Whole-Cell (WC) Matrix Assisted Laser Desorption Ionization-Time-of-Flight (MALDI-TOF) mass spectrometry (MS), correlate delta-toxin expression with accessory gene regulator (agr) status, and assess the prevalence of agr deficiency in clinical isolates with and without resistance to methicillin and glycopeptides. The position of the delta-toxin peak in the mass spectrum was identified using purified delta-toxin and isogenic wild type and mutant strains for agr-rnaIII, which encodes delta-toxin. Correlation between delta-toxin production and agr RNAIII expression was assessed by northern blotting. A series of 168 consecutive clinical isolates and 23 unrelated glycopeptide-intermediate S. aureus strains (GISA/heterogeneous GISA) were then tested by WC-MALDI-TOF MS. The delta-toxin peak was detected at 3005±5 Thomson, as expected for the naturally formylated delta toxin, or at 3035±5 Thomson for its G10S variant. Multivariate analysis showed that chronicity of S. aureus infection and glycopeptide resistance were significantly associated with delta-toxin deficiency (p = 0.048; CI 95%: 1.01-10.24; p = 0.023; CI 95%: 1.20-12.76, respectively). In conclusion, the S. aureus delta-toxin was identified in the WC-MALDI-TOF MS spectrum generated during routine identification procedures. Consequently, agr status can potentially predict infectious complications and rationalise application of novel virulence factor-based therapies.
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Affiliation(s)
- Julie Gagnaire
- Hospices Civils de Lyon, Centre National de Référence des Staphylocoques, Centre de Biologie et de Pathologie Est, Bron, France
| | - Olivier Dauwalder
- Hospices Civils de Lyon, Centre National de Référence des Staphylocoques, Centre de Biologie et de Pathologie Est, Bron, France
- Université de Lyon, Domaine de la Buire, Lyon, France
- INSERM U851, Bacterial Pathogenesis and Innate Immunity laboratory, Lyon, France
| | - Sandrine Boisset
- Hospices Civils de Lyon, Centre National de Référence des Staphylocoques, Centre de Biologie et de Pathologie Est, Bron, France
- Université de Lyon, Domaine de la Buire, Lyon, France
- INSERM U851, Bacterial Pathogenesis and Innate Immunity laboratory, Lyon, France
| | - David Khau
- Hospices Civils de Lyon, Centre National de Référence des Staphylocoques, Centre de Biologie et de Pathologie Est, Bron, France
| | - Anne-Marie Freydière
- Hospices Civils de Lyon, Centre National de Référence des Staphylocoques, Centre de Biologie et de Pathologie Est, Bron, France
| | - Florence Ader
- INSERM U851, Bacterial Pathogenesis and Innate Immunity laboratory, Lyon, France
- Hospices Civils de Lyon, Service de Maladies Infectieuses, Lyon, France
| | - Michèle Bes
- Hospices Civils de Lyon, Centre National de Référence des Staphylocoques, Centre de Biologie et de Pathologie Est, Bron, France
- INSERM U851, Bacterial Pathogenesis and Innate Immunity laboratory, Lyon, France
| | - Gerard Lina
- Hospices Civils de Lyon, Centre National de Référence des Staphylocoques, Centre de Biologie et de Pathologie Est, Bron, France
- Université de Lyon, Domaine de la Buire, Lyon, France
- INSERM U851, Bacterial Pathogenesis and Innate Immunity laboratory, Lyon, France
| | - Anne Tristan
- Hospices Civils de Lyon, Centre National de Référence des Staphylocoques, Centre de Biologie et de Pathologie Est, Bron, France
- Université de Lyon, Domaine de la Buire, Lyon, France
- INSERM U851, Bacterial Pathogenesis and Innate Immunity laboratory, Lyon, France
| | - Marie-Elisabeth Reverdy
- Hospices Civils de Lyon, Centre National de Référence des Staphylocoques, Centre de Biologie et de Pathologie Est, Bron, France
| | - Adrienne Marchand
- Laboratoire de Chimie et Microbiologie de l’Eau - UMR 6008 CNRS, IBMIG - UFR Sciences Fondamentales et Appliquées, Université de Poitiers, Poitiers, France
| | - Thomas Geissmann
- Université de Lyon, Domaine de la Buire, Lyon, France
- INSERM U851, Bacterial Pathogenesis and Innate Immunity laboratory, Lyon, France
| | - Yvonne Benito
- Hospices Civils de Lyon, Centre National de Référence des Staphylocoques, Centre de Biologie et de Pathologie Est, Bron, France
- Université de Lyon, Domaine de la Buire, Lyon, France
- INSERM U851, Bacterial Pathogenesis and Innate Immunity laboratory, Lyon, France
| | - Géraldine Durand
- bioMérieux S.A, Microbiology Research & Development unit, La Balme Les Grottes, France
| | - Jean-Philippe Charrier
- bioMérieux S.A, Technology Research Department, Technology platform, Marcy L’Etoile France
| | - Jerome Etienne
- Hospices Civils de Lyon, Centre National de Référence des Staphylocoques, Centre de Biologie et de Pathologie Est, Bron, France
- Université de Lyon, Domaine de la Buire, Lyon, France
- INSERM U851, Bacterial Pathogenesis and Innate Immunity laboratory, Lyon, France
| | - Martin Welker
- bioMérieux S.A, Microbiology Research & Development unit, La Balme Les Grottes, France
| | - Alex Van Belkum
- bioMérieux S.A, Microbiology Research & Development unit, La Balme Les Grottes, France
| | - François Vandenesch
- Hospices Civils de Lyon, Centre National de Référence des Staphylocoques, Centre de Biologie et de Pathologie Est, Bron, France
- Université de Lyon, Domaine de la Buire, Lyon, France
- INSERM U851, Bacterial Pathogenesis and Innate Immunity laboratory, Lyon, France
- * E-mail:
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Comparative study using phenotypic, genotypic, and proteomics methods for identification of coagulase-negative staphylococci. J Clin Microbiol 2012; 50:1437-9. [PMID: 22238435 DOI: 10.1128/jcm.06746-11] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Five methods were compared to determine the most accurate method for identification of coagulase-negative staphylococci (CoNS) (n = 142 strains). Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) showed the best results for rapid and accurate CoNS differentiation (99.3% of strains correctly identified). An alternative to this approach could be Vitek2 combined with partial tuf gene sequencing (100% of strains correctly identified when both methods are performed simultaneously).
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Tuf gene sequence analysis has greater discriminatory power than 16S rRNA sequence analysis in identification of clinical isolates of coagulase-negative staphylococci. J Clin Microbiol 2011; 49:4142-9. [PMID: 21998419 DOI: 10.1128/jcm.05213-11] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We compared and analyzed 16S rRNA and tuf gene sequences for 97 clinical isolates of coagulase-negative staphylococci (CNS) by use of the GenBank, MicroSeq, EzTaxon, and BIBI databases. Discordant results for definitive identification were observed and differed according to the different databases and target genes. Although higher percentages of sequence identity were obtained with GenBank and MicroSeq for 16S rRNA analysis, the BIBI and EzTaxon databases produced less ambiguous results. Greater discriminatory power and fewer multiple probable identifications were observed with tuf gene analysis than with 16S rRNA analysis. The most pertinent results for tuf gene analysis were obtained with the GenBank database when the cutoff values for the percentage of identity were adjusted to be greater than or equal to 98.0%, with >0.8% separation between species. Analysis of the tuf gene proved to be more discriminative for certain CNS species; further, this method exhibited better distinction in the identification of CNS clinical isolates.
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Tuf gene sequence analysis has greater discriminatory power than 16S rRNA sequence analysis in identification of clinical isolates of coagulase-negative staphylococci. J Clin Microbiol 2011. [PMID: 21998419 DOI: 10.1128/jcm.05213-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We compared and analyzed 16S rRNA and tuf gene sequences for 97 clinical isolates of coagulase-negative staphylococci (CNS) by use of the GenBank, MicroSeq, EzTaxon, and BIBI databases. Discordant results for definitive identification were observed and differed according to the different databases and target genes. Although higher percentages of sequence identity were obtained with GenBank and MicroSeq for 16S rRNA analysis, the BIBI and EzTaxon databases produced less ambiguous results. Greater discriminatory power and fewer multiple probable identifications were observed with tuf gene analysis than with 16S rRNA analysis. The most pertinent results for tuf gene analysis were obtained with the GenBank database when the cutoff values for the percentage of identity were adjusted to be greater than or equal to 98.0%, with >0.8% separation between species. Analysis of the tuf gene proved to be more discriminative for certain CNS species; further, this method exhibited better distinction in the identification of CNS clinical isolates.
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Haenni M, Châtre P, Boisset S, Carricajo A, Bes M, Laurent F, Madec JY. Staphylococcal nasal carriage in calves: multiresistant Staphylococcus sciuri and immune evasion cluster (IEC) genes in methicillin-resistant Staphylococcus aureus ST398. J Antimicrob Chemother 2011; 66:1927-8. [PMID: 21609981 DOI: 10.1093/jac/dkr196] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Carpaij N, Willems RJL, Bonten MJM, Fluit AC. Comparison of the identification of coagulase-negative staphylococci by matrix-assisted laser desorption ionization time-of-flight mass spectrometry and tuf sequencing. Eur J Clin Microbiol Infect Dis 2011; 30:1169-72. [PMID: 21359622 PMCID: PMC3172412 DOI: 10.1007/s10096-011-1204-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 02/11/2011] [Indexed: 11/30/2022]
Abstract
The increasing incidence of coagulase-negative staphylococci (CoNS) in hospital-acquired infections underlines the need for an accurate and simple identification of Staphylococcus isolates at the species level. Sequencing of the tuf gene has been shown to be the most accurate for the species identification of CoNS. We determined the species of 62 consecutive clinical and 31 reference CoNS isolates by tuf gene sequencing and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Species assignment by MALDI-TOF-MS and tuf sequencing was congruent in all cases. We conclude that MALDI-TOF-MS is accurate for identifying CoNS in routine clinical practice. The study also identified an unexpectedly high number of cases of Staphylococcus capitis infections among 62 consecutive CoNS isolates in 2009 at the University Medical Center Utrecht, the Netherlands.
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Affiliation(s)
- N Carpaij
- Department of Medical Microbiology, University Medical Center Utrecht, room G04.614, PO Box 85500, 3508 GA Utrecht, The Netherlands.
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Rood IGH, de Korte D, Ramírez-Arcos S, Savelkoul PHM, Pettersson A. Distribution, origin and contamination risk of coagulase-negative staphylococci from platelet concentrates. J Med Microbiol 2011; 60:592-599. [PMID: 21212143 DOI: 10.1099/jmm.0.023176-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Transfusion-associated bacterial sepsis is the most common microbiological risk of transfusion and is caused mostly by platelet concentrates (PCs). The most frequently identified bacterial contaminants of PCs are coagulase-negative staphylococci (CNS). In order to learn more about the distribution, source and risk of the CNS that are involved in bacterial contamination of PCs, CNS strains isolated during platelet screening were collected and characterized to the species level with three different methods: 16S rRNA and sodA gene sequencing, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and amplified fragment length polymorphism (AFLP) analysis. AFLP analysis was also used for the typing of the CNS strains. A total of 83 CNS strains were analysed by sequencing and 8 different CNS species were identified, with Staphylococcus epidermidis being the predominant species. MALDI-TOF MS and AFLP analysis confirmed these results to a large extent. However, MALDI_TOF MS could not identify all strains to the species level and AFLP analysis revealed an additional, likely novel, CNS species. The species identified are mainly recognized as being part of the normal skin flora. Typing of the CNS strains by AFLP analysis showed that there was not a unique strain which is significantly more often present during bacterial contamination of PCs.
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Affiliation(s)
- Ineke G H Rood
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
- Department of Blood Cell Research, Sanquin Research, Amsterdam, The Netherlands
| | - Dirk de Korte
- Department of Blood Cell Research, Sanquin Research, Amsterdam, The Netherlands
| | | | - Paul H M Savelkoul
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - Annika Pettersson
- Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
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