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Ballah FM, Hoque MN, Islam MS, Faisal GM, Rahman AMMT, Khatun MM, Rahman M, Hassan J, Rahman MT. Genomic Insights of a Methicillin-Resistant Biofilm-Producing Staphylococcus aureus Strain Isolated From Food Handlers. BIOMED RESEARCH INTERNATIONAL 2024; 2024:5516117. [PMID: 39071244 PMCID: PMC11283335 DOI: 10.1155/2024/5516117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/27/2024] [Accepted: 06/24/2024] [Indexed: 07/30/2024]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is an important zoonotic pathogen associated with a wide range of infections in humans and animals. Thus, the emergence of MRSA clones poses an important threat to human and animal health. This study is aimed at elucidating the genomics insights of a strong biofilm-producing and multidrug-resistant (MDR) S. aureus MTR_BAU_H1 strain through whole-genome sequencing (WGS). The S. aureus MTR_BAU_H1 strain was isolated from food handlers' hand swabs in Bangladesh and phenotypically assessed for antimicrobial susceptibility and biofilm production assays. The isolate was further undergone to high throughput WGS and analysed using different bioinformatics tools to elucidate the genetic diversity, molecular epidemiology, sequence type (ST), antimicrobial resistance, and virulence gene distribution. Phenotypic analyses revealed that the S. aureus MTR_BAU_H1 strain is a strong biofilm-former and carries both antimicrobial resistance (e.g., methicillin resistance; mecA, beta-lactam resistance; blaZ and tetracycline resistance; tetC) and virulence (e.g., sea, tsst, and PVL) genes. The genome of the S. aureus MTR_BAU_H1 belonged to ST1930 that possessed three plasmid replicons (e.g., rep16, rep7c, and rep19), seven prophages, and two clustered regularly interspaced short palindromic repeat (CRISPR) arrays of varying sizes. Phylogenetic analysis showed a close evolutionary relationship between the MTR_BAU_H1 genome and other MRSA clones of diverse hosts and demographics. The MTR_BAU_H1 genome harbours 42 antimicrobial resistance genes (ARGs), 128 virulence genes, and 273 SEED subsystems coding for the metabolism of amino acids, carbohydrates, proteins, cofactors, vitamins, minerals, and lipids. This is the first-ever WGS-based study of a strong biofilm-producing and MDR S. aureus strain isolated from human hand swabs in Bangladesh that unveils new information on the resistomes (ARGs and correlated mechanisms) and virulence potentials that might be linked to staphylococcal pathogenesis in both humans and animals.
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Affiliation(s)
- Fatimah Muhammad Ballah
- Department of Microbiology and HygieneFaculty of Veterinary ScienceBangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - M. Nazmul Hoque
- Molecular Biology and Bioinformatics LaboratoryDepartment of GynaecologyObstetrics and Reproductive HealthBangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Md. Saiful Islam
- Department of Microbiology and HygieneFaculty of Veterinary ScienceBangladesh Agricultural University, Mymensingh 2202, Bangladesh
- Department of Animal SciencesUniversity of California-Davis, Davis, California CA 95616, USA
| | - Golam Mahbub Faisal
- Molecular Biology and Bioinformatics LaboratoryDepartment of GynaecologyObstetrics and Reproductive HealthBangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | | | - Mst. Minara Khatun
- Department of Microbiology and HygieneFaculty of Veterinary ScienceBangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Marzia Rahman
- Department of Microbiology and HygieneFaculty of Veterinary ScienceBangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Jayedul Hassan
- Department of Microbiology and HygieneFaculty of Veterinary ScienceBangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Md. Tanvir Rahman
- Department of Microbiology and HygieneFaculty of Veterinary ScienceBangladesh Agricultural University, Mymensingh 2202, Bangladesh
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Huang L, Zhu L, Yan J, Lin Y, Ding D, He L, Li Y, Ying Y, Shen L, Jiang Y, Cai H, Jiang T. Genomic characterization and outbreak investigations of methicillin-resistant Staphylococcus aureus in a county-level hospital in China. Front Microbiol 2024; 15:1387855. [PMID: 38638904 PMCID: PMC11025083 DOI: 10.3389/fmicb.2024.1387855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 03/11/2024] [Indexed: 04/20/2024] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a common pathogen contributing to healthcare-associated infections, which can result in multiple sites infections. The epidemiological characteristics of MRSA exhibit variability among distinct regions and healthcare facilities. The aim of this study was to investigate the molecular epidemiology and nosocomial outbreak characteristics of MRSA in a county-level hospital in China. A total of 130 non-repetitive MRSA strains were collected from December 2020 to November 2021. Whole-genome sequencing (WGS) was performed to identify antimicrobial resistance and virulence factors. Phylogenetic analysis was conducted to ascertain genetic diversity and phylogenetic relationships. Independent transmission scenarios were determined by the phylogeny derived from single nucleotide polymorphisms (SNPs) within the core genome. All the MRSA isolates were collected from the intensive care unit (30.00%, 39/130), the department of otorhinolaryngology (10.00%, 13/130) and the department of burn unit (9.23%, 12/130). The clinical samples mainly included phlegm (53.85%, 70/130), purulent fluid (24.62%, 32/130), and secretions (8.46%, 11/130). The resistance rates to erythromycin, clindamycin and ciprofloxacin were 75.38, 40.00, and 39.23%, respectively. All the isolates belonged to 11 clonal complexes (CCs), with the major prevalent types were CC5, CC59, and CC398, accounting for 30.00% (39/130), 29.23% (38/130), and 16.92% (22/130), respectively. Twenty sequence types (STs) were identified, and ST59 (25.38%, 33/130) was the dominant lineage, followed by ST5 (23.84%, 31/130) and ST398 (16.92%, 22/130). Three different SCCmec types were investigated, most of isolates were type IV (33.85%, 44/130), followed by type II (27.69%, 36/130) and type III (0.77%, 1/130). The common clonal structures included CC5-ST5-t2460-SCCmec IIa, CC59-ST59-t437-SCCmec IV and CC398-ST398-t034-SCCmec (-), with rates of 16.92% (22/130), 14.62% (19/130), and 13.84% (18/130), respectively. Only 12 panton-valentine leucocidin (PVL) positive strains were identified. Two independent clonal outbreaks were detected, one consisting of 22 PVL-negative strains belongs to CC5-ST5-t2460-SCCmec IIa and the other consisting of 8 PVL-negative strains belongs to CC5-ST5-t311-SCCmec IIa. Overall, our study indicated that the CC5 lineage emerged as the predominant epidemic clone of MRSA, responsible for nosocomial outbreaks and transmission within a county-level hospital in China, highlighting the necessity to strengthen infection control measures for MRSA in such healthcare facilities.
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Affiliation(s)
- Linyao Huang
- Department of Clinical Laboratory, The First People's Hospital of Wenling, Affiliated Wenling Hospital, Wenzhou Medical University, Wenling, China
| | - Liangrong Zhu
- Department of Pharmacy, Wenling Hospital of Traditional Chinese Medicine, Affiliated Wenling Traditional Chinese Medicine Hospital, Zhejiang Chinese Medical University, Wenling, China
| | - Jianxin Yan
- Department of Clinical Laboratory, The First People's Hospital of Wenling, Affiliated Wenling Hospital, Wenzhou Medical University, Wenling, China
| | - Yajing Lin
- Department of Clinical Laboratory, The First People's Hospital of Wenling, Affiliated Wenling Hospital, Wenzhou Medical University, Wenling, China
| | - Ding Ding
- Department of Clinical Laboratory, The First People's Hospital of Wenling, Affiliated Wenling Hospital, Wenzhou Medical University, Wenling, China
| | - Long He
- Department of Clinical Laboratory, The First People's Hospital of Wenling, Affiliated Wenling Hospital, Wenzhou Medical University, Wenling, China
| | - Yexuzi Li
- Department of Critical Care Medicine, The First People's Hospital of Wenling, Affiliated Wenling Hospital, Wenzhou Medical University, Wenling, China
| | - Yi Ying
- Department of Traditional Chinese Medicine, The Affiliated Xianju’s Hospital, Hangzhou Medical College, Xianju, China
| | - Lijiong Shen
- Department of Clinical Laboratory, The First People's Hospital of Wenling, Affiliated Wenling Hospital, Wenzhou Medical University, Wenling, China
| | - Yuhan Jiang
- School of Public Health, Hangzhou Medical College, Hangzhou, China
| | - Haijun Cai
- Burn Unit, The First People's Hospital of Wenling, Affiliated Wenling Hospital, Wenzhou Medical University, Wenling, China
| | - Tian Jiang
- Department of Clinical Laboratory, The First People's Hospital of Wenling, Affiliated Wenling Hospital, Wenzhou Medical University, Wenling, China
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Rong D, Liu Z, Huang J, Zhang F, Wu Q, Dai J, Li Y, Zhao M, Li Q, Zhang J, Wu S. Prevalence and characterization of Staphylococcus aureus and Staphylococcus argenteus isolated from rice and flour products in Guangdong, China. Int J Food Microbiol 2023; 406:110348. [PMID: 37573713 DOI: 10.1016/j.ijfoodmicro.2023.110348] [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: 03/29/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/15/2023]
Abstract
Staphylococcus aureus and Staphylococcus argenteus have been implicated in food poisoning outbreaks, and have been found in various types of food products according to our previous study. Rice and flour products are popular and widely consumed around the world. However, limited data are available on the microbial safety of S. aureus in rice and flour products, and S. argenteus has never been reported. Thus, this study aimed to investigate the contamination of S. aureus and S. argenteus in 250 fresh rice and flour product samples from five cities in Guangdong, China. According to qualitative and quantitative analyses, 68 (27.2 %) and 11 (4.4 %) samples were positive for S. aureus and S. argenteus, including 9 samples that exceeded 100 MPN/g. For antibiotics susceptibility tests in 16 antibiotics, the S. aureus isolates exhibited higher rates of resistance and multidrug resistance than S. argenteus. The S. aureus and S. argenteus isolates were mainly resistant to penicillin (70.21 %; 79.17 %), tetracycline (20.21 %; 58.33 %) and azithromycin (19.68 %, 8.33 %). However, the other antibiotic resistance rates were <10 %. Furthermore, the genetic background of the isolates was analyzed by whole-genome sequencing (WGS). As a result, the S. aureus isolates were divided into 18 known sequence types (STs) and 4 novel STs (ST7675, ST7679, ST7680 and ST7682), which mainly belonged to ST188 (20.6 %) and ST6 (14.7 %). The S. argenteus isolates mainly belonged to ST2250 (90.9 %), with a novel type (ST7683). In total, 36 and 16 antibiotic resistance genes (ARGs) were found in S. aureus and S. argenteus isolates, respectively. In addition, 91 virulence genes (VFs) were detected in S. aureus isolates as well as 90 % of core VFs were similar to S. argenteus. More than 20 % of the S. aureus isolates carried the classic enterotoxin gene (sea-sec), but chp, cna and map were free in all S. argenteus isolates. Importantly, 33.8 % of S. aureus isolates belonged to the immune evasion cluster (IEC) type B, whereas most of S. argenteus isolates (90.9 %) belong to IEC type E. According to the phylogenetic analysis, the S. aureus and S. argenteus isolates in fresh rice and flour products may indicate loss or acquisition of ARGs and VFs to survive and adapt to the environment. Our study confirmed the presence of S. argenteus in rice and flour products at first and focused on the multi-dimensional systematic comparative analysis of S. aureus and S. argenteus to reveal their ubiquity and similarities or differences, and provide more accurate and effective basic information for follow-up monitoring and tracking.
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Affiliation(s)
- Dongli Rong
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Zhenjie Liu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Jiahui Huang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Feng Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Jingsha Dai
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Yuanyu Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Miao Zhao
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Qi Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Shi Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China.
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Dendani Chadi Z, Arcangioli MA. Pulsed-Field Gel Electrophoresis Analysis of Bovine Associated Staphylococcus aureus: A Review. Pathogens 2023; 12:966. [PMID: 37513813 PMCID: PMC10385338 DOI: 10.3390/pathogens12070966] [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: 06/09/2023] [Revised: 07/10/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
For decades now, DNA fingerprinting by means of pulsed-field gel electrophoresis (PFGE) continues to be the most widely used to separate large DNA molecules and distinguish between different strains in alternating pulses. This is done by isolating intact chromosomal DNA and using restriction enzymes with specific restriction sites to generate less than 30 restriction fragments from 50 Kb to 10 Mbp. These results make clone-specific band profiles easy to compare. Specialized equipment is required for the optimization of DNA separation and resolution, among which a contour-clamped homogeneous electric field (CHEF) apparatus is the most commonly used. As a result, the PFGE analysis of a bacterial genome provides useful information in terms of epidemiological investigations of different bacterial pathogens. For Staphylococcus aureus subtyping, despite its limitations and the emergence of alternative methods, PFGE analysis has proven to be an adequate choice and the gold standard for determining genetic relatedness, especially in outbreak detection and short-term surveillance in the veterinary field.
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Affiliation(s)
- Zoubida Dendani Chadi
- Laboratory of Biodiversity and Pollution of Ecosystems, Department of Veterinary Medicine, Faculty of Natural Science and Life, University of Chadli Bendjedid, El Tarf 36000, Algeria
| | - Marie-Anne Arcangioli
- VetAgro Sup, Université de Lyon, UMR Mycoplasmoses Animales, 69280 Marcy l'Etoile, France
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Lawal OU, Ayobami O, Abouelfetouh A, Mourabit N, Kaba M, Egyir B, Abdulgader SM, Shittu AO. A 6-Year Update on the Diversity of Methicillin-Resistant Staphylococcus aureus Clones in Africa: A Systematic Review. Front Microbiol 2022; 13:860436. [PMID: 35591993 PMCID: PMC9113548 DOI: 10.3389/fmicb.2022.860436] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Background Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of hospital-associated (HA) and community-associated (CA) infections globally. The multi-drug resistant nature of this pathogen and its capacity to cause outbreaks in hospital and community settings highlight the need for effective interventions, including its surveillance for prevention and control. This study provides an update on the clonal distribution of MRSA in Africa. Methods A systematic review was conducted by screening for eligible English, French, and Arabic articles from November 2014 to December 2020, using six electronic databases (PubMed, EBSCOhost, Web of Science, Scopus, African Journals Online, and Google Scholar). Data were retrieved and analyzed according to the Preferred Reporting Items for Systematic Review and Meta-Analysis guidelines (registered at PROSPERO: CRD42021277238). Genotyping data was based primarily on multilocus sequence types (STs) and Staphylococcal Cassette Chromosome mec (SCCmec) types. We utilized the Phyloviz algorithm in the cluster analysis and categorization of the MRSA STs into various clonal complexes (CCs). Results We identified 65 studies and 26 publications from 16 of 54 (30%) African countries that provided sufficient genotyping data. MRSA with diverse staphylococcal protein A (spa) and SCCmec types in CC5 and CC8 were reported across the continent. The ST5-IV [2B] and ST8-IV [2B] were dominant clones in Angola and the Democratic Republic of Congo (DRC), respectively. Also, ST88-IV [2B] was widely distributed across the continent, particularly in three Portuguese-speaking countries (Angola, Cape Verde, and São Tomé and Príncipe). The ST80-IV [2B] was described in Algeria and Egypt, while the HA-ST239/ST241-III [3A] was only identified in Egypt, Ghana, Kenya, and South Africa. ST152-MRSA was documented in the DRC, Kenya, Nigeria, and South Africa. Panton-Valentine leukocidin (PVL)-positive MRSA was observed in several CCs across the continent. The median prevalence of PVL-positive MRSA was 33% (ranged from 0 to 77%; n = 15). Conclusion We observed an increase in the distribution of ST1, ST22, and ST152, but a decline of ST239/241 in Africa. Data on MRSA clones in Africa is still limited. There is a need to strengthen genomic surveillance capacity based on a "One-Health" strategy to prevent and control MRSA in Africa.
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Affiliation(s)
- Opeyemi Uwangbaoje Lawal
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
| | - Olaniyi Ayobami
- Unit for Healthcare-Associated Infections, Surveillance of Antimicrobial Resistance and Consumption, Robert Koch Institute, Berlin, Germany
| | - Alaa Abouelfetouh
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt.,Department of Microbiology and Immunology, Faculty of Pharmacy, AlAlamein International University, Alalamein, Egypt
| | - Nadira Mourabit
- Biotechnology, Environmental Technology and Valorisation of Bio-Resources Team, Department of Biology, Faculty of Sciences and Techniques of Al Hoceima, Abdelmalek Essaadi University, Tetouan, Morocco
| | - Mamadou Kaba
- Division of Medical Microbiology, Department of Clinical Laboratory Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Beverly Egyir
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Shima M Abdulgader
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa
| | - Adebayo Osagie Shittu
- Department of Microbiology, Obafemi Awolowo University, Ile-Ife, Nigeria.,Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
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Nouws S, Bogaerts B, Verhaegen B, Denayer S, Laeremans L, Marchal K, Roosens NHC, Vanneste K, De Keersmaecker SCJ. Whole Genome Sequencing Provides an Added Value to the Investigation of Staphylococcal Food Poisoning Outbreaks. Front Microbiol 2021; 12:750278. [PMID: 34795649 PMCID: PMC8593433 DOI: 10.3389/fmicb.2021.750278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/04/2021] [Indexed: 12/13/2022] Open
Abstract
Through staphylococcal enterotoxin (SE) production, Staphylococcus aureus is a common cause of food poisoning. Detection of staphylococcal food poisoning (SFP) is mostly performed using immunoassays, which, however, only detect five of 27 SEs described to date. Polymerase chain reactions are, therefore, frequently used in complement to identify a bigger arsenal of SE at the gene level (se) but are labor-intensive. Complete se profiling of isolates from different sources, i.e., food and human cases, is, however, important to provide an indication of their potential link within foodborne outbreak investigation. In addition to complete se gene profiling, relatedness between isolates is determined with more certainty using pulsed-field gel electrophoresis, Staphylococcus protein A gene typing and other methods, but these are shown to lack resolution. We evaluated how whole genome sequencing (WGS) can offer a solution to these shortcomings. By WGS analysis of a selection of S. aureus isolates, including some belonging to a confirmed foodborne outbreak, its added value as the ultimate multiplexing method was demonstrated. In contrast to PCR-based se gene detection for which primers are sometimes shown to be non-specific, WGS enabled complete se gene profiling with high performance, provided that a database containing reference sequences for all se genes was constructed and employed. The custom compiled database and applied parameters were made publicly available in an online user-friendly interface. As an all-in-one approach with high resolution, WGS additionally allowed inferring correct isolate relationships. The different DNA extraction kits that were tested affected neither se gene profiling nor relatedness determination, which is interesting for data sharing during SFP outbreak investigation. Although confirming the production of enterotoxins remains important for SFP investigation, we delivered a proof-of-concept that WGS is a valid alternative and/or complementary tool for outbreak investigation.
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Affiliation(s)
- Stéphanie Nouws
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium.,IDLab, Department of Information Technology, Ghent University - IMEC, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Bert Bogaerts
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium.,IDLab, Department of Information Technology, Ghent University - IMEC, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Bavo Verhaegen
- National Reference Laboratory for Foodborne Outbreaks (NRL-FBO) and for Coagulase Positive Staphylococci (NRL-CPS), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Sarah Denayer
- National Reference Laboratory for Foodborne Outbreaks (NRL-FBO) and for Coagulase Positive Staphylococci (NRL-CPS), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Lasse Laeremans
- Organic Contaminants and Additives, Sciensano, Brussels, Belgium
| | - Kathleen Marchal
- IDLab, Department of Information Technology, Ghent University - IMEC, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
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Genomic Epidemiology and Characterization of Methicillin-Resistant Staphylococcus aureus from Bloodstream Infections in China. mSystems 2021; 6:e0083721. [PMID: 34726482 PMCID: PMC8562482 DOI: 10.1128/msystems.00837-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Since 2010, methicillin-resistant Staphylococcus aureus (MRSA) ST59 began to increase in prevalence in China, gradually replacing ST239 and has become the dominant clone in most hospitals in China. Here, we investigated the changing epidemiology, phylogenetic reconstruction, and genomic characterization of MRSA clones in China to identify the genomic driving factors in the prevalence of ST59. Most MRSA isolates were identified as ST59 (36.98%; 277/749), which increased from 25.09% in 2014 to 35.53% in 2019. The phylogenetic analysis of the 749 MRSA isolates showed a high level of diversity and the copresence of hospital-associated, community-associated, livestock-associated, and hypervirulent clones. Furthermore, minimum spanning trees revealed that ST59 MRSA clones from different hospitals and regions were integrated, suggesting that frequent exchanges had occurred between regions and hospitals. ST59 clones displayed higher susceptibility to antimicrobials than did ST239 and ST5 MRSA clones, indicating that resistance to non-β-lactam and fluoroquinolone antibiotics may be not critical for the epidemic success of ST59 clones. Virulence factors detection showed that sak and chp genes enriched in MRSA ST59 may be associated with the enhanced spreading success of ST59, whereas qacA may have contributed to the predominance of ST5 in East China. Our refined analysis of different clones among ST239, ST5, ST59, and ST398 demonstrated the existence of potential driving factors for the evolution of nosocomial MRSA populations and diversity of the evolutionary events surrounding clonal replacement. IMPORTANCE As a developing country, China has an unbalanced health care system due to regional differences in economic development. However, China is also a country worthy of study with regard to the population dynamics of MRSA within the more resource-rich health care systems. In this study, we carried out genomic analysis to investigate the genomic epidemiology and characterization of MRSA isolated from bloodstream infections over a timespan of 6 years. Our refined analysis of different MRSA clones among ST59, ST5, ST239, and ST398 demonstrated the existence of driving factors for the evolution of nosocomial MRSA populations and diversity of the evolutionary events surrounding clonal replacement.
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Toleman MS, Reuter S, Jamrozy D, Wilson HJ, Blane B, Harrison EM, Coll F, Hope RJ, Kearns A, Parkhill J, Peacock SJ, Török ME. Prospective genomic surveillance of methicillin-resistant Staphylococcus aureus (MRSA) associated with bloodstream infection, England, 1 October 2012 to 30 September 2013. ACTA ACUST UNITED AC 2020; 24. [PMID: 30696529 PMCID: PMC6351993 DOI: 10.2807/1560-7917.es.2019.24.4.1800215] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BackgroundMandatory reporting of methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infections (BSI) has occurred in England for over 15years. Epidemiological information is recorded, but routine collection of isolates for characterisation has not been routinely undertaken. Ongoing developments in whole-genome sequencing (WGS) have demonstrated its value in outbreak investigations and for determining the spread of antimicrobial resistance and bacterial population structure. Benefits of adding genomics to routine epidemiological MRSA surveillance are unknown.AimTo determine feasibility and potential utility of adding genomics to epidemiological surveillance of MRSA.MethodsWe conducted an epidemiological and genomic survey of MRSA BSI in England over a 1-year period (1 October 2012--30 September 2013).ResultsDuring the study period, 903 cases of MRSA BSI were reported; 425 isolates were available for sequencing of which, 276 (65%) were clonal complex (CC) 22. Addition of 64 MRSA genomes from published outbreak investigations showed that the study genomes could provide context for outbreak isolates and supported cluster identification. Comparison to other MRSA genome collections demonstrated variation in clonal diversity achieved through different sampling strategies and identified potentially high-risk clones e.g. USA300 and local expansion of CC5 MRSA in South West England.ConclusionsWe demonstrate the potential utility of combined epidemiological and genomic MRSA BSI surveillance to determine the national population structure of MRSA, contextualise previous MRSA outbreaks, and detect potentially high-risk lineages. These findings support the integration of epidemiological and genomic surveillance for MRSA BSI as a step towards a comprehensive surveillance programme in England.
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Affiliation(s)
- Michelle S Toleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom.,Wellcome Sanger Institute, Hinxton, United Kingdom.,University of Cambridge, Department of Medicine, Cambridge, United Kingdom
| | - Sandra Reuter
- University of Freiburg, Institute for Infection Prevention and Hospital Epidemiology, Freiburg, Germany
| | | | - Hayley J Wilson
- University of Cambridge, Department of Medicine, Cambridge, United Kingdom
| | - Beth Blane
- University of Cambridge, Department of Medicine, Cambridge, United Kingdom
| | - Ewan M Harrison
- Wellcome Sanger Institute, Hinxton, United Kingdom.,University of Cambridge, Department of Medicine, Cambridge, United Kingdom
| | - Francesc Coll
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Russell J Hope
- Public Health England, National Infection Service, Colindale, London, United Kingdom
| | - Angela Kearns
- Public Health England, National Infection Service, Colindale, London, United Kingdom
| | | | - Sharon J Peacock
- London School of Hygiene and Tropical Medicine, London, United Kingdom.,Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom.,Wellcome Sanger Institute, Hinxton, United Kingdom.,University of Cambridge, Department of Medicine, Cambridge, United Kingdom
| | - M Estée Török
- Public Health England, Clinical Microbiology and Public Health Laboratory, Cambridge, United Kingdom.,Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom.,University of Cambridge, Department of Medicine, Cambridge, United Kingdom
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9
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Brancaccio M, Mennitti C, Laneri S, Franco A, De Biasi MG, Cesaro A, Fimiani F, Moscarella E, Gragnano F, Mazzaccara C, Limongelli G, Frisso G, Lombardo B, Pagliuca C, Colicchio R, Salvatore P, Calabrò P, Pero R, Scudiero O. Methicillin-Resistant Staphylococcus aureus: Risk for General Infection and Endocarditis Among Athletes. Antibiotics (Basel) 2020; 9:E332. [PMID: 32570705 PMCID: PMC7345113 DOI: 10.3390/antibiotics9060332] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/04/2020] [Accepted: 06/09/2020] [Indexed: 12/23/2022] Open
Abstract
The first studies on Staphylococcus aureus (SA) infections in athletes were conducted in the 1980s, and examined athletes that perform in close physical contact, with particular attention to damaged or infected skin. Recent studies have used molecular epidemiology to shed light on the transmission of SA in professional athletes. These studies have shown that contact between athletes is prolonged and constant, and that these factors influence the appearance of infections caused by SA. These results support the need to use sanitary measures designed to prevent the appearance of SA infections. The factors triggering the establishment of SA within professional sports groups are the nasal colonization of SA, contact between athletes and sweating. Hence, there is a need to use the most modern molecular typing methods to evaluate the appearance of cutaneous SA disease. This review aims to summarize both the current SA infections known in athletes and the diagnostic methods employed for recognition, pointing to possible preventive strategies and the factors that can act as a springboard for the appearance of SA and subsequent transmission between athletes.
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Affiliation(s)
- Mariarita Brancaccio
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
| | - Cristina Mennitti
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S.Pansini 5, 80131 Naples, Italy; (C.M.); (C.M.); (G.F.); (B.L.); (C.P.); (R.C.); (P.S.)
| | - Sonia Laneri
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy; (S.L.); (A.F.); (M.G.D.B.)
| | - Adelaide Franco
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy; (S.L.); (A.F.); (M.G.D.B.)
| | - Margherita G. De Biasi
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy; (S.L.); (A.F.); (M.G.D.B.)
| | - Arturo Cesaro
- Department of Cardio-Thoracic and Respiratory Sciences, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Napoli, Italy; (A.C.); (G.L.)
| | - Fabio Fimiani
- Center of Excellence for Research on Cardiovascular Diseases Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Napoli, Italy;
| | - Elisabetta Moscarella
- Department of Translational Medical Sciences, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Napoli, Italy; (E.M.); (P.C.)
| | - Felice Gragnano
- Division of Cardiology, Department of Translational Medical Sciences, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Napoli, Italy;
| | - Cristina Mazzaccara
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S.Pansini 5, 80131 Naples, Italy; (C.M.); (C.M.); (G.F.); (B.L.); (C.P.); (R.C.); (P.S.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80100 Naples, Italy
| | - Giuseppe Limongelli
- Department of Cardio-Thoracic and Respiratory Sciences, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Napoli, Italy; (A.C.); (G.L.)
| | - Giulia Frisso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S.Pansini 5, 80131 Naples, Italy; (C.M.); (C.M.); (G.F.); (B.L.); (C.P.); (R.C.); (P.S.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80100 Naples, Italy
| | - Barbara Lombardo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S.Pansini 5, 80131 Naples, Italy; (C.M.); (C.M.); (G.F.); (B.L.); (C.P.); (R.C.); (P.S.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80100 Naples, Italy
| | - Chiara Pagliuca
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S.Pansini 5, 80131 Naples, Italy; (C.M.); (C.M.); (G.F.); (B.L.); (C.P.); (R.C.); (P.S.)
| | - Roberta Colicchio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S.Pansini 5, 80131 Naples, Italy; (C.M.); (C.M.); (G.F.); (B.L.); (C.P.); (R.C.); (P.S.)
| | - Paola Salvatore
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S.Pansini 5, 80131 Naples, Italy; (C.M.); (C.M.); (G.F.); (B.L.); (C.P.); (R.C.); (P.S.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80100 Naples, Italy
- Ceinge Biotecnologie Avanzate S. C. a R. L., 80131 Naples, Italy
| | - Paolo Calabrò
- Department of Translational Medical Sciences, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Napoli, Italy; (E.M.); (P.C.)
| | - Raffaela Pero
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S.Pansini 5, 80131 Naples, Italy; (C.M.); (C.M.); (G.F.); (B.L.); (C.P.); (R.C.); (P.S.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80100 Naples, Italy
| | - Olga Scudiero
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S.Pansini 5, 80131 Naples, Italy; (C.M.); (C.M.); (G.F.); (B.L.); (C.P.); (R.C.); (P.S.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80100 Naples, Italy
- Ceinge Biotecnologie Avanzate S. C. a R. L., 80131 Naples, Italy
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10
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Mizusawa M, Carroll KC. Novel strategies for rapid identification and susceptibility testing of MRSA. Expert Rev Anti Infect Ther 2020; 18:759-778. [PMID: 32329637 DOI: 10.1080/14787210.2020.1760842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Methicillin-resistant Staphylococcus aureus (MRSA) is associated with adverse clinical outcomes and increased morbidity, mortality, length of hospital stay, and health-care costs. Rapid diagnosis of MRSA infections has been associated with positive impact on clinical outcomes. AREAS COVERED We searched relevant papers in PubMed for the last 10 years. In major papers, we scanned the bibliographies to ensure that important articles were included. This review describes screening and diagnostic test methods for MRSA and their analytical performances with a focus on rapid molecular-based assays including those that are on the horizon. Future novel technologies will allow more rapid detection of phenotypic resistance. In the case of whole-genome sequencing, detection of mutations may predict resistance, transmission, and virulence. EXPERT OPINION Currently there are many diagnostic options for the detection of MRSA in surveillance and clinical samples. In general, these are highly accurate and have resulted in improvements in targeted management and reduction in hospital or intensive care unit length of stay for both MSSA and MRSA. Impact on mortality has been variable. Promising novel technologies will not only accurately identify pathogens and detect their resistance markers but will allow discovery of virulence determinants that might further affect patient management.
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Affiliation(s)
- Masako Mizusawa
- Section of Infectious Diseases, Department of Internal Medicine, University of Missouri , Kansas, MO, USA
| | - Karen C Carroll
- Department of Pathology, Division of Medical Microbiology, The Johns Hopkins University School of Medicine , Baltimore, MD, USA
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11
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Chaudhry V, Patil PB. Evolutionary insights into adaptation of Staphylococcus haemolyticus to human and non-human niches. Genomics 2019; 112:2052-2062. [PMID: 31785311 DOI: 10.1016/j.ygeno.2019.11.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 11/16/2019] [Accepted: 11/26/2019] [Indexed: 11/16/2022]
Abstract
Staphylococcus haemolyticus is a well-known member of human skin microbiome and an emerging opportunistic human pathogen. Presently, evolutionary studies are limited to human isolates even though it is reported from plants with beneficial properties and in environmental settings. In the present study, we report isolation of novel S. haemolyticus strains from surface sterilized rice seeds and compare their genome to other isolates from diverse niches available in public domain. The study showed expanding nature of pan-genome and revealed set of genes with putative functions related to its adaptability. This is seen by presence of type II lanthipeptide cluster in rice isolates, metal homeostasis genes in an isolate from copper coin and gene encoding methicillin resistance in human isolates. The present study on differential genome dynamics and role of horizontal gene transfers has provided novel insights into capability for ecological diversification of a bacterium of significance to human health.
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Affiliation(s)
- Vasvi Chaudhry
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Sector - 39A, Chandigarh 160036, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Sector - 39A, Chandigarh 160036, India.
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12
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Kristinsdottir I, Haraldsson A, Thorkelsson T, Haraldsson G, Kristinsson KG, Larsen J, Larsen AR, Thors V. MRSA outbreak in a tertiary neonatal intensive care unit in Iceland. Infect Dis (Lond) 2019; 51:815-823. [PMID: 31507231 DOI: 10.1080/23744235.2019.1662083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Introduction: Preventing the spread of methicillin-resistant Staphylococcus aureus (MRSA) and understanding the pathophysiology and transmission is essential. This study describes an MRSA outbreak in a neonatal intensive care unit in Reykjavik, Iceland at a time where no screening procedures were active. Materials and methods: After isolating MRSA in the neonatal intensive care unit in 2015, neonates, staff members and parents of positive patients were screened and environmental samples collected. The study period was from 14 April 2015 until 31 August 2015. Antimicrobial susceptibility testing, spa-typing and whole genome sequencing were done on MRSA isolates. Results: During the study period, 96/143 admitted patients were screened for colonization. Non-screened infants had short admissions not including screening days. MRSA was isolated from nine infants and seven parents. All tested staff members were negative. Eight infants and six parents carried MRSA ST30-IVc with spa-type t253 and one infant and its parent carried MRSA CC9-IVa (spa-type t4845) while most environmental samples were MRSA CC9-IVa (spa-type t4845). Whole genome sequencing revealed close relatedness between all ST30-IVc and CC9-IVa isolates, respectively. All colonized infants received decolonization treatment, but 3/9 were still positive when last sampled. Discussion: The main outbreak source was a single MRSA ST30-IVc (spa-type t253), isolated for the first time in Iceland. A new CC9-IVa (spa-type t4845) was also identified, most abundant on environmental surfaces but only in one patient. The reason for the differences in the epidemiology of the two strains is not clear. The study highlights a need for screening procedures in high-risk settings and guidelines for neonatal decolonization.
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Affiliation(s)
| | - Asgeir Haraldsson
- Faculty of Medicine, University of Iceland , Reykjavík , Iceland.,Children's Hospital Iceland, Landspitali University Hospital , Reykjavík , Iceland
| | - Thordur Thorkelsson
- Faculty of Medicine, University of Iceland , Reykjavík , Iceland.,Children's Hospital Iceland, Landspitali University Hospital , Reykjavík , Iceland
| | - Gunnsteinn Haraldsson
- Faculty of Medicine, University of Iceland , Reykjavík , Iceland.,Department of Clinical Microbiology, Landspitali University Hospital , Reykjavík , Iceland
| | - Karl G Kristinsson
- Faculty of Medicine, University of Iceland , Reykjavík , Iceland.,Department of Clinical Microbiology, Landspitali University Hospital , Reykjavík , Iceland
| | - Jesper Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institute , Copenhagen , Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institute , Copenhagen , Denmark
| | - Valtyr Thors
- Faculty of Medicine, University of Iceland , Reykjavík , Iceland.,Children's Hospital Iceland, Landspitali University Hospital , Reykjavík , Iceland
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13
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Jauneikaite E, Ferguson T, Mosavie M, Fallowfield JL, Davey T, Thorpe N, Allsopp A, Shaw AM, Fudge D, O'Shea MK, Wilson D, Morgan M, Pichon B, Kearns AM, Sriskandan S, Lamb LE. Staphylococcus aureus colonization and acquisition of skin and soft tissue infection among Royal Marines recruits: a prospective cohort study. Clin Microbiol Infect 2019; 26:381.e1-381.e6. [PMID: 31357012 DOI: 10.1016/j.cmi.2019.07.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 07/03/2019] [Accepted: 07/13/2019] [Indexed: 10/26/2022]
Abstract
OBJECTIVES Skin and soft tissue infections (SSTIs) are a serious health issue for military personnel. Of particular importance are those caused by methicillin-resistant Staphylococcus aureus and Panton-Valentine leucocidin (PVL)-positive S. aureus (PVL-SA), as they have been associated with outbreaks of SSTIs. A prospective observational study was conducted in Royal Marine (RM) recruits to investigate the prevalence of PVL-SA carriage and any association with SSTIs. METHODS A total of 1012 RM recruits were followed through a 32-week training programme, with nose and throat swabs obtained at weeks 1, 6, 15 and 32. S. aureus isolates were characterized by antibiotic susceptibility testing, spa typing, presence of mecA/C and PVL genes. Retrospective review of the clinical notes for SSTI acquisition was conducted. RESULTS S. aureus colonization decreased from Week 1 to Week 32 (41% to 26%, p < 0.0001). Of 1168 S. aureus isolates, three out of 1168 (0.3%) were MRSA and ten out of 1168 (0.9%) PVL-positive (all MSSA) and 169 out of 1168 (14.5%) were resistant to clindamycin. Isolates showed genetic diversity with 238 different spa types associated with 25 multi-locus sequence type (MLST) clonal complexes. SSTIs were seen in 35% (351/989) of recruits with 3 training days lost per recruit. SSTI acquisition rate was reduced amongst persistent carriers (p < 0.0283). CONCLUSIONS Nose and throat carriage of MRSA and PVL-SA was low among recruits, despite a high incidence of SSTIs being reported, particularly cellulitis. Carriage strains were predominantly MSSA with a marked diversity of genotypes. Persistent nose and/or throat carriage was not associated with SSTI acquisition. Putative person-to-person transmission within troops was identified based on spa typing requiring further research to confirm and explore potential transmission routes.
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Affiliation(s)
- E Jauneikaite
- Department of Medicine, Imperial College London, London, UK; NIHR Health Protection Research Unit in Antimicrobial Resistance and Healthcare-associated Infections, Imperial College London, London, UK; Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - T Ferguson
- Department of Medicine, Imperial College London, London, UK
| | - M Mosavie
- Department of Medicine, Imperial College London, London, UK; NIHR Health Protection Research Unit in Antimicrobial Resistance and Healthcare-associated Infections, Imperial College London, London, UK
| | | | - T Davey
- Institute of Naval Medicine, Alverstoke, UK
| | - N Thorpe
- Institute of Naval Medicine, Alverstoke, UK
| | - A Allsopp
- Institute of Naval Medicine, Alverstoke, UK
| | - A M Shaw
- Institute of Naval Medicine, Alverstoke, UK
| | - D Fudge
- Academic Department of Military Medicine, Royal Centre for Defence Medicine (Research and Academia), Birmingham, UK
| | - M K O'Shea
- Academic Department of Military Medicine, Royal Centre for Defence Medicine (Research and Academia), Birmingham, UK; Institute of Microbiology and Infection, The University of Birmingham, Birmingham, UK
| | - D Wilson
- Academic Department of Military Medicine, Royal Centre for Defence Medicine (Research and Academia), Birmingham, UK
| | - M Morgan
- Department of Microbiology, Royal Devon and Exeter Hospital, Exeter, UK
| | - B Pichon
- Healthcare Associated Infections and Antimicrobial Resistance Division, National Infection Service, Public Health England, London, UK
| | - A M Kearns
- Healthcare Associated Infections and Antimicrobial Resistance Division, National Infection Service, Public Health England, London, UK
| | - S Sriskandan
- Department of Medicine, Imperial College London, London, UK; NIHR Health Protection Research Unit in Antimicrobial Resistance and Healthcare-associated Infections, Imperial College London, London, UK
| | - L E Lamb
- Department of Medicine, Imperial College London, London, UK; Academic Department of Military Medicine, Royal Centre for Defence Medicine (Research and Academia), Birmingham, UK; Royal Free London NHS Foundation Trust, London, UK.
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14
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Humphreys H, Coleman D. Contribution of whole-genome sequencing to understanding of the epidemiology and control of meticillin-resistant Staphylococcus aureus. J Hosp Infect 2019; 102:189-199. [DOI: 10.1016/j.jhin.2019.01.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 01/29/2019] [Indexed: 02/06/2023]
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15
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Muthuirulandi Sethuvel DP, Devanga Ragupathi NK, Bakthavatchalam YD, Vijayakumar S, Varghese R, Shankar C, Jacob JJ, Vasudevan K, Elangovan D, Balaji V. Current strategy for local- to global-level molecular epidemiological characterisation of global antimicrobial resistance surveillance system pathogens. Indian J Med Microbiol 2019; 37:147-162. [PMID: 31745014 DOI: 10.4103/ijmm.ijmm_19_396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The prime goal of molecular epidemiology is to identify the origin and evolution of pathogens, which can potentially influence the public health worldwide. Traditional methods provide limited information which is not sufficient for outbreak investigation and studying transmission dynamics. The recent advancement of next-generation sequencing had a major impact on molecular epidemiological studies. Currently, whole-genome sequencing (WGS) has become the gold standard typing method, especially for clinically significant pathogens. Here, we aimed to describe the application of appropriate molecular typing methods for global antimicrobial resistance surveillance system pathogens based on the level of discrimination and epidemiological settings. This shows that sequence-based methods such as multi-locus sequence typing (MLST) are widely used due to cost-effectiveness and database accessibility. However, WGS is the only method of choice for studying Escherichia coli and Shigella spp. WGS is shown to have higher discrimination than other methods in typing Klebsiella pneumoniae, Acinetobacter baumannii and Salmonella spp. due to its changing accessory genome content. For Gram positives such as Streptococcus pneumoniae, WGS would be preferable to understand the evolution of the strains. Similarly, for Staphylococcus aureus, combination of MLST, staphylococcal protein A or SCCmec typing along with WGS could be the choice for epidemiological typing of hospital- and community-acquired strains. This review highlights that combinations of different typing methods should be used to get complete information since no one standalone method is sufficient to study the varying genome diversity.
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Affiliation(s)
| | | | | | - Saranya Vijayakumar
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Rosemol Varghese
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Chaitra Shankar
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Karthick Vasudevan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Divyaa Elangovan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Veeraraghavan Balaji
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
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16
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Earls MR, Shore AC, Brennan GI, Simbeck A, Schneider-Brachert W, Vremerǎ T, Dorneanu OS, Slickers P, Ehricht R, Monecke S, Coleman DC. A novel multidrug-resistant PVL-negative CC1-MRSA-IV clone emerging in Ireland and Germany likely originated in South-Eastern Europe. INFECTION GENETICS AND EVOLUTION 2019; 69:117-126. [PMID: 30677533 DOI: 10.1016/j.meegid.2019.01.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/20/2018] [Accepted: 01/15/2019] [Indexed: 12/19/2022]
Abstract
This study investigated the recent emergence of multidrug-resistant Panton-Valentine leukocidin (PVL)-negative CC1-MRSA-IV in Ireland and Germany. Ten CC1-MSSA and 139 CC1-MRSA isolates recovered in Ireland between 2004 and 2017 were investigated. These were compared to 21 German CC1-MRSA, 10 Romanian CC1-MSSA, five Romanian CC1-MRSA and two UAE CC1-MRSA, which were selected from an extensive global database, based on similar DNA microarray profiles to the Irish isolates. All isolates subsequently underwent whole-genome sequencing, core-genome single nucleotide polymorphism (cgSNP) analysis and enhanced SCCmec subtyping. Two PVL-negative clades (A and B1) were identified among four main clades. Clade A included 20 German isolates, 119 Irish isolates, and all Romanian MRSA and MSSA isolates, the latter of which differed from clade A MRSA by 47-130 cgSNPs. Eighty-six Irish clade A isolates formed a tight subclade (A1) exhibiting 0-49 pairwise cgSNPs, 80 of which harboured a 46 kb conjugative plasmid carrying both ileS2, encoding high-level mupirocin resistance, and qacA, encoding chlorhexidine resistance. The resistance genes aadE, aphA3 and sat were detected in all clade A MRSA and the majority (8/10) of clade A MSSA isolates. None of the clade A isolates harboured any enterotoxin genes other than seh, which is universally present in CC1. Clade B1 included the remaining German isolate, 17 Irish isolates and the two UAE isolates, all of which corresponded to the Western Australia MRSA-1 (WA MRSA-1) clone based on genotypic characteristics. MRSA within clades A and B1 differed by 188 cgSNPs and clade-specific SCCmec characteristics were identified, indicating independent acquisition of the SCCmec element. This study demonstrated the existence of a European PVL-negative CC1-MRSA-IV clone that is distinctly different from the well-defined PVL-negative CC1-MRSA-IV clone, WA MRSA-1. Furthermore, cgSNP analysis revealed that this newly defined clone may have originated in South-Eastern Europe, before spreading to both Ireland and Germany.
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Affiliation(s)
- Megan R Earls
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, Trinity College, University of Dublin, Dublin, Ireland.
| | - Anna C Shore
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, Trinity College, University of Dublin, Dublin, Ireland.
| | - Gráinne I Brennan
- National MRSA Reference Laboratory, St. James's Hospital, James's Street, Dublin, Ireland.
| | - Alexandra Simbeck
- Institute for Clinical Microbiology and Hygiene, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany.
| | - Wulf Schneider-Brachert
- Institute for Clinical Microbiology and Hygiene, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany.
| | - Teodora Vremerǎ
- Microbiology Unit, Department of Preventive and Interdisciplinary Medicine, University of Medicine & Pharmacy "Grigore T Popa", Iaşi, Romania.
| | - Olivia S Dorneanu
- Microbiology Unit, Department of Preventive and Interdisciplinary Medicine, University of Medicine & Pharmacy "Grigore T Popa", Iaşi, Romania.
| | - Peter Slickers
- Abbott (Alere Technologies GmbH), Jena, Germany; InfectoGnostics Research Campus, Jena, Germany.
| | - Ralf Ehricht
- InfectoGnostics Research Campus, Jena, Germany; Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany.
| | - Stefan Monecke
- InfectoGnostics Research Campus, Jena, Germany; Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany; Institute for Medical Microbiology and Hygiene, Medical Faculty "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany.
| | - David C Coleman
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, Trinity College, University of Dublin, Dublin, Ireland.
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17
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Ray SM. Preventing Methicillin-Resistant Staphylococcus aureus (MRSA) Disease in Urban US Hospitals-Now for the Hard Part: More Evidence Pointing to the Community as the Source of MRSA Acquisition. J Infect Dis 2018; 215:1631-1633. [PMID: 28486618 DOI: 10.1093/infdis/jix109] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 02/21/2017] [Indexed: 11/14/2022] Open
Affiliation(s)
- Susan M Ray
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine/Grady Health System, Atlanta, Georgia
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18
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Gray J, Oppenheim B, Mahida N. The Journal of Hospital Infection - a history of infection prevention and control in 100 volumes. J Hosp Infect 2018; 100:1-8. [PMID: 30173875 DOI: 10.1016/j.jhin.2018.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 07/04/2018] [Indexed: 02/04/2023]
Affiliation(s)
- J Gray
- Journal of Hospital Infection, London, UK.
| | | | - N Mahida
- Journal of Hospital Infection, London, UK
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19
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Accuracy of Different Bioinformatics Methods in Detecting Antibiotic Resistance and Virulence Factors from Staphylococcus aureus Whole-Genome Sequences. J Clin Microbiol 2018; 56:JCM.01815-17. [PMID: 29925638 DOI: 10.1128/jcm.01815-17] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 05/09/2018] [Indexed: 01/08/2023] Open
Abstract
In principle, whole-genome sequencing (WGS) can predict phenotypic resistance directly from a genotype, replacing laboratory-based tests. However, the contribution of different bioinformatics methods to genotype-phenotype discrepancies has not been systematically explored to date. We compared three WGS-based bioinformatics methods (Genefinder [read based], Mykrobe [de Bruijn graph based], and Typewriter [BLAST based]) for predicting the presence/absence of 83 different resistance determinants and virulence genes and overall antimicrobial susceptibility in 1,379 Staphylococcus aureus isolates previously characterized by standard laboratory methods (disc diffusion, broth and/or agar dilution, and PCR). In total, 99.5% (113,830/114,457) of individual resistance-determinant/virulence gene predictions were identical between all three methods, with only 627 (0.5%) discordant predictions, demonstrating high overall agreement (Fleiss' kappa = 0.98, P < 0.0001). Discrepancies when identified were in only one of the three methods for all genes except the cassette recombinase, ccrC(b). The genotypic antimicrobial susceptibility prediction matched the laboratory phenotype in 98.3% (14,224/14,464) of cases (2,720 [18.8%] resistant, 11,504 [79.5%] susceptible). There was greater disagreement between the laboratory phenotypes and the combined genotypic predictions (97 [0.7%] phenotypically susceptible, but all bioinformatic methods reported resistance; 89 [0.6%] phenotypically resistant, but all bioinformatics methods reported susceptible) than within the three bioinformatics methods (54 [0.4%] cases, 16 phenotypically resistant, 38 phenotypically susceptible). However, in 36/54 (67%) cases, the consensus genotype matched the laboratory phenotype. In this study, the choice between these three specific bioinformatic methods to identify resistance determinants or other genes in S. aureus did not prove critical, with all demonstrating high concordance with each other and phenotypic/molecular methods. However, each has some limitations; therefore, consensus methods provide some assurance.
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Earls MR, Coleman DC, Brennan GI, Fleming T, Monecke S, Slickers P, Ehricht R, Shore AC. Intra-Hospital, Inter-Hospital and Intercontinental Spread of ST78 MRSA From Two Neonatal Intensive Care Unit Outbreaks Established Using Whole-Genome Sequencing. Front Microbiol 2018; 9:1485. [PMID: 30022976 PMCID: PMC6039561 DOI: 10.3389/fmicb.2018.01485] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/14/2018] [Indexed: 01/22/2023] Open
Abstract
From 2009 to 2011 [transmission period (TP) 1] and 2014 to 2017 (TP2), two outbreaks involving community-associated clonal complex (CC) 88-MRSA spa types t186 and t786, respectively, occurred in the Neonatal Intensive Care Unit (NICU) of an Irish hospital (H1). This study investigated the relatedness of these isolates, their relationship to other CC88 MRSA from Ireland and their likely geographic origin, using whole-genome sequencing (WGS). All 28 CC88-MRSA isolates identified at the Irish National MRSA Reference Laboratory between 2009 and 2017 were investigated including 20 H1 patient isolates, two H1 isolates recovered from a single healthcare worker (HCW) 2 years apart, three patient isolates from a second hospital (H2) and one patient isolate from each of three different hospitals (H3, H4, and H5). All isolates underwent DNA microarray profiling. Thirteen international isolates with similar microarray profiles to at least one Irish isolate were selected from an extensive global database. All isolates underwent Illumina MiSeq WGS. The majority of Irish isolates (25/28; all H1 isolates, two H2 isolates and the H3 isolate) were identified as ST78-MRSA-IVa and formed a large cluster, exhibiting 1–71 pairwise allelic differences, in a whole-genome MLST-based minimum spanning tree (MST) involving all Irish isolates. A H1/H2, H1/H3, and H1 HCW/patient isolate pair each exhibited one allelic difference. The TP2 isolates were characterised by a different spa type and the loss of hsdS. The three remaining Irish isolates (from H2, H4, and H5) were identified as ST88-MRSA-IVa and dispersed at the opposite end of the MST, exhibiting 81–211 pairwise allelic differences. Core-genome MLST and sequence-based plasmid analysis revealed the recent shared ancestry of Irish and Australian ST78-MRSA-IVa, and of Irish and French/Egyptian ST88-MRSA-IVa. This study revealed the homogeneity of isolates recovered during two NICU outbreaks (despite spa type and hsdS carriage variances), HCW involvement in the outbreak transmission chain and the strain's spread to two other Irish hospitals. The outbreak strain, CC88/ST78-MRSA-IVa, was likely imported from Australia, where it is prevalent. CC88/ST88-MRSA-IVa was also identified in Irish hospitals and was likely imported from Africa, where it is predominant, and/or a country with a large population of African descent.
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Affiliation(s)
- Megan R Earls
- Microbiology Research Unit, Dublin Dental University Hospital, Trinity College, University of Dublin, Dublin, Ireland
| | - David C Coleman
- Microbiology Research Unit, Dublin Dental University Hospital, Trinity College, University of Dublin, Dublin, Ireland
| | - Gráinne I Brennan
- National MRSA Reference Laboratory, St. James's Hospital, Dublin, Ireland
| | - Tanya Fleming
- National MRSA Reference Laboratory, St. James's Hospital, Dublin, Ireland
| | - Stefan Monecke
- Abbott (Alere Technologies GmbH), Jena, Germany.,InfectGnostics Research Campus, Jena, Germany
| | - Peter Slickers
- Abbott (Alere Technologies GmbH), Jena, Germany.,InfectGnostics Research Campus, Jena, Germany
| | - Ralf Ehricht
- Abbott (Alere Technologies GmbH), Jena, Germany.,InfectGnostics Research Campus, Jena, Germany
| | - Anna C Shore
- Microbiology Research Unit, Dublin Dental University Hospital, Trinity College, University of Dublin, Dublin, Ireland
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Raven K, Blane B, Churcher C, Parkhill J, Peacock SJ. Are commercial providers a viable option for clinical bacterial sequencing? Microb Genom 2018; 4. [PMID: 29620501 PMCID: PMC5989584 DOI: 10.1099/mgen.0.000173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Bacterial whole-genome sequencing in the clinical setting has the potential to bring major improvements to infection control and clinical practice. Sequencing instruments are not currently available in the majority of routine microbiology laboratories worldwide, but an alternative is to use external sequencing providers. To foster discussion around this we investigated whether send-out services were a viable option. Four providers offering MiSeq sequencing were selected based on cost and evaluated based on the service provided and sequence data quality. DNA was prepared from five methicillin-resistant Staphylococcus aureus (MRSA) isolates, four of which were investigated during a previously published outbreak in the UK together with a reference MRSA isolate (ST22 HO 5096 0412). Cost of sequencing per isolate ranged from £155 to £342 and turnaround times from DNA postage to arrival of sequence data ranged from 12 to 63 days. Comparison of commercially generated genomes against the original sequence data demonstrated very high concordance, with no more than one single nucleotide polymorphism (SNP) difference on core genome mapping between the original sequences and the new sequence for all four providers. Multilocus sequence type could not be assigned based on assembly for the two cheapest sequence providers due to fragmented assemblies probably caused by a lower output of sequence data per isolate. Our results indicate that external providers returned highly accurate genome data, but that improvements are required in turnaround time to make this a viable option for use in clinical practice.
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Affiliation(s)
- Kathy Raven
- 1Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Beth Blane
- 1Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Carol Churcher
- 1Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Julian Parkhill
- 2Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Sharon J Peacock
- 1Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK.,2Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,3London School of Hygiene and Tropical Medicine, London, UK
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Kashyap PC, Chia N, Nelson H, Segal E, Elinav E. Microbiome at the Frontier of Personalized Medicine. Mayo Clin Proc 2017; 92:1855-1864. [PMID: 29202942 PMCID: PMC5730337 DOI: 10.1016/j.mayocp.2017.10.004] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/13/2017] [Accepted: 10/09/2017] [Indexed: 12/21/2022]
Abstract
The genomic revolution promises to transform our approach to treat patients by individualizing treatments, reducing adverse events, and decreasing health care costs. The early advances using this have been realized primarily by optimizing preventive and therapeutic approaches in cancer using human genome sequencing. The ability to characterize the microbiome, which includes all the microbes that reside within and upon us and all their genetic elements, using next-generation sequencing allows us to now incorporate this important contributor to human disease into developing new preventive and therapeutic strategies. In this review we highlight the importance of the microbiome in all aspects of human disease, including pathogenesis, phenotype, prognosis, and response to treatment, as well as their role as diagnostic and therapeutic biomarkers. We provide a role for next-generation sequencing in both precise microbial identification of infectious diseases and characterization of microbial communities and their function. Taken together, the microbiome is emerging as an integral part of precision medicine approach as it not only contributes to interindividual variability in all aspects of a disease but also represents a potentially modifiable factor that is amenable to targeting by therapeutics.
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Affiliation(s)
- Purna C Kashyap
- Enteric Neuroscience Program, Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN.
| | | | - Heidi Nelson
- Department of Surgery, Mayo Clinic, Rochester, MN
| | - Eran Segal
- Department of Computer Science, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Elinav
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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23
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He X, Jin Y, Ye M, Chen N, Zhu J, Wang J, Jiang L, Wu R. Bacterial Genetic Architecture of Ecological Interactions in Co-culture by GWAS-Taking Escherichia coli and Staphylococcus aureus as an Example. Front Microbiol 2017; 8:2332. [PMID: 29230205 PMCID: PMC5712204 DOI: 10.3389/fmicb.2017.02332] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 11/13/2017] [Indexed: 11/22/2022] Open
Abstract
How a species responds to such a biotic environment in the community, ultimately leading to its evolution, has been a topic of intense interest to ecological evolutionary biologists. Until recently, limited knowledge was available regarding the genotypic changes that underlie phenotypic changes. Our study implemented GWAS (Genome-Wide Association Studies) to illustrate the genetic architecture of ecological interactions that take place in microbial populations. By choosing 45 such interspecific pairs of Escherichia coli and Staphylococcus aureus strains that were all genotyped throughout the entire genome, we employed Q-ROADTRIPS to analyze the association between single SNPs and microbial abundance measured at each time point for bacterial populations reared in monoculture and co-culture, respectively. We identified a large number of SNPs and indels across the genomes (35.69 G clean data of E. coli and 50.41 G of S. aureus). We reported 66 and 111 SNPs that were associated with interaction in E. coli and S. aureus, respectively. 23 out of 66 polymorphic changes resulted in amino acid alterations.12 significant genes, such as murE, treA, argS, and relA, which were also identified in previous evolutionary studies. In S. aureus, 111 SNPs detected in coding sequences could be divided into 35 non-synonymous and 76 synonymous SNPs. Our study illustrated the potential of genome-wide association methods for studying rapidly evolving traits in bacteria. Genetic association study methods will facilitate the identification of genetic elements likely to cause phenotypes of interest and provide targets for further laboratory investigation.
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Affiliation(s)
- Xiaoqing He
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yi Jin
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Meixia Ye
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Nan Chen
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jing Zhu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jingqi Wang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Libo Jiang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.,Center for Statistical Genetics, Pennsylvania State University, Hershey, PA, United States
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24
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First Complete Genome Sequence of Methicillin-Resistant Staphylococcus aureus Strain SO-1977 Isolated from Khartoum, Sudan. GENOME ANNOUNCEMENTS 2017; 5:5/42/e00945-17. [PMID: 29051236 PMCID: PMC5646389 DOI: 10.1128/genomea.00945-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Methicillin-resistant Staphylococcus aureus is increasingly becoming resistant to most antibiotics and consequently has become a challenging public health problem in Sudan. The present study documented the first complete genome sequence of strain SO-1977, isolated from a contaminated wound in Sudan.
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Gagnaire J, Verhoeven PO, Grattard F, Rigaill J, Lucht F, Pozzetto B, Berthelot P, Botelho-Nevers E. Epidemiology and clinical relevance of Staphylococcus aureus intestinal carriage: a systematic review and meta-analysis. Expert Rev Anti Infect Ther 2017; 15:767-785. [PMID: 28726558 DOI: 10.1080/14787210.2017.1358611] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Recent data highlight the importance of screening more than one site for improving the detection of S. aureus colonization. Intestinal carriage is frequently under-investigated and its clinical impact ought to be defined a better way. Areas covered: This review and meta-analysis provide an updated overview of prevalence, characteristics and clinical significance of S. aureus intestinal carriage in different populations, both for methicillin-susceptible and -resistant S. aureus strains. Expert commentary: Intestinal S. aureus carriage is documented with higher prevalence in children and in patients with S. aureus skin and soft tissue infections. This site of colonization was shown to be associated with a high risk of dissemination in the environment and with S. aureus infection. Intestinal carriage is frequently retrieved in nasal carriers, reflecting probably an association with a high bacterial load. Exclusive intestinal carriage present in one third of intestinal carriers can be associated with infection. Comparative genotyping analysis of different strains from nasal and extra-nasal sites of carriage, including the intestinal ones, in the same individuals, would allow a better comprehension of the pathophysiology of S. aureus endogenous infection. It could also permit to improve the prevention of these infections by decolonization of sites implicated in infection genesis.
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Affiliation(s)
- Julie Gagnaire
- a GIMAP EA 3064 (Groupe Immunité des Muqueuses et Agents Pathogènes) , University of Lyon , Saint-Etienne , France.,b Infectious Diseases Department , University Hospital of Saint-Etienne , Saint-Etienne , France
| | - Paul O Verhoeven
- a GIMAP EA 3064 (Groupe Immunité des Muqueuses et Agents Pathogènes) , University of Lyon , Saint-Etienne , France.,c Laboratory of Infectious Agents and Hygiene , University Hospital of Saint-Etienne , Saint-Etienne , France
| | - Florence Grattard
- a GIMAP EA 3064 (Groupe Immunité des Muqueuses et Agents Pathogènes) , University of Lyon , Saint-Etienne , France.,c Laboratory of Infectious Agents and Hygiene , University Hospital of Saint-Etienne , Saint-Etienne , France
| | - Josselin Rigaill
- a GIMAP EA 3064 (Groupe Immunité des Muqueuses et Agents Pathogènes) , University of Lyon , Saint-Etienne , France.,c Laboratory of Infectious Agents and Hygiene , University Hospital of Saint-Etienne , Saint-Etienne , France
| | - Frédéric Lucht
- a GIMAP EA 3064 (Groupe Immunité des Muqueuses et Agents Pathogènes) , University of Lyon , Saint-Etienne , France.,b Infectious Diseases Department , University Hospital of Saint-Etienne , Saint-Etienne , France
| | - Bruno Pozzetto
- a GIMAP EA 3064 (Groupe Immunité des Muqueuses et Agents Pathogènes) , University of Lyon , Saint-Etienne , France.,c Laboratory of Infectious Agents and Hygiene , University Hospital of Saint-Etienne , Saint-Etienne , France
| | - Philippe Berthelot
- a GIMAP EA 3064 (Groupe Immunité des Muqueuses et Agents Pathogènes) , University of Lyon , Saint-Etienne , France.,b Infectious Diseases Department , University Hospital of Saint-Etienne , Saint-Etienne , France.,c Laboratory of Infectious Agents and Hygiene , University Hospital of Saint-Etienne , Saint-Etienne , France
| | - Elisabeth Botelho-Nevers
- a GIMAP EA 3064 (Groupe Immunité des Muqueuses et Agents Pathogènes) , University of Lyon , Saint-Etienne , France.,b Infectious Diseases Department , University Hospital of Saint-Etienne , Saint-Etienne , France
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26
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Abstract
The community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) epidemic in the United States is largely attributable to the meteoric rise of a single clone, referred to as USA300. This strain not only spread across the United States in just a few years to become the predominant cause of staphylococcal disease, but it also appears to have increased the overall number of skin and soft-tissue infections (SSTIs), increasing the overall disease burden. While USA300 still constitutes a major public health burden, its prevalence may be decreasing in some parts of the United States. Other than an epidemic in South America due to a closely related strain, USA300 also seems to have been largely unable to establish itself as an endemic infection in other geographic locations. While there have been several hypotheses put forward to explain the enormous success of USA300, the reasons for its failures and its potential fall remain obscure. Far from being unique to USA300, the rise and fall of specific clones of S. aureus in human populations seems to be a common process that has occurred multiple times and in multiple locations. This review charts the rise of USA300 and the evidence that suggests that it may be in decline, and it considers how best to understand the future spread, containment, and possible extinction of CA-MRSA.
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Affiliation(s)
- Paul J Planet
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York.,Pediatric Infectious Disease Division, Children's Hospital of Philadelphia.,Perelman School of Medicine, University of Pennsylvania, Philadelphia
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27
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Earls MR, Kinnevey PM, Brennan GI, Lazaris A, Skally M, O’Connell B, Humphreys H, Shore AC, Coleman DC. The recent emergence in hospitals of multidrug-resistant community-associated sequence type 1 and spa type t127 methicillin-resistant Staphylococcus aureus investigated by whole-genome sequencing: Implications for screening. PLoS One 2017; 12:e0175542. [PMID: 28399151 PMCID: PMC5388477 DOI: 10.1371/journal.pone.0175542] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/28/2017] [Indexed: 11/19/2022] Open
Abstract
Community-associated spa type t127/t922 methicillin-resistant Staphylococcus aureus (MRSA) prevalence increased from 1%-7% in Ireland between 2010–2015. This study tracked the spread of 89 such isolates from June 2013-June 2016. These included 78 healthcare-associated and 11 community associated-MRSA isolates from a prolonged hospital outbreak (H1) (n = 46), 16 other hospitals (n = 28), four other healthcare facilities (n = 4) and community-associated sources (n = 11). Isolates underwent antimicrobial susceptibility testing, DNA microarray profiling and whole-genome sequencing. Minimum spanning trees were generated following core-genome multilocus sequence typing and pairwise single nucleotide variation (SNV) analysis was performed. All isolates were sequence type 1 MRSA staphylococcal cassette chromosome mec type IV (ST1-MRSA-IV) and 76/89 were multidrug-resistant. Fifty isolates, including 40/46 from H1, were high-level mupirocin-resistant, carrying a conjugative 39 kb iles2-encoding plasmid. Two closely related ST1-MRSA-IV strains (I and II) and multiple sporadic strains were identified. Strain I isolates (57/89), including 43/46 H1 and all high-level mupirocin-resistant isolates, exhibited ≤80 SNVs. Two strain I isolates from separate H1 healthcare workers differed from other H1/strain I isolates by 7–47 and 12–53 SNVs, respectively, indicating healthcare worker involvement in this outbreak. Strain II isolates (19/89), including the remaining H1 isolates, exhibited ≤127 SNVs. For each strain, the pairwise SNVs exhibited by healthcare-associated and community-associated isolates indicated recent transmission of ST1-MRSA-IV within and between multiple hospitals, healthcare facilities and communities in Ireland. Given the interchange between healthcare-associated and community-associated isolates in hospitals, the risk factors that inform screening for MRSA require revision.
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Affiliation(s)
- Megan R. Earls
- Microbiology Research Unit, Dublin Dental University Hospital, University of Dublin, Trinity College, Dublin, Ireland
| | - Peter M. Kinnevey
- Microbiology Research Unit, Dublin Dental University Hospital, University of Dublin, Trinity College, Dublin, Ireland
| | - Gráinne I. Brennan
- Microbiology Research Unit, Dublin Dental University Hospital, University of Dublin, Trinity College, Dublin, Ireland
- National MRSA Reference Laboratory, St. James’s Hospital, Dublin 8, Ireland
| | - Alexandros Lazaris
- Microbiology Research Unit, Dublin Dental University Hospital, University of Dublin, Trinity College, Dublin, Ireland
| | - Mairead Skally
- Department of Microbiology, Beaumont Hospital, Dublin, Ireland
| | - Brian O’Connell
- National MRSA Reference Laboratory, St. James’s Hospital, Dublin 8, Ireland
- Department of Clinical Microbiology, School of Medicine, Trinity College Dublin, St. James’s Hospital, Dublin 8, Ireland
| | - Hilary Humphreys
- Department of Microbiology, Beaumont Hospital, Dublin, Ireland
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland Education and Research Centre, Beaumont Hospital, Dublin, Ireland
| | - Anna C. Shore
- Microbiology Research Unit, Dublin Dental University Hospital, University of Dublin, Trinity College, Dublin, Ireland
| | - David C. Coleman
- Microbiology Research Unit, Dublin Dental University Hospital, University of Dublin, Trinity College, Dublin, Ireland
- * E-mail:
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28
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Planet PJ, Narechania A, Chen L, Mathema B, Boundy S, Archer G, Kreiswirth B. Architecture of a Species: Phylogenomics of Staphylococcus aureus. Trends Microbiol 2016; 25:153-166. [PMID: 27751626 DOI: 10.1016/j.tim.2016.09.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/07/2016] [Accepted: 09/22/2016] [Indexed: 12/11/2022]
Abstract
A deluge of whole-genome sequencing has begun to give insights into the patterns and processes of microbial evolution, but genome sequences have accrued in a haphazard manner, with biased sampling of natural variation that is driven largely by medical and epidemiological priorities. For instance, there is a strong bias for sequencing epidemic lineages of methicillin-resistant Staphylococcus aureus (MRSA) over sensitive isolates (methicillin-sensitive S. aureus: MSSA). As more diverse genomes are sequenced the emerging picture is of a highly subdivided species with a handful of relatively clonal groups (complexes) that, at any given moment, dominate in particular geographical regions. The establishment of hegemony of particular clones appears to be a dynamic process of successive waves of replacement of the previously dominant clone. Here we review the phylogenomic structure of a diverse range of S. aureus, including both MRSA and MSSA. We consider the utility of the concept of the 'core' genome and the impact of recombination and horizontal transfer. We argue that whole-genome surveillance of S. aureus populations could lead to better forecasting of antibiotic resistance and virulence of emerging clones, and a better understanding of the elusive biological factors that determine repeated strain replacement.
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Affiliation(s)
- Paul J Planet
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA; Department of Pediatrics, Division of Pediatric Infectious Diseases, Children's Hospital of Philadelphia & University of Pennsylvania, Philadelphia, PA, USA.
| | - Apurva Narechania
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Liang Chen
- Public Health Research Institute Center, New Jersey Medical School, Rutgers, Newark, NJ, USA
| | - Barun Mathema
- Public Health Research Institute Center, New Jersey Medical School, Rutgers, Newark, NJ, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Sam Boundy
- Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Gordon Archer
- Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Barry Kreiswirth
- Public Health Research Institute Center, New Jersey Medical School, Rutgers, Newark, NJ, USA
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29
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Coia J. MRSA – seeing the bigger picture. J Hosp Infect 2016; 93:364-5. [DOI: 10.1016/j.jhin.2016.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 05/31/2016] [Indexed: 10/21/2022]
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30
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Brehony C, Hill DM, Lucidarme J, Borrow R, Maiden MC. Meningococcal vaccine antigen diversity in global databases. ACTA ACUST UNITED AC 2016; 20:30084. [PMID: 26676305 DOI: 10.2807/1560-7917.es.2015.20.49.30084] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 07/09/2015] [Indexed: 11/20/2022]
Abstract
The lack of an anti-capsular vaccine against serogroup B meningococcal disease has necessitated the exploration of alternative vaccine candidates, mostly proteins exhibiting varying degrees of antigenic variation. Analysis of variants of antigen-encoding genes is facilitated by publicly accessible online sequence repositories, such as the Neisseria PubMLST database and the associated Meningitis Research Foundation Meningococcus Genome Library (MRF-MGL). We investigated six proposed meningococcal vaccine formulations by deducing the prevalence of their components in the isolates represented in these repositories. Despite high diversity, a limited number of antigenic variants of each of the vaccine antigens were prevalent, with strong associations of particular variant combinations with given serogroups and genotypes. In the MRF-MGL and globally, the highest levels of identical sequences were observed with multicomponent/multivariant vaccines. Our analyses further demonstrated that certain combinations of antigen variants were prevalent over periods of decades in widely differing locations, indicating that vaccine formulations containing a judicious choice of antigen variants have potential for long-term protection across geographic regions. The data further indicated that formulations with multiple variants would be especially relevant at times of low disease incidence, as relative diversity was higher. Continued surveillance is required to monitor the changing prevalence of these vaccine antigens.
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Affiliation(s)
- Carina Brehony
- Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom
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31
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Monaco M, Pimentel de Araujo F, Cruciani M, Coccia EM, Pantosti A. Worldwide Epidemiology and Antibiotic Resistance of Staphylococcus aureus. Curr Top Microbiol Immunol 2016; 409:21-56. [PMID: 27025380 DOI: 10.1007/82_2016_3] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Staphylococcus aureus is an important human pathogen, responsible for infections in the community and the healthcare setting. Although much of the attention is focused on the methicillin-resistant "variant" MRSA, the methicillin-susceptible counterpart (MSSA) remains a prime species in infections. The epidemiology of S. aureus, especially of MRSA, showed a rapid evolution in the last years. After representing a typical nosocomial multidrug-resistant pathogen, MRSA has recently emerged in the community and among farmed animals thanks to its ability to evolve and adapt to different settings. Global surveillance has shown that MRSA represents a problem in all continents and countries where studies have been carried out, determining an increase in mortality and the need to use last-resource expensive antibiotics. S. aureus can easily acquire resistance to antibiotics and MRSA is characteristically multidrug resistant. Resistance to vancomycin, the principal anti-MRSA antibiotic is rare, although isolates with decreased susceptibility are recovered in many areas. Resistance to the more recently introduced antibiotics, linezolid and daptomycin, has emerged; however, they remain substantially active against the large majority of MSSA and MRSA. Newer antistaphylococcal drugs have been developed, but since their clinical use has been very limited so far, little is known about the emergence of resistance. Molecular typing techniques have allowed to identify the major successful clones and lineages of MSSA and MRSA, including high-risk clones, and to trace their diffusion. In the face of a continuously evolving scenario, this review depicts the most common clones circulating in different geographical areas and in different settings at present. Since the evolution of S. aureus will continue, it is important to maintain the attention on the epidemiology of S. aureus in the future with a global view.
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Affiliation(s)
- Monica Monaco
- Department of Infectious, Parasitic and Immuno-mediated Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Fernanda Pimentel de Araujo
- Department of Infectious, Parasitic and Immuno-mediated Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Melania Cruciani
- Department of Infectious, Parasitic and Immuno-mediated Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Eliana M Coccia
- Department of Infectious, Parasitic and Immuno-mediated Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Annalisa Pantosti
- Department of Infectious, Parasitic and Immuno-mediated Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
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Williamson DA, Heffernan H, Nimmo G. Contemporary genomic approaches in the diagnosis and typing of Staphylococcus aureus. Pathology 2015; 47:270-5. [PMID: 25764206 DOI: 10.1097/pat.0000000000000236] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Staphylococcus aureus is a major human pathogen, causing disease in both community and healthcare settings. Over the past two decades, the epidemiology of S. aureus disease has changed dramatically, with the emergence and spread of community-associated methicillin-resistant S. aureus clones. This epidemiological shift, coupled with the association between delayed antimicrobial therapy and increased mortality in S. aureus bacteraemia, has greatly facilitated advances in the rapid molecular diagnosis of S. aureus. Rapid molecular testing for S. aureus can greatly reduce laboratory turnaround time, and in some circumstances, may lead to improved clinical outcomes. In addition, advances in DNA sequencing technology and bioinformatic analysis have shed new lights on the molecular epidemiology and transmission dynamics of S. aureus. In this context, we provide an overview of the key advances in the molecular diagnosis and typing of S. aureus, with a particular focus on the clinical impact and utility of genomic technologies.
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Affiliation(s)
- Deborah A Williamson
- 1Institute of Environmental Science and Research, Wellington 2Department of Pathology, University of Otago, Wellington, New Zealand 3Pathology Queensland Central Laboratory, Brisbane 4Griffith University School of Medicine, Gold Coast, Qld, Australia
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Ueda O, Tanaka S, Nagasawa Z, Hanaki H, Shobuike T, Miyamoto H. Development of a novel matrix-assisted laser desorption/ionization time-of-flight mass spectrum (MALDI-TOF-MS)-based typing method to identify meticillin-resistant Staphylococcus aureus clones. J Hosp Infect 2015; 90:147-55. [PMID: 25922338 DOI: 10.1016/j.jhin.2014.11.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 11/18/2014] [Indexed: 11/25/2022]
Abstract
BACKGROUND Mass spectrum analysis enables species- and subspecies-level identification, and can be used as an epidemiological tool in outbreak management. However, its reliability at clonal level has yet to be established. AIM To establish a matrix-assisted laser desorption/ionization time-of-flight mass-spectrum-based method that enables bacterial clone identification with accuracy equivalent to pulsed-field gel electrophoresis/phage open-reading frame typing (PFGE/POT). METHODS Meticillin-resistant Staphylococcus aureus (MRSA) was used in this study. Mass spectra were obtained from a standard strain of S. aureus (ATCC29213) and 57 clinically isolated strains, categorized according to POT. Peaks associated with MRSA clone identification (N = 67) were extracted. Based on this peak information, the feasibility of MRSA clone identification was examined by cluster analysis. FINDINGS In addition to the 58 strains used for peak extraction, mass spectrum analysis of 24 clinically isolated outbreak strains revealed that peak data could be used for successful identification of clones. These typing results were fully consistent with the PFGE and POT results. CONCLUSION This novel method enables simple and rapid typing with accuracy equivalent to PFGE/POT. This method would be suited to rapid outbreak analysis, offering accurate information to combat infectious diseases.
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Affiliation(s)
- O Ueda
- Microbiology Group, MM Business Unit, Siemens Healthcare Diagnostics KK, Tokyo, Japan; Department of Pathology and Microbiology, Faculty of Medicine, Saga University, Saga, Japan
| | - S Tanaka
- Department of Clinical Laboratory, Saga University Hospital, Saga, Japan
| | - Z Nagasawa
- Department of Medical Technology and Sciences, School of Health Sciences at Fukuoka, International University of Health and Welfare, Fukuoka, Japan
| | - H Hanaki
- Kitasato University Research Centre for Anti-infectious Drugs, Tokyo, Japan
| | - T Shobuike
- Department of Pathology and Microbiology, Faculty of Medicine, Saga University, Saga, Japan
| | - H Miyamoto
- Department of Pathology and Microbiology, Faculty of Medicine, Saga University, Saga, Japan.
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Moore G, Cookson B, Gordon NC, Jackson R, Kearns A, Singleton J, Smyth D, Wilson APR. Whole-genome sequencing in hierarchy with pulsed-field gel electrophoresis: the utility of this approach to establish possible sources of MRSA cross-transmission. J Hosp Infect 2015; 90:38-45. [PMID: 25648940 DOI: 10.1016/j.jhin.2014.12.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 12/18/2014] [Indexed: 10/24/2022]
Abstract
BACKGROUND In order to study the micro-epidemiology of meticillin-resistant Staphylococcus aureus (MRSA) effectively, the molecular typing method used must be able to distinguish between different MRSA strains. Pulsed-field gel electrophoresis (PFGE) can detect small genetic differences but is limited in its potential to distinguish isolates within a major lineage. Whole-genome sequencing (WGS) provides sufficient resolution to support or exclude links between otherwise indistinguishable isolates, but lacks the practical utility of conventional typing methods. AIM To explore the utility of WGS in a hierarchical approach with PFGE to help establish possible sources of MRSA cross-transmission in the intensive care setting. METHODS Possible transmission routes from donor to recipient via the hands of staff, the air or environmental surfaces were identified. Focused molecular typing used PFGE to explore these transmission hypotheses. WGS was applied when an acquisition event involved a common PFGE pulsotype. FINDINGS Thirty-eight of the 78 acquisition events could not be explored as clinical isolates were not available. PFGE excluded all potential donors from 26 of the remaining 40 acquisition events, but did identify a probable source in 14 new colonizations. Within the hypotheses tested, PFGE supported links between patients occupying the same bay, the same bed space, adjacent isolation rooms and different wards. When a patient source was not identified, PFGE implicated the ward environment and the hands of staff. However, WGS disproved three of these transmission pathways. CONCLUSION WGS can complement conventional typing methods by confirming or refuting possible MRSA transmission hypotheses. Epidemiological data are crucial in this process.
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Affiliation(s)
- G Moore
- Clinical Microbiology and Virology, University College London Hospitals NHS Foundation Trust, London, UK; Biosafety Investigation Unit, Public Health England, Porton Down, Salisbury, UK.
| | - B Cookson
- Staphylococcus Reference Unit, Antimicrobial Resistance and Healthcare Associated Infections, Public Health England Colindale, London, UK; Division of Infection and Immunity, University College London, London, UK
| | - N C Gordon
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - R Jackson
- Clinical Microbiology and Virology, University College London Hospitals NHS Foundation Trust, London, UK
| | - A Kearns
- Staphylococcus Reference Unit, Antimicrobial Resistance and Healthcare Associated Infections, Public Health England Colindale, London, UK
| | - J Singleton
- Department of Intensive Care, Royal Free Hampstead NHS Trust, London, UK
| | - D Smyth
- Clinical Microbiology and Virology, University College London Hospitals NHS Foundation Trust, London, UK
| | - A P R Wilson
- Clinical Microbiology and Virology, University College London Hospitals NHS Foundation Trust, London, UK
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Inouye M, Dashnow H, Raven LA, Schultz MB, Pope BJ, Tomita T, Zobel J, Holt KE. SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Med 2014. [PMID: 25422674 DOI: 10.1186/s13073–014–0090–6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet routine use of whole genome sequencing (WGS) for these purposes poses significant challenges. Here we present SRST2, a read mapping-based tool for fast and accurate detection of genes, alleles and multi-locus sequence types (MLST) from WGS data. Using >900 genomes from common pathogens, we show SRST2 is highly accurate and outperforms assembly-based methods in terms of both gene detection and allele assignment. We include validation of SRST2 within a public health laboratory, and demonstrate its use for microbial genome surveillance in the hospital setting. In the face of rising threats of antimicrobial resistance and emerging virulence among bacterial pathogens, SRST2 represents a powerful tool for rapidly extracting clinically useful information from raw WGS data. Source code is available from http://katholt.github.io/srst2/.
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Affiliation(s)
- Michael Inouye
- Medical Systems Biology, Department of Pathology, The University of Melbourne, Parkville, Victoria Australia ; Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria Australia
| | - Harriet Dashnow
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010 Australia ; Victorian Life Sciences Computation Initiative, The University of Melbourne, 187 Grattan Street Carlton, Melbourne, Victoria Australia
| | - Lesley-Ann Raven
- Medical Systems Biology, Department of Pathology, The University of Melbourne, Parkville, Victoria Australia
| | - Mark B Schultz
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010 Australia
| | - Bernard J Pope
- Victorian Life Sciences Computation Initiative, The University of Melbourne, 187 Grattan Street Carlton, Melbourne, Victoria Australia ; Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia
| | - Takehiro Tomita
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria Australia ; Microbiological Diagnostic Unit, The University of Melbourne, Parkville, Victoria Australia
| | - Justin Zobel
- Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010 Australia
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Inouye M, Dashnow H, Raven LA, Schultz MB, Pope BJ, Tomita T, Zobel J, Holt KE. SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Med 2014; 6:90. [PMID: 25422674 PMCID: PMC4237778 DOI: 10.1186/s13073-014-0090-6] [Citation(s) in RCA: 707] [Impact Index Per Article: 70.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/16/2014] [Indexed: 01/06/2023] Open
Abstract
Rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet routine use of whole genome sequencing (WGS) for these purposes poses significant challenges. Here we present SRST2, a read mapping-based tool for fast and accurate detection of genes, alleles and multi-locus sequence types (MLST) from WGS data. Using >900 genomes from common pathogens, we show SRST2 is highly accurate and outperforms assembly-based methods in terms of both gene detection and allele assignment. We include validation of SRST2 within a public health laboratory, and demonstrate its use for microbial genome surveillance in the hospital setting. In the face of rising threats of antimicrobial resistance and emerging virulence among bacterial pathogens, SRST2 represents a powerful tool for rapidly extracting clinically useful information from raw WGS data. Source code is available from http://katholt.github.io/srst2/.
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Affiliation(s)
- Michael Inouye
- Medical Systems Biology, Department of Pathology, The University of Melbourne, Parkville, Victoria Australia ; Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria Australia
| | - Harriet Dashnow
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010 Australia ; Victorian Life Sciences Computation Initiative, The University of Melbourne, 187 Grattan Street Carlton, Melbourne, Victoria Australia
| | - Lesley-Ann Raven
- Medical Systems Biology, Department of Pathology, The University of Melbourne, Parkville, Victoria Australia
| | - Mark B Schultz
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010 Australia
| | - Bernard J Pope
- Victorian Life Sciences Computation Initiative, The University of Melbourne, 187 Grattan Street Carlton, Melbourne, Victoria Australia ; Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia
| | - Takehiro Tomita
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria Australia ; Microbiological Diagnostic Unit, The University of Melbourne, Parkville, Victoria Australia
| | - Justin Zobel
- Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010 Australia
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Absence of patient-to-patient intrahospital transmission of Staphylococcus aureus as determined by whole-genome sequencing. mBio 2014; 5:e01692-14. [PMID: 25293757 PMCID: PMC4196229 DOI: 10.1128/mbio.01692-14] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Nosocomial transmission of pathogens is a major health care challenge. The increasing spread of antibiotic-resistant strains represents an ongoing threat to public health. Previous Staphylococcus aureus transmission studies have focused on transmission of S. aureus between asymptomatic carriers or used low-resolution typing methods such as multilocus sequence typing (MLST) or spa typing. To identify patient-to-patient intrahospital transmission using high-resolution genetic analysis, we sequenced the genomes of a consecutive set of 398 S. aureus isolates from sterile-site infections. The S. aureus strains were collected from four hospitals in the Houston Methodist Hospital System over a 6-month period. Importantly, we discovered no evidence of transmission of S. aureus between patients with sterile-site infections. The lack of intrahospital transmission may reflect a fundamental difference between day-to-day transmission events in the hospital setting and the more frequently studied outbreak scenarios. Previous studies have suggested that nosocomial transmission of S. aureus is common. Our data revealed an unexpected lack of evidence for intrahospital transmission of S. aureus between patients with invasive infections. This finding has important implications for hospital infection control and public health efforts. In addition, our data demonstrate that highly related pools of S. aureus strains exist in the community which may complicate outbreak investigations.
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Palomino JC, Vandamme P, Martin A. Classical and new assays for detecting drug resistance in tuberculosis. Biomark Med 2014; 8:1105-14. [DOI: 10.2217/bmm.14.73] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Tuberculosis is a public health concern worldwide. Particularly worrying is the emergence of severe forms of drug resistance, such as extensively drug resistant and totally drug resistant tuberculosis, with few treatment options for the afflicted patients. To avoid further spread of drug resistance, its early detection is extremely important. Conventional phenotypic procedures to detect drug resistance depended on the in vitro slow growth of the bacteria. More recent molecular approaches such as reverse-hybridization assays and real-time PCR tests have been introduced. Newer options proposed include, faster culture-based methods and whole-genome sequencing and nanotechnology. Not yet available is a real point-of-care test, applied directly in clinical samples and reliable enough for guiding a treatment option.
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Affiliation(s)
- Juan Carlos Palomino
- Laboratory of Microbiology, Department of Biochemistry & Microbiology, Ghent University, KL Ledeganckstraat 35, 9000 Gent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry & Microbiology, Ghent University, KL Ledeganckstraat 35, 9000 Gent, Belgium
| | - Anandi Martin
- Laboratory of Microbiology, Department of Biochemistry & Microbiology, Ghent University, KL Ledeganckstraat 35, 9000 Gent, Belgium
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Fossum Moen AE, Holberg-Petersen M, Andresen LL, Blomfeldt A. spa typing alone is not sufficient to demonstrate endemic establishment of meticillin-resistant Staphylococcus aureus in a low-prevalence country. J Hosp Infect 2014; 88:72-7. [PMID: 25085462 DOI: 10.1016/j.jhin.2014.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 06/17/2014] [Indexed: 11/25/2022]
Abstract
BACKGROUND The prevalence of meticillin-resistant Staphylococcus aureus (MRSA) in Norway is low but increasing. Over the last decade, numerous nursing homes have experienced MRSA outbreaks. One genetic lineage, spa type t304, has been identified at multiple nursing homes and has caused large outbreaks lasting for several years. AIM To evaluate whether spa typing is sufficient for the detection of MRSA spread and endemic establishment in a low-prevalence area, using spa type t304 as the test organism. METHODS All spa type t304 isolates detected in 1991-2010 in the most densely populated area of Norway were included. Time and place of bacterial sampling were recorded. The isolates were analysed using multi-locus sequence typing, staphylococcal cassette chromosome mec typing, detection of lukS/F-PV and pulsed-field gel electrophoresis (PFGE). FINDINGS In total, 181 spa type t304 isolates were identified in three of 23 municipalities. Most (91%) of the isolates could be linked to 13 nursing homes, eight of which experienced outbreaks. PFGE analysis revealed three PFGE types, consisting of 19 PFGE patterns; 95% of the isolates were PFGE type 2. In total, PFGE types 2 and 3 accounted for 99% of all nursing home isolates, and included isolates from different nursing homes, different outbreaks and different time periods. Additional genetic analyses did not further differentiate between the spa type t304 isolates. CONCLUSION MRSA spa type t304 appears to have established itself as an endemic genetic lineage in the study area. spa typing does not provide sufficient resolution when investigating the spread of an endemic-like genetic lineage in a low-prevalence area, and should be supplemented by additional typing techniques.
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Affiliation(s)
- A E Fossum Moen
- Section of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital and Institute of Clinical Medicine, University of Oslo, Lørenskog, Norway.
| | - M Holberg-Petersen
- Department of Microbiology, Division of Diagnostics and Intervention, Oslo University Hospital, Ullevål, Oslo, Norway
| | - L L Andresen
- Department of Microbiology, Division of Diagnostics and Intervention, Oslo University Hospital, Ullevål, Oslo, Norway
| | - A Blomfeldt
- Department of Microbiology and Infection Control, Division of Diagnostics and Technology, Akershus University Hospital, Lørenskog, Norway
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Caboche S, Audebert C, Hot D. High-Throughput Sequencing, a VersatileWeapon to Support Genome-Based Diagnosis in Infectious Diseases: Applications to Clinical Bacteriology. Pathogens 2014; 3:258-79. [PMID: 25437800 PMCID: PMC4243446 DOI: 10.3390/pathogens3020258] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 02/28/2014] [Accepted: 03/20/2014] [Indexed: 12/19/2022] Open
Abstract
The recent progresses of high-throughput sequencing (HTS) technologies enable easy and cost-reduced access to whole genome sequencing (WGS) or re-sequencing. HTS associated with adapted, automatic and fast bioinformatics solutions for sequencing applications promises an accurate and timely identification and characterization of pathogenic agents. Many studies have demonstrated that data obtained from HTS analysis have allowed genome-based diagnosis, which has been consistent with phenotypic observations. These proofs of concept are probably the first steps toward the future of clinical microbiology. From concept to routine use, many parameters need to be considered to promote HTS as a powerful tool to help physicians and clinicians in microbiological investigations. This review highlights the milestones to be completed toward this purpose.
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Affiliation(s)
- Ségolène Caboche
- FRE 3642 Molecular and Cellular Medecine, CNRS, Institut Pasteur de Lille and University Lille Nord de France, Lille 59019, France.
| | | | - David Hot
- FRE 3642 Molecular and Cellular Medecine, CNRS, Institut Pasteur de Lille and University Lille Nord de France, Lille 59019, France.
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Molecular Diagnosis Contributing for Multi-Drug Resistant Infection Control. CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES 2014. [DOI: 10.1007/s40506-013-0006-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Miller RM, Price JR, Batty EM, Didelot X, Wyllie D, Golubchik T, Crook DW, Paul J, Peto TEA, Wilson DJ, Cule M, Ip CLC, Day NPJ, Moore CE, Bowden R, Llewelyn MJ. Healthcare-associated outbreak of meticillin-resistant Staphylococcus aureus bacteraemia: role of a cryptic variant of an epidemic clone. J Hosp Infect 2013; 86:83-9. [PMID: 24433924 PMCID: PMC3924019 DOI: 10.1016/j.jhin.2013.11.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 11/20/2013] [Indexed: 12/21/2022]
Abstract
Background New strains of meticillin-resistant Staphylococcus aureus (MRSA) may be associated with changes in rates of disease or clinical presentation. Conventional typing techniques may not detect new clonal variants that underlie changes in epidemiology or clinical phenotype. Aim To investigate the role of clonal variants of MRSA in an outbreak of MRSA bacteraemia at a hospital in England. Methods Bacteraemia isolates of the major UK lineages (EMRSA-15 and -16) from before and after the outbreak were analysed by whole-genome sequencing in the context of epidemiological and clinical data. For comparison, EMRSA-15 and -16 isolates from another hospital in England were sequenced. A clonal variant of EMRSA-16 was identified at the outbreak hospital and a molecular signature test designed to distinguish variant isolates among further EMRSA-16 strains. Findings By whole-genome sequencing, EMRSA-16 isolates during the outbreak showed strikingly low genetic diversity (P < 1 × 10−6, Monte Carlo test), compared with EMRSA-15 and EMRSA-16 isolates from before the outbreak or the comparator hospital, demonstrating the emergence of a clonal variant. The variant was indistinguishable from the ancestral strain by conventional typing. This clonal variant accounted for 64/72 (89%) of EMRSA-16 bacteraemia isolates at the outbreak hospital from 2006. Conclusions Evolutionary changes in epidemic MRSA strains not detected by conventional typing may be associated with changes in disease epidemiology. Rapid and affordable technologies for whole-genome sequencing are becoming available with the potential to identify and track the emergence of variants of highly clonal organisms.
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Affiliation(s)
- R M Miller
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - J R Price
- Department of Microbiology and Infectious Diseases, Brighton and Sussex University Hospital NHS Trust, Brighton, UK
| | - E M Batty
- Department of Statistics, University of Oxford, Oxford, UK
| | - X Didelot
- Department of Statistics, University of Oxford, Oxford, UK
| | - D Wyllie
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - T Golubchik
- Department of Statistics, University of Oxford, Oxford, UK
| | - D W Crook
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - J Paul
- Public Health England, Royal Sussex County Hospital, Brighton, UK
| | - T E A Peto
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - D J Wilson
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M Cule
- Department of Statistics, University of Oxford, Oxford, UK
| | - C L C Ip
- Department of Statistics, University of Oxford, Oxford, UK
| | - N P J Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Rajthevee, Bangkok, Thailand; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - C E Moore
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Oxford University Collaborative Laboratory, Angkor Hospital for Children, Siem Reap, Cambodia
| | - R Bowden
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK; Department of Statistics, University of Oxford, Oxford, UK; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M J Llewelyn
- Department of Microbiology and Infectious Diseases, Brighton and Sussex University Hospital NHS Trust, Brighton, UK.
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Price JR, Golubchik T, Cole K, Wilson DJ, Crook DW, Thwaites GE, Bowden R, Walker AS, Peto TEA, Paul J, Llewelyn MJ. Whole-genome sequencing shows that patient-to-patient transmission rarely accounts for acquisition of Staphylococcus aureus in an intensive care unit. Clin Infect Dis 2013; 58:609-18. [PMID: 24336829 PMCID: PMC3922217 DOI: 10.1093/cid/cit807] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
An assessment of Staphylococcus aureus acquisition among intensive care patients using serial sampling and whole-genome sequencing found less than a fifth of acquisitions resulted from patient-to-patient transmission. Whole-genome sequencing identified transmission more accurately than spa-typing and patient stay data. Background. Strategies to prevent Staphylococcus aureus infection in hospitals focus on patient-to-patient transmission. We used whole-genome sequencing to investigate the role of colonized patients as the source of new S. aureus acquisitions, and the reliability of identifying patient-to-patient transmission using the conventional approach of spa typing and overlapping patient stay. Methods. Over 14 months, all unselected patients admitted to an adult intensive care unit (ICU) were serially screened for S. aureus. All available isolates (n = 275) were spa typed and underwent whole-genome sequencing to investigate their relatedness at high resolution. Results. Staphylococcus aureus was carried by 185 of 1109 patients sampled within 24 hours of ICU admission (16.7%); 59 (5.3%) patients carried methicillin-resistant S. aureus (MRSA). Forty-four S. aureus (22 MRSA) acquisitions while on ICU were detected. Isolates were available for genetic analysis from 37 acquisitions. Whole-genome sequencing indicated that 7 of these 37 (18.9%) were transmissions from other colonized patients. Conventional methods (spa typing combined with overlapping patient stay) falsely identified 3 patient-to-patient transmissions (all MRSA) and failed to detect 2 acquisitions and 4 transmissions (2 MRSA). Conclusions. Only a minority of S. aureus acquisitions can be explained by patient-to-patient transmission. Whole-genome sequencing provides the resolution to disprove transmission events indicated by conventional methods and also to reveal otherwise unsuspected transmission events. Whole-genome sequencing should replace conventional methods for detection of nosocomial S. aureus transmission.
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Affiliation(s)
- James R Price
- Department of Microbiology and Infection, Royal Sussex County Hospital, Brighton
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Prosperi M, Veras N, Azarian T, Rathore M, Nolan D, Rand K, Cook RL, Johnson J, Morris JG, Salemi M. Molecular epidemiology of community-associated methicillin-resistant Staphylococcus aureus in the genomic era: a cross-sectional study. Sci Rep 2013; 3:1902. [PMID: 23712667 PMCID: PMC3664956 DOI: 10.1038/srep01902] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 05/07/2013] [Indexed: 11/16/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of healthcare-associated infections and significant contributor to healthcare cost. Community-associated-MRSA (CA-MRSA) strains have now invaded healthcare settings. A convenience sample of 97 clinical MRSA isolates was obtained from seven hospitals during a one-week period in 2010. We employed a framework integrating Staphylococcus protein A typing and full-genome next-generation sequencing. Single nucleotide polymorphisms were analyzed using phylodynamics. Twenty-six t002, 48 t008, and 23 other strains were identified. Phylodynamic analysis of 30 t008 strains showed ongoing exponential growth of the effective population size the basic reproductive number (R0) ranging from 1.24 to 1.34. No evidence of hospital clusters was identified. The lack of phylogeographic clustering suggests that community introduction is a major contributor to emergence of CA-MRSA strains within hospitals. Phylodynamic analysis provides a powerful framework to investigate MRSA transmission between the community and hospitals, an understanding of which is essential for control.
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Affiliation(s)
- Mattia Prosperi
- College of Medicine, Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Jacksonville, FL, USA
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Gunes H, Gulen D, Mutlu R, Gumus A, Tas T, Topkaya AE. Antibacterial effects of curcumin: An in vitro minimum inhibitory concentration study. Toxicol Ind Health 2013; 32:246-50. [PMID: 24097361 DOI: 10.1177/0748233713498458] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
AIM To evaluate the antibacterial effect of curcumin with the minimum inhibitory concentration (MIC) method in standard bacterial strains. METHODS The in vitro antibacterial activity of curcumin was evaluated against methicillin-sensitive Staphylococcus aureus (MSSA) (ATCC 29213), methicillin-resistant Staphylococcus aureus (MRSA) (ATCC 43300), Enterococcus faecalis (ATCC 29212), Bacillus subtilis (ATCC 6633), Pseudomonas aeruginosa (ATCC 27853), Escherichia coli (ATCC 25922) and Klebsiella pneumoniae (ATCC 700603) using the macrodilution broth susceptibility test method. After incubation in tubes, the antibacterial activity of curcumin was detected by a lack of turbidity, which indicated the inhibition of bacterial growth. The concentration in the tube with the highest dilution showing no turbidity was defined as the MIC. RESULTS The curcumin MIC values were 175 µg/ml, 129 µg/ml, 219 µg/ml, 217 µg/ml, 163 µg/ml, 293 µg/ml and 216 µg/ml against P. aeruginosa, B. subtilis, MSSA, MRSA, E. coli, E. faecalis and K. Pneumonia, respectively. CONCLUSION This study revealed antibacterial effects of curcumin against standard bacterial strains in high concentrations. Animal experiments have demonstrated that curcumin applied at high doses has strong antibacterial activity. There is a need for further in vivo studies to shed light on antibacterial effects of curcumin with high concentrations.
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Affiliation(s)
- Hayati Gunes
- Department of Medical Microbiology, Medical Faculty, Namik Kemal University, Tekirdag, Turkey
| | - Dumrul Gulen
- Department of Medical Microbiology, Medical Faculty, Namik Kemal University, Tekirdag, Turkey
| | - Reyhan Mutlu
- Department of Medical Microbiology, Medical Faculty, Namik Kemal University, Tekirdag, Turkey
| | - Abdullah Gumus
- Department of Medical Microbiology, Medical Faculty, Namik Kemal University, Tekirdag, Turkey
| | - Tekin Tas
- Department of Medical Microbiology, Medical Faculty, Abant Izzet Baysal University, Bolu, Turkey
| | - Aynur Eren Topkaya
- Department of Medical Microbiology, Medical Faculty, Namik Kemal University, Tekirdag, Turkey
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Kirkup BC, Mahlen S, Kallstrom G. Future-Generation Sequencing and Clinical Microbiology. Clin Lab Med 2013; 33:685-704. [DOI: 10.1016/j.cll.2013.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Humphreys H, Coleman DC. Whole genome sequencing and the prevention and control of meticillin-resistant Staphylococcus aureus infection. J Hosp Infect 2013; 85:85-6. [PMID: 23871767 DOI: 10.1016/j.jhin.2013.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 05/03/2013] [Indexed: 10/26/2022]
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