1
|
Shepherd MJ, Fu T, Harrington NE, Kottara A, Cagney K, Chalmers JD, Paterson S, Fothergill JL, Brockhurst MA. Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance. Nat Rev Microbiol 2024:10.1038/s41579-024-01041-1. [PMID: 38689039 DOI: 10.1038/s41579-024-01041-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2024] [Indexed: 05/02/2024]
Abstract
The ecological and evolutionary mechanisms of antimicrobial resistance (AMR) emergence within patients and how these vary across bacterial infections are poorly understood. Increasingly widespread use of pathogen genome sequencing in the clinic enables a deeper understanding of these processes. In this Review, we explore the clinical evidence to support four major mechanisms of within-patient AMR emergence in bacteria: spontaneous resistance mutations; in situ horizontal gene transfer of resistance genes; selection of pre-existing resistance; and immigration of resistant lineages. Within-patient AMR emergence occurs across a wide range of host niches and bacterial species, but the importance of each mechanism varies between bacterial species and infection sites within the body. We identify potential drivers of such differences and discuss how ecological and evolutionary analysis could be embedded within clinical trials of antimicrobials, which are powerful but underused tools for understanding why these mechanisms vary between pathogens, infections and individuals. Ultimately, improving understanding of how host niche, bacterial species and antibiotic mode of action combine to govern the ecological and evolutionary mechanism of AMR emergence in patients will enable more predictive and personalized diagnosis and antimicrobial therapies.
Collapse
Affiliation(s)
- Matthew J Shepherd
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK.
| | - Taoran Fu
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Niamh E Harrington
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Anastasia Kottara
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Kendall Cagney
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Steve Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Joanne L Fothergill
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Michael A Brockhurst
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK.
| |
Collapse
|
2
|
Bivona D, Bonomo C, Colombini L, Bonacci PG, Privitera GF, Caruso G, Caraci F, Santoro F, Musso N, Bongiorno D, Iannelli F, Stefani S. Generation and Characterization of Stable Small Colony Variants of USA300 Staphylococcus aureus in RAW 264.7 Murine Macrophages. Antibiotics (Basel) 2024; 13:264. [PMID: 38534699 DOI: 10.3390/antibiotics13030264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024] Open
Abstract
Intracellular survival and immune evasion are typical features of staphylococcal infections. USA300 is a major clone of methicillin-resistant S. aureus (MRSA), a community- and hospital-acquired pathogen capable of disseminating throughout the body and evading the immune system. Carnosine is an endogenous dipeptide characterized by antioxidant and anti-inflammatory properties acting on the peripheral (macrophages) and tissue-resident (microglia) immune system. In this work, RAW 264.7 murine macrophages were infected with the USA300 ATCC BAA-1556 S. aureus strain and treated with 20 mM carnosine and/or 32 mg/L erythromycin. Stable small colony variant (SCV) formation on blood agar medium was obtained after 48 h of combined treatment. Whole genome sequencing of the BAA-1556 strain and its stable derivative SCVs when combining Illumina and nanopore technologies revealed three single nucleotide differences, including a nonsense mutation in the shikimate kinase gene aroK. Gene expression analysis showed a significant up-regulation of the uhpt and sdrE genes in the stable SCVs compared with the wild-type, likely involved in adaptation to the intracellular milieu.
Collapse
Affiliation(s)
- Dalida Bivona
- Medical Molecular Microbiology and Antibiotic Resistance Laboratory (MMARLab), Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95123 Catania, Italy
| | - Carmelo Bonomo
- Medical Molecular Microbiology and Antibiotic Resistance Laboratory (MMARLab), Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95123 Catania, Italy
| | - Lorenzo Colombini
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Paolo G Bonacci
- Medical Molecular Microbiology and Antibiotic Resistance Laboratory (MMARLab), Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95123 Catania, Italy
| | - Grete F Privitera
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
| | - Giuseppe Caruso
- Department of Drug and Health Sciences, University of Catania, 95125 Catania, Italy
- Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Filippo Caraci
- Department of Drug and Health Sciences, University of Catania, 95125 Catania, Italy
- Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Francesco Santoro
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Nicolò Musso
- Biochemical Section, Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95123 Catania, Italy
| | - Dafne Bongiorno
- Medical Molecular Microbiology and Antibiotic Resistance Laboratory (MMARLab), Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95123 Catania, Italy
| | - Francesco Iannelli
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Stefania Stefani
- Medical Molecular Microbiology and Antibiotic Resistance Laboratory (MMARLab), Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95123 Catania, Italy
| |
Collapse
|
3
|
Yi EJ, Nguyen TTM, Jin X, Bellere AD, Kim MJ, Yi TH. Human Milk-Derived Enterococcus faecalis HM20: A Potential Alternative Agent of Antimicrobial Effect against Methicillin-Resistant Staphylococcus aureus (MRSA). Microorganisms 2024; 12:306. [PMID: 38399710 PMCID: PMC10892211 DOI: 10.3390/microorganisms12020306] [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: 12/28/2023] [Revised: 01/22/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
The increasing global impact of skin diseases, fueled by methicillin-resistant Staphylococcus aureus (MRSA), emphasizes the necessity for alternative therapies with lower toxicity, such as lactic acid bacteria (LAB). This study aims to isolate potential LAB from human milk and evaluate their efficacy against MRSA using various methods, including well diffusion, microdilution, crystal violet assay, enzymatic characterization, SDS-PAGE, and scanning electron microscopy (SEM). Among the 26 LAB screened, the human milk-derived strain HM20 exhibited significant antimicrobial activity against S. aureus CCARM 3089 (MRSA), which is a highly resistant skin pathogen. Through 16S rRNA sequencing, strain HM20 was identified as closely related to Enterococcus faecalis ATCC 19433T, which was subsequently designated as Enterococcus faecalis HM20. The minimum inhibitory concentration (MIC) of the cell-free supernatant (CFS) of HM20 against S. aureus KCTC 3881 and S. aureus CCARM 3089 was determined to be 6.25% and 12.5%, respectively. Furthermore, the effective inhibition of biofilm formation in S. aureus KCTC 3881 and S. aureus CCARM 3089 was observed at concentrations of 12.5% and 25% or higher, respectively. The antibacterial effect of the CFS was attributed to the presence of organic acids, hydrogen peroxide, and bacteriocins. Additionally, the antimicrobial peptides produced by HM20 were found to be stable under heat treatment and analyzed to have a size below 5 kDa. SEM image observations confirmed that the CFS of HM20 caused damage to the cell wall, forming pores and wrinkles on S. aureus KCTC 3881 and S. aureus CCARM 3089. This comprehensive investigation on strain HM20 conducted in this study provides foundational data for potential developments in functional materials aimed at addressing skin infections and antibiotic-resistant strains in the future.
Collapse
Affiliation(s)
- Eun-Ji Yi
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea; (E.-J.Y.); (T.T.M.N.); (A.D.B.)
| | - Trang Thi Minh Nguyen
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea; (E.-J.Y.); (T.T.M.N.); (A.D.B.)
| | - Xiangji Jin
- Department of Dermatology, School of Medicine, Graduate School, Kyung Hee University, 26 Kyungheedae-ro, Dong-daemun, Seoul 02447, Republic of Korea;
| | - Arce Defeo Bellere
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea; (E.-J.Y.); (T.T.M.N.); (A.D.B.)
| | - Mi-Ju Kim
- Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Tae-Hoo Yi
- Graduate School of Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea; (E.-J.Y.); (T.T.M.N.); (A.D.B.)
| |
Collapse
|
4
|
Hamushan M, Yu J, Jiang F, Wang B, Li M, Hu Y, Wang J, Wu Q, Tang J, Han P, Shen H. Adaptive evolution of the Clf-Sdr subfamily contributes to Staphylococcus aureus musculoskeletal infection: Evidence from comparative genomics. Microbiol Res 2024; 278:127502. [PMID: 37832395 DOI: 10.1016/j.micres.2023.127502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023]
Abstract
Persistent Staphylococcus aureus infections of the musculoskeletal system are a challenge in clinical practice. Although extensive studies on the genotypic changes in S. aureus in soft tissue and blood system infections have been conducted, little is known about how S. aureus adapts to the microenvironment of the musculoskeletal system. Here, we used comparative genomics to analyze the isolates from patients with an S. aureus infection of the musculoskeletal system. We observed that mutations in the Clf-Sdr subfamily proteins frequently occurred during persistent infections. Furthermore, these mutations were primarily located in the non-active site (R region), rather than in the active site (A region). Mechanistically, the clfA/B mutation enhanced the S. aureus biofilm formation ability through the binding to fibrinogen and intercellular adhesion. Complementation studies using the USA300-ΔMSCRAMMs strains clfA and clfB revealed that mutations in both the A and R regions could enhance their corresponding function. The results of protein structure prediction and ligand-binding simulations suggest that these mutations influence the protein structure and ligand binding. In conclusion, our study suggests that the Clf-Sdr subfamily mutations may be one of the mechanisms contributing to persistent S. aureus infections of the musculoskeletal system.
Collapse
Affiliation(s)
- Musha Hamushan
- Orthopaedic Department, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Microsurgery on Extremities, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinlong Yu
- Orthopaedic Department, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Feng Jiang
- Orthopaedic Department, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Microsurgery on Extremities, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Boyong Wang
- Orthopaedic Department, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Microsurgery on Extremities, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingzhang Li
- Orthopaedic Department, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Microsurgery on Extremities, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yujie Hu
- Orthopaedic Department, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Microsurgery on Extremities, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianqiang Wang
- Department of Clinical Laboratory, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiong Wu
- Department of Clinical Laboratory, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jin Tang
- Department of Clinical Laboratory, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Pei Han
- Orthopaedic Department, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Microsurgery on Extremities, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Hao Shen
- Orthopaedic Department, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Microsurgery on Extremities, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| |
Collapse
|
5
|
Li T, Luo D, Ning N, Liu X, Chen F, Zhang L, Bao C, Li Z, Li D, Gu H, Qu F, Yang X, Huang Y, Li B, Wang H. Acinetobacter baumannii adaptation to the host pH microenvironment is mediated by allelic variation in a single residue of BauA protein. PNAS NEXUS 2023; 2:pgad079. [PMID: 37065616 PMCID: PMC10098034 DOI: 10.1093/pnasnexus/pgad079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 02/20/2023] [Accepted: 02/28/2023] [Indexed: 04/18/2023]
Abstract
Acinetobacter baumannii has been listed as one of the most critical pathogens in nosocomial infections; however, the key genes and mechanisms to adapt to the host microenvironment lack in-depth understanding. In this study, a total of 76 isolates (from 8 to 12 isolates per patient, spanning 128 to 188 days) were longitudinally collected from eight patients to investigate the within-host evolution of A. baumannii. A total of 70 within-host mutations were identified, 80% of which were nonsynonymous, indicating the important role of positive selection. Several evolutionary strategies of A. baumannii to increase its potential to adapt to the host microenvironment were identified, including hypermutation and recombination. Six genes were mutated in isolates from two or more patients, including two TonB-dependent receptor genes (bauA and BJAB07104_RS00665). In particular, the siderophore receptor gene bauA was mutated in multiple isolates from four patients with three MLST types, and all mutations were at amino acid 391 in ligand-binding sites. With 391T or 391A, BauA was more strongly bound to siderophores, which promoted the iron-absorption activity of A. baumannii at acidic or neutral pH, respectively. Through the A/T mutation at site 391 of BauA, A. baumannii displayed two reversible phases to adapt to distinct pH microenvironments. In conclusion, we demonstrated the comprehensive within-host evolutionary dynamics of A. baumannii, and discovered a key mutation of BauA site 391 as a genetic switch to adapt to different pH values, which may represent a model in the pathogen evolutionary adaption of the host microenvironment.
Collapse
Affiliation(s)
- Tao Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Deyan Luo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Nianzhi Ning
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Xiong Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Fanghong Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Liangyan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Chunmei Bao
- Department of Clinical Laboratory, The Fifth Medical Center of PLA General Hospital, No. 100 West Fourth Ring Road, Beijing 100039, China
| | - Zhan Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Deyu Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Hongjing Gu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Fen Qu
- Department of Clinical Laboratory, The Fifth Medical Center of PLA General Hospital, No. 100 West Fourth Ring Road, Beijing 100039, China
| | - Xiaolan Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Yanyu Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Boan Li
- Department of Clinical Laboratory, The Fifth Medical Center of PLA General Hospital, No. 100 West Fourth Ring Road, Beijing 100039, China
| | - Hui Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| |
Collapse
|
6
|
Hu J, Chen L, Li G, Pan Y, Lu Y, Chen J, Xiong W, Zeng Z. Prevalence and genetic characteristics of fosB-positive Staphylococcus aureus in duck farms in Guangdong, China in 2020. J Antimicrob Chemother 2023; 78:802-809. [PMID: 36691844 DOI: 10.1093/jac/dkad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 01/03/2023] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVES To investigate the epidemiology of fosB-positive Staphylococcus aureus in waterfowl farms in the Pearl River tributaries in Guangdong Province, China in 2020. METHODS A total of 63 S. aureus were recovered from 315 samples collected from six duck farms and one goose farm. PFGE, WGS and analysis were performed on 19 fosB-positive S. aureus. RESULTS The fosfomycin resistance rate of the strains was as high as 52.4% (33/63), and 30.1% (19/63) of the strains carried fosB. Resistance gene prediction results showed that duck farm environment-derived strains contained the oxazolidinone drug resistance gene optrA. All fosB-positive S. aureus were MRSA and most of them were MDR, mainly ST9-t899 and ST164-t899. PFGE showed that fosB-positive S. aureus from humans and ducks could be clustered into the same clade. In addition, core-genome SNP analysis showed that clonal transmission of S. aureus occurred between humans and water. Pan-genome analysis showed that S. aureus had an open pangenome. The fosB gene was located on 2610-2615 bp plasmids, which all contained a broad host-range plasmid replication protein family 13. Small plasmids carrying the fosB gene could be found in different multilocus STs of S. aureus. CONCLUSIONS This study indicated that duck farms in Guangdong, China could be an important reservoir of fosB-positive S. aureus. The spread of drug-resistant bacteria in waterfowl farms requires further monitoring.
Collapse
Affiliation(s)
- Jianxin Hu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, South China Agricultural University, Guangzhou 510642, China
| | - Lin Chen
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, South China Agricultural University, Guangzhou 510642, China
| | - Guihua Li
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, South China Agricultural University, Guangzhou 510642, China
| | - Yu Pan
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, South China Agricultural University, Guangzhou 510642, China
| | - Yixing Lu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, South China Agricultural University, Guangzhou 510642, China
| | - Jin Chen
- National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, South China Agricultural University, Guangzhou 510642, China
| | - Wenguang Xiong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, South China Agricultural University, Guangzhou 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhenling Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.,National Risk Assessment Laboratory for Antimicrobial Resistant of Microorganisms in Animals, South China Agricultural University, Guangzhou 510642, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| |
Collapse
|
7
|
Zhang H, Tian L, Chen T, Chen W, Ge Y, Bi J, Fang Z, Chen M. Prevalence and WGS-based characteristics of MRSA isolates in hospitals in Shanghai, China. Front Microbiol 2022; 13:1002691. [PMID: 36406454 PMCID: PMC9668878 DOI: 10.3389/fmicb.2022.1002691] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/15/2022] [Indexed: 11/02/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) isolates remain a serious threat to global health despite a decrease in MRSA infections since 2005. MRSA isolates exhibit great diversity worldwide, and their lineages show geographic variation. In this study, we used whole genome sequencing (WGS) to analyze antibiotic resistance genes and virulence genes, spa, staphylococcal cassette chromosome mec, sequence types (STs), and core genome multilocus sequence typing (cgMLST) of MRSA isolates from patients and environmental surface in hospitals in China to determine their prevalence and molecular traits. The highest number of infections by MRSA isolates was observed in patients aged ≥60 years (69.8%, P < 0.05). We identified a total of 19 STs from 162 MRSA isolates from patients. A significant increase was observed in the incidence of ST764-t002-II MRSA infection, which is replacing ST5-t002-II MRSA as the predominant ST. Similarly, isolates from environmental surface were predominantly ST764-t002-II (47%). Notably, most ST764 isolates (97.7%) carried seb, but not arginine catabolic mobile element (ACME), which differed from ST764 isolates in Japan and Thailand. The potential danger of spreading requires rigorous surveillance of emerging ST764 MRSA isolates. We also found higher resistance to seven antimicrobials [OXA, cefoxitin (FOX), ERY, CFZ, ciprofloxacin (CIP), levofloxacin (LEV), and moxifloxacin (MXF)]. Resistance to gentamicin (38.3%), tetracycline (55.9%), and minocycline (41.5%) were also common. Phenotypic resistance to antimicrobials was associated with resistance genes to its content, and cgMLST clustering suggested a strong link between these strains. Overall, our findings revealed the prevalence and molecular characteristics of MRSA isolates in Shanghai, China, providing a theoretical reference for preventing and controlling clonal transmission of MRSA isolates in hospitals in China.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Min Chen
- Department for Pathogen Identification, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| |
Collapse
|
8
|
Cetik Yildiz S. Staphylococcus aureus and Methicillin Resistant Staphylococcus aureus (MRSA) Carriage and Infections. Infect Dis (Lond) 2022. [DOI: 10.5772/intechopen.107138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Staphylococcus aureus is among the most common opportunistic infections worldwide, as it is found as part of the flora in many parts of the body. S. aureus is the leading cause of nosocomial infections with its ability to rapidly colonize the infected area, high virulence, rapid adaptation to environmental conditions, and the ability to develop very fast and effective resistance even to new generation antibiotics. Methicillin-resistant Staphylococcus aureus (MRSA), first identified in the 1960s, is one of the most successful modern pathogens, becoming an important factor in hospitals in the 1980s. MRSA is an important factor, especially in hospitalized patients and healthcare-associated infections. Patients colonized with S. aureus and MRSA are at risk for community-acquired infections. It is critical that multidrug resistance reduces treatment options in MRSA infections and MRSA strains. These microorganisms have been the subject of research for years as they spread and become resistant in both social and medical settings and cause great morbidity and mortality. With the rapid spread of resistance among bacteria, antibiotic resistance has increased the cost of health care, and this has become the factor limiting the production of new antibiotics.
Collapse
|
9
|
Lagos AC, Sundqvist M, Dyrkell F, Stegger M, Söderquist B, Mölling P. Evaluation of within-host evolution of methicillin-resistant Staphylococcus aureus (MRSA) by comparing cgMLST and SNP analysis approaches. Sci Rep 2022; 12:10541. [PMID: 35732699 PMCID: PMC9214674 DOI: 10.1038/s41598-022-14640-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022] Open
Abstract
Whole genome sequencing (WGS) of methicillin-resistant Staphylococcus aureus (MRSA) provides high-resolution typing, facilitating surveillance and outbreak investigations. The aim of this study was to evaluate the genomic variation rate in MRSA, by comparing commonly used core genome multilocus sequencing (cgMLST) against single nucleotide polymorphism (SNP) analyses. WGS was performed on 95 MRSA isolates, collected from 20 carriers during years 2003–2019. To assess variation and methodological-related differences, two different cgMLST schemes were obtained using Ridom SeqSphere+ and the cloud-based 1928 platform. In addition, two SNP methods, 1928 platform and Northern Arizona SNP Pipeline (NASP) were used. The cgMLST using Ridom SeqSphere+ and 1928 showed a median of 5.0 and 2.0 allele variants/year, respectively. In the SNP analysis, performed with two reference genomes COL and Newman, 1928 showed a median of 13 and 24 SNPs (including presumed recombination) and 3.8 respectively 4.0 SNPs (without recombination) per individual/year. Accordantly, NASP showed a median of 5.5 and 5.8 SNPs per individual/year. In conclusion, an estimated genomic variation rate of 2.0–5.8 genetic events per year (without recombination), is suggested as a general guideline to be used at clinical laboratories for surveillance and outbreak investigations independently of analysis approach used.
Collapse
Affiliation(s)
- Amaya Campillay Lagos
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
| | - Martin Sundqvist
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | | | - Marc Stegger
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Bo Söderquist
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Paula Mölling
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| |
Collapse
|
10
|
Crespo-Piazuelo D, Lawlor PG. Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) prevalence in humans in close contact with animals and measures to reduce on-farm colonisation. Ir Vet J 2021; 74:21. [PMID: 34362463 PMCID: PMC8348836 DOI: 10.1186/s13620-021-00200-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/13/2021] [Indexed: 12/14/2022] Open
Abstract
Since the 1940s, Staphylococcus aureus has adapted to the use of different antimicrobials to treat infections. Although S. aureus can act as a commensal bacterium, some strains are facultative pathogens and acquiring them can be fatal. In particular, treating infections caused by S. aureus with acquired antimicrobial resistance is problematic, as their treatment is more difficult. Some of these S. aureus variants are methicillin-resistant S. aureus (MRSA) with prevalence across the globe in health-care facilities, community settings and on livestock farms. Apart from humans, MRSA can colonise other animal species, and because of this, resistance to new antimicrobials can appear and jump between species. Livestock and companion animals are particularly important in this regard considering the relatively high usage of antimicrobials in these species. There is a risk to humans who come into direct contact with animals acquiring MRSA but there is also the risk of animals acquiring MRSA from colonised humans. In this review, we summarise studies conducted worldwide to characterise the prevalence of MRSA in veterinarians, farmers and other personnel who come into close contact with animals. Finally, alternative treatment, preventive measures and on-farm strategies to reduce MRSA introduction to a farm and carriage within a herd are discussed.
Collapse
Affiliation(s)
- Daniel Crespo-Piazuelo
- Teagasc, Pig Development Department, Animal & Grassland Research & Innovation Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland
| | - Peadar G Lawlor
- Teagasc, Pig Development Department, Animal & Grassland Research & Innovation Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland.
| |
Collapse
|
11
|
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus. NPJ Syst Biol Appl 2021; 7:30. [PMID: 34188046 PMCID: PMC8241996 DOI: 10.1038/s41540-021-00188-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 05/25/2021] [Indexed: 12/19/2022] Open
Abstract
Staphylococcus aureus is a high-priority pathogen causing severe infections with high morbidity and mortality worldwide. Many S. aureus strains are methicillin-resistant (MRSA) or even multi-drug resistant. It is one of the most successful and prominent modern pathogens. An effective fight against S. aureus infections requires novel targets for antimicrobial and antistaphylococcal therapies. Recent advances in whole-genome sequencing and high-throughput techniques facilitate the generation of genome-scale metabolic models (GEMs). Among the multiple applications of GEMs is drug-targeting in pathogens. Hence, comprehensive and predictive metabolic reconstructions of S. aureus could facilitate the identification of novel targets for antimicrobial therapies. This review aims at giving an overview of all available GEMs of multiple S. aureus strains. We downloaded all 114 available GEMs of S. aureus for further analysis. The scope of each model was evaluated, including the number of reactions, metabolites, and genes. Furthermore, all models were quality-controlled using MEMOTE, an open-source application with standardized metabolic tests. Growth capabilities and model similarities were examined. This review should lead as a guide for choosing the appropriate GEM for a given research question. With the information about the availability, the format, and the strengths and potentials of each model, one can either choose an existing model or combine several models to create models with even higher predictive values. This facilitates model-driven discoveries of novel antimicrobial targets to fight multi-drug resistant S. aureus strains.
Collapse
|
12
|
Gatt YE, Margalit H. Common Adaptive Strategies Underlie Within-Host Evolution of Bacterial Pathogens. Mol Biol Evol 2021; 38:1101-1121. [PMID: 33118035 PMCID: PMC7947768 DOI: 10.1093/molbev/msaa278] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Within-host adaptation is a hallmark of chronic bacterial infections, involving substantial genomic changes. Recent large-scale genomic data from prolonged infections allow the examination of adaptive strategies employed by different pathogens and open the door to investigate whether they converge toward similar strategies. Here, we compiled extensive data of whole-genome sequences of bacterial isolates belonging to miscellaneous species sampled at sequential time points during clinical infections. Analysis of these data revealed that different species share some common adaptive strategies, achieved by mutating various genes. Although the same genes were often mutated in several strains within a species, different genes related to the same pathway, structure, or function were changed in other species utilizing the same adaptive strategy (e.g., mutating flagellar genes). Strategies exploited by various bacterial species were often predicted to be driven by the host immune system, a powerful selective pressure that is not species specific. Remarkably, we find adaptive strategies identified previously within single species to be ubiquitous. Two striking examples are shifts from siderophore-based to heme-based iron scavenging (previously shown for Pseudomonas aeruginosa) and changes in glycerol-phosphate metabolism (previously shown to decrease sensitivity to antibiotics in Mycobacterium tuberculosis). Virulence factors were often adaptively affected in different species, indicating shifts from acute to chronic virulence and virulence attenuation during infection. Our study presents a global view on common within-host adaptive strategies employed by different bacterial species and provides a rich resource for further studying these processes.
Collapse
Affiliation(s)
- Yair E Gatt
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| |
Collapse
|
13
|
Haim MS, Zaheer R, Bharat A, Di Gregorio S, Di Conza J, Galanternik L, Lubovich S, Golding GR, Graham MR, Van Domselaar G, Cardona ST, Mollerach M. Comparative genomics of ST5 and ST30 methicillin-resistant Staphylococcus aureus sequential isolates recovered from paediatric patients with cystic fibrosis. Microb Genom 2021; 7:mgen000510. [PMID: 33599606 PMCID: PMC8190608 DOI: 10.1099/mgen.0.000510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/21/2020] [Indexed: 12/28/2022] Open
Abstract
Staphylococcus aureus chronic airway infection in patients with cystic fibrosis (CF) allows this pathogen to adapt over time in response to different selection pressures. We have previously shown that the main sequence types related to community-acquired methicillin-resistant S. aureus (MRSA) infections in Argentina - ST5 and ST30 - are also frequently isolated from the sputum of patients with CF, but in these patients they usually display multi-drug antimicrobial resistance. In this study, we sequenced the genomes of MRSA from four paediatric CF patients with the goal of identifying mutations among sequential isolates, especially those possibly related to antimicrobial resistance and virulence, which might contribute to the adaptation of the pathogen in the airways of patients with CF. Our results revealed genetic differences in sequential MRSA strains isolated from patients with CF in both their core and accessory genomes. Although the genetic adaptation of S. aureus was distinct in different hosts, we detected independent mutations in thyA, htrA, rpsJ and gyrA - which are known to have crucial roles in S. aureus virulence and antimicrobial resistance - in isolates recovered from multiple patients. Moreover, we identified allelic variants that were detected in all of the isolates recovered after a certain time point; these non-synonymous mutations were in genes associated with antimicrobial resistance, virulence, iron scavenging and oxidative stress resistance. In conclusion, our results provide evidence of genetic variability among sequential MRSA isolates that could be implicated in the adaptation of these strains during chronic CF airway infection.
Collapse
Affiliation(s)
- María Sol Haim
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Rahat Zaheer
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Amrita Bharat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Sabrina Di Gregorio
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - José Di Conza
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | | | - Silvina Lubovich
- Hospital de Niños 'Dr Ricardo Gutiérrez', Buenos Aires, Argentina
| | - George R. Golding
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Disease, University of Manitoba, Winnipeg, Canada
| | - Morag R. Graham
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Disease, University of Manitoba, Winnipeg, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Disease, University of Manitoba, Winnipeg, Canada
| | - Silvia T. Cardona
- Department of Medical Microbiology and Infectious Disease, University of Manitoba, Winnipeg, Canada
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Marta Mollerach
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| |
Collapse
|
14
|
Huemer M, Mairpady Shambat S, Brugger SD, Zinkernagel AS. Antibiotic resistance and persistence-Implications for human health and treatment perspectives. EMBO Rep 2020; 21:e51034. [PMID: 33400359 PMCID: PMC7726816 DOI: 10.15252/embr.202051034] [Citation(s) in RCA: 191] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/13/2020] [Accepted: 11/02/2020] [Indexed: 12/24/2022] Open
Abstract
Antimicrobial resistance (AMR) and persistence are associated with an elevated risk of treatment failure and relapsing infections. They are thus important drivers of increased morbidity and mortality rates resulting in growing healthcare costs. Antibiotic resistance is readily identifiable with standard microbiological assays, and the threat imposed by antibiotic resistance has been well recognized. Measures aiming to reduce resistance development and spreading of resistant bacteria are being enforced. However, the phenomenon of bacteria surviving antibiotic exposure despite being fully susceptible, so-called antibiotic persistence, is still largely underestimated. In contrast to antibiotic resistance, antibiotic persistence is difficult to measure and therefore often missed, potentially leading to treatment failures. In this review, we focus on bacterial mechanisms allowing evasion of antibiotic killing and discuss their implications on human health. We describe the relationship between antibiotic persistence and bacterial heterogeneity and discuss recent studies that link bacterial persistence and tolerance with the evolution of antibiotic resistance. Finally, we review persister detection methods, novel strategies aiming at eradicating bacterial persisters and the latest advances in the development of new antibiotics.
Collapse
Affiliation(s)
- Markus Huemer
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital ZurichUniversity of ZurichZurichSwitzerland
| | - Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital ZurichUniversity of ZurichZurichSwitzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital ZurichUniversity of ZurichZurichSwitzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital ZurichUniversity of ZurichZurichSwitzerland
| |
Collapse
|
15
|
Coll F, Raven KE, Knight GM, Blane B, Harrison EM, Leek D, Enoch DA, Brown NM, Parkhill J, Peacock SJ. Definition of a genetic relatedness cutoff to exclude recent transmission of meticillin-resistant Staphylococcus aureus: a genomic epidemiology analysis. LANCET MICROBE 2020; 1:e328-e335. [PMID: 33313577 PMCID: PMC7721685 DOI: 10.1016/s2666-5247(20)30149-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Background Whole-genome sequencing (WGS) can be used in genomic epidemiology investigations to confirm or refute outbreaks of bacterial pathogens, and to support targeted and efficient infection control interventions. We aimed to define a genetic relatedness cutoff, quantified as a number of single-nucleotide polymorphisms (SNP), for meticillin-resistant Staphylococcus aureus (MRSA), above which recent (ie, within 6 months) patient-to-patient transmission could be ruled out. Methods We did a retrospective genomic and epidemiological analysis of MRSA data from two prospective observational cohort studies in the UK to establish SNP cutoffs for genetic relatedness, above which recent transmission was unlikely. We used three separate approaches to calculate these thresholds. First, we applied a linear mixed model to estimate the S aureus substitution rate and 95th percentile within-host diversity in a cohort in which multiple isolates were sequenced per individual. Second, we applied a simulated transmission model to this same genomic dataset. Finally, in a second cohort, we determined the genetic distance (ie, the number of SNPs) that would capture 95% of epidemiologically linked cases. We applied the three approaches to both whole-genome and core-genome sequences. Findings In the linear mixed model, the estimated substitution rate was roughly 5 whole-genome SNPs (wgSNPs) or 3 core-genome SNPs (cgSNPs) per genome per year, and the 95th percentile within-host diversity was 19 wgSNPs or 10 cgSNPs. The combined SNP cutoffs for detection of MRSA transmission within 6 months per this model were thus 24 wgSNPs or 13 cgSNPs. The simulated transmission model suggested that cutoffs of 17 wgSNPs or 12 cgSNPs would detect 95% of MRSA transmission events within the same timeframe. Finally, in the second cohort, cutoffs of 22 wgSNPs or 11 cgSNPs captured 95% of epidemiologically linked cases within 6 months. Interpretation On the basis of our results, we propose conservative cutoffs of 25 wgSNPs or 15 cgSNPS above which transmission of MRSA within the previous 6 months can be ruled out. These cutoffs could potentially be used as part of a genomic sequencing approach to the management of outbreaks of MRSA in conjunction with traditional epidemiological techniques. Funding UK Department of Health, Wellcome Trust, UK National Institute for Health Research.
Collapse
Affiliation(s)
- Francesc Coll
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Correspondence to: Dr Francesc Coll, Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Kathy E Raven
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gwenan M Knight
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Beth Blane
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ewan M Harrison
- Department of Medicine, University of Cambridge, Cambridge, UK
- Human Genetics Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Danielle Leek
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, UK
- Public Health England, London, UK
| |
Collapse
|
16
|
Mobile genetic elements responsible for discordant Staphylococcus aureus phenotypes and genotypes in the same blood culture bottle. Diagn Microbiol Infect Dis 2020; 98:115175. [PMID: 32947112 DOI: 10.1016/j.diagmicrobio.2020.115175] [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] [Received: 06/10/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 11/22/2022]
Abstract
Approximately 15-20% of the S. aureus genome contains mobile genetic elements that can cause discrepancies between phenotypic and genotypic identification methods. Three blood culture bottles (each from a different patient) that showed discordant results, were shown to contain 2 S. aureus isolates after additional subcultures. One bottle had MRSA and MSSA that by DNA sequence analysis differed only by 31 kb; however, the deletions encompassed parts of SCCmec including mecA and SCCM1. The second bottle contained MRSA and MSSA that differed by 124 kb; the MSSA was missing the entire SCCmec and spa regions. The last bottle contained 2 MRSA, one with ACME II disrupting SCCmec and a 24 bp spa deletion. The deletions in SCCmec and the other elements gave rise to the discrepancies between molecular and the original culture results. Such discrepancies should prompt a search for additional strains in the blood culture bottle.
Collapse
|
17
|
Roe C, Stegger M, Lilje B, Johannesen TB, Ng KL, Sieber RN, Driebe E, Engelthaler DM, Andersen PS. Genomic analyses of Staphylococcus aureus clonal complex 45 isolates does not distinguish nasal carriage from bacteraemia. Microb Genom 2020; 6:mgen000403. [PMID: 32667872 PMCID: PMC7641415 DOI: 10.1099/mgen.0.000403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 06/16/2020] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus is a colonizing opportunistic pathogen and a leading cause of bloodstream infection with high morbidity and mortality. S. aureus carriage frequency is reportedly between 20 and 40 % among healthy adults, with S. aureus colonization considered to be a risk factor for S. aureus bacteraemia. It is unknown whether a genetic component of the bacterium is associated with S. aureus bacteraemia in comparison to nasal carriage strains. Previous association studies primarily focusing on the clinical outcome of an S. aureus infection have produced conflicting results, often limited by study design challenged by sample collections and the clonal diversity of S. aureus. To date, no study has investigated whether genomic features separate nasal carriage isolates from S. aureus bacteraemia isolates within a single clonal lineage. Here we have investigated whether genomic features, including single-nucleotide polymorphisms (SNPs), genes, or kmers, distinguish S. aureus nasal carriage isolates from bacteraemia isolates that all belong to the same clonal lineage [clonal complex 45 (CC45)] using whole-genome sequencing (WGS) and a genome-wide association (GWA) approach. From CC45, 100 isolates (50 bacteraemia and 50 nasal carriage, geographically and temporally matched) from Denmark were whole-genome sequenced and subjected to GWA analyses involving gene copy number variation, SNPs, gene content, kmers and gene combinations, while correcting for lineage effects. No statistically significant association involving SNPs, specific genes, gene variants, gene copy number variation, or a combination of genes was identified that could distinguish bacteraemia isolates from nasal carriage isolates. The presented results suggest that all S. aureus nasal CC45 isolates carry the potential to cause invasive disease, as no core or accessory genome content or variations were statistically associated with invasiveness.
Collapse
Affiliation(s)
- Chandler Roe
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- Northern Arizona University, Flagstaff, AZ, USA
| | - Marc Stegger
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Berit Lilje
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Kim Lee Ng
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Raphael N. Sieber
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | | | - Paal Skytt Andersen
- Translational Genomics Research Institute, Flagstaff, AZ, USA
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| |
Collapse
|
18
|
Methicillin-resistant Staphylococcus aureus: an overview of basic and clinical research. Nat Rev Microbiol 2020; 17:203-218. [PMID: 30737488 DOI: 10.1038/s41579-018-0147-4] [Citation(s) in RCA: 872] [Impact Index Per Article: 218.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most successful modern pathogens. The same organism that lives as a commensal and is transmitted in both health-care and community settings is also a leading cause of bacteraemia, endocarditis, skin and soft tissue infections, bone and joint infections and hospital-acquired infections. Genetically diverse, the epidemiology of MRSA is primarily characterized by the serial emergence of epidemic strains. Although its incidence has recently declined in some regions, MRSA still poses a formidable clinical threat, with persistently high morbidity and mortality. Successful treatment remains challenging and requires the evaluation of both novel antimicrobials and adjunctive aspects of care, such as infectious disease consultation, echocardiography and source control. In this Review, we provide an overview of basic and clinical MRSA research and summarize the expansive body of literature on the epidemiology, transmission, genetic diversity, evolution, surveillance and treatment of MRSA.
Collapse
|
19
|
Azarian T, Ridgway JP, Yin Z, David MZ. Long-Term Intrahost Evolution of Methicillin Resistant Staphylococcus aureus Among Cystic Fibrosis Patients With Respiratory Carriage. Front Genet 2019; 10:546. [PMID: 31244886 PMCID: PMC6581716 DOI: 10.3389/fgene.2019.00546] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/22/2019] [Indexed: 12/29/2022] Open
Abstract
Staphylococcus aureus is the most commonly identified airway colonizer of cystic fibrosis (CF) patients, and infections with methicillin-resistant S. aureus (MRSA) are associated with poor outcomes. Yet, little is known about the intrahost evolution of S. aureus among CF patients. We investigated convergent evolution and adaptation of MRSA among four CF patients with long-term respiratory carriage. For each patient, we performed whole-genome sequencing on an average of 21 isolates (range: 19–23) carried for a mean of 1,403 days (range: 903–1,679), including 25 pairs of isolates collected on the same day. We assessed intrahost diversity, population structure, evolutionary history, evidence of switched intergenic regions (IGRs), and signatures of adaptation in the context of patient age, antibiotic treatment, and co-colonizing microbes. Phylogenetic analysis delineated distinct multilocus sequence type ST5 (n = 3) and ST72 (n = 1) clonal populations in addition to sporadic, non-clonal isolates, and uncovered a putative transmission event. Variation in antibiotic resistance was observed within clonal populations, even among isolates collected on the same day. Rates of molecular evolution ranged from 2.21 to 8.64 nucleotide polymorphisms per year, and lineage ages were consistent with acquisition of colonization in early childhood followed by subsequent persistence of multiple sub-populations. Selection analysis of 1,622 core genes present in all four clonal populations (n = 79) found 11 genes variable in three subjects – most notably, ATP-dependent protease clpX, 2-oxoglutarate dehydrogenase odhA, fmtC, and transcription-repair coupling factor mfd. Only one gene, staphylococcal protein A (spa), was found to have evidence of gene-wide diversifying selection. We identified three instances of intrahost IGR switching events, two of which flanked genes related to quorum sensing. The complex microbial ecology of the CF airway poses challenges for management. We illustrate appreciable intrahost diversity as well as persistence of a dominant lineage. We also show that intrahost adaptation is a continual process, despite purifying selective pressure, and provide targets that should be investigated further for their function in CF adaptation.
Collapse
Affiliation(s)
- Taj Azarian
- College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Jessica P Ridgway
- Department of Medicine, University of Chicago, Chicago, IL, United States
| | - Zachary Yin
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Michael Z David
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| |
Collapse
|
20
|
Millar EV, Rice GK, Schlett CD, Elassal EM, Cer RZ, Frey KG, Hamilton T, Ellis MW, Tribble DR, Bishop-Lilly KA, Bennett JW. Genomic epidemiology of MRSA infection and colonization isolates among military trainees with skin and soft tissue infection. Infection 2019; 47:729-737. [DOI: 10.1007/s15010-019-01282-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/12/2019] [Indexed: 10/27/2022]
|
21
|
Rigat F, Bartolini E, Dalsass M, Kumar N, Marchi S, Speziale P, Maione D, Chen L, Romano MR, Alegre ML, Bagnoli F, Daum RS, David MZ. Retrospective Identification of a Broad IgG Repertoire Differentiating Patients With S. aureus Skin and Soft Tissue Infections From Controls. Front Immunol 2019; 10:114. [PMID: 30792711 PMCID: PMC6375365 DOI: 10.3389/fimmu.2019.00114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 01/15/2019] [Indexed: 12/12/2022] Open
Abstract
Background: Although the relevance of humoral immunity for protection against S. aureus skin and soft tissue infections (SSTIs) has been suggested by several animal and human studies, the question of which human antibodies may be protective has so far impeded the development of a safe and effective vaccine. Because most adults have developed certain anti-S. aureus antibodies due to S. aureus colonization or infection, we hypothesized that the titers of antibodies to S. aureus in uninfected controls would differ from those in infected patients and would also differ in infected patients from the time of acute infection to a 40-day convalescent serum. Methods: To test these hypotheses, we measured human antibody levels against a panel of 134 unique antigens comprising the S. aureus surfome and secretome in subjects with active culture-confirmed S. aureus SSTIs (cases) and in controls with no infection, using a novel S. aureus protein microarray. Results: Most S. aureus SSTI patients (n = 60) and controls (n = 142) had antibodies to many of the tested S. aureus antigens. Univariate analysis showed statistically weak differences in the IgG levels to some antigens in the SSTI patient (case) sera compared with controls. Antibody levels to most tested antigens did not increase comparing acute with 40-day serum. Multiple logistic regression identified a rich subset of antigens that, by their antibody levels, together correctly differentiated all cases from all controls. Conclusions: Antibodies directed against S. aureus antigens were present both in patients with S. aureus SSTIs and in uninfected control patients. We found that SSTI patients and controls could be distinguished only based on differences in antibody levels to many staphylococcal surface and secreted antigens. Our results demonstrate that in the studied population, the levels of anti-S. aureus antibodies appear largely fixed, suggesting that there may be some level of unresponsiveness to natural infection.
Collapse
Affiliation(s)
- Fabio Rigat
- GSK Pharmaceuticals R&D, Stevenage, United Kingdom
| | | | | | - Neha Kumar
- Department of Pediatrics, University of Chicago, Chicago, IL, United States
| | | | - Pietro Speziale
- Department of Engineering, University of Pavia, Pavia, Italy
- Biochemistry Section, Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | | | - Luqiu Chen
- Department of Medicine, University of Chicago, Chicago, IL, United States
| | | | - Maria-Luisa Alegre
- Department of Medicine, University of Chicago, Chicago, IL, United States
| | | | - Robert S. Daum
- Department of Pediatrics, University of Chicago, Chicago, IL, United States
| | - Michael Z. David
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| |
Collapse
|
22
|
Read TD, Petit RA, Yin Z, Montgomery T, McNulty MC, David MZ. USA300 Staphylococcus aureus persists on multiple body sites following an infection. BMC Microbiol 2018; 18:206. [PMID: 30518317 PMCID: PMC6282268 DOI: 10.1186/s12866-018-1336-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 11/12/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND USA300 methicillin-resistant Staphylococcus aureus (MRSA) is a community- and hospital-acquired pathogen that frequently causes infections but also can survive on the human body asymptomatically as a part of the normal microbiota. We devised a comparative genomic strategy to track colonizing USA300 at different body sites after an initial infection. We sampled ST8 S. aureus from subjects at the site of a first known MRSA infection. Within 60 days of this infection and again 12 months later, each subject was tested for asymptomatic colonization in the nose, throat and perirectal region. 93 S. aureus strains underwent whole genome shotgun sequencing. RESULTS Among 28 subjects at the initial sampling time, we isolated S. aureus from the nose, throat and perirectal sites from 15, 11 and 15 of them, respectively. Twelve months later we isolated S. aureus from 9 subjects, with 6, 3 and 3 strains from the nose, throat and perirectal area, respectively. Genome sequencing revealed that 23 patients (ages 0-66 years) carried USA300 intra-subject lineages (ISLs), defined as having an index infection isolate and closely related colonizing strains. Pairwise distance between strains in different ISLs was 48 to 162 single nucleotide polymorphisms (SNPs) across the core regions of the chromosome, whereas within the same ISL it was 0 to 26 SNPs. Strains in ISLs from the same subject differed in plasmid and prophage content, and contained deletions that removed the mecA-containing SCCmec and ACME regions. Five strains contained frameshift mutations in agr toxin-regulating genes. Persistence of an ISL was not associated with clinical or demographic subject characteristics. We inferred that colonization with the ISL occurred about 18 weeks before the first assessment of asymptomatic colonization. CONCLUSIONS Clonal lineages of USA300 may continue to colonize people at one or more anatomic sites up to a year after an initial infection and experience loss of the SCCmec, loss and gain of other mobile genetic elements, and mutations in the agr operon.
Collapse
Affiliation(s)
- Timothy D. Read
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA USA
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA USA
| | - Robert A. Petit
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA USA
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA USA
| | - Zachary Yin
- Department of Pediatrics, Section of Infectious Diseases, University of Chicago, Chicago, IL USA
| | - Tuyaa Montgomery
- Department of Pediatrics, Section of Infectious Diseases, University of Chicago, Chicago, IL USA
| | - Moira C. McNulty
- Department of Medicine, Section of Infectious Diseases and Global Health, University of Chicago, Chicago, IL USA
| | - Michael Z. David
- Department of Medicine, Division of Infectious Diseases, University of Pennsylvania, Philadelphia, PA USA
| |
Collapse
|
23
|
Genome Plasticity of agr-Defective Staphylococcus aureus during Clinical Infection. Infect Immun 2018; 86:IAI.00331-18. [PMID: 30061376 PMCID: PMC6204747 DOI: 10.1128/iai.00331-18] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/21/2018] [Indexed: 01/05/2023] Open
Abstract
Therapy for bacteremia caused by Staphylococcus aureus is often ineffective, even when treatment conditions are optimal according to experimental protocols. Adapted subclones, such as those bearing mutations that attenuate agr-mediated virulence activation, are associated with persistent infection and patient mortality. Therapy for bacteremia caused by Staphylococcus aureus is often ineffective, even when treatment conditions are optimal according to experimental protocols. Adapted subclones, such as those bearing mutations that attenuate agr-mediated virulence activation, are associated with persistent infection and patient mortality. To identify additional alterations in agr-defective mutants, we sequenced and assembled the complete genomes of clone pairs from colonizing and infected sites of several patients in whom S. aureus demonstrated a within-host loss of agr function. We report that events associated with agr inactivation result in agr-defective blood and nares strain pairs that are enriched in mutations compared to pairs from wild-type controls. The random distribution of mutations between colonizing and infecting strains from the same patient, and between strains from different patients, suggests that much of the genetic complexity of agr-defective strains results from prolonged infection or therapy-induced stress. However, in one of the agr-defective infecting strains, multiple genetic changes resulted in increased virulence in a murine model of bloodstream infection, bypassing the mutation of agr and raising the possibility that some changes were selected. Expression profiling correlated the elevated virulence of this agr-defective mutant to restored expression of the agr-regulated ESAT6-like type VII secretion system, a known virulence factor. Thus, additional mutations outside the agr locus can contribute to diversification and adaptation during infection by S. aureus agr mutants associated with poor patient outcomes.
Collapse
|
24
|
Benoit JB, Frank DN, Bessesen MT. Genomic evolution of Staphylococcus aureus isolates colonizing the nares and progressing to bacteremia. PLoS One 2018; 13:e0195860. [PMID: 29723202 PMCID: PMC5933776 DOI: 10.1371/journal.pone.0195860] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 03/31/2018] [Indexed: 12/21/2022] Open
Abstract
Background Nasal colonization by Staphylococcus aureus is a key risk factor for bacteremia. The objective of this study is to identify genomic modifications occurring in nasal carriage strains of S. aureus as they progress to bacteremia in a cohort of hospitalized patients. Methods Eight patients with S. aureus bacteremia were identified. Genomic sequences of the bloodstream isolates were compared with 57 nasal isolates collected longitudinally prior to the occurrence of bacteremia, which covered a timespan of up to 326 days before bacteremia. Results Within each subject, nasal colonizing strains were closely related to bacteremia strains. Within a subject, the number of single nucleotide polymorphisms (SNPs) observed between time points was greater than within a single time point. Co-colonization and strain replacement were observed in one case. In all cases colonization progressed to bacteremia without addition of new virulence genes. In one case, a mutation in the accessory gene regulator gene caused abrogation of agr function. Conclusion S. aureus evolves in the human nares at a variable rate. Progression of S. aureus nasal colonization to nosocomial infection is seldom associated with acquisition of new virulence determinants. Mutation in the agr gene with abrogation of function was associated with progression to bacteremia in one case.
Collapse
Affiliation(s)
- Jeanne B. Benoit
- Division of Infectious Diseases, Department of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
- Department of Veterans Affairs Eastern Colorado Healthcare System, Denver, Colorado, United States of America
| | - Daniel N. Frank
- Division of Infectious Diseases, Department of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
- Department of Veterans Affairs Eastern Colorado Healthcare System, Denver, Colorado, United States of America
| | - Mary T. Bessesen
- Division of Infectious Diseases, Department of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
- Department of Veterans Affairs Eastern Colorado Healthcare System, Denver, Colorado, United States of America
- * E-mail:
| |
Collapse
|
25
|
Choe D, Szubin R, Dahesh S, Cho S, Nizet V, Palsson B, Cho BK. Genome-scale analysis of Methicillin-resistant Staphylococcus aureus USA300 reveals a tradeoff between pathogenesis and drug resistance. Sci Rep 2018; 8:2215. [PMID: 29396540 PMCID: PMC5797083 DOI: 10.1038/s41598-018-20661-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 01/18/2018] [Indexed: 12/15/2022] Open
Abstract
Staphylococcus aureus infection is a rising public health care threat. S. aureus is believed to have elaborate regulatory networks that orchestrate its virulence. Despite its importance, the systematic understanding of the transcriptional landscape of S. aureus is limited. Here, we describe the primary transcriptome landscape of an epidemic USA300 isolate of community-acquired methicillin-resistant S. aureus. We experimentally determined 1,861 transcription start sites with their principal promoter elements, including well-conserved -35 and -10 elements and weakly conserved -16 element and 5' untranslated regions containing AG-rich Shine-Dalgarno sequence. In addition, we identified 225 genes whose transcription was initiated from multiple transcription start sites, suggesting potential regulatory functions at transcription level. Along with the transcription unit architecture derived by integrating the primary transcriptome analysis with operon prediction, the measurement of differential gene expression revealed the regulatory framework of the virulence regulator Agr, the SarA-family transcriptional regulators, and β-lactam resistance regulators. Interestingly, we observed a complex interplay between virulence regulation, β-lactam resistance, and metabolism, suggesting a possible tradeoff between pathogenesis and drug resistance in the USA300 strain. Our results provide platform resource for the location of transcription initiation and an in-depth understanding of transcriptional regulation of pathogenesis, virulence, and antibiotic resistance in S. aureus.
Collapse
Affiliation(s)
- Donghui Choe
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Richard Szubin
- Department of Bioengineering, University of California San Diego, La Jolla, 92023, CA, USA
| | - Samira Dahesh
- University of California San Diego School of Medicine, La Jolla, 92023, CA, USA
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Victor Nizet
- University of California San Diego School of Medicine, La Jolla, 92023, CA, USA.
| | - Bernhard Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, 92023, CA, USA.
- University of California San Diego School of Medicine, La Jolla, 92023, CA, USA.
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
- KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
| |
Collapse
|
26
|
Harkins CP, Pettigrew KA, Oravcová K, Gardner J, Hearn RMR, Rice D, Mather AE, Parkhill J, Brown SJ, Proby CM, Holden MTG. The Microevolution and Epidemiology of Staphylococcus aureus Colonization during Atopic Eczema Disease Flare. J Invest Dermatol 2017; 138:336-343. [PMID: 28951239 PMCID: PMC5780352 DOI: 10.1016/j.jid.2017.09.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/11/2017] [Accepted: 09/12/2017] [Indexed: 01/24/2023]
Abstract
Staphylococcus aureus is an opportunistic pathogen and variable component of the human microbiota. A characteristic of atopic eczema (AE) is colonization by S. aureus, with exacerbations associated with an increased bacterial burden of the organism. Despite this, the origins and genetic diversity of S. aureus colonizing individual patients during AE disease flares is poorly understood. To examine the microevolution of S. aureus colonization, we deep sequenced S. aureus populations from nine children with moderate to severe AE and 18 non-atopic children asymptomatically carrying S. aureus nasally. Colonization by clonal S. aureus populations was observed in both AE patients and control participants, with all but one of the individuals carrying colonies belonging to a single sequence type. Phylogenetic analysis showed that disease flares were associated with the clonal expansion of the S. aureus population, occurring over a period of weeks to months. There was a significant difference in the genetic backgrounds of S. aureus colonizing AE cases versus controls (Fisher exact test, P = 0.03). Examination of intra-host genetic heterogeneity of the colonizing S. aureus populations identified evidence of within-host selection in the AE patients, with AE variants being potentially selectively advantageous for intracellular persistence and treatment resistance.
Collapse
Affiliation(s)
- Catriona P Harkins
- School of Medicine, University of St Andrews, St Andrews, UK; Department of Dermatology, Ninewells Hospital, Dundee, UK; School of Medicine, University of Dundee, Dundee, UK.
| | | | - Katarina Oravcová
- School of Medicine, University of St Andrews, St Andrews, UK; Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - June Gardner
- Department of Dermatology, Ninewells Hospital, Dundee, UK
| | - R M Ross Hearn
- Department of Dermatology, Ninewells Hospital, Dundee, UK
| | - Debbie Rice
- Scottish Children's Research Network, MACH 2 Building, Level 5, Ninewells Hospital, Dundee, UK
| | - Alison E Mather
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Sara J Brown
- Department of Dermatology, Ninewells Hospital, Dundee, UK; Skin Research Group, Division of Cancer Research, School of Medicine, University of Dundee, UK
| | - Charlotte M Proby
- Department of Dermatology, Ninewells Hospital, Dundee, UK; School of Medicine, University of Dundee, Dundee, UK
| | | |
Collapse
|
27
|
Graña-Miraglia L, Lozano LF, Velázquez C, Volkow-Fernández P, Pérez-Oseguera Á, Cevallos MA, Castillo-Ramírez S. Rapid Gene Turnover as a Significant Source of Genetic Variation in a Recently Seeded Population of a Healthcare-Associated Pathogen. Front Microbiol 2017; 8:1817. [PMID: 28979253 PMCID: PMC5611417 DOI: 10.3389/fmicb.2017.01817] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/06/2017] [Indexed: 12/11/2022] Open
Abstract
Genome sequencing has been useful to gain an understanding of bacterial evolution. It has been used for studying the phylogeography and/or the impact of mutation and recombination on bacterial populations. However, it has rarely been used to study gene turnover at microevolutionary scales. Here, we sequenced Mexican strains of the human pathogen Acinetobacter baumannii sampled from the same locale over a 3 year period to obtain insights into the microevolutionary dynamics of gene content variability. We found that the Mexican A. baumannii population was recently founded and has been emerging due to a rapid clonal expansion. Furthermore, we noticed that on average the Mexican strains differed from each other by over 300 genes and, notably, this gene content variation has accrued more frequently and faster than the accumulation of mutations. Moreover, due to its rapid pace, gene content variation reflects the phylogeny only at very short periods of time. Additionally, we found that the external branches of the phylogeny had almost 100 more genes than the internal branches. All in all, these results show that rapid gene turnover has been of paramount importance in producing genetic variation within this population and demonstrate the utility of genome sequencing to study alternative forms of genetic variation.
Collapse
Affiliation(s)
- Lucía Graña-Miraglia
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico
| | - Luis F Lozano
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico
| | - Consuelo Velázquez
- Departamento de Enfermedades Infecciosas, Instituto Nacional de CancerologíaMexico, Mexico
| | | | - Ángeles Pérez-Oseguera
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico
| | - Miguel A Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Génomicas, Universidad Nacional Autónoma de MéxicoCuernavaca, Mexico
| |
Collapse
|
28
|
Millar EV, Rice GK, Elassal EM, Schlett CD, Bennett JW, Redden CL, Mor D, Law NN, Tribble DR, Hamilton T, Ellis MW, Bishop-Lilly KA. Genomic Characterization of USA300 Methicillin-Resistant Staphylococcus aureus (MRSA) to Evaluate Intraclass Transmission and Recurrence of Skin and Soft Tissue Infection (SSTI) Among High-Risk Military Trainees. Clin Infect Dis 2017; 65:461-468. [PMID: 28419202 PMCID: PMC5849051 DOI: 10.1093/cid/cix327] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/10/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Military trainees are at increased risk for methicillin-resistant Staphylococcus aureus (MRSA) skin and soft tissue infection (SSTI). Whole genome sequencing (WGS) can refine our understanding of MRSA transmission and microevolution in congregate settings. METHODS We conducted a prospective case-control study of SSTI among US Army infantry trainees at Fort Benning, Georgia, from July 2012 to December 2014. We identified clusters of USA300 MRSA SSTI within select training classes and performed WGS on clinical isolates. We then linked genomic, phylogenetic, epidemiologic, and clinical data in order to evaluate intra- and interclass disease transmission. Furthermore, among cases of recurrent MRSA SSTI, we evaluated the intrahost relatedness of infecting strains. RESULTS Nine training classes with ≥5 cases of USA300 MRSA SSTI were selected. Eighty USA300 MRSA clinical isolates from 74 trainees, 6 (8.1%) of whom had recurrent infection, were subjected to WGS. We identified 2719 single nucleotide variants (SNVs). The overall median (range) SNV difference between isolates was 173 (1-339). Intraclass median SNV differences ranged from 23 to 245. Two phylogenetic clusters were suggestive of interclass MRSA transmission. One of these clusters stemmed from 2 classes that were separated by a 13-month period but housed in the same barracks. Among trainees with recurrent MRSA SSTI, the intrahost median SNV difference was 7.5 (1-48). CONCLUSIONS Application of WGS revealed intra- and interclass transmission of MRSA among military trainees. An interclass cluster between 2 noncontemporaneous classes suggests a long-term reservoir for MRSA in this setting.
Collapse
Affiliation(s)
- Eugene V Millar
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville
| | - Gregory K Rice
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick
| | - Emad M Elassal
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville
| | - Carey D Schlett
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville
| | - Jason W Bennett
- Walter Reed Army Institute of Research, Silver Spring
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Cassie L Redden
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick
| | - Deepika Mor
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville
| | - Natasha N Law
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville
- Martin Army Community Hospital, Fort Benning, Georgia
| | - David R Tribble
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda
| | - Theron Hamilton
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick
| | - Michael W Ellis
- University of Toledo College of Medicine and Life Sciences, Ohio
| | - Kimberly A Bishop-Lilly
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick
| |
Collapse
|
29
|
Didelot X, Fraser C, Gardy J, Colijn C. Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks. Mol Biol Evol 2017; 34:997-1007. [PMID: 28100788 PMCID: PMC5850352 DOI: 10.1093/molbev/msw275] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genomic data are increasingly being used to understand infectious disease epidemiology. Isolates from a given outbreak are sequenced, and the patterns of shared variation are used to infer which isolates within the outbreak are most closely related to each other. Unfortunately, the phylogenetic trees typically used to represent this variation are not directly informative about who infected whom-a phylogenetic tree is not a transmission tree. However, a transmission tree can be inferred from a phylogeny while accounting for within-host genetic diversity by coloring the branches of a phylogeny according to which host those branches were in. Here we extend this approach and show that it can be applied to partially sampled and ongoing outbreaks. This requires computing the correct probability of an observed transmission tree and we herein demonstrate how to do this for a large class of epidemiological models. We also demonstrate how the branch coloring approach can incorporate a variable number of unique colors to represent unsampled intermediates in transmission chains. The resulting algorithm is a reversible jump Monte-Carlo Markov Chain, which we apply to both simulated data and real data from an outbreak of tuberculosis. By accounting for unsampled cases and an outbreak which may not have reached its end, our method is uniquely suited to use in a public health environment during real-time outbreak investigations. We implemented this transmission tree inference methodology in an R package called TransPhylo, which is freely available from https://github.com/xavierdidelot/TransPhylo.
Collapse
Affiliation(s)
- Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, United Kingdom
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, United Kingdom
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jennifer Gardy
- Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Caroline Colijn
- Department of Mathematics, Imperial College, London, United Kingdom
| |
Collapse
|
30
|
Bayliss SC, Verner-Jeffreys DW, Bartie KL, Aanensen DM, Sheppard SK, Adams A, Feil EJ. The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens. Front Microbiol 2017; 8:121. [PMID: 28217117 PMCID: PMC5290457 DOI: 10.3389/fmicb.2017.00121] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/17/2017] [Indexed: 01/23/2023] Open
Abstract
Aquaculture is the fastest growing food-producing sector, and the sustainability of this industry is critical both for global food security and economic welfare. The management of infectious disease represents a key challenge. Here, we discuss the opportunities afforded by whole genome sequencing of bacterial and viral pathogens of aquaculture to mitigate disease emergence and spread. We outline, by way of comparison, how sequencing technology is transforming the molecular epidemiology of pathogens of public health importance, emphasizing the importance of community-oriented databases and analysis tools.
Collapse
Affiliation(s)
- Sion C Bayliss
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath Bath, UK
| | | | - Kerry L Bartie
- Institute of Aquaculture, University of Stirling Stirling, UK
| | - David M Aanensen
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College LondonLondon, UK; The Centre for Genomic Pathogen Surveillance, Wellcome Genome CampusCambridge, UK
| | - Samuel K Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath Bath, UK
| | - Alexandra Adams
- Institute of Aquaculture, University of Stirling Stirling, UK
| | - Edward J Feil
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath Bath, UK
| |
Collapse
|
31
|
Cella E, Ceccarelli G, Vita S, Lai A, Presti AL, Blasi A, Palco ML, Guarino MPL, Zehender G, Angeletti S, Ciccozzi M. First epidemiological and phylogenetic analysis of Hepatitis B virus infection in migrants from Mali. J Med Virol 2016; 89:639-646. [PMID: 27576107 DOI: 10.1002/jmv.24671] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2016] [Indexed: 12/17/2022]
Abstract
The armed conflict in Mali caused a migration crisis since 2012. Most Malian refugees were in Italy. In Sub-Saharan Africa, the seroprevalence of anti-HBV antibodies is particularly high. Genotype E is the most prevalent throughout a crescent covering area from Angola to Senegal, including Mali. We report 16 HBV positive individual from 136 Malian asylum seekers in order to investigate the genetic diversity of HBV in this population. Sequencing and phylogenetic analysis has been used. The HBV genotype E isolates from Mali did not cluster together but were intermixed, with the other African sequences. Only three supported clade were evidenced and closely related to sequences from Burkina Faso. The estimated evolutionary rate was 9.29 × 104 . The root of the tree dated back to February 2008 in (95% HPD: 2006-2011). From this ancestor six main statistically supported clusters (pp > 0.80) were identified. The most recent Clade dated back to May 2015. The BSP showed that the effective number of infections softly increased from 2011 to the 2015. Phylogenetic analysis helped in understanding how two on sixteen individuals, have been infected in Italy, and give an important improvement in prevention campaigns and monitoring of the viral infection in migrants. J. Med. Virol. 89:639-646, 2017. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Eleonora Cella
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Epidemiology Unit, Istituto Superiore di Sanità, Rome, Italy.,Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Giancarlo Ceccarelli
- Public Health and Infectious Diseases, Sapienza University, Rome, Italy.,Migrant Health Research Organisation (Mi-HeRO) - Centro di Ricerca sulla Salute delle Popolazioni Mobili e Globale, Italy
| | - Serena Vita
- Public Health and Infectious Diseases, Sapienza University, Rome, Italy.,Migrant Health Research Organisation (Mi-HeRO) - Centro di Ricerca sulla Salute delle Popolazioni Mobili e Globale, Italy
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy
| | - Alessandra Lo Presti
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Epidemiology Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Aletheia Blasi
- Clinical Pathology and Microbiology Unit, University Campus Bio-Medico of Rome, Italy
| | - Maurizio Lo Palco
- Sanitary Bureau of Asylum Seekers Center of Castelnuovo di Porto, Rome, Italy.,Auxilium Società Cooperativa Sociale, Senise (PZ), Italy
| | | | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, Milan, Italy
| | - Silvia Angeletti
- Clinical Pathology and Microbiology Unit, University Campus Bio-Medico of Rome, Italy
| | - Massimo Ciccozzi
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Epidemiology Unit, Istituto Superiore di Sanità, Rome, Italy.,Clinical Pathology and Microbiology Unit, University Campus Bio-Medico of Rome, Italy
| | | |
Collapse
|