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Zhou J, He C, Yang H, Shu W, Liu Q. Integrative omics analysis reveals insights into small colony variants of Staphylococcus aureus induced by sulfamethoxazole-trimethoprim. BMC Microbiol 2024; 24:212. [PMID: 38877418 PMCID: PMC11179224 DOI: 10.1186/s12866-024-03364-8] [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: 09/05/2023] [Accepted: 06/04/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND Long-term treatment with trimethoprim-sulfamethoxazole (SXT) can lead to the formation of small-colony variants (SCVs) of Staphylococcus aureus. However, the mechanism behind SCVs formation remains poorly understood. In this study, we explored the phenotype and omics-based characterization of S. aureus SCVs induced by SXT and shed light on the potential causes of SCV formation. METHODS Stable SCVs were obtained by continuously treating S. aureus isolates using 12/238 µg/ml of SXT, characterized by growth kinetics, antibiotic susceptibility testing, and auxotrophism test. Subsequently, a pair of representative strains (SCV and its parental strain) were selected for genomic, transcriptomic and metabolomic analysis. RESULTS Three stable S. aureus SCVs were successfully screened and proven to be homologous to their corresponding parental strains. Phenotypic tests showed that all SCVs were non-classical mechanisms associated with impaired utilization of menadione, heme and thymine, and exhibited slower growth and higher antibiotic minimum inhibitory concentrations (MICs), compared to their corresponding parental strains. Genomic data revealed 15 missense mutations in 13 genes in the representative SCV, which were involved in adhesion, intramolecular phosphate transfer on ribose, transport pathways, and phage-encoded proteins. The combination analysis of transcriptome and metabolome identified 35 overlapping pathways possible associated with the phenotype switching of S. aureus. These pathways mainly included changes in metabolism, such as purine metabolism, pyruvate metabolism, amino acid metabolism, and ABC transporters, which could play a crucial role in promoting SCVs development by affecting nucleic acid synthesis and energy metabolism in bacteria. CONCLUSION This study provides profound insights into the causes of S. aureus SCV formation induced by SXT. The findings may offer valuable clues for developing new strategies to combat S. aureus SCV infections.
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Affiliation(s)
- Jingwen Zhou
- Department of Clinical Laboratory, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 274 Zhijiang Middle Rd, Shanghai, 200071, People's Republic of China
| | - Chunyan He
- Department of Clinical Laboratory, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Han Yang
- Department of Clinical Laboratory, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Wen Shu
- Department of Clinical Laboratory, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qingzhong Liu
- Department of Clinical Laboratory, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 274 Zhijiang Middle Rd, Shanghai, 200071, People's Republic of China.
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2
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Carrel M, Smith M, Shi Q, Hasegawa S, Clore GS, Perencevich EN, Goto M. Antimicrobial Resistance Patterns of Outpatient Staphylococcus aureus Isolates. JAMA Netw Open 2024; 7:e2417199. [PMID: 38874923 PMCID: PMC11179135 DOI: 10.1001/jamanetworkopen.2024.17199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/17/2024] [Indexed: 06/15/2024] Open
Abstract
Importance Oral non-β-lactam antibiotics are commonly used for empirical therapy of Staphylococcus aureus infections, especially in outpatient settings. However, little is known about potential geographic heterogeneity and temporal trends in the prevalence of S aureus resistance to non-β-lactams in the US. Objective To characterize the spatiotemporal trends of resistance to non-β-lactam antibiotics among community-onset S aureus infections, including regional variation in resistance rates and geographical heterogeneity in multidrug resistance. Design, Setting, and Participants This cross-sectional study used data from Veterans Health Administration clinics collected from adult outpatients with S aureus infection in the conterminous 48 states and Washington, DC, from January 1, 2010, to December 31, 2019. Data were analyzed from January to November 2023. Exposures Resistance to lincosamides (clindamycin), tetracyclines, sulfonamides (trimethoprim-sulfamethoxazole [TMP-SMX]), and macrolides. Main Outcomes and Measures Spatiotemporal variation of S aureus resistance to these 4 classes of non-β-lactam antibiotics, stratified by methicillin-resistant S aureus (MRSA) and methicillin-sensitive S aureus (MSSA), and subdivided by regions of the US (Northeast, Midwest, South, and West). Trend tests and bivariate mapping were used to determine significant changes in resistant proportions over time and identify counties where rates of resistance to multiple non-β-lactams were high. Results A total of 382 149 S aureus isolates from 268 214 unique outpatients (mean [SD] age, 63.4 [14.8] years; 252 910 males [94.29%]) were analyzed. There was a decrease in the proportion of MRSA nationwide, from 53.6% in 2010 to 38.8% in 2019. Among MRSA isolates, we observed a significant increase in tetracycline resistance (from 3.6% in 2010 to 12.8% in 2019; P for trend < .001) and TMP-SMX resistance (from 2.6% in 2010 to 9.2% in 2019; P for trend < .001), modest and not significant increases in clindamycin resistance (from 24.2% in 2010 to 30.6% in 2019; P for trend = .34), and a significant decrease in macrolide resistance (from 73.5% in 2010 to 60.2% in 2019; P for trend < .001). Among MSSA isolates, significant upward trends in clindamycin, tetracyclines, and TMP-SMX resistance were observed. For example, tetracycline resistance increased from 3.7% in 2010 to 9.1% in 2019 (P for trend < .001). Regional stratification over time showed that the Northeast had slightly higher rates of clindamycin resistance but lower rates of tetracycline resistance, while the South had notably higher rates of resistance to tetracyclines and TMP-SMX, particularly among MRSA isolates. Bivariate mapping at the county scale did not indicate clear regional patterns of shared high levels of resistance to the 4 classes of antimicrobials studied. Conclusions and Relevance In this study of outpatient S aureus isolates, MRSA became less common over the 10-year period, and MRSA isolates were increasingly resistant to tetracyclines and TMP-SMX. Geographic analysis indicated no spatial overlap in counties with high rates of resistance to both tetracyclines and TMP-SMX. Examining the regional spatial variation of antibiotic resistance can inform empirical therapy recommendations and help to understand the evolution of S aureus antibiotic resistance mechanisms.
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Affiliation(s)
- Margaret Carrel
- Department of Geographical and Sustainability Sciences, University of Iowa, Iowa City
| | - Matthew Smith
- Department of Internal Medicine, University of Iowa, Iowa City
- Center for Access & Delivery Research and Evaluation, Iowa City Veterans Affairs Health Care System, Iowa City, Iowa
| | - Qianyi Shi
- Department of Internal Medicine, University of Iowa, Iowa City
| | - Shinya Hasegawa
- Department of Internal Medicine, University of Iowa, Iowa City
- Center for Access & Delivery Research and Evaluation, Iowa City Veterans Affairs Health Care System, Iowa City, Iowa
| | - Gosia S Clore
- Department of Internal Medicine, University of Iowa, Iowa City
- Center for Access & Delivery Research and Evaluation, Iowa City Veterans Affairs Health Care System, Iowa City, Iowa
| | - Eli N Perencevich
- Department of Internal Medicine, University of Iowa, Iowa City
- Center for Access & Delivery Research and Evaluation, Iowa City Veterans Affairs Health Care System, Iowa City, Iowa
- Associate Editor, JAMA Network Open
| | - Michihiko Goto
- Department of Internal Medicine, University of Iowa, Iowa City
- Center for Access & Delivery Research and Evaluation, Iowa City Veterans Affairs Health Care System, Iowa City, Iowa
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Wolfe KH, Pierce VM, Humphries RM. How New Regulation of Laboratory-Developed Antimicrobial Susceptibility Tests Will Affect Infectious Diseases Clinical Practice. Clin Infect Dis 2024; 78:1140-1147. [PMID: 38573057 DOI: 10.1093/cid/ciae075] [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: 11/14/2023] [Indexed: 04/05/2024] Open
Abstract
Antimicrobial resistance (AMR) affects 2.8 million Americans annually. AMR is identified through antimicrobial susceptibility testing (AST), but current and proposed regulatory policies from the United States Food and Drug Administration (FDA) jeopardize the future availability of AST for many microorganisms. Devices that perform AST must be cleared by the FDA using their susceptibility test interpretive criteria, also known as breakpoints. The FDA list of breakpoints is relatively short. Today, laboratories supplement FDA breakpoints using breakpoints published by the Clinical and Laboratory Standards Institute, using legacy devices and laboratory-developed tests (LDTs). FDA proposes to regulate LDTs, and with no FDA breakpoints for many drug-bug combinations, the risk is loss of AST for key clinical indications and stifling innovation in technology development. Effective solutions require collaboration between manufacturers, infectious diseases clinicians, pharmacists, laboratories, and the FDA.
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Affiliation(s)
- Kaleb H Wolfe
- Department of Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Virginia M Pierce
- Department of Pathology, University of Michigan Medical School, Ann Arbor
| | - Romney M Humphries
- Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
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Vaňková E, Julák J, Machková A, Obrová K, Klančnik A, Smole Možina S, Scholtz V. Overcoming antibiotic resistance: non-thermal plasma and antibiotics combination inhibits important pathogens. Pathog Dis 2024; 82:ftae007. [PMID: 38730561 PMCID: PMC11094553 DOI: 10.1093/femspd/ftae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/27/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024] Open
Abstract
Antibiotic resistance (ATBR) is increasing every year as the overuse of antibiotics (ATBs) and the lack of newly emerging antimicrobial agents lead to an efficient pathogen escape from ATBs action. This trend is alarming and the World Health Organization warned in 2021 that ATBR could become the leading cause of death worldwide by 2050. The development of novel ATBs is not fast enough considering the situation, and alternative strategies are therefore urgently required. One such alternative may be the use of non-thermal plasma (NTP), a well-established antimicrobial agent actively used in a growing number of medical fields. Despite its efficiency, NTP alone is not always sufficient to completely eliminate pathogens. However, NTP combined with ATBs is more potent and evidence has been emerging over the last few years proving this is a robust and highly effective strategy to fight resistant pathogens. This minireview summarizes experimental research addressing the potential of the NTP-ATBs combination, particularly for inhibiting planktonic and biofilm growth and treating infections in mouse models caused by methicillin-resistant Staphylococcus aureus or Pseudomonas aeruginosa. The published studies highlight this combination as a promising solution to emerging ATBR, and further research is therefore highly desirable.
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Affiliation(s)
- Eva Vaňková
- Department of Physics and Measurements, University of Chemistry and Technology in Prague, 160 00 Prague, Czech Republic
- Department of Biotechnology, University of Chemistry and Technology in Prague, 160 00 Prague, Czech Republic
| | - Jaroslav Julák
- Department of Physics and Measurements, University of Chemistry and Technology in Prague, 160 00 Prague, Czech Republic
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University in Prague, 160 00 Prague, Czech Republic
| | - Anna Machková
- Department of Physics and Measurements, University of Chemistry and Technology in Prague, 160 00 Prague, Czech Republic
| | - Klára Obrová
- Department of Physics and Measurements, University of Chemistry and Technology in Prague, 160 00 Prague, Czech Republic
| | - Anja Klančnik
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Sonja Smole Možina
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Vladimír Scholtz
- Department of Physics and Measurements, University of Chemistry and Technology in Prague, 160 00 Prague, Czech Republic
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Liu J, Huang T, Soteyome T, Miao J, Yu G, Chen D, Ye C, Yang L, Xu Z. Antimicrobial Resistance, SCC mec, Virulence and Genotypes of MRSA in Southern China for 7 Years: Filling the Gap of Molecular Epidemiology. Antibiotics (Basel) 2023; 12:antibiotics12020368. [PMID: 36830279 PMCID: PMC9952273 DOI: 10.3390/antibiotics12020368] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/06/2022] [Accepted: 01/16/2023] [Indexed: 02/12/2023] Open
Abstract
As the prevalence of Staphylococcus aureus infections is of worldwide concern, phenotype and genotype in prevalent MRSA strains require longitudinal investigation. In this study, the antibiotic resistance, virulence gene acquisition, and molecular type were determined on a large scale of nosocomial S. aureus strains in Southern China during 2009-2015. Bacterial identification and antimicrobial susceptibility to 10 antibiotics were tested by Vitek-2. Virulence genes encoding staphylococcal enterotoxins (SEA, SEB, SEC, SED, and SEE), exfoliative toxins (ETA and ETB), Panton-Valentine leukocidin (PVL), and toxic shock syndrome toxin (TSST) were detected by PCR, with SCCmec typing also conducted by multiplex PCR strategy. Genotypes were discriminated by MLST and spaA typing. MLST was performed by amplification of the internal region of seven housekeeping genes. PCR amplification targeting the spa gene was performed for spa typing. No resistance to vancomycin, linezolid, or quinupristin and increase in the resistance to trimethoprim/sulfamethoxazole (55.5%) were identified. A total of nine SCCmec types and subtypes, thirteen STs clustered into thirteen spa types were identified, with ST239-SCCmec III-t037 presenting the predominant methicillin-resistant S. aureus (MRSA) clone. Typically, SCCmec type IX and ST546 were emergent types in China. Isolates positive for both pvl and tsst genes and for both eta and etb genes were also identified. Important findings in this study include: firstly, we have provided comprehensive knowledge on the molecular epidemiology of MRSA in Southern China which fills the gap since 2006 or 2010 from previous studies. Secondly, we have presented the correlation between virulence factors (four major groups) and genotypes (SCCmec, ST and spa types). Thirdly, we have shown evidence for earliest emergence of type I SCCmec from 2012, type VI from 2009 and type XI from 2012 in MRSA from Southern China.
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Affiliation(s)
- Junyan Liu
- College of Light Industry and Food Science, Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, Academy of Contemporary Agricultural Engineering Innovations, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Processing and Intelligent Manufacturing of Lingnan Specialty Food, Ministry of Agriculture, Guangzhou 510225, China
| | - Tengyi Huang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515063, China
| | - Thanapop Soteyome
- Home Economics Technology, Rajamangala University of Technology Phra Nakhon, Bangkok 10300, Thailand
| | - Jian Miao
- Graduate Program in Pharmaceutical Sciences, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Guangchao Yu
- Center of Clinical Laboratory Medicine, First Affiliated Hospital of Jinan University, Guangzhou 510620, China
| | - Dingqiang Chen
- Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Congxiu Ye
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yan-Sen University, Guangzhou 510630, China
| | - Ling Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
| | - Zhenbo Xu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515063, China
- Correspondence: ; Tel./Fax: +86-20-8711-3252
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Zelmer AR, Nelson R, Richter K, Atkins GJ. Can intracellular Staphylococcus aureus in osteomyelitis be treated using current antibiotics? A systematic review and narrative synthesis. Bone Res 2022; 10:53. [PMID: 35961964 PMCID: PMC9374758 DOI: 10.1038/s41413-022-00227-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/26/2022] [Accepted: 06/15/2022] [Indexed: 11/09/2022] Open
Abstract
Approximately 40% of treatments of chronic and recurrent osteomyelitis fail in part due to bacterial persistence. Staphylococcus aureus, the predominant pathogen in human osteomyelitis, is known to persist by phenotypic adaptation as small-colony variants (SCVs) and by formation of intracellular reservoirs, including those in major bone cell types, reducing susceptibility to antibiotics. Intracellular infections with S. aureus are difficult to treat; however, there are no evidence-based clinical guidelines addressing these infections in osteomyelitis. We conducted a systematic review of the literature to determine the demonstrated efficacy of all antibiotics against intracellular S. aureus relevant to osteomyelitis, including protein biosynthesis inhibitors (lincosamides, streptogramins, macrolides, oxazolidines, tetracyclines, fusidic acid, and aminoglycosides), enzyme inhibitors (fluoroquinolones and ansamycines), and cell wall inhibitors (beta-lactam inhibitors, glycopeptides, fosfomycin, and lipopeptides). The PubMed and Embase databases were screened for articles related to intracellular S. aureus infections that compared the effectiveness of multiple antibiotics or a single antibiotic together with another treatment, which resulted in 34 full-text articles fitting the inclusion criteria. The combined findings of these studies were largely inconclusive, most likely due to the plethora of methodologies utilized. Therefore, the reported findings in the context of the models employed and possible solutions for improved understanding are explored here. While rifampicin, oritavancin, linezolid, moxifloxacin and oxacillin were identified as the most effective potential intracellular treatments, the scientific evidence for these is still relatively weak. We advocate for more standardized research on determining the intracellular effectiveness of antibiotics in S. aureus osteomyelitis to improve treatments and patient outcomes.
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Affiliation(s)
- Anja R Zelmer
- Centre for Orthopaedic and Trauma Research, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5000, Australia
| | - Renjy Nelson
- Department of Infectious Diseases, Central Adelaide Local Health Network, Adelaide, SA, 5000, Australia.,Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
| | - Katharina Richter
- Richter Lab, Department of Surgery, Basil Hetzel Institute for Translational Health Research, University of Adelaide, Adelaide, SA, 5011, Australia
| | - Gerald J Atkins
- Centre for Orthopaedic and Trauma Research, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, 5000, Australia.
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