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Jugas R, Vitkova H. ProcaryaSV: structural variation detection pipeline for bacterial genomes using short-read sequencing. BMC Bioinformatics 2024; 25:233. [PMID: 38982375 PMCID: PMC11234778 DOI: 10.1186/s12859-024-05843-1] [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: 01/31/2024] [Accepted: 06/13/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND Structural variations play an important role in bacterial genomes. They can mediate genome adaptation quickly in response to the external environment and thus can also play a role in antibiotic resistance. The detection of structural variations in bacteria is challenging, and the recognition of even small rearrangements can be important. Even though most detection tools are aimed at and benchmarked on eukaryotic genomes, they can also be used on prokaryotic genomes. The key features of detection are the ability to detect small rearrangements and support haploid genomes. Because of the limiting performance of a single detection tool, combining the detection abilities of multiple tools can lead to more robust results. There are already available workflows for structural variation detection for long-reads technologies and for the detection of single-nucleotide variation and indels, both aimed at bacteria. Yet we are unaware of structural variations detection workflows for the short-reads sequencing platform. Motivated by this gap we created our workflow. Further, we were interested in increasing the detection performance and providing more robust results. RESULTS We developed an open-source bioinformatics pipeline, ProcaryaSV, for the detection of structural variations in bacterial isolates from paired-end short sequencing reads. Multiple tools, starting with quality control and trimming of sequencing data, alignment to the reference genome, and multiple structural variation detection tools, are integrated. All the partial results are then processed and merged with an in-house merging algorithm. Compared with a single detection approach, ProcaryaSV has improved detection performance and is a reproducible easy-to-use tool. CONCLUSIONS The ProcaryaSV pipeline provides an integrative approach to structural variation detection from paired-end next-generation sequencing of bacterial samples. It can be easily installed and used on Linux machines. It is publicly available on GitHub at https://github.com/robinjugas/ProcaryaSV .
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Affiliation(s)
- Robin Jugas
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Helena Vitkova
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic.
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2
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Zhou C, Pawline MB, Pironti A, Morales SM, Perault AI, Ulrich RJ, Podkowik M, Lejeune A, DuMont A, Stubbe FX, Korman A, Jones DR, Schluter J, Richardson AR, Fey PD, Drlica K, Cadwell K, Torres VJ, Shopsin B. Microbiota and metabolic adaptation shape Staphylococcus aureus virulence and antimicrobial resistance during intestinal colonization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.11.593044. [PMID: 38766195 PMCID: PMC11100824 DOI: 10.1101/2024.05.11.593044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Depletion of microbiota increases susceptibility to gastrointestinal colonization and subsequent infection by opportunistic pathogens such as methicillin-resistant Staphylococcus aureus (MRSA). How the absence of gut microbiota impacts the evolution of MRSA is unknown. The present report used germ-free mice to investigate the evolutionary dynamics of MRSA in the absence of gut microbiota. Through genomic analyses and competition assays, we found that MRSA adapts to the microbiota-free gut through sequential genetic mutations and structural changes that enhance fitness. Initially, these adaptations increase carbohydrate transport; subsequently, evolutionary pathways largely diverge to enhance either arginine metabolism or cell wall biosynthesis. Increased fitness in arginine pathway mutants depended on arginine catabolic genes, especially nos and arcC, which promote microaerobic respiration and ATP generation, respectively. Thus, arginine adaptation likely improves redox balance and energy production in the oxygen-limited gut environment. Findings were supported by human gut metagenomic analyses, which suggest the influence of arginine metabolism on colonization. Surprisingly, these adaptive genetic changes often reduced MRSA's antimicrobial resistance and virulence. Furthermore, resistance mutation, typically associated with decreased virulence, also reduced colonization fitness, indicating evolutionary trade-offs among these traits. The presence of normal microbiota inhibited these adaptations, preserving MRSA's wild-type characteristics that effectively balance virulence, resistance, and colonization fitness. The results highlight the protective role of gut microbiota in preserving a balance of key MRSA traits for long-term ecological success in commensal populations, underscoring the potential consequences on MRSA's survival and fitness during and after host hospitalization and antimicrobial treatment.
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Affiliation(s)
- Chunyi Zhou
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Miranda B. Pawline
- Department of Medicine, Division of Infectious Diseases, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Alejandro Pironti
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY 10016, USA
- Microbial Computational Genomic Core Lab, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Sabrina M. Morales
- Department of Medicine, Division of Infectious Diseases, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Andrew I. Perault
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Robert J. Ulrich
- Department of Medicine, Division of Infectious Diseases, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Magdalena Podkowik
- Department of Medicine, Division of Infectious Diseases, New York University Grossman School of Medicine, New York, NY 10016, USA
- Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Alannah Lejeune
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ashley DuMont
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | | | - Aryeh Korman
- Metabolomics Core Resource Laboratory, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Drew R. Jones
- Metabolomics Core Resource Laboratory, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jonas Schluter
- Institute for Systems Genetics, Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Anthony R. Richardson
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Paul D. Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Karl Drlica
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07102, USA
- Department of Microbiology, Biochemistry & Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ 07102, USA
| | - Ken Cadwell
- Division of Gastroenterology and Hepatology, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University, Grossman School of Medicine, New York, NY 10016, USA
| | - Victor J. Torres
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Bo Shopsin
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Department of Medicine, Division of Infectious Diseases, New York University Grossman School of Medicine, New York, NY 10016, USA
- Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY 10016, USA
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3
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Ulrich RJ, Podkowik M, Tierce R, Irnov I, Putzel G, Samhadaneh N, Lacey KA, Boff D, Morales SM, Makita S, Karagounis TK, Zwack EE, Zhou C, Kim R, Drlica K, Pironti A, van Bakel H, Torres VJ, Shopsin B. Prophage-encoded methyltransferase drives adaptation of community-acquired methicillin-resistant Staphylococcus aureus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.17.589803. [PMID: 38659881 PMCID: PMC11042277 DOI: 10.1101/2024.04.17.589803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
We recently described the evolution of a community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) USA300 variant responsible for an outbreak of skin and soft tissue infections. Acquisition of a mosaic version of the Φ11 prophage (mΦ11) that increases skin abscess size was an early step in CA-MRSA adaptation that primed the successful spread of the clone. The present report shows how prophage mΦ11 exerts its effect on virulence for skin infection without encoding a known toxin or fitness genes. Abscess size and skin inflammation were associated with DNA methylase activity of an mΦ11-encoded adenine methyltransferase (designated pamA). pamA increased expression of fibronectin-binding protein A (fnbA; FnBPA), and inactivation of fnbA eliminated the effect of pamA on abscess virulence without affecting strains lacking pamA. Thus, fnbA is a pamA-specific virulence factor. Mechanistically, pamA was shown to promote biofilm formation in vivo in skin abscesses, a phenotype linked to FnBPA's role in biofilm formation. Collectively, these data reveal a novel mechanism-epigenetic regulation of staphylococcal gene expression-by which phage can regulate virulence to drive adaptive leaps by S. aureus.
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Affiliation(s)
- Robert J. Ulrich
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Magdalena Podkowik
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
- Antimicrobial-Resistant Pathogens Program, NYU Grossman School of Medicine, New York, NY, USA
| | - Rebecca Tierce
- Division of Comparative Medicine, NYU Langone Health, New York, NY, USA
| | - Irnov Irnov
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Gregory Putzel
- Antimicrobial-Resistant Pathogens Program, NYU Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Nora Samhadaneh
- Antimicrobial-Resistant Pathogens Program, NYU Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Keenan A. Lacey
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Daiane Boff
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Sabrina M. Morales
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Sohei Makita
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Theodora K. Karagounis
- Ronald O. Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY, USA
| | - Erin E. Zwack
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Chunyi Zhou
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Randie Kim
- Ronald O. Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY, USA
| | - Karl Drlica
- Department of Microbiology, Biochemistry & Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Alejandro Pironti
- Antimicrobial-Resistant Pathogens Program, NYU Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Victor J. Torres
- Antimicrobial-Resistant Pathogens Program, NYU Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
- Department of Host-Microbe Interactions, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Bo Shopsin
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
- Antimicrobial-Resistant Pathogens Program, NYU Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
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Shields KE, Ranava D, Tan Y, Zhang D, Yap MNF. Epitranscriptional m6A modification of rRNA negatively impacts translation and host colonization in Staphylococcus aureus. PLoS Pathog 2024; 20:e1011968. [PMID: 38252661 PMCID: PMC10833563 DOI: 10.1371/journal.ppat.1011968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 02/01/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Macrolides, lincosamides, and streptogramin B (MLS) are structurally distinct molecules that are among the safest antibiotics for prophylactic use and for the treatment of bacterial infections. The family of erythromycin resistance methyltransferases (Erm) invariantly install either one or two methyl groups onto the N6,6-adenosine of 2058 nucleotide (m6A2058) of the bacterial 23S rRNA, leading to bacterial cross-resistance to all MLS antibiotics. Despite extensive structural studies on the mechanism of Erm-mediated MLS resistance, how the m6A epitranscriptomic mark affects ribosome function and bacterial physiology is not well understood. Here, we show that Staphylococcus aureus cells harboring m6A2058 ribosomes are outcompeted by cells carrying unmodified ribosomes during infections and are severely impaired in colonization in the absence of an unmodified counterpart. The competitive advantage of m6A2058 ribosomes is manifested only upon antibiotic challenge. Using ribosome profiling (Ribo-Seq) and a dual-fluorescence reporter to measure ribosome occupancy and translational fidelity, we found that specific genes involved in host interactions, metabolism, and information processing are disproportionally deregulated in mRNA translation. This dysregulation is linked to a substantial reduction in translational capacity and fidelity in m6A2058 ribosomes. These findings point to a general "inefficient translation" mechanism of trade-offs associated with multidrug-resistant ribosomes.
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Affiliation(s)
- Kathryn E. Shields
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - David Ranava
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Yongjun Tan
- Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, Missouri, United States of America
| | - Dapeng Zhang
- Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, Missouri, United States of America
- Program of Bioinformatics and Computational Biology, College of Arts and Sciences, St. Louis, Missouri, United States of America
| | - Mee-Ngan F. Yap
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
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5
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Jiang JH, Cameron DR, Nethercott C, Aires-de-Sousa M, Peleg AY. Virulence attributes of successful methicillin-resistant Staphylococcus aureus lineages. Clin Microbiol Rev 2023; 36:e0014822. [PMID: 37982596 PMCID: PMC10732075 DOI: 10.1128/cmr.00148-22] [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] [Indexed: 11/21/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of severe and often fatal infections. MRSA epidemics have occurred in waves, whereby a previously successful lineage has been replaced by a more fit and better adapted lineage. Selection pressures in both hospital and community settings are not uniform across the globe, which has resulted in geographically distinct epidemiology. This review focuses on the mechanisms that trigger the establishment and maintenance of current, dominant MRSA lineages across the globe. While the important role of antibiotic resistance will be mentioned throughout, factors which influence the capacity of S. aureus to colonize and cause disease within a host will be the primary focus of this review. We show that while MRSA possesses a diverse arsenal of toxins including alpha-toxin, the success of a lineage involves more than just producing toxins that damage the host. Success is often attributed to the acquisition or loss of genetic elements involved in colonization and niche adaptation such as the arginine catabolic mobile element, as well as the activity of regulatory systems, and shift metabolism accordingly (e.g., the accessory genome regulator, agr). Understanding exactly how specific MRSA clones cause prolonged epidemics may reveal targets for therapies, whereby both core (e.g., the alpha toxin) and acquired virulence factors (e.g., the Panton-Valentine leukocidin) may be nullified using anti-virulence strategies.
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Affiliation(s)
- Jhih-Hang Jiang
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - David R. Cameron
- Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Cara Nethercott
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Marta Aires-de-Sousa
- Laboratory of Molecular Genetics, Institutode Tecnologia Químicae Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
- Escola Superior de Saúde da Cruz Vermelha Portuguesa-Lisboa (ESSCVP-Lisboa), Lisbon, Portugal
| | - Anton Y. Peleg
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Centre to Impact Antimicrobial Resistance, Monash University, Clayton, Melbourne, Victoria, Australia
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6
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Miele L, Evans RML, Cunniffe NJ, Torres-Barceló C, Bevacqua D. Evolutionary Epidemiology Consequences of Trait-Dependent Control of Heterogeneous Parasites. Am Nat 2023; 202:E130-E146. [PMID: 37963120 DOI: 10.1086/726062] [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] [Indexed: 11/16/2023]
Abstract
AbstractDisease control can induce both demographic and evolutionary responses in host-parasite systems. Foreseeing the outcome of control therefore requires knowledge of the eco-evolutionary feedback between control and system. Previous work has assumed that control strategies have a homogeneous effect on the parasite population. However, this is not true when control targets those traits that confer to the parasite heterogeneous levels of resistance, which can additionally be related to other key parasite traits through evolutionary trade-offs. In this work, we develop a minimal model coupling epidemiological and evolutionary dynamics to explore possible trait-dependent effects of control strategies. In particular, we consider a parasite expressing continuous levels of a trait-determining resource exploitation and a control treatment that can be either positively or negatively correlated with that trait. We demonstrate the potential of trait-dependent control by considering that the decision maker may want to minimize both the damage caused by the disease and the use of treatment, due to possible environmental or economic costs. We identify efficient strategies showing that the optimal type of treatment depends on the amount applied. Our results pave the way for the study of control strategies based on evolutionary constraints, such as collateral sensitivity and resistance costs, which are receiving increasing attention for both public health and agricultural purposes.
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André C, Lebreton F, Van Tyne D, Cadorette J, Boody R, Gilmore MS, Bispo PJM. Microbiology of Eye Infections at the Massachusetts Eye and Ear: An 8-Year Retrospective Review Combined With Genomic Epidemiology. Am J Ophthalmol 2023; 255:43-56. [PMID: 37343741 PMCID: PMC10592486 DOI: 10.1016/j.ajo.2023.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/28/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
PURPOSE Ocular bacterial infections are important causes of morbidity and vision loss. Early antimicrobial therapy is necessary to save vision, but their efficacy is increasingly compromised by antimicrobial resistance (AMR). We assessed the etiology of ocular bacterial infections seen at Massachusetts Eye and Ear and investigated the molecular epidemiology and AMR profiles of contemporary isolates. DESIGN Laboratory investigation. METHODS We used a combination of phenotypic tests and genome sequencing to identify the predominant lineages of leading ocular pathogens and their AMR profiles. RESULTS A total of 1601 isolates were collected from 2014 to 2021, with Staphylococcus aureus (n = 621), coagulase-negative staphylococci (CoNS) (n = 234), Pseudomonas aeruginosa (n = 213), Enterobacteriaceae (n = 167), and Streptococcus pneumoniae (n = 95) being the most common. Resistance was high among staphylococci, with methicillin resistance (MR) detected in 28% of S aureus and 39.8% of CoNS isolates. Multidrug resistance (MDR) was frequent among MR staphylococci (MRSA 60%, MRCoNS 76.1%). The population of S aureus isolates consisted mainly of 2 clonal complexes (CCs): CC8 (26.1%) and CC5 (24.1%). CC5 strains carried a variety of AMR markers, resulting in high levels of resistance to first-line therapies. Similarly, the population of ocular Staphylococcus epidermidis was homogenous with most belonging to CC2 (85%), which were commonly MDR (48%). Conversely, ocular S pneumoniae, P aeruginosa, and Enterobacteriaceae were often susceptible to first-line therapies and grouped into highly diverse genetic populations. CONCLUSION Our data showed that ocular bacterial infections in our patient population are disproportionately caused by strains that are resistant to clinically relevant antibiotics and are associated with major epidemic genotypes with both community and hospital associations.
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Affiliation(s)
- Camille André
- From the Department of Ophthalmology (C.A., F.L., D.V., J.C., R.B., M.S.G., P.J.M.B.), Massachusetts Eye and Ear Infirmary
| | - François Lebreton
- From the Department of Ophthalmology (C.A., F.L., D.V., J.C., R.B., M.S.G., P.J.M.B.), Massachusetts Eye and Ear Infirmary; Department of Microbiology and Immunology (F.L., D.V., M.S.G.), Harvard Medical School, Boston, Massachusetts, USA
| | - Daria Van Tyne
- From the Department of Ophthalmology (C.A., F.L., D.V., J.C., R.B., M.S.G., P.J.M.B.), Massachusetts Eye and Ear Infirmary; Department of Microbiology and Immunology (F.L., D.V., M.S.G.), Harvard Medical School, Boston, Massachusetts, USA
| | - James Cadorette
- From the Department of Ophthalmology (C.A., F.L., D.V., J.C., R.B., M.S.G., P.J.M.B.), Massachusetts Eye and Ear Infirmary
| | - Rick Boody
- From the Department of Ophthalmology (C.A., F.L., D.V., J.C., R.B., M.S.G., P.J.M.B.), Massachusetts Eye and Ear Infirmary
| | - Michael S Gilmore
- From the Department of Ophthalmology (C.A., F.L., D.V., J.C., R.B., M.S.G., P.J.M.B.), Massachusetts Eye and Ear Infirmary; Department of Microbiology and Immunology (F.L., D.V., M.S.G.), Harvard Medical School, Boston, Massachusetts, USA
| | - Paulo J M Bispo
- From the Department of Ophthalmology (C.A., F.L., D.V., J.C., R.B., M.S.G., P.J.M.B.), Massachusetts Eye and Ear Infirmary.
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8
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Martínez JRW, Planet PJ, Spencer-Sandino M, Rivas L, Díaz L, Moustafa AM, Quesille-Villalobos A, Riquelme-Neira R, Alcalde-Rico M, Hanson B, Carvajal LP, Rincón S, Reyes J, Lam M, Calderon JF, Araos R, García P, Arias CA, Munita JM. Dynamics of the MRSA Population in a Chilean Hospital: a Phylogenomic Analysis (2000-2016). Microbiol Spectr 2023; 11:e0535122. [PMID: 37338398 PMCID: PMC10433796 DOI: 10.1128/spectrum.05351-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/29/2023] [Indexed: 06/21/2023] Open
Abstract
The global dissemination of methicillin-resistant Staphylococcus aureus (MRSA) is associated with the emergence and establishment of clones in specific geographic areas. The Chilean-Cordobes clone (ChC) (ST5-SCCmecI) has been the predominant MRSA clone in Chile since its first description in 1998, despite the report of other emerging MRSA clones in recent years. Here, we characterize the evolutionary history of MRSA from 2000 to 2016 in a Chilean tertiary health care center using phylogenomic analyses. We sequenced 469 MRSA isolates collected between 2000 and 2016. We evaluated the temporal trends of the circulating clones and performed a phylogenomic reconstruction to characterize the clonal dynamics. We found a significant increase in the diversity and richness of sequence types (STs; Spearman r = 0.8748, P < 0.0001) with a Shannon diversity index increasing from 0.221 in the year 2000 to 1.33 in 2016, and an effective diversity (Hill number; q = 2) increasing from 1.12 to 2.71. The temporal trend analysis revealed that in the period 2000 to 2003 most of the isolates (94.2%; n = 98) belonged to the ChC clone. However, since then, the frequency of the ChC clone has decreased over time, accounting for 52% of the collection in the 2013 to 2016 period. This decline was accompanied by the rise of two emerging MRSA lineages, ST105-SCCmecII and ST72-SCCmecVI. In conclusion, the ChC clone remains the most frequent MRSA lineage, but this lineage is gradually being replaced by several emerging clones, the most important of which is clone ST105-SCCmecII. To the best of our knowledge, this is the largest study of MRSA clonal dynamics performed in South America. IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is a major public health pathogen that disseminates through the emergence of successful dominant clones in specific geographic regions. Knowledge of the dissemination and molecular epidemiology of MRSA in Latin America is scarce and is largely based on small studies or more limited typing techniques that lack the resolution to represent an accurate description of the genomic landscape. We used whole-genome sequencing to study 469 MRSA isolates collected between 2000 and 2016 in Chile providing the largest and most detailed study of clonal dynamics of MRSA in South America to date. We found a significant increase in the diversity of MRSA clones circulating over the 17-year study period. Additionally, we describe the emergence of two novel clones (ST105-SCCmecII and ST72-SCCmecVI), which have been gradually increasing in frequency over time. Our results drastically improve our understanding of the dissemination and update our knowledge about MRSA in Latin America.
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Affiliation(s)
- José R. W. Martínez
- Genomics & Resistant Microbes (GeRM), ICIM, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Paul J. Planet
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- American Museum of Natural History, New York, New York, USA
| | - Maria Spencer-Sandino
- Genomics & Resistant Microbes (GeRM), ICIM, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Lina Rivas
- Genomics & Resistant Microbes (GeRM), ICIM, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Lorena Díaz
- Genomics & Resistant Microbes (GeRM), ICIM, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogotá, Colombia
| | - Ahmed M. Moustafa
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ana Quesille-Villalobos
- Genomics & Resistant Microbes (GeRM), ICIM, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Roberto Riquelme-Neira
- Genomics & Resistant Microbes (GeRM), ICIM, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago, Chile
| | - Manuel Alcalde-Rico
- Genomics & Resistant Microbes (GeRM), ICIM, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
- Grupo de Resistencia a los Antibióticos en Bacterias Patógenas y Ambientales (GRABPA), Pontificia Univ. Católica de Valparaíso, Valparaiso, Chile
| | - Blake Hanson
- Center for Antimicrobial Resistance and Microbial Genomics, Univ. of Texas Health Science Center, McGovern Medical School, Houston, Texas, USA
| | - Lina P. Carvajal
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogotá, Colombia
| | - Sandra Rincón
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogotá, Colombia
| | - Jinnethe Reyes
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogotá, Colombia
| | - Marusella Lam
- Departamento de Laboratorios Clínicos, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan F. Calderon
- Centro de Genética y Genómica Instituto de Ciencias e Innovación en Medicina Facultad de Medicina Clínica Alemana Universidad Del Desarrollo, Santiago, Chile
- Research Center for the Development of Novel Therapeutic Alternatives for Alcohol Use Disorders, Santiago, Chile
| | - Rafael Araos
- Genomics & Resistant Microbes (GeRM), ICIM, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Patricia García
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
- Departamento de Laboratorios Clínicos, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - César A. Arias
- Division of Infectious Diseases, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases, Houston Methodist Research Institution, Houston, Texas, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - José M. Munita
- Genomics & Resistant Microbes (GeRM), ICIM, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Multidisciplinary Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
- Hospital Padre Hurtado, Santiago, Chile
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9
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Torres NJ, Rizzo DN, Reinberg MA, Jobson ME, Totzke BC, Jackson JK, Yu W, Shaw LN. The identification of two M20B family peptidases required for full virulence in Staphylococcus aureus. Front Cell Infect Microbiol 2023; 13:1176769. [PMID: 37538308 PMCID: PMC10394242 DOI: 10.3389/fcimb.2023.1176769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/13/2023] [Indexed: 08/05/2023] Open
Abstract
We have previously demonstrated that deletion of an intracellular leucine aminopeptidase results in attenuated virulence of S. aureus. Herein we explore the role of 10 other aminopeptidases in S. aureus pathogenesis. Using a human blood survival assay we identified mutations in two enzymes from the M20B family (PepT1 and PepT2) as having markedly decreased survival compared to the parent. We further reveal that pepT1, pepT2 and pepT1/2 mutant strains are impaired in their ability to resist phagocytosis by, and engender survival within, human macrophages. Using a co-infection model of murine sepsis, we demonstrate impairment of dissemination and survival for both single mutants that is even more pronounced in the double mutant. We show that these enzymes are localized to the cytosol and membrane but are not necessary for peptide-based nutrition, a hallmark of cell-associated aminopeptidases. Furthermore, none of the survival defects appear to be the result of altered virulence factor production. An exploration of their regulation reveals that both are controlled by known regulators of the S. aureus virulence process, including Agr, Rot and/or SarA, and that this cascade may be mediated by FarR. Structural modeling of PepT1 reveals it bears all the hallmarks of a tripeptidase, whilst PepT2 differs significantly in its catalytic pocket, suggesting a broader substrate preference. In sum, we have identified two M20B aminopeptidases that are integral to S. aureus pathogenesis. The future identification of protein and/or peptide targets for these proteases will be critical to understanding their important virulence impacting functions.
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Affiliation(s)
| | | | | | | | | | | | | | - Lindsey N. Shaw
- Department of Molecular Biosciences, University of South Florida, Tampa, FL, United States
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10
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Kim J, Kim GL, Norambuena J, Boyd JM, Parker D. Impact of the pentose phosphate pathway on metabolism and pathogenesis of Staphylococcus aureus. PLoS Pathog 2023; 19:e1011531. [PMID: 37440594 PMCID: PMC10368262 DOI: 10.1371/journal.ppat.1011531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/25/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Staphylococcus aureus is an important pathogen that leads to significant disease through multiple routes of infection. We recently published a transposon sequencing (Tn-seq) screen in a mouse acute pneumonia model and identified a hypothetical gene (SAUSA300_1902, pgl) with similarity to a lactonase of Escherichia coli involved in the pentose phosphate pathway (PPP) that was conditionally essential. Limited studies have investigated the role of the PPP in physiology and pathogenesis of S. aureus. We show here that mutation of pgl significantly impacts ATP levels and respiration. RNA-seq analysis of the pgl mutant and parent strains identified compensatory changes in gene expression for glucose and gluconate as well as reductions in the pyrimidine biosynthesis locus. These differences were also evident through unbiased metabolomics studies and 13C labeling experiments that showed mutation of pgl led to reductions in pyrimidine metabolism including decreases in ribose-5P, UMP and GMP. These nucleotide reductions impacted the amount of extracellular DNA in biofilms and reduced biofilm formation. Mutation also limited the capacity of the strain to resist oxidant damage induced by hydrogen peroxide and paraquat and subsequent intracellular survival inside macrophages. Changes in wall teichoic acid impacted susceptibility to hydrogen peroxide. We demonstrated the importance of these changes on virulence in three different models of infection, covering respiratory, skin and septicemia, demonstrating the need for proper PPP function in all models. This work demonstrates the multifaceted role metabolism can play in multiple aspects of S. aureus pathogenesis.
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Affiliation(s)
- Jisun Kim
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
| | - Gyu-Lee Kim
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
| | - Javiera Norambuena
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Jeffrey M. Boyd
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Dane Parker
- Department of Pathology, Immunology and Laboratory Medicine, Center for Immunity and Inflammation, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
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11
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Fitzgerald BA, Wadud A, Slimak Z, Slonczewski JL. Enterococcus faecalis OG1RF Evolution at Low pH Selects Fusidate-Sensitive Mutants in Elongation Factor G and at High pH Selects Defects in Phosphate Transport. Appl Environ Microbiol 2023; 89:e0046623. [PMID: 37272807 PMCID: PMC10304957 DOI: 10.1128/aem.00466-23] [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: 03/21/2023] [Accepted: 05/15/2023] [Indexed: 06/06/2023] Open
Abstract
Enterococcus bacteria inhabit human and soil environments that show a wide range of pH values. Strains include commensals as well as antibiotic-resistant pathogens. We investigated the adaptation to pH stress in E. faecalis OG1RF by conducting experimental evolution under acidic (pH 4.8), neutral pH (pH 7.0), and basic (pH 9.0) conditions. A serial planktonic culture was performed for 500 generations and in a high-pH biofilm culture for 4 serial bead transfers. Nearly all of the mutations led to nonsynonomous codons, indicating adaptive selection. All of the acid-adapted clones from the planktonic culture showed a mutation in fusA (encoding elongation factor G). The acid-adapted fusA mutants had a trade-off of decreased resistance to fusidic acid (fusidate). All of the base-adapted clones from the planktonic cultures as well as some from the biofilm-adapted cultures showed mutations that affected the Pst phosphate ABC transporter (pstA, pstB, pstB2, pstC) and pyrR (pyrimidine biosynthesis regulator/uracil phosphoribosyltransferase). The biofilm cultures produced small-size colonies on brain heart infusion agar. These variants each contained a single mutation in pstB2, pstC, or pyrR. The pst and pyrR mutants outgrew the ancestral strain at pH 9.2, with a trade-off of lower growth at pH 4.8. Additional genes that had a mutation in multiple clones that evolved at high pH (but not at low pH) include opp1BCDF (oligopeptide ABC transporter), ccpA (catabolite control protein A), and ftsZ (septation protein). Overall, the experimental evolution of E. faecalis showed a strong pH dependence, favoring the fusidate-sensitive elongation factor G modification at low pH and the loss of phosphate transport genes at high pH. IMPORTANCE E. faecalis bacteria are found in dental biofilms, where they experience low pH as a result of fermentative metabolism. Thus, the effect of pH on antibiotic resistance has clinical importance. The loss of fusidate resistance is notable for OG1RF strains in which fusidate resistance is assumed to be a stable genetic marker. In endodontal infections, enterococci can resist calcium hydroxide therapy that generates extremely high pH values. In other environments, such as the soil and plant rhizosphere, enterococci experience acidification that is associated with climate change. Thus, the pH modulation of natural selection in enterococci is important for human health as well as for understanding soil environments.
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Affiliation(s)
| | - Ayman Wadud
- Department of Biology, Kenyon College, Gambier, Ohio, USA
| | - Zachary Slimak
- Department of Biology, Kenyon College, Gambier, Ohio, USA
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12
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Shinohara K, Uehara Y, Teruya K, Sasaki T, Baba T, Nakaminami H, Kananizadeh P, Morimoto Y, Kikuchi Y, Oka S. Emergence of community-associated methicillin-resistant Staphylococcus aureus ΨUSA300 among Japanese people with HIV, resulted from stepwise mutations in 2010s. Sci Rep 2023; 13:8322. [PMID: 37221358 DOI: 10.1038/s41598-023-35171-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 05/14/2023] [Indexed: 05/25/2023] Open
Abstract
Although infection with the methicillin-resistant Staphylococcus aureus (MRSA) clone USA300 is extremely rare in Japan, the uniquely evolved clone ΨUSA300 has been reported in Japan. An outbreak of a distinct USA300 clone was recently reported in an HIV/AIDS referral hospital in Tokyo. The present study investigated the evolutionary origin and genetic diversity of USA300-related clones causing regional outbreaks among people living with HIV (PLWHIV) in Tokyo. MRSA isolates collected from PLWHIV in an HIV/AIDS referral center in Tokyo were subjected to whole-genome sequencing and their genetic features were compared with those of previously described USA300 MRSA genomes. Of the 28 MRSAs isolated in 2016-2019, 23 (82.1%) were identified as USA300, with 22 (95.6%) of the latter identified as ΨUSA300. Although the genomic structure of ΨUSA300 was identical to the structures of reference USA300 strains, one clade (cluster A) was found to have acquired 29 previously identified lineage-specific mutations in a stepwise manner. The estimated divergence dates of ΨUSA300 and Cluster A were 2009 and 2012, respectively. These findings suggested that the ΨUSA300 clone had spread among PLWHIVs in Tokyo in the early 2010s, with stepwise acquisition of lineage-specific nonsynonymous mutations.
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Affiliation(s)
- Koh Shinohara
- AIDS Clinical Center, The National Center for Global Health and Medicine, Tokyo, Japan
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yuki Uehara
- Department of Microbiology, Faculty of Medicine, Juntendo University, Tokyo, Japan.
- Department of Infectious Diseases, Fujita Health University School of Medicine, 1-98, Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan.
| | - Katsuji Teruya
- AIDS Clinical Center, The National Center for Global Health and Medicine, Tokyo, Japan
| | - Takashi Sasaki
- Animal Research Center, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tadashi Baba
- Graduate School of Nursing, Seisen Jogakuin College, Nagano, Japan
| | - Hidemasa Nakaminami
- Department of Microbiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Pegah Kananizadeh
- Department of Microbiology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Yuh Morimoto
- Faculty of Health Science, Juntendo University, Tokyo, Japan
| | - Yoshimi Kikuchi
- AIDS Clinical Center, The National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinichi Oka
- AIDS Clinical Center, The National Center for Global Health and Medicine, Tokyo, Japan
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13
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Martínez JRW, Alcalde-Rico M, Jara-Videla E, Rios R, Moustafa AM, Hanson B, Rivas L, Carvajal LP, Rincon S, Diaz L, Reyes J, Quesille-Villalobos A, Riquelme-Neira R, Undurraga EA, Olivares-Pacheco J, García P, Araos R, Planet PJ, Arias CA, Munita JM. Heavy Metal Pollution From a Major Earthquake and Tsunami in Chile Is Associated With Geographic Divergence of Clinical Isolates of Methicillin-Resistant Staphylococcus aureus in Latin America. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.18.541300. [PMID: 37293062 PMCID: PMC10245734 DOI: 10.1101/2023.05.18.541300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a priority pathogen listed by the World Health Organization. The global spread of MRSA is characterized by successive waves of epidemic clones that predominate in specific geographical regions. The acquisition of genes encoding resistance to heavy-metals is thought to be a key feature in the divergence and geographical spread of MRSA. Increasing evidence suggests that extreme natural events, such as earthquakes and tsunamis, could release heavy-metals into the environment. However, the impact of environmental exposition to heavy-metals on the divergence and spread of MRSA clones has been insufficiently explored. We assess the association between a major earthquake and tsunami in an industrialized port in southern Chile and MRSA clone divergence in Latin America. We performed a phylogenomic reconstruction of 113 MRSA clinical isolates from seven Latin American healthcare centers, including 25 isolates collected in a geographic area affected by an earthquake and tsunami that led to high levels of heavy-metal environmental contamination. We found a divergence event strongly associated with the presence of a plasmid harboring heavy-metal resistance genes in the isolates obtained in the area where the earthquake and tsunami occurred. Moreover, clinical isolates carrying this plasmid showed increased tolerance to mercury, arsenic, and cadmium. We also observed a physiological burden in the plasmid-carrying isolates in absence of heavy-metals. Our results are the first evidence that suggests that heavy-metal contamination, in the aftermath of an environmental disaster, appears to be a key evolutionary event for the spread and dissemination of MRSA in Latin America.
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Affiliation(s)
- Jose RW Martínez
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
| | - Manuel Alcalde-Rico
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
- Grupo de Resistencia a los Antibióticos en Bacterias Patógenas y Ambientales (GRABPA), Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Chile
| | - Estefanía Jara-Videla
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
| | - Rafael Rios
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogota, Colombia
| | - Ahmed M. Moustafa
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Blake Hanson
- Center for Antimicrobial Resistance and Microbial Genomics and Division of Infectious Diseases, University of Texas Health Science Center, McGovern Medical School, Houston, Texas, USA
| | - Lina Rivas
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
| | - Lina P. Carvajal
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogota, Colombia
| | - Sandra Rincon
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogota, Colombia
| | - Lorena Diaz
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
| | - Jinnethe Reyes
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogota, Colombia
| | - Ana Quesille-Villalobos
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
| | - Roberto Riquelme-Neira
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de las Américas, Santiago, Chile
| | - Eduardo A. Undurraga
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
- Escuela de Gobierno, Pontificia Universidad Católica de Chile, Santiago, RM, Chile
- Research Center for Integrated Disaster Risk Management (CIGIDEN), Santiago, Chile
- CIFAR Azrieli Global Scholars program, CIFAR, Toronto, Canada
| | - Jorge Olivares-Pacheco
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
- Grupo de Resistencia a los Antibióticos en Bacterias Patógenas y Ambientales (GRABPA), Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Chile
| | - Patricia García
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
- Departamento de Enfermedades Infecciosas, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rafael Araos
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
| | - Paul J. Planet
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- American Museum of Natural History, New York, NY 10024, USA
| | - César A. Arias
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogota, Colombia
- Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA
- Center for Infectious Diseases Research, Houston Methodist Research Institution, Houston, TX, USA
| | - Jose M. Munita
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Chile
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14
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Long DR, Penewit K, Lo HY, Almazan J, Holmes EA, Bryan AB, Wolter DJ, Lewis JD, Waalkes A, Salipante SJ. In Vitro Selection Identifies Staphylococcus aureus Genes Influencing Biofilm Formation. Infect Immun 2023; 91:e0053822. [PMID: 36847490 PMCID: PMC10016075 DOI: 10.1128/iai.00538-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/13/2023] [Indexed: 03/01/2023] Open
Abstract
Staphylococcus aureus generates biofilms during many chronic human infections, which contributes to its growth and persistence in the host. Multiple genes and pathways necessary for S. aureus biofilm production have been identified, but knowledge is incomplete, and little is known about spontaneous mutations that increase biofilm formation as infection progresses. Here, we performed in vitro selection of four S. aureus laboratory strains (ATCC 29213, JE2, N315, and Newman) to identify mutations associated with enhanced biofilm production. Biofilm formation increased in passaged isolates from all strains, exhibiting from 1.2- to 5-fold the capacity of parental lines. Whole-genome sequencing identified nonsynonymous mutations affecting 23 candidate genes and a genomic duplication encompassing sigB. Six candidate genes significantly impacted biofilm formation as isogenic transposon knockouts: three were previously reported to impact S. aureus biofilm formation (icaR, spdC, and codY), while the remaining three (manA, narH, and fruB) were newly implicated by this study. Plasmid-mediated genetic complementation of manA, narH, and fruB transposon mutants corrected biofilm deficiencies, with high-level expression of manA and fruB further enhancing biofilm formation over basal levels. This work recognizes genes not previously identified as contributing to biofilm formation in S. aureus and reveals genetic changes able to augment biofilm production by that organism.
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Affiliation(s)
- Dustin R. Long
- Division of Critical Care Medicine, Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Kelsi Penewit
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Hsin-Yu Lo
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Jared Almazan
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Elizabeth A. Holmes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Andrew B. Bryan
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Daniel J. Wolter
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Janessa D. Lewis
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Adam Waalkes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Stephen J. Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
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15
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Martínez JRW, Planet PJ, Maria SS, Lina R, Lorena D, Ana QV, Roberto RN, Manuel AR, Blake H, Carvajal LP, Sandra R, Jinnethe R, Marusella L, Rafael A, Patricia G, Arias CA, Munita JM. Dynamics of the MRSA Population in A Chilean Hospital: A Phylogenomic Analysis (2000-2016). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.06.526811. [PMID: 36798318 PMCID: PMC9934535 DOI: 10.1101/2023.02.06.526811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The global dissemination of methicillin-resistant Staphylococcus aureus (MRSA) is associated with the emergence and establishment of clones in specific geographic areas. The Chilean-Cordobes clone (ChC) (ST5-SCC mec I) has been the predominant MRSA clone in Chile since its first description in 1998, despite the report of other emerging MRSA clones in the last years. Here, we characterize the evolutionary history of MRSA from 2000 to 2016 in a Chilean tertiary healthcare center using phylogenomic analyses. We sequenced 469 MRSA isolates collected between 2000-2016 in a tertiary healthcare center in Chile. We evaluated the temporal trends of the circulating clones and performed a phylogenomic reconstruction to characterize the clonal dynamics. We found a significant increase in the diversity and richness of sequence types (STs; Spearman r=0.8748, p<0.0001) with a Shannon diversity index increasing from 0.221 in the year 2000 to 1.33 in 2016. The temporal trend analysis revealed that in the period 2000-2003 most of the isolates (94.2%; n=98) belonged to the ChC clone. However, since then, the frequency of the ChC clone has decreased over time, accounting for 52% of the collection in the 2013-2016 period. This decline was accompanied by the rise of two emerging MRSA lineages, ST105-SCC mec II and ST72-SCC mec VI. In conclusion, the ChC clone remains the most frequent MRSA lineage in Chile. However, this lineage is gradually being replaced by several emerging clones, the most important of which is clone ST105-SCC mec II. To the best of our knowledge, this is the largest study of MRSA clonal dynamics performed in South America. Importance Methicillin-resistant Staphylococcus aureus (MRSA) is a major public health pathogen that disseminates through the emergence of successful dominant clones in specific geographic regions. Knowledge of the dissemination and molecular epidemiology of MRSA in Latin America is scarce and is largely based on small studies or classical typing techniques with several limitations to depict an accurate description of their genomic landscape. We used whole-genome sequencing to study 469 MRSA isolates collected between 2000-2016 in Chile to provide the largest and most detailed study of clonal dynamics of MRSA carried out in South America to date. We found a significant increase in the diversity of MRSA clones circulating over the 17-year study period. Additionally, we describe the emergence of two novel clones (ST105-SCCmecII and ST72-SCCmecVI), which have been gradually increasing their frequency over time. Our results drastically improve our understanding of the dissemination and update our knowledge about MRSA in Latin America.
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16
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Bianco CM, Moustafa AM, O’Brien K, Martin MA, Read TD, Kreiswirth BN, Planet PJ. Pre-epidemic evolution of the MRSA USA300 clade and a molecular key for classification. Front Cell Infect Microbiol 2023; 13:1081070. [PMID: 36761897 PMCID: PMC9902376 DOI: 10.3389/fcimb.2023.1081070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/04/2023] [Indexed: 01/26/2023] Open
Abstract
Introduction USA300 has remained the dominant community and healthcare associated methicillin-resistant Staphylococcus aureus (MRSA) clone in the United States and in northern South America for at least the past 20 years. In this time, it has experienced epidemic spread in both of these locations. However, its pre-epidemic evolutionary history and origins are incompletely understood. Large sequencing databases, such as NCBI, PATRIC, and Staphopia, contain clues to the early evolution of USA300 in the form of sequenced genomes of USA300 isolates that are representative of lineages that diverged prior to the establishment of the South American epidemic (SAE) clade and North American epidemic (NAE) clade. In addition, historical isolates collected prior to the emergence of epidemics can help reconstruct early events in the history of this lineage. Methods Here, we take advantage of the accrued, publicly available data, as well as two newly sequenced pre-epidemic historical isolates from 1996, and a very early diverging ACME-negative NAE genome, to understand the pre-epidemic evolution of USA300. We use database mining techniques to emphasize genomes similar to pre-epidemic isolates, with the goal of reconstructing the early molecular evolution of the USA300 lineage. Results Phylogenetic analysis with these genomes confirms that the NAE and SAE USA300 lineages diverged from a most recent common ancestor around 1970 with high confidence, and it also pinpoints the independent acquisition events of the of the ACME and COMER loci with greater precision than in previous studies. We provide evidence for a North American origin of the USA300 lineage and identify multiple introductions of USA300 into South and North America. Notably, we describe a third major USA300 clade (the pre-epidemic branching clade; PEB1) consisting of both MSSA and MRSA isolates circulating around the world that diverged from the USA300 lineage prior to the establishment of the South and North American epidemics. We present a detailed analysis of specific sequence characteristics of each of the major clades, and present diagnostic positions that can be used to classify new genomes.
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Affiliation(s)
- Colleen M. Bianco
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Ahmed M. Moustafa
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Kelsey O’Brien
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Michael A. Martin
- Division of Infectious Diseases & Department of Human Genetics Emory University School of Medicine, Atlanta, GA, United States
| | - Timothy D. Read
- Division of Infectious Diseases & Department of Human Genetics Emory University School of Medicine, Atlanta, GA, United States
| | - Barry N. Kreiswirth
- Center for Discovery & Innovation, Hackensack Meridian Health, Nutley, NJ, United States
| | - Paul J. Planet
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, PA, United States,American Museum of Natural History, New York, NY, United States,*Correspondence: Paul J. Planet,
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Botelho J, Cazares A, Schulenburg H. The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements. Nucleic Acids Res 2023; 51:236-252. [PMID: 36610752 PMCID: PMC9841420 DOI: 10.1093/nar/gkac1220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 01/09/2023] Open
Abstract
Mobile genetic elements (MGEs) mediate the shuffling of genes among organisms. They contribute to the spread of virulence and antibiotic resistance (AMR) genes in human pathogens, such as the particularly problematic group of ESKAPE pathogens. Here, we performed the first systematic analysis of MGEs, including plasmids, prophages, and integrative and conjugative/mobilizable elements (ICEs/IMEs), across all ESKAPE pathogens. We found that different MGE types are asymmetrically distributed across these pathogens, and that most horizontal gene transfer (HGT) events are restricted by phylum or genus. We show that the MGEs proteome is involved in diverse functional processes and distinguish widespread proteins within the ESKAPE context. Moreover, anti-CRISPRs and AMR genes are overrepresented in the ESKAPE mobilome. Our results also underscore species-specific trends shaping the number of MGEs, AMR, and virulence genes across pairs of conspecific ESKAPE genomes with and without CRISPR-Cas systems. Finally, we observed that CRISPR spacers found on prophages, ICEs/IMEs, and plasmids have different targeting biases: while plasmid and prophage CRISPRs almost exclusively target other plasmids and prophages, respectively, ICEs/IMEs CRISPRs preferentially target prophages. Overall, our study highlights the general importance of the ESKAPE mobilome in contributing to the spread of AMR and mediating conflict among MGEs.
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Affiliation(s)
- João Botelho
- To whom correspondence should be addressed. Tel: +49 431 880 4143;
| | - Adrian Cazares
- EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK,Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Hinrich Schulenburg
- Antibiotic Resistance Evolution Group, Max Planck Institute for Evolutionary Biology, Plön, Germany,Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian Albrechts University, Kiel, Germany
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18
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Barakat NA, Rasmy SA, Hosny AEDMS, Kashef MT. Effect of povidone-iodine and propanol-based mecetronium ethyl sulphate on antimicrobial resistance and virulence in Staphylococcus aureus. Antimicrob Resist Infect Control 2022; 11:139. [PMID: 36369050 PMCID: PMC9652812 DOI: 10.1186/s13756-022-01178-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022] Open
Abstract
Background Reports are available on cross-resistance between antibiotics and biocides. We evaluated the effect of povidone-iodine (PVP-I) and propanol-based mecetronium ethyl sulphate (PBM) on resistance development, antibiotics cross-resistance, and virulence in Staphylococcus aureus. Methods The minimum inhibitory concentration (MIC) of PVP-I and PBM were determined against S. aureus ATCC 25923 using the agar-dilution method. Staphylococcus aureus ATCC 25923 was subjected to subinhibitory concentrations of the tested biocides in ten consecutive passages followed by five passages in a biocide-free medium; MIC was determined after each passage and after the fifth passage in the biocide-free medium. The developed resistant mutant was tested for cross-resistance to different antibiotics using Kirby-Bauer disk diffusion method. Antibiotic susceptibility profiles as well as biocides’ MIC were determined for 97 clinical S. aureus isolates. Isolates were categorized into susceptible and resistant to the tested biocides based on MIC distribution pattern. The virulence of the biocide-resistant mutant and the effect of subinhibitory concentrations of biocides on virulence (biofilm formation, hemolysin activity, and expression of virulence-related genes) were tested. Results PVP-I and PBM MIC were 5000 μg/mL and 664 μg/mL. No resistance developed to PVP-I but a 128-fold increase in PBM MIC was recorded, by repeated exposure. The developed PBM-resistant mutant acquired resistance to penicillin, cefoxitin, and ciprofloxacin. No clinical isolates were PVP-I-resistant while 48.5% were PBM-resistant. PBM-resistant isolates were more significantly detected among multidrug-resistant isolates. PVP-I subinhibitory concentrations (¼ and ½ of MIC) completely inhibited biofilm formation and significantly reduced hemolysin activity (7% and 0.28%, respectively). However, subinhibitory concentrations of PBM caused moderate reduction in biofilm activity and non-significant reduction in hemolysin activity. The ½ MIC of PVP-I significantly reduced the expression of hla, ebps, eno, fib, icaA, and icaD genes. The virulence of the biocide-resistant mutant was similar to that of parent strain. Conclusion PVP-I is a highly recommended antiseptic for use in healthcare settings to control the evolution of high-risk clones. Exposure to PVP-I causes no resistance-development risk in S. aureus, with virulence inhibition by subinhibitory concentrations. Also, special protocols need to be followed during PBM use in hospitals to avoid the selection of resistant strains. Supplementary Information The online version contains supplementary material available at 10.1186/s13756-022-01178-9.
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Silva V, Monteiro A, Pereira JE, Maltez L, Igrejas G, Poeta P. MRSA in Humans, Pets and Livestock in Portugal: Where We Came from and Where We Are Going. Pathogens 2022; 11:1110. [PMID: 36297167 PMCID: PMC9608539 DOI: 10.3390/pathogens11101110] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 09/10/2023] Open
Abstract
Over the years, molecular typing of methicillin-resistant S. aureus (MRSA) has allowed for the identification of endemic MRSA strains and pathogenic strains. After reaching a peak of predominance in a given geographic region, MRSA strains are usually replaced by a new strain. This process is called clonal replacement and is observed worldwide. The worldwide spread of hospital-associated MRSA (HA-MRSA), community-associated MRSA (CA-MRSA) and livestock-associated MRSA (LA-MRSA) clones over the last few decades has allowed this microorganism to be currently considered a pandemic. In Portugal, most HA-MRSA infections are associated with EMRSA-15 (S22-IV), New York/Japan (ST5-II) and Iberian (ST247-I) clones. Regarding the strains found in the community, many of them are frequently associated with the hospital environment, namely the Pediatric, Brazilian and Iberian clones. On the other hand, a strain that is typically found in animals, MRSA clonal complex (CC) 398, has been described in humans as colonizing and causing infections. The ST398 clone is found across all animal species, particularly in farm animals where the economic impact of LA-MRSA infections can have disastrous consequences for industries. In contrast, the EMRSA-15 clone seems to be more related to companion animals. The objective of this review is to better understand the MRSA epidemiology because it is, undoubtedly, an important public health concern that requires more attention, in order to achieve an effective response in all sectors.
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Affiliation(s)
- Vanessa Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 2829-516 Caparica, Portugal
| | - Andreia Monteiro
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - José Eduardo Pereira
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Luís Maltez
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 2829-516 Caparica, Portugal
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
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20
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Li X, Wang Y, Jiang X, Zeng Y, Zhao X, Washio J, Takahashi N, Zhang L. Investigation of drug resistance of caries-related streptococci to antimicrobial peptide GH12. Front Cell Infect Microbiol 2022; 12:991938. [PMID: 36159653 PMCID: PMC9492880 DOI: 10.3389/fcimb.2022.991938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Dental caries is associated with caries-related streptococci and antimicrobial agents have been widely used for caries control, but troubled by antibiotic resistance. This study aimed to investigate the intrinsic and acquired resistance of caries-related streptococci to antimicrobial peptide GH12, which was proven promising for caries control, and preliminarily explore the phenotypic changes and whole genome of stable acquired resistant strains. In this study, susceptibility assays and resistance assays were performed, followed by stability assays of resistance, to evaluate the intrinsic resistance and the potential resistance of caries-related streptococci. Then, the phenotypic changes of the stable acquired resistant strain were explored. The whole genome of the resistant strain was sequenced and analyzed by second-generation and third-generation high-throughput sequencing technologies. Streptococcus gordonii and Streptococcus sanguinis were intrinsically resistant to GH12 compared to cariogenic Streptococcus mutans. Acquired GH12 resistance in one S. sanguinis and four S. mutans clinical strains was transient but stable in one S. mutans strain (COCC33-14). However, acquired resistance to daptomycin (DAP) and chlorhexidine in all strains was stable. Furthermore, the COCC33-14 showed cross-resistance to DAP and delayed growth rates and a lower population. However, no drug-resistant gene mutation was detected in this strain, but 6 new and 5 missing genes were found. Among them, annotation of one new gene (gene 1782|COCC33-14R) is related to the integral component of the membrane, and one missing gene rpsN is associated with the metabolism and growth of bacteria. The results indicate that stable resistant mutants of caries-related streptococci could hardly be selected by exposure to consecutive sublethal GH12, but the risk still existed. Resistance in COCC33-14R is mainly related to changes in the cell envelope.
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Affiliation(s)
- Xinwei Li
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Stomatology, Chengdu Second People’s Hospital, Chengdu, China
| | - Yufei Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xuelian Jiang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuhao Zeng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xinran Zhao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jumpei Washio
- Division of Oral Ecology and Biochemistry, Graduate School of Dentistry, Tohoku University, Sendai, Japan
| | - Nobuhiro Takahashi
- Division of Oral Ecology and Biochemistry, Graduate School of Dentistry, Tohoku University, Sendai, Japan
| | - Linglin Zhang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- *Correspondence: Linglin Zhang,
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21
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Garrett SR, Mariano G, Dicks J, Palmer T. Homologous recombination between tandem paralogues drives evolution of a subset of type VII secretion system immunity genes in firmicute bacteria. Microb Genom 2022; 8. [PMID: 35960642 PMCID: PMC9484751 DOI: 10.1099/mgen.0.000868] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The type VII secretion system (T7SS) is found in many Gram-positive firmicutes and secretes protein toxins that mediate bacterial antagonism. Two T7SS toxins have been identified in Staphylococcus aureus, EsaD a nuclease toxin that is counteracted by the EsaG immunity protein, and TspA, which has membrane depolarising activity and is neutralised by TsaI. Both toxins are polymorphic, and strings of non-identical esaG and tsaI immunity genes are encoded in all S. aureus strains. To investigate the evolution of esaG repertoires, we analysed the sequences of the tandem esaG genes and their encoded proteins. We identified three blocks of high sequence similarity shared by all esaG genes and identified evidence of extensive recombination events between esaG paralogues facilitated through these conserved sequence blocks. Recombination between these blocks accounts for loss and expansion of esaG genes in S. aureus genomes and we identified evidence of such events during evolution of strains in clonal complex 8. TipC, an immunity protein for the TelC lipid II phosphatase toxin secreted by the streptococcal T7SS, is also encoded by multiple gene paralogues. Two blocks of high sequence similarity locate to the 5′ and 3′ end of tipC genes, and we found strong evidence for recombination between tipC paralogues encoded by Streptococcus mitis BCC08. By contrast, we found only a single homology block across tsaI genes, and little evidence for intergenic recombination within this gene family. We conclude that homologous recombination is one of the drivers for the evolution of T7SS immunity gene clusters.
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Affiliation(s)
- Stephen R Garrett
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Giuseppina Mariano
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Jo Dicks
- Culture Collections, UK Health Security Agency, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Tracy Palmer
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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22
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Convergence of virulence and antimicrobial resistance in increasingly prevalent Escherichia coli ST131 papGII+ sublineages. Commun Biol 2022; 5:752. [PMID: 35902767 PMCID: PMC9334617 DOI: 10.1038/s42003-022-03660-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 06/29/2022] [Indexed: 12/26/2022] Open
Abstract
Escherichia coli lineage ST131 is an important cause of urinary tract and bloodstream infections worldwide and is highly resistant to antimicrobials. Specific ST131 lineages carrying invasiveness-associated papGII pathogenicity islands (PAIs) were previously described, but it is unknown how invasiveness relates to the acquisition of antimicrobial resistance (AMR). In this study, we analysed 1638 ST131 genomes and found that papGII+ isolates carry significantly more AMR genes than papGII-negative isolates, suggesting a convergence of virulence and AMR. The prevalence of papGII+ isolates among human clinical ST131 isolates increased dramatically since 2005, accounting for half of the recent E. coli bloodstream isolates. Emerging papGII+ lineages within clade C2 were characterized by a chromosomally integrated blaCTX-M-15 and the loss and replacement of F2:A1:B- plasmids. Convergence of virulence and AMR is worrying, and further dissemination of papGII+ ST131 lineages may lead to a rise in severe and difficult-to-treat extraintestinal infections. Genomic analyses indicate that the ST131 lineage of E. coli, responsible for urinary and bloodstream infections globally, is evolving towards both increased virulence and increased resistance to antimicrobials.
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Huang S, He J, Zhang Y, Su L, Tong L, Sun Y, Zhou M, Chen Z. The Correlation Between Biofilm-Forming Ability of Community-Acquired Methicillin-Resistant Staphylococcus aureus Isolated from the Respiratory Tract and Clinical Characteristics in Children. Infect Drug Resist 2022; 15:3657-3668. [PMID: 35855760 PMCID: PMC9288189 DOI: 10.2147/idr.s370755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/17/2022] [Indexed: 01/09/2023] Open
Abstract
Objective This study aimed to investigate the biofilm-forming ability, molecular typing, and antimicrobial resistance of community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) strains isolated from the respiratory tract of children and their correlation with clinical characteristics. Methods All CA-MRSA strains were isolated from hospitalized children, and their presentation, molecular typing, antimicrobial susceptibility, and biofilm formation were investigated. The clinical characteristics were compared between the strong and weak biofilm producer groups. Results Fifty-three CA-MRSA strains were isolated from the respiratory samples of 53 children, with nearly half of them being young infants (0-12 months). Approximately, 88.7% (47/53) of the isolates were resistant to four or more antibiotics, mainly β-lactam antibiotics, lincosamides, and macrolides. Twelve sequence types (STs) and 20 subtypes of staphylococcal protein A (spa) typing were identified, with ST59-t437 (39.6%, 21/53) as the predominant subtype. All strains showed the ability to form biofilms. When compared to children with weak biofilm-forming CA-MRSA strains, those with strong biofilm-forming strains had higher proportions of lower respiratory tract infections (LRTI) (88.5% vs 59.3%), obvious cough symptoms (84.6% vs 51.9%), and severe chest imaging manifestations (76.9% vs 37.0%). Furthermore, a strong biofilm-forming ability significantly increased the risk of prolonged cough in children with LRTI (44.4% vs 14.3%), and a positive correlation between the duration of cough and the extent of biofilm formation was observed. Medical history investigation revealed that the strong biofilm-forming group had a much higher percentage of macrolides intake than the weak biofilm-forming group in the last month before admission (61.5% vs 14.8%). Conclusion ST59-t437 was the most prevalent clone in CA-MRSA respiratory isolates among the hospitalized children. All CA-MRSA strains formed biofilms. The stronger the biofilm-forming ability, the more serious and prolonged were the respiratory symptoms.
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Affiliation(s)
- Shumin Huang
- Department of Pulmonology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, People’s Republic of China,National Clinical Research Center for Child Health, National Children’s Regional Medical Center, Hangzhou, 310052, People’s Republic of China
| | - Jing He
- Department of Pulmonology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, People’s Republic of China,National Clinical Research Center for Child Health, National Children’s Regional Medical Center, Hangzhou, 310052, People’s Republic of China
| | - Yiting Zhang
- Department of Pulmonology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, People’s Republic of China,National Clinical Research Center for Child Health, National Children’s Regional Medical Center, Hangzhou, 310052, People’s Republic of China
| | - Lin Su
- Department of Pulmonology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, People’s Republic of China,National Clinical Research Center for Child Health, National Children’s Regional Medical Center, Hangzhou, 310052, People’s Republic of China
| | - Lin Tong
- Department of Pulmonology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, People’s Republic of China,National Clinical Research Center for Child Health, National Children’s Regional Medical Center, Hangzhou, 310052, People’s Republic of China
| | - Ying Sun
- Department of Pulmonology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, People’s Republic of China,National Clinical Research Center for Child Health, National Children’s Regional Medical Center, Hangzhou, 310052, People’s Republic of China
| | - Mingming Zhou
- National Clinical Research Center for Child Health, National Children’s Regional Medical Center, Hangzhou, 310052, People’s Republic of China,Department of Clinical Laboratory, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, People’s Republic of China
| | - Zhimin Chen
- Department of Pulmonology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, 310052, People’s Republic of China,National Clinical Research Center for Child Health, National Children’s Regional Medical Center, Hangzhou, 310052, People’s Republic of China,Correspondence: Zhimin Chen, Email
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Goncheva MI, Chin D, Heinrichs DE. Nucleotide biosynthesis: the base of bacterial pathogenesis. Trends Microbiol 2022; 30:793-804. [PMID: 35074276 DOI: 10.1016/j.tim.2021.12.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 01/08/2023]
Abstract
Most free-living organisms require the synthesis and/or acquisition of purines and pyrimidines, which form the basis of nucleotides, to survive. In most bacteria, the nucleotides are synthesized de novo and the products are used in many cell functions, including DNA replication, energy storage, and as signaling molecules. Due to their central role in the metabolism of bacteria, both nucleotide biosynthesis pathways have strong links with the virulence of opportunistic and bona fide bacterial pathogens. Recent findings have established a new, shared link in the control of nucleotide biosynthesis and the production of virulence factors. Furthermore, targeting of these pathways forms the basis of interspecies competition and can provide an open source for new antimicrobial compounds. Here, we highlight the contribution of nucleotide biosynthesis to bacterial pathogenesis in a plethora of different diseases and speculate on how they can be targeted by intervention strategies.
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Affiliation(s)
- Mariya I Goncheva
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada N6A 5C1
| | - Denny Chin
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada N6A 5C1
| | - David E Heinrichs
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada N6A 5C1.
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Lokken-Toyli KL, de Steenhuijsen Piters WAA, Zangari T, Martel R, Kuipers K, Shopsin B, Loomis C, Bogaert D, Weiser JN. Decreased production of epithelial-derived antimicrobial molecules at mucosal barriers during early life. Mucosal Immunol 2021; 14:1358-1368. [PMID: 34465896 PMCID: PMC8542637 DOI: 10.1038/s41385-021-00438-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/12/2021] [Accepted: 08/01/2021] [Indexed: 02/04/2023]
Abstract
Young age is a risk factor for respiratory and gastrointestinal infections. Here, we compared infant and adult mice to identify age-dependent mechanisms that drive susceptibility to mucosal infections during early life. Transcriptional profiling of the upper respiratory tract (URT) epithelium revealed significant dampening of early life innate mucosal defenses. Epithelial-mediated production of the most abundant antimicrobial molecules, lysozyme, and lactoferrin, and the polymeric immunoglobulin receptor (pIgR), responsible for IgA transcytosis, was expressed in an age-dependent manner. This was attributed to delayed functional development of serous cells. Absence of epithelial-derived lysozyme and the pIgR was also observed in the small intestine during early life. Infection of infant mice with lysozyme-susceptible strains of Streptococcus pneumoniae or Staphylococcus aureus in the URT or gastrointestinal tract, respectively, demonstrated an age-dependent regulation of lysozyme enzymatic activity. Lysozyme derived from maternal milk partially compensated for the reduction in URT lysozyme activity of infant mice. Similar to our observations in mice, expression of lysozyme and the pIgR in nasopharyngeal samples collected from healthy human infants during the first year of life followed an age-dependent regulation. Thus, a global pattern of reduced antimicrobial and IgA-mediated defenses may contribute to increased susceptibility of young children to mucosal infections.
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Affiliation(s)
- Kristen L. Lokken-Toyli
- Department of Microbiology, New York University School of Medicine, New York, New York USA.,for correspondence: Kristen L. Lokken-Toyli, PhD, New York University School of Medicine, Alexandria Center for Life Sciences - West Tower, 430 East 29th Street, Room 560, New York, NY 10016, Tel: (212) 263-1080, Fax: (646) 501-4645,
| | - Wouter A. A. de Steenhuijsen Piters
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital/University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands; National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands
| | - Tonia Zangari
- Department of Microbiology, New York University School of Medicine, New York, New York USA
| | - Rachel Martel
- Department of Microbiology, New York University School of Medicine, New York, New York USA
| | - Kirsten Kuipers
- Department of Microbiology, New York University School of Medicine, New York, New York USA
| | - Bo Shopsin
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA; Division of Infectious Diseases, Department of Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Cynthia Loomis
- Department of Pathology, New York University School of Medicine, New York, New York USA
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital/University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands; National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands; University of Edinburgh Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK.
| | - Jeffrey N. Weiser
- Department of Microbiology, New York University School of Medicine, New York, New York USA
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An Enzybiotic Regimen for the Treatment of Methicillin-Resistant Staphylococcus aureus Orthopaedic Device-Related Infection. Antibiotics (Basel) 2021; 10:antibiotics10101186. [PMID: 34680767 PMCID: PMC8533017 DOI: 10.3390/antibiotics10101186] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/21/2021] [Accepted: 09/24/2021] [Indexed: 12/31/2022] Open
Abstract
Orthopaedic device-related infection (ODRI) presents a significant challenge to the field of orthopaedic and trauma surgery. Despite extensive treatment involving surgical debridement and prolonged antibiotic therapy, outcomes remain poor. This is largely due to the unique abilities of Staphylococcus aureus, the most common causative agent of ODRI, to establish and protect itself within the host by forming biofilms on implanted devices and staphylococcal abscess communities (SACs). There is a need for novel antimicrobials that can readily target such features. Enzybiotics are a class of antimicrobial enzymes derived from bacteria and bacteriophages, which function by enzymatically degrading bacterial polymers essential to bacterial survival or biofilm formation. Here, we apply an enzybiotic-based combination regimen to a set of in vitro models as well as in a murine ODRI model to evaluate their usefulness in eradicating established S. aureus infection, compared to classical antibiotics. We show that two chimeric endolysins previously selected for their functional efficacy in human serum in combination with a polysaccharide depolymerase reduce bacterial CFU numbers 10,000-fold in a peg model and in an implant model of biofilm. The enzyme combination also completely eradicates S. aureus in a SAC in vitro model where classical antibiotics are ineffective. In an in vivo ODRI model in mice, the antibiofilm effects of this enzyme regimen are further enhanced when combined with a classical gentamicin/vancomycin treatment. In a mouse model of methicillin-resistant S. aureus (MRSA) ODRI following a fracture repair, a combined local enzybiotic/antibiotic treatment regimen showed a significant CFU reduction in the device and the surrounding soft tissue, as well as significant prevention of weight loss. These outcomes were superior to treatment with antibiotics alone. Overall, this study demonstrates that the addition of enzybiotics, which are distinguished by their extremely rapid killing efficacy and antibiofilm activities, can enhance the treatment of severe MRSA ODRI.
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Abstract
Microbes are constantly evolving. Laboratory studies of bacterial evolution increase our understanding of evolutionary dynamics, identify adaptive changes, and answer important questions that impact human health. During bacterial infections in humans, however, the evolutionary parameters acting on infecting populations are likely to be much more complex than those that can be tested in the laboratory. Nonetheless, human infections can be thought of as naturally occurring in vivo bacterial evolution experiments, which can teach us about antibiotic resistance, pathogenesis, and transmission. Here, we review recent advances in the study of within-host bacterial evolution during human infection and discuss practical considerations for conducting such studies. We focus on 2 possible outcomes for de novo adaptive mutations, which we have termed "adapt-and-live" and "adapt-and-die." In the adapt-and-live scenario, a mutation is long lived, enabling its transmission on to other individuals, or the establishment of chronic infection. In the adapt-and-die scenario, a mutation is rapidly extinguished, either because it carries a substantial fitness cost, it arises within tissues that block transmission to new hosts, it is outcompeted by more fit clones, or the infection resolves. Adapt-and-die mutations can provide rich information about selection pressures in vivo, yet they can easily elude detection because they are short lived, may be more difficult to sample, or could be maladaptive in the long term. Understanding how bacteria adapt under each of these scenarios can reveal new insights about the basic biology of pathogenic microbes and could aid in the design of new translational approaches to combat bacterial infections.
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Affiliation(s)
- Matthew J. Culyba
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Daria Van Tyne
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
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Patel A, Lighter J, Fulmer Y, Copin R, Ratner AJ, Shopsin B. Retapamulin Activity Against Pediatric Strains of Mupirocin-resistant Methicillin-resistant Staphylococcus aureus. Pediatr Infect Dis J 2021; 40:637-638. [PMID: 33657598 PMCID: PMC8713557 DOI: 10.1097/inf.0000000000003123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Retapamulin activity against 53 isolates obtained from a mupirocin-resistant community-acquired methicillin-resistant Staphylococcus aureus pediatric disease cluster was evaluated using broth microdilution. All strains were susceptible to retapamulin with minimum inhibitory concentrations ≤ 0.5 μg/mL. DNA sequence analysis of rplC and cfr identified one rplC strain variant that did not demonstrate reduced phenotypic susceptibility to retapamulin. These results demonstrate that retapamulin may be a useful alternative therapy for mupirocin-resistant community-acquired methicillin-resistant S. aureus, especially in disease clusters.
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Affiliation(s)
- Ami Patel
- Department of Pediatrics, Division of Pediatric Infectious Diseases, New York University (NYU) School of Medicine/NYU Langone Health, New York, NY
| | - Jennifer Lighter
- Department of Pediatrics, Division of Pediatric Infectious Diseases, New York University (NYU) School of Medicine/NYU Langone Health, New York, NY
- Department of Infection Prevention and Control, New York University (NYU) School of Medicine/NYU Langone Health, New York, NY
| | - Yi Fulmer
- Department of Microbiology, New York University (NYU) School of Medicine/NYU Langone Health, New York, NY
| | - Richard Copin
- Department of Microbiology, New York University (NYU) School of Medicine/NYU Langone Health, New York, NY
| | - Adam J. Ratner
- Department of Pediatrics, Division of Pediatric Infectious Diseases, New York University (NYU) School of Medicine/NYU Langone Health, New York, NY
- Department of Microbiology, New York University (NYU) School of Medicine/NYU Langone Health, New York, NY
| | - Bo Shopsin
- Department of Microbiology, New York University (NYU) School of Medicine/NYU Langone Health, New York, NY
- Department of Medicine, Division of Infectious Diseases, New York University (NYU) School of Medicine/NYU Langone Health, New York, NY
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Rzycki M, Drabik D, Szostak-Paluch K, Hanus-Lorenz B, Kraszewski S. Unraveling the mechanism of octenidine and chlorhexidine on membranes: Does electrostatics matter? Biophys J 2021; 120:3392-3408. [PMID: 34214528 PMCID: PMC8391085 DOI: 10.1016/j.bpj.2021.06.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/26/2021] [Accepted: 06/22/2021] [Indexed: 11/20/2022] Open
Abstract
The increasing problem of antibiotic resistance in bacteria requires the development of new antimicrobial candidates. There are several well-known substances with commercial use, but their molecular mode of action is not fully understood. In this work, we focus on two commonly used antimicrobial agents from the detergent family—octenidine dichloride (OCT) and chlorhexidine digluconate (CHX). Both of them are reported to be agents selectively attacking the cell membrane through interaction inducing membrane disruption by emulsification. They are believed to present electrostatic selectivity toward charged lipids. In this study, we tested this hypothesis and revised previously proposed molecular mechanisms of action. Employing a variety of techniques such as molecular dynamics, ζ potential with dynamic light scattering, vesicle fluctuation spectroscopy, carboxyfluorescein leakage measurement, and fluorescence trimethylammonium-diphenylhexatriene- and diphenylhexatriene-based studies for determination of OCT and CHX membrane location, we performed experimental studies using two model membrane systems—zwitterionic PC and negatively charged PG (18:1/18:1):PC (16:0/18:1) 3:7, respectively. These studies were extended by molecular dynamics simulations performed on a three-component bacterial membrane model system to further test interactions with another negatively charged lipid, cardiolipin. In summary, our study demonstrated that detergent selectivity is far more complicated than supposed simple electrostatic interactions. Although OCT does disrupt the membrane, our results suggest that its primary selectivity was more linked to mechanical properties of the membrane. On the other hand, CHX did not disrupt membranes as a primary activity, nor did it show any sign of electrostatic selectivity toward negatively charged membranes at any stage of interactions, which suggests membrane disruption by influencing more discrete membrane properties.
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Affiliation(s)
- Mateusz Rzycki
- Department of Experimental Physics, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wroclaw, Poland; Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wroclaw, Poland.
| | - Dominik Drabik
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wroclaw, Poland; Laboratory of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Kamila Szostak-Paluch
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wroclaw, Poland; Research and Development Center, Regional Specialized Hospital, Wroclaw, Poland
| | - Beata Hanus-Lorenz
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Sebastian Kraszewski
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wroclaw, Poland
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Smith JT, Eckhardt EM, Hansel NB, Eliato TR, Martin IW, Andam CP. Genomic epidemiology of methicillin-resistant and -susceptible Staphylococcus aureus from bloodstream infections. BMC Infect Dis 2021; 21:589. [PMID: 34154550 PMCID: PMC8215799 DOI: 10.1186/s12879-021-06293-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/01/2021] [Indexed: 01/13/2023] Open
Abstract
Background Bloodstream infections due to Staphylococcus aureus cause significant patient morbidity and mortality worldwide. Of major concern is the emergence and spread of methicillin-resistant S. aureus (MRSA) in bloodstream infections, which are associated with therapeutic failure and increased mortality. Methods We generated high quality draft genomes from 323 S. aureus blood culture isolates from patients diagnosed with bloodstream infection at the Dartmouth-Hitchcock Medical Center, New Hampshire, USA in 2010–2018. Results In silico detection of antimicrobial resistance genes revealed that 133/323 isolates (41.18%) carry horizontally acquired genes conferring resistance to at least three antimicrobial classes, with resistance determinants for aminoglycosides, beta-lactams and macrolides being the most prevalent. The most common resistance genes were blaZ and mecA, which were found in 262/323 (81.11%) and 104/323 (32.20%) isolates, respectively. Majority of the MRSA (102/105 isolates or 97.14%) identified using in vitro screening were related to two clonal complexes (CC) 5 and 8. The two CCs emerged in the New Hampshire population at separate times. We estimated that the time to the most recent common ancestor of CC5 was 1973 (95% highest posterior density (HPD) intervals: 1966–1979) and 1946 for CC8 (95% HPD intervals: 1924–1959). The effective population size of CC8 increased until the late 1960s when it started to level off until late 2000s. The levelling off of CC8 in 1968 coincided with the acquisition of SCCmec Type IV in majority of the strains. The plateau in CC8 also coincided with the acceleration in the population growth of CC5 carrying SCCmec Type II in the early 1970s, which eventually leveled off in the early 1990s. Lastly, we found evidence for frequent recombination in the two clones during their recent clonal expansion, which has likely contributed to their success in the population. Conclusions We conclude that the S. aureus population was shaped mainly by the clonal expansion, recombination and co-dominance of two major MRSA clones in the last five decades in New Hampshire, USA. These results have important implications on the development of effective and robust strategies for intervention, control and treatment of life-threatening bloodstream infections. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06293-3.
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Affiliation(s)
- Joshua T Smith
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA
| | - Elissa M Eckhardt
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH, 03756, USA
| | - Nicole B Hansel
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH, 03756, USA
| | | | - Isabella W Martin
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH, 03756, USA.
| | - Cheryl P Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, 12222, USA.
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Choi SH, Lee J, Jung J, Kim ES, Kim MJ, Chong YP, Kim SH, Lee SO, Choi SH, Woo JH, Kim YS. A Longitudinal Study of Adult Patients with Staphylococcus aureus Bacteremia over 11 Years in Korea. J Korean Med Sci 2021; 36:e104. [PMID: 33904260 PMCID: PMC8076844 DOI: 10.3346/jkms.2021.36.e104] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 02/04/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The temporal changes in the Staphylococcus aureus genotypes causing S. aureus bacteremia (SAB) and the corresponding clinical changes over the last decade in South Korea are rarely investigated. METHODS A longitudinal study of adult SAB patients was conducted in a large referral hospital in Seoul, South Korea. Adult monomicrobial SAB patients were enrolled between August 2008 and December 2018. Genotyping was performed by multilocus sequence typing (MLST) and staphylococcal protein A (spa) typing. Trends in changes were identified by linear regression analysis. RESULTS Of 1782 adult SAB patients, the blood isolates of 1,778 (99.8%) and 1,634 (91.7%) were determined to be MLST and spa type, respectively. ST5 (-2.626%/year) and ST239 (-0.354%/year) decreased during the study period (P < 0.001 for both), but ST72 (2.009%/yr)-and ST8 (0.567%/yr) increased (P < 0.001 for both). The most common genotype was changed from ST5 in 2008 (44.9%) to ST72 in 2018 (36.3%). Panton-Valentine leukocidin-positive spa-t008-MRSA (USA300) was found in 28.6%. Central venous catheter (CVC)-related SAB (-2.440%/yr) and persistent SAB (-1.016%/yr) decreased, but mortality and recurrence rates were unchanged. CONCLUSION Over the last decade, the hospital clones ST5 and ST239 have been replaced by community genotype ST72. This was associated with decreased CVC-related and persistent SAB. Increased USA300 was observed in community and hospital settings. Further research is required to identify the reasons for the ST72 epidemic and predict the impending epidemic of ST8 strains, including USA300.
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Affiliation(s)
- Seong Ho Choi
- Division of Infectious Diseases, Department of Internal Medicine, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, Korea
| | - Jeongsoo Lee
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jiwon Jung
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Eun Sil Kim
- Asan Institute of Life Sciences, Asan Medical Center, Seoul, Korea
- Center for Antimicrobial Resistance and Microbial Genetics, University of Ulsan, Seoul, Korea
| | - Min Jae Kim
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Yong Pil Chong
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sung Han Kim
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sang Oh Lee
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sang Ho Choi
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jun Hee Woo
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Yang Soo Kim
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Asan Institute of Life Sciences, Asan Medical Center, Seoul, Korea
- Center for Antimicrobial Resistance and Microbial Genetics, University of Ulsan, Seoul, Korea.
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Clinical relevance of topical antibiotic use in co-selecting for multidrug-resistant Staphylococcus aureus: Insights from in vitro and ex vivo models. Antimicrob Agents Chemother 2021; 95:AAC.02048-20. [PMID: 33593834 PMCID: PMC8092865 DOI: 10.1128/aac.02048-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Topical antibiotic preparations, such as fusidic acid (FA) or mupirocin, are used in the prevention and treatment of superficial skin infections caused by staphylococci. Previous genomic epidemiology work has suggested an association between the widespread use of topical antibiotics and the emergence of methicillin resistant Staphylococcus aureus in some settings. In this study, we provide experimental proof of co-selection for multidrug resistance in S. aureus following exposure to FA or mupirocin. Through targeted mutagenesis and phenotypic analyses, we confirmed that fusC carriage confers resistance to FA, and mupA carriage confers high-level resistance to mupirocin in multiple S. aureus genetic backgrounds. In vitro experiments demonstrated that carriage of fusC and mupA confer a competitive advantage in the presence of sub-inhibitory concentrations of FA and mupirocin, respectively. Further, we used a porcine skin colonisation model to show that clinically relevant concentrations of topical antibiotics can co-select for presence of unrelated antimicrobial resistance determinants, such as mecA, blaZ, and qacA, in fusC or mupA harbouring S. aureus These findings provide valuable insights on the role of acquired FA or mupirocin resistance in co-selecting for broader antibiotic resistance in S. aureus, prompting greater need for judicious use of topical antibiotics.
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Alizon S. Treating symptomatic infections and the co-evolution of virulence and drug resistance. PEER COMMUNITY JOURNAL 2021; 1:e47. [PMID: 38707518 PMCID: PMC7615929 DOI: 10.24072/pcjournal.38] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Antimicrobial therapeutic treatments are by definition applied after the onset of symptoms, which tend to correlate with infection severity. Using mathematical epidemiology models, I explore how this link affects the coevolutionary dynamics between the virulence of an infection, measured via host mortality rate, and its susceptibility to chemotherapy. I show that unless resistance pre-exists in the population, drug-resistant infections are initially more virulent than drug-sensitive ones. As the epidemic unfolds, virulence is more counter-selected in drug-sensitive than in drug-resistant infections. This difference decreases over time and, eventually, the exact shape of genetic trade-offs govern long-term evolutionary dynamics. Using adaptive dynamics, I show that two types of evolutionary stable strategies (ESS) may be reached in the context of this simple model and that, depending on the parameter values, an ESS may only be locally stable. In general, the more the treatment rate increases with virulence, the lower the ESS value. Overall, both on the short-term and long-term, having treatment rate depend on infection virulence tend to favour less virulent strains in drug-sensitive infections. These results highlight the importance of the feedbacks between epidemiology, public health policies and parasite evolution, and have implications for the monitoring of virulence evolution.
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Affiliation(s)
- Samuel Alizon
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, Paris, France
- MIVEGEC, CNRS, IRD, Université de Montpellier, France
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Cieśluk M, Deptuła P, Piktel E, Fiedoruk K, Suprewicz Ł, Paprocka P, Kot P, Pogoda K, Bucki R. Physics Comes to the Aid of Medicine-Clinically-Relevant Microorganisms through the Eyes of Atomic Force Microscope. Pathogens 2020; 9:pathogens9110969. [PMID: 33233696 PMCID: PMC7699805 DOI: 10.3390/pathogens9110969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 12/01/2022] Open
Abstract
Despite the hope that was raised with the implementation of antibiotics to the treatment of infections in medical practice, the initial enthusiasm has substantially faded due to increasing drug resistance in pathogenic microorganisms. Therefore, there is a need for novel analytical and diagnostic methods in order to extend our knowledge regarding the mode of action of the conventional and novel antimicrobial agents from a perspective of single microbial cells as well as their communities growing in infected sites, i.e., biofilms. In recent years, atomic force microscopy (AFM) has been mostly used to study different aspects of the pathophysiology of noninfectious conditions with attempts to characterize morphological and rheological properties of tissues, individual mammalian cells as well as their organelles and extracellular matrix, and cells’ mechanical changes upon exposure to different stimuli. At the same time, an ever-growing number of studies have demonstrated AFM as a valuable approach in studying microorganisms in regard to changes in their morphology and nanomechanical properties, e.g., stiffness in response to antimicrobial treatment or interaction with a substrate as well as the mechanisms behind their virulence. This review summarizes recent developments and the authors’ point of view on AFM-based evaluation of microorganisms’ response to applied antimicrobial treatment within a group of selected bacteria, fungi, and viruses. The AFM potential in development of modern diagnostic and therapeutic methods for combating of infections caused by drug-resistant bacterial strains is also discussed.
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Affiliation(s)
- Mateusz Cieśluk
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Bialystok, Poland; (M.C.); (P.D.); (E.P.); (K.F.); (Ł.S.)
| | - Piotr Deptuła
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Bialystok, Poland; (M.C.); (P.D.); (E.P.); (K.F.); (Ł.S.)
| | - Ewelina Piktel
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Bialystok, Poland; (M.C.); (P.D.); (E.P.); (K.F.); (Ł.S.)
| | - Krzysztof Fiedoruk
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Bialystok, Poland; (M.C.); (P.D.); (E.P.); (K.F.); (Ł.S.)
| | - Łukasz Suprewicz
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Bialystok, Poland; (M.C.); (P.D.); (E.P.); (K.F.); (Ł.S.)
| | - Paulina Paprocka
- Department of Microbiology and Immunology, Institute of Medical Science, Collegium Medicum, Jan Kochanowski University in Kielce, PL-25317 Kielce, Poland; (P.P.); (P.K.)
| | - Patrycja Kot
- Department of Microbiology and Immunology, Institute of Medical Science, Collegium Medicum, Jan Kochanowski University in Kielce, PL-25317 Kielce, Poland; (P.P.); (P.K.)
| | - Katarzyna Pogoda
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31342 Krakow, Poland;
| | - Robert Bucki
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Bialystok, Poland; (M.C.); (P.D.); (E.P.); (K.F.); (Ł.S.)
- Correspondence:
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Peng M, Biswas D. Environmental Influences of High-Density Agricultural Animal Operation on Human Forearm Skin Microflora. Microorganisms 2020; 8:microorganisms8101481. [PMID: 32993188 PMCID: PMC7650789 DOI: 10.3390/microorganisms8101481] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/17/2020] [Accepted: 09/23/2020] [Indexed: 12/18/2022] Open
Abstract
The human forearm skin microbiome ecosystem contains rich and diverse microbes, which are influenced by environmental exposures. The microbial representatives can be exchanged between human and environment, specifically animals, by which they share certain or similar epidermal microbes. Livestock and poultry are the microbial sources that are associated with the transmission of community-based pathogenic infections. Here, in this study, we proposed investigating the environmental influences introduced by livestock/poultry operations on forearm skin microflora of on-site farm workers. A total of 30 human skin swab samples were collected from 20 animal workers in dairy or integrated farms and 10 healthy volunteer controls. The skin microbiome was 16S metagenomics that were sequenced with Illumina MiSeq system. For skin microbial community analysis, the abundance of major phyla and genera as well as alpha and beta diversities were compared across groups. We identified distinctive microbial compositional patterns on skin of workers in farm with different animal commodities. Workers in integrated farms containing various animals were associated with higher abundances of epidermal Proteobacteria, especially Pseudomonas and Acinetobacter, but lower Actinobacteria, especially Corynebacterium and Propionibacterium. For those workers with frequent dairy cattle operations, their Firmicutes in the forearm skin microbiota were enriched. Furthermore, farm animal operations also reduced Staphylococcus and Streptococcus, as well as modulated the microbial biodiversity in farm workers' skin microbiome. The alterations of forearm skin microflora in farm workers, influenced by their frequent farm animal operations, may increase their risk in skin infections with unusual pathogens and epidermal diseases.
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Affiliation(s)
- Mengfei Peng
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA;
| | - Debabrata Biswas
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA;
- Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA
- Correspondence: ; Tel.: +1-301-405-3791
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Song J, Niu W, Wu R, Wang J, Lei L, Han W, Gu J. The Phage Holin HolGH15 Exhibits Potential As an Antibacterial Agent to Control Listeria monocytogenes. Foodborne Pathog Dis 2020; 18:574-581. [PMID: 32955931 DOI: 10.1089/fpd.2020.2833] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Listeria monocytogenes is an important foodborne pathogen that is a serious threat to public health security, and new strategies to control this bacterium in food are needed. HolGH15, derived from Staphylococcus aureus phage GH15, has shown antibacterial activity against several bacterial species. In this work, the antilisterial behavior and effectiveness of HolGH15 are further studied. To elucidate its antimicrobial modes against L. monocytogenes, cell integrity and membrane permeabilization assays were performed. When treated with HolGH15, the release of 260-nm-absorbing materials of L. monocytogenes was rapidly increased. HolGH15 triggered a significant increase in fluorescence intensity by flow cytometry. In membrane permeabilization assays, the cytoplasmic β-galactosidase of L. monocytogenes treated with HolGH15 was released via an increase in the permeability of the membrane. HolGH15 caused changes in the structural properties of L. monocytogenes cells resulting in shrinkage, which evoked the release and removal of cellular contents and finally lead to cell death. Electron microscopy observations indicated that HolGH15 exhibited excellent bactericidal potency by permeabilizing the cell membrane, damaging membrane integrity, and inducing cellular content shrinkage or loss. Moreover, HolGH15 (at the final concentration of 240 μg/mL) reduced L. monocytogenes (at the initial concentration of 106 colony-forming unit/mL) to an undetectable level at 4°C. Collectively, HolGH15 has potential as a novel antimicrobial agent against L. monocytogenes in the manufacture and store of food by spraying or soaking, especially at refrigerated temperature.
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Affiliation(s)
- Jun Song
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China.,Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Wenchao Niu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Rui Wu
- Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jianfa Wang
- Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Liancheng Lei
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Wenyu Han
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
| | - Jingmin Gu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
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37
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Cetylpyridinium Chloride: Mechanism of Action, Antimicrobial Efficacy in Biofilms, and Potential Risks of Resistance. Antimicrob Agents Chemother 2020; 64:AAC.00576-20. [PMID: 32513792 DOI: 10.1128/aac.00576-20] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial resistance is a serious issue for public health care all over the world. While resistance toward antibiotics has attracted strong interest among researchers and the general public over the last 2 decades, the directly related problem of resistance toward antiseptics and biocides has been somewhat left untended. In the field of dentistry, antiseptics are routinely used in professional care, but they are also included in lots of oral care products such as mouthwashes or dentifrices, which are easily available for consumers over-the-counter. Despite this fact, there is little awareness among the dental community about potential risks of the widespread, unreflected, and potentially even needless use of antiseptics in oral care. Cetylpyridinium chloride (CPC), a quaternary ammonium compound, which was first described in 1939, is one of the most commonly used antiseptics in oral care products and included in a wide range of over-the-counter products such as mouthwashes and dentifrices. The aim of the present review is to summarize the current literature on CPC, particularly focusing on its mechanism of action, its antimicrobial efficacy toward biofilms, and on potential risks of resistance toward this antiseptic as well as underlying mechanisms. Furthermore, this work aims to raise awareness among the dental community about the risk of resistance toward antiseptics in general.
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38
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Young TK, Gutierrez D, Meehan SA, Pellett Madan R, Oza VS. Neutrophilic panniculitis arising from hematogenous spread of methicillin-resistant Staphylococcus aureus. Pediatr Dermatol 2020; 37:531-533. [PMID: 32124476 DOI: 10.1111/pde.14123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Infectious panniculitis from hematogenous spread is uncommon and usually occurs in immunocompromised patients. Dissemination of gram-positive organisms to the subcutaneous tissue is rare with only several reports of disseminated panniculitis caused by Streptococcal species. We report a case of an immunocompetent 2-year-old boy presenting with diffuse neutrophilic panniculitis arising from methicillin-resistant Staphylococcus aureus septicemia. This case represents a highly atypical manifestation of severe MRSA infection and serves as a reminder to consider MRSA as a cause of disseminated neutrophilic panniculitis, particularly in high-risk populations.
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Affiliation(s)
- Trevor K Young
- The Ronald O. Perelman Department of Dermatology, New York University Grossman School of Medicine, New York, NY, USA
| | - Daniel Gutierrez
- The Ronald O. Perelman Department of Dermatology, New York University Grossman School of Medicine, New York, NY, USA
| | - Shane A Meehan
- The Ronald O. Perelman Department of Dermatology, New York University Grossman School of Medicine, New York, NY, USA
| | - Rebecca Pellett Madan
- Department of Pediatrics, New York University Grossman School of Medicine, New York, NY, USA
| | - Vikash S Oza
- The Ronald O. Perelman Department of Dermatology, New York University Grossman School of Medicine, New York, NY, USA
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39
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Moustafa AM, Lal A, Planet PJ. Comparative genomics in infectious disease. Curr Opin Microbiol 2020; 53:61-70. [PMID: 32248056 DOI: 10.1016/j.mib.2020.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 02/07/2023]
Abstract
With more than one million bacterial genome sequences uploaded to public databases in the last 25 years, genomics has become a powerful tool for studying bacterial biology. Here, we review recent approaches that leverage large numbers of whole genome sequences to decipher the spread and pathogenesis of bacterial infectious diseases.
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Affiliation(s)
- Ahmed M Moustafa
- Division of Pediatric Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Arnav Lal
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Paul J Planet
- Division of Pediatric Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA.
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40
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Susceptibility of Cutibacterium acnes to topical minocycline foam. Anaerobe 2020; 62:102169. [DOI: 10.1016/j.anaerobe.2020.102169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/13/2020] [Accepted: 01/27/2020] [Indexed: 11/19/2022]
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41
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Wu L, Wang H, Xia Y, Xi R. CNV-BAC: Copy number Variation Detection in Bacterial Circular Genome. Bioinformatics 2020; 36:3890-3891. [DOI: 10.1093/bioinformatics/btaa208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 03/14/2020] [Accepted: 03/23/2020] [Indexed: 11/14/2022] Open
Abstract
Abstract
Motivation
Whole-genome sequencing (WGS) is widely used for copy number variation (CNV) detection. However, for most bacteria, their circular genome structure and high replication rate make reads more enriched near the replication origin. CNV detection based on read depth could be seriously influenced by such replication bias.
Results
We show that the replication bias is widespread using ∼200 bacterial WGS data. We develop CNV-BAC (CNV-Bacteria) that can properly normalize the replication bias and other known biases in bacterial WGS data and can accurately detect CNVs. Simulation and real data analysis show that CNV-BAC achieves the best performance in CNV detection compared with available algorithms.
Availability and implementation
CNV-BAC is available at https://github.com/XiDsLab/CNV-BAC.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Han Wang
- School of Mathematical Sciences
- Center for Statistical Science, Peking University, Beijing 100871, China
| | - Yuchao Xia
- School of Applied Science, Beijing Information Science and Technology University, Beijing 100101, China
| | - Ruibin Xi
- School of Mathematical Sciences
- Center for Statistical Science, Peking University, Beijing 100871, China
- Department of Biostatistics, Peking University, Beijing 100871, China
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42
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Yeung F, Chen YH, Lin JD, Leung JM, McCauley C, Devlin JC, Hansen C, Cronkite A, Stephens Z, Drake-Dunn C, Fulmer Y, Shopsin B, Ruggles KV, Round JL, Loke P, Graham AL, Cadwell K. Altered Immunity of Laboratory Mice in the Natural Environment Is Associated with Fungal Colonization. Cell Host Microbe 2020; 27:809-822.e6. [PMID: 32209432 DOI: 10.1016/j.chom.2020.02.015] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/11/2019] [Accepted: 02/28/2020] [Indexed: 12/21/2022]
Abstract
Free-living mammals, such as humans and wild mice, display heightened immune activation compared with artificially maintained laboratory mice. These differences are partially attributed to microbial exposure as laboratory mice infected with pathogens exhibit immune profiles more closely resembling that of free-living animals. Here, we examine how colonization by microorganisms within the natural environment contributes to immune system maturation by releasing inbred laboratory mice into an outdoor enclosure. In addition to enhancing differentiation of T cell populations previously associated with pathogen exposure, outdoor release increased circulating granulocytes. However, these "rewilded" mice were not infected by pathogens previously implicated in immune activation. Rather, immune system changes were associated with altered microbiota composition with notable increases in intestinal fungi. Fungi isolated from rewilded mice were sufficient in increasing circulating granulocytes. These findings establish a model to investigate how the natural environment impacts immune development and show that sustained fungal exposure impacts granulocyte numbers.
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Affiliation(s)
- Frank Yeung
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Sackler Institute of Graduate Biomedical Sciences, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ying-Han Chen
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jian-Da Lin
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jacqueline M Leung
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Caroline McCauley
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Joseph C Devlin
- Sackler Institute of Graduate Biomedical Sciences, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Christina Hansen
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Alex Cronkite
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Zac Stephens
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Charlotte Drake-Dunn
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Yi Fulmer
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA; Division of Infectious Disease, Department of Medicine, New York University Langone Health, New York, NY 10016, USA
| | - Bo Shopsin
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA; Division of Infectious Disease, Department of Medicine, New York University Langone Health, New York, NY 10016, USA
| | - Kelly V Ruggles
- Division of Translational Medicine, Department of Medicine, New York University Langone Health, New York, NY 10016, USA; Applied Bioinformatics Laboratories, New York Unversity Grossman School of Medicine, New York, NY 10016, USA
| | - June L Round
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - P'ng Loke
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Andrea L Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Ken Cadwell
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA; Division of Gastroenterology and Hepatology, Department of Medicine, New York University Langone Health, New York, NY 10016, USA.
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43
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Banaszkiewicz S, Calland JK, Mourkas E, Sheppard SK, Pascoe B, Bania J. Genetic Diversity of Composite Enterotoxigenic Staphylococcus epidermidis Pathogenicity Islands. Genome Biol Evol 2020; 11:3498-3509. [PMID: 31769803 PMCID: PMC6931896 DOI: 10.1093/gbe/evz259] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2019] [Indexed: 02/07/2023] Open
Abstract
The only known elements encoding enterotoxins in coagulase-negative staphylococci are composite Staphylococcus epidermidis pathogenicity islands (SePIs), including SePI and S. epidermidis composite insertion (SeCI) regions. We investigated 1545 Staphylococcus spp. genomes using whole-genome MLST, and queried them for genes of staphylococcal enterotoxin family and for 29 ORFs identified in prototype SePI from S. epidermidis FRI909. Enterotoxin-encoding genes were identified in 97% of Staphylococcus aureus genomes, in one Staphylococcus argenteus genome and in nine S. epidermidis genomes. All enterotoxigenic S. epidermidis strains carried composite SePI, encoding sec and sel enterotoxin genes, and were assigned to a discrete wgMLST cluster also containing genomes with incomplete islands located in the same region as complete SePI in enterotoxigenic strains. Staphylococcus epidermidis strains without SeCI and SePI genes, and strains with complete SeCI and no SePI genes were identified but no strains were found to carry only SePI and not SeCI genes. The systematic differences between SePI and SeCI regions imply a lineage-specific pattern of inheritance and support independent acquisition of the two elements in S. epidermidis. We provided evidence of reticulate evolution of mobile elements that contain elements with different putative ancestry, including composite SePI that contains genes found in other coagulase-negative staphylococci (SeCI), as well as in S. aureus (SePI-like elements). We conclude that SePI-associated elements present in nonenterotoxigenic S. epidermidis represent a scaffold associated with acquisition of virulence-associated genes. Gene exchange between S. aureus and S. epidermidis may promote emergence of new pathogenic S. epidermidis clones.
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Affiliation(s)
- Sylwia Banaszkiewicz
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Poland
| | | | | | | | - Ben Pascoe
- The Milner Centre for Evolution, University of Bath, United Kingdom
| | - Jacek Bania
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Poland
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44
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Multitasking Actors of Staphylococcus aureus Metabolism and Virulence. Trends Microbiol 2020; 28:6-9. [DOI: 10.1016/j.tim.2019.10.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 01/10/2023]
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45
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Giulieri SG, Tong SYC, Williamson DA. Using genomics to understand meticillin- and vancomycin-resistant Staphylococcus aureus infections. Microb Genom 2020; 6:e000324. [PMID: 31913111 PMCID: PMC7067033 DOI: 10.1099/mgen.0.000324] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/12/2019] [Indexed: 12/15/2022] Open
Abstract
Resistance to meticillin and vancomycin in Staphylococcus aureus significantly complicates the management of severe infections like bacteraemia, endocarditis or osteomyelitis. Here, we review the molecular mechanisms and genomic epidemiology of resistance to these agents, with a focus on how genomics has provided insights into the emergence and evolution of major meticillin-resistant S. aureus clones. We also provide insights on the use of bacterial whole-genome sequencing to inform management of S. aureus infections and for control of transmission at the hospital and in the community.
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Affiliation(s)
- Stefano G. Giulieri
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Infectious Disease Department, Austin Health, Melbourne, Australia
| | - Steven Y. C. Tong
- Victorian Infectious Disease Service, Royal Melbourne Hospital, and Doherty Department University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
- Menzies School of Health Research, Darwin, Australia
| | - Deborah A. Williamson
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute of Infection and Immunity, Melbourne, Australia
- Microbiology, Royal Melbourne Hospital, Melbourne, Australia
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46
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López Y, Tato M, Gargallo-Viola D, Cantón R, Vila J, Zsolt I. Mutant prevention concentration of ozenoxacin for quinolone-susceptible or -resistant Staphylococcus aureus and Staphylococcus epidermidis. PLoS One 2019; 14:e0223326. [PMID: 31596898 PMCID: PMC6785070 DOI: 10.1371/journal.pone.0223326] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/18/2019] [Indexed: 11/17/2022] Open
Abstract
Ozenoxacin (OZN) belongs to a new generation of non-fluorinated quinolones for the topical treatment of skin infections which has shown to be effective in the treatment of susceptible and resistant Gram-positive cocci. The mutant prevention concentration (MPC) of ozenoxacin, levofloxacin and ciprofloxacin was determined in quinolone-susceptible and -resistant strains including methicillin-susceptible S. aureus, methicillin-resistant S. aureus, methicillin-susceptible S. epidermidis and methicillin-resistant S. epidermidis with different profile of mutation in the quinolone resistance determining regions (QRDR). The MPC value of OZN for the methicillin-susceptible S. aureus strain susceptible to quinolones, without mutations in QRDR, was 0.05 mg/L, being 280-fold lower than that observed with ciprofloxacin and levofloxacin. In methicillin-susceptible and–resistant S. aureus strains with mutations in the gyrA or/and grlA genes the MPC of OZN went from 0.1 to 6 mg/L, whereas the MPC of levofloxacin and ciprofloxacin was > 50 mg/L for the same strains. For methicillin-susceptible and–resistant S. epidermidis the results were similar to those abovementioned for S. aureus. According to our results, the MPC of OZN was far below the quantity of ozenoxacin achieved in the epidermal layer, suggesting that the in vivo selection of mutants, if it occurs, will take place at low frequency. Ozenoxacin is an excellent candidate for the treatment of bacterial infections caused by susceptible and quinolone-resistant staphylococci isolated usually from skin infections.
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Affiliation(s)
- Y López
- Institute of Global Health of Barcelona, Barcelona, Spain
| | - M Tato
- Department of Clinical Microbiology, Hospital Universitario Ramón y Cajal & Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | | | - R Cantón
- Department of Clinical Microbiology, Hospital Universitario Ramón y Cajal & Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - J Vila
- Institute of Global Health of Barcelona, Barcelona, Spain.,Department of Clinical Microbiology, Hospital Clinic, School of Medicine, University of Barcelona, Spain
| | - I Zsolt
- Medical Department, Ferrer Internacional, Barcelona, Spain
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47
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DuChane CM, Karpin GW, Ehrich M, Falkinham JO, Merola JS. Iridium piano stool complexes with activity against S. aureus and MRSA: it is past time to truly think outside of the box. MEDCHEMCOMM 2019; 10:1391-1398. [PMID: 31534656 PMCID: PMC6748342 DOI: 10.1039/c9md00140a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/09/2019] [Indexed: 01/21/2023]
Abstract
A new class of piano-stool iridium complexes with 1,2-diaminoethane ligands are shown to be effective and safe antimicrobials with activity against Staphylococcus aureus, including various isolates of methicillin-resistant strains (MRSA). Comparison to other piano stool complexes with activity against mycobacteria are made along with a discussion of structure-activity relationships. The structures of one the most active complexes with the ligand cis-1,2-diaminocyclohexane and one of the least active complexes with the ligand trans-1,2-diaminocyclohexane are compared and discussed with respect to their drastically different activities. In vitro toxicity studies for all of the complexes are described. In addition, a mouse study with one of the complexes, [(pentamethylcyclopentadienyl)(cis-1,2-diaminocyclohexane)(chloro)iridium]chloride, showed no ill effects on the mice at high doses.
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Affiliation(s)
- Christine M DuChane
- Virginia Tech Center for Drug Discovery , Blacksburg , VA 24061 , USA .
- Department of Chemistry , Virginia Tech , Blacksburg , VA 24061 , USA
| | - George W Karpin
- Virginia Tech Center for Drug Discovery , Blacksburg , VA 24061 , USA .
- Department of Chemistry , Virginia Tech , Blacksburg , VA 24061 , USA
| | - Marion Ehrich
- Virginia Tech Center for Drug Discovery , Blacksburg , VA 24061 , USA .
- Virginia-Maryland College of Veterinary Medicine , Virginia Tech , Blacksburg , VA 24061 , USA
| | - Joseph O Falkinham
- Virginia Tech Center for Drug Discovery , Blacksburg , VA 24061 , USA .
- Department of Biological Sciences , Virginia Tech , Blacksburg , VA 24061 , USA
| | - Joseph S Merola
- Virginia Tech Center for Drug Discovery , Blacksburg , VA 24061 , USA .
- Department of Chemistry , Virginia Tech , Blacksburg , VA 24061 , USA
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48
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Kavanagh KT. Control of MSSA and MRSA in the United States: protocols, policies, risk adjustment and excuses. Antimicrob Resist Infect Control 2019; 8:103. [PMID: 31244994 PMCID: PMC6582558 DOI: 10.1186/s13756-019-0550-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 05/28/2019] [Indexed: 12/17/2022] Open
Abstract
Data released by the U.S. Centers for Disease Control and Prevention (CDC) on March 5, 2019 showed that Staph aureus infections are a major problem in the United States, with 119,000 infections and almost 20,000 deaths in 2017. Rates of decline for hospital-onset MRSA have slowed since 2012 and the United States is not on track for meeting the 2015 U.S. Dept. of Health and Human Services’ goal of a 50% reduction by 2020. There is a need for improved standards for control of dangerous pathogens. Currently, the World Health Organization’s recommendation of preoperatively screening patients for Staph aureus has not become a standard of care in the United States. The U.S. Veterans Health Administration also released data which found a much larger decrease in hospital-onset MRSA infections as opposed to hospital-onset MSSA using various infectious disease bundles that all included universal MRSA surveillance and isolation for MRSA carriers. These results mirror the results obtained by the United Kingdom’s National Health Service. These findings support the contention that the marked decline in hospital-onset MRSA infections observed in these studies is due to interventions which are specifically targeted towards MRSA. A case is made that concerns with the integrity of healthcare policy research, along with industrial conflicts-of-interest have inhibited effective formulation of infectious disease policy in the United States. Because MRSA has become endemic in the general U.S. population (approximately 2%), the author advocates that universal facility-wide screening of MRSA on admission be included in infection prevention bundles used at U.S. hospital.
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49
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Peng KT, Huang TY, Chiang YC, Hsu YY, Chuang FY, Lee CW, Chang PJ. Comparison of Methicillin-Resistant Staphylococcus aureus Isolates from Cellulitis and from Osteomyelitis in a Taiwan Hospital, 2016-2018. J Clin Med 2019; 8:E816. [PMID: 31181643 PMCID: PMC6617150 DOI: 10.3390/jcm8060816] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/27/2019] [Accepted: 06/06/2019] [Indexed: 01/21/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) causes superficial infections such as cellulitis or invasive infections such as osteomyelitis; however, differences in MRSA isolates from cellulitis (CL-MRSA) and from osteomyelitis (OM-MRSA) at the same local area remain largely unknown. A total of 221 MRSA isolates including 106 CL-MRSA strains and 115 OM-MRSA strains were collected at Chang-Gung Memorial Hospital in Taiwan between 2016 and 2018, and their genotypic and phenotypic characteristics were compared. We found that OM-MRSA isolates significantly exhibited higher rates of resistance to multiple antibiotics than CL-MRSA isolates. Genotypically, OM-MRSA isolates had higher proportions of the SCCmec type III, the sequence type ST239, and the spa type t037 than CL-MRSA isolates. Besides the multidrug-resistant lineage ST239-t037-SCCmecIII more prevalent in OM-MRSA, higher antibiotic resistance rates were also observed in several other prevalent lineages in OM-MRSA as compared to the same lineages in CL-MRSA. Furthermore, when prosthetic joint infection (PJI) associated and non-PJI-associated MRSA strains in osteomyelitis were compared, no significant differences were observed in antibiotic resistance rates between the two groups, albeit more diverse genotypes were found in non-PJI-associated MRSA. Our findings therefore suggest that deep infections may allow MRSA to evade antibiotic attack and facilitate the convergent evolution and selection of multidrug-resistant lineages.
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Affiliation(s)
- Kuo-Ti Peng
- Department of Orthopaedic Surgery, Chang Gung Memorial Hospital, Chiayi 61363, Taiwan.
- College of Medicine, Chang Gung University, Taoyuan 33303, Taiwan.
| | - Tsung-Yu Huang
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital, Chiayi 61363, Taiwan.
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan 33303, Taiwan.
| | - Yao-Chang Chiang
- Department of Nursing, Chang Gung University of Science and Technology, Chiayi 61363, Taiwan.
- Division of Basic Medical Sciences, and Chronic Diseases and Health Promotion Research Center, Chang Gung University of Science and Technology, Chiayi 61363, Taiwan.
| | - Yu-Yi Hsu
- Department of Orthopaedic Surgery, Chang Gung Memorial Hospital, Chiayi 61363, Taiwan.
| | - Fang-Yi Chuang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Chiayi 61363, Taiwan.
| | - Chiang-Wen Lee
- Department of Nursing, Chang Gung University of Science and Technology, Chiayi 61363, Taiwan.
- Division of Basic Medical Sciences, and Chronic Diseases and Health Promotion Research Center, Chang Gung University of Science and Technology, Chiayi 61363, Taiwan.
- Research Center for Industry of Human Ecology and Research Center for Chinese Herbal Medicine, Chang Gung University of Science and Technology, Taoyuan 33303, Taiwan.
- Department of Rehabilitation, Chang Gung Memorial Hospital, Chiayi 61363, Taiwan.
| | - Pey-Jium Chang
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan 33303, Taiwan.
- Department of Nephrology, Chang Gung Memorial Hospital, Chiayi 61363, Taiwan.
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50
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Cieplik F, Jakubovics NS, Buchalla W, Maisch T, Hellwig E, Al-Ahmad A. Resistance Toward Chlorhexidine in Oral Bacteria - Is There Cause for Concern? Front Microbiol 2019; 10:587. [PMID: 30967854 PMCID: PMC6439480 DOI: 10.3389/fmicb.2019.00587] [Citation(s) in RCA: 195] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 03/07/2019] [Indexed: 12/20/2022] Open
Abstract
The threat of antibiotic resistance has attracted strong interest during the last two decades, thus stimulating stewardship programs and research on alternative antimicrobial therapies. Conversely, much less attention has been given to the directly related problem of resistance toward antiseptics and biocides. While bacterial resistances toward triclosan or quaternary ammonium compounds have been considered in this context, the bis-biguanide chlorhexidine (CHX) has been put into focus only very recently when its use was associated with emergence of stable resistance to the last-resort antibiotic colistin. The antimicrobial effect of CHX is based on damaging the bacterial cytoplasmic membrane and subsequent leakage of cytoplasmic material. Consequently, mechanisms conferring resistance toward CHX include multidrug efflux pumps and cell membrane changes. For instance, in staphylococci it has been shown that plasmid-borne qac ("quaternary ammonium compound") genes encode Qac efflux proteins that recognize cationic antiseptics as substrates. In Pseudomonas stutzeri, changes in the outer membrane protein and lipopolysaccharide profiles have been implicated in CHX resistance. However, little is known about the risk of resistance toward CHX in oral bacteria and potential mechanisms conferring this resistance or even cross-resistances toward antibiotics. Interestingly, there is also little awareness about the risk of CHX resistance in the dental community even though CHX has been widely used in dental practice as the gold-standard antiseptic for more than 40 years and is also included in a wide range of oral care consumer products. This review provides an overview of general resistance mechanisms toward CHX and the evidence for CHX resistance in oral bacteria. Furthermore, this work aims to raise awareness among the dental community about the risk of resistance toward CHX and accompanying cross-resistance to antibiotics. We propose new research directions related to the effects of CHX on bacteria in oral biofilms.
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Affiliation(s)
- Fabian Cieplik
- Department of Conservative Dentistry and Periodontology, University Medical Center Regensburg, Regensburg, Germany
| | - Nicholas S Jakubovics
- Centre for Oral Health Research, School of Dental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Wolfgang Buchalla
- Department of Conservative Dentistry and Periodontology, University Medical Center Regensburg, Regensburg, Germany
| | - Tim Maisch
- Department of Dermatology, University Medical Center Regensburg, Regensburg, Germany
| | - Elmar Hellwig
- Department of Operative Dentistry and Periodontology, Center for Dental Medicine, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Ali Al-Ahmad
- Department of Operative Dentistry and Periodontology, Center for Dental Medicine, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
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