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Lucena ACR, Ferrarini MG, de Oliveira WK, Marcon BH, Morello LG, Alves LR, Faoro H. Modulation of Klebsiella pneumoniae Outer Membrane Vesicle Protein Cargo under Antibiotic Treatment. Biomedicines 2023; 11:1515. [PMID: 37371610 DOI: 10.3390/biomedicines11061515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/14/2023] [Accepted: 05/14/2023] [Indexed: 06/29/2023] Open
Abstract
Klebsiella pneumoniae is a nosocomial pathogen and an important propagator of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains. Like other Gram-negative bacteria, they secrete outer membrane vesicles (OMVs) that distribute virulence and resistance factors. Here, we subjected a K. pneumoniae-XDR to subinhibitory concentrations of meropenem, amikacin, polymyxin B, and a combination of these agents to evaluate changes in the protein cargo of OMVs through liquid chromatography-tandem mass spectrometry (LC-MS/MS). Genome sequencing of the clinical isolate K. pneumoniae strain HCD1 (KpHCD1) revealed the presence of 41 resistance genes and 159 virulence factors. We identified 64 proteins in KpHCD1-OMVs modulated with different antibiotic treatments involved in processing genetic information, environmental information, cell envelope formation, energy metabolism, and drug resistance. The OMV proteome expression profile suggests that OMVs may be associated with pathogenicity, survival, stress response, and resistance dissemination.
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Affiliation(s)
- Aline Castro Rodrigues Lucena
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
| | - Mariana Galvão Ferrarini
- Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, Université de Lyon, Université Lyon 1, 69622 Villeurbanne, France
| | - Willian Klassen de Oliveira
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
| | - Bruna Hilzendeger Marcon
- Laboratory for Basic Biology of Stem Cells, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
| | - Luis Gustavo Morello
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
| | - Lysangela Ronalte Alves
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
- CHU de Quebec Research Center, Department of Microbiology, Infectious Disease and Immunology, University Laval, Quebec, QC G1V 0A6, Canada
| | - Helisson Faoro
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
- CHU de Quebec Research Center, Department of Microbiology, Infectious Disease and Immunology, University Laval, Quebec, QC G1V 0A6, Canada
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Patil R, Dehari D, Chaudhuri A, Kumar DN, Kumar D, Singh S, Nath G, Agrawal AK. Recent advancements in nanotechnology-based bacteriophage delivery strategies against bacterial ocular infections. Microbiol Res 2023; 273:127413. [PMID: 37216845 DOI: 10.1016/j.micres.2023.127413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 05/24/2023]
Abstract
Antibiotic resistance is growing as a critical challenge in a variety of disease conditions including ocular infections leading to disastrous effects on the human eyes. Staphylococcus aureus (S. aureus) mediated ocular infections are very common affecting different parts of the eye viz. vitreous chamber, conjunctiva, cornea, anterior and posterior chambers, tear duct, and eyelids. Blepharitis, dacryocystitis, conjunctivitis, keratitis, endophthalmitis, and orbital cellulitis are some of the commonly known ocular infections caused by S. aureus. Some of these infections are so fatal that they could cause bilateral blindness like panophthalmitis and orbital cellulitis, which is caused by methicillin-resistant S. aureus (MRSA) and vancomycin-resistance S. aureus (VRSA). The treatment of S. aureus infections with known antibiotics is becoming gradually difficult because of the development of resistance against multiple antibiotics. Apart from the different combinations and formulation strategies, bacteriophage therapy is growing as an effective alternative to treat such infections. Although the superiority of bacteriophage therapy is well established, yet physical factors (high temperatures, acidic pH, UV-rays, and ionic strength) and pharmaceutical barriers (poor stability, low in-vivo retention, controlled and targeted delivery, immune system neutralization, etc.) have the greatest influence on the viability of phage virions (also phage proteins). A variety of Nanotechnology based formulations such as polymeric nanoparticles, liposomes, dendrimers, nanoemulsions, and nanofibres have been recently reported to overcome the above-mentioned obstacles. In this review, we have compiled all these recent reports and discussed bacteriophage-based nanoformulations techniques for the successful treatment of ocular infections caused by multidrug-resistant S. aureus and other bacteria.
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Affiliation(s)
- Rohit Patil
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, U.P., India
| | - Deepa Dehari
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, U.P., India
| | - Aiswarya Chaudhuri
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, U.P., India
| | - Dulla Naveen Kumar
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, U.P., India
| | - Dinesh Kumar
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, U.P., India
| | - Sanjay Singh
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, U.P., India; Babasaheb Bhimrao Ambedkar University, Lucknow 226025, U.P., India
| | - Gopal Nath
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, U.P., India
| | - Ashish Kumar Agrawal
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, U.P., India.
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Keller MR, Dörr T. Bacterial metabolism and susceptibility to cell wall-active antibiotics. Adv Microb Physiol 2023; 83:181-219. [PMID: 37507159 PMCID: PMC11024984 DOI: 10.1016/bs.ampbs.2023.04.002] [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: 07/30/2023]
Abstract
Bacterial infections are increasingly resistant to antimicrobial therapy. Intense research focus has thus been placed on identifying the mechanisms that bacteria use to resist killing or growth inhibition by antibiotics and the ways in which bacteria share these traits with one another. This work has led to the advancement of new drugs, combination therapy regimens, and a deeper appreciation for the adaptability seen in microorganisms. However, while the primary mechanisms of action of most antibiotics are well understood, the more subtle contributions of bacterial metabolic state to repairing or preventing damage caused by antimicrobials (thereby promoting survival) are still understudied. Here, we review a modern viewpoint on a classical system: examining bacterial metabolism's connection to antibiotic susceptibility. We dive into the relationship between metabolism and antibiotic efficacy through the lens of growth rate, energy state, resource allocation, and the infection environment, focusing on cell wall-active antibiotics.
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Affiliation(s)
- Megan Renee Keller
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, United States; Department of Microbiology, Cornell University, Ithaca, NY, United States; Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY, United States.
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Varela MF, Stephen J, Bharti D, Lekshmi M, Kumar S. Inhibition of Multidrug Efflux Pumps Belonging to the Major Facilitator Superfamily in Bacterial Pathogens. Biomedicines 2023; 11:1448. [PMID: 37239119 PMCID: PMC10216197 DOI: 10.3390/biomedicines11051448] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Bacterial pathogens resistant to multiple structurally distinct antimicrobial agents are causative agents of infectious disease, and they thus constitute a serious concern for public health. Of the various bacterial mechanisms for antimicrobial resistance, active efflux is a well-known system that extrudes clinically relevant antimicrobial agents, rendering specific pathogens recalcitrant to the growth-inhibitory effects of multiple drugs. In particular, multidrug efflux pump members of the major facilitator superfamily constitute central resistance systems in bacterial pathogens. This review article addresses the recent efforts to modulate these antimicrobial efflux transporters from a molecular perspective. Such investigations can potentially restore the clinical efficacy of infectious disease chemotherapy.
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Affiliation(s)
- Manuel F. Varela
- Department of Biology, Eastern New Mexico University, Station 33, Portales, NM 88130, USA
| | - Jerusha Stephen
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India; (J.S.); (D.B.); (M.L.); (S.K.)
| | - Deeksha Bharti
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India; (J.S.); (D.B.); (M.L.); (S.K.)
| | - Manjusha Lekshmi
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India; (J.S.); (D.B.); (M.L.); (S.K.)
| | - Sanath Kumar
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India; (J.S.); (D.B.); (M.L.); (S.K.)
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Grudlewska-Buda K, Bauza-Kaszewska J, Wiktorczyk-Kapischke N, Budzyńska A, Gospodarek-Komkowska E, Skowron K. Antibiotic Resistance in Selected Emerging Bacterial Foodborne Pathogens-An Issue of Concern? Antibiotics (Basel) 2023; 12:antibiotics12050880. [PMID: 37237783 DOI: 10.3390/antibiotics12050880] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/30/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Antibiotic resistance (AR) and multidrug resistance (MDR) have been confirmed for all major foodborne pathogens: Campylobacter spp., Salmonella spp., Escherichia coli and Listeria monocytogenes. Of great concern to scientists and physicians are also reports of antibiotic-resistant emerging food pathogens-microorganisms that have not previously been linked to food contamination or were considered epidemiologically insignificant. Since the properties of foodborne pathogens are not always sufficiently recognized, the consequences of the infections are often not easily predictable, and the control of their activity is difficult. The bacteria most commonly identified as emerging foodborne pathogens include Aliarcobacter spp., Aeromonas spp., Cronobacter spp., Vibrio spp., Clostridioides difficile, Escherichia coli, Mycobacterium paratuberculosis, Salmonella enterica, Streptocccus suis, Campylobacter jejuni, Helicobacter pylori, Listeria monocytogenes and Yersinia enterocolitica. The results of our analysis confirm antibiotic resistance and multidrug resistance among the mentioned species. Among the antibiotics whose effectiveness is steadily declining due to expanding resistance among bacteria isolated from food are β-lactams, sulfonamides, tetracyclines and fluoroquinolones. Continuous and thorough monitoring of strains isolated from food is necessary to characterize the existing mechanisms of resistance. In our opinion, this review shows the scale of the problem of microbes related to health, which should not be underestimated.
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Affiliation(s)
- Katarzyna Grudlewska-Buda
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
| | - Justyna Bauza-Kaszewska
- Department of Microbiology and Food Technology, Bydgoszcz University of Science and Technology, 85-029 Bydgoszcz, Poland
| | - Natalia Wiktorczyk-Kapischke
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
| | - Anna Budzyńska
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
| | - Eugenia Gospodarek-Komkowska
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
| | - Krzysztof Skowron
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland
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Darby EM, Trampari E, Siasat P, Gaya MS, Alav I, Webber MA, Blair JMA. Molecular mechanisms of antibiotic resistance revisited. Nat Rev Microbiol 2023; 21:280-295. [PMID: 36411397 DOI: 10.1038/s41579-022-00820-y] [Citation(s) in RCA: 195] [Impact Index Per Article: 195.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2022] [Indexed: 11/22/2022]
Abstract
Antibiotic resistance is a global health emergency, with resistance detected to all antibiotics currently in clinical use and only a few novel drugs in the pipeline. Understanding the molecular mechanisms that bacteria use to resist the action of antimicrobials is critical to recognize global patterns of resistance and to improve the use of current drugs, as well as for the design of new drugs less susceptible to resistance development and novel strategies to combat resistance. In this Review, we explore recent advances in understanding how resistance genes contribute to the biology of the host, new structural details of relevant molecular events underpinning resistance, the identification of new resistance gene families and the interactions between different resistance mechanisms. Finally, we discuss how we can use this information to develop the next generation of antimicrobial therapies.
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Affiliation(s)
- Elizabeth M Darby
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | - Pauline Siasat
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | - Ilyas Alav
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
- Medical School, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Jessica M A Blair
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
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Puzia W, Gawor J, Gromadka R, Skoczyńska A, Sadowy E. Comparative genomic analysis of two ST320 Streptococcus pneumoniae isolates, representing serotypes 19A and 19F. BMC Genom Data 2023; 24:19. [PMID: 37032356 PMCID: PMC10084702 DOI: 10.1186/s12863-023-01118-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 03/03/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND Streptococcus pneumoniae (pneumococcus) represents an important human pathogen, responsible for respiratory and invasive infections in the community. The efficacy of polysaccharide conjugate vaccines formulated against pneumococci is reduced by the phenomenon of serotype replacement in population of this pathogen. The aim of the current study was to obtain and compare complete genomic sequences of two pneumococcal isolates, both belonging to ST320 but differing by the serotype. RESULTS Here, we report genomic sequences of two isolates of important human pathogen, S. pneumoniae. Genomic sequencing resulted in complete sequences of chromosomes of both isolates, 2,069,241 bp and 2,103,144 bp in size, and confirmed the presence of cps loci specific for serotypes 19A and 19F. The comparative analysis of these genomes revealed several instances of recombination, which involved not only S. pneumoniae but also presumably other streptococci as donors. CONCLUSIONS We report the complete genomic sequences of two S. pneumoniae isolates of ST320 and serotypes 19A and 19F. The detailed comparative analysis of these genomes revealed the history of several recombination events, clustered in the region including the cps locus.
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Affiliation(s)
- Weronika Puzia
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | - Jan Gawor
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | - Robert Gromadka
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics PAS, Warsaw, Poland
| | - Anna Skoczyńska
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
- National Reference Centre for Bacterial Meningitis, National Medicines Institute, Warsaw, Poland
| | - Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, Ul. Chelmska 30/34, 00-725, Warsaw, Poland.
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Mi HF, Shen X, Chen XQ, Zhang XL, Ke WJ, Xiao Y. Association between treatment failure in patients with early syphilis and penicillin resistance-related gene mutations of Treponema pallidum: Protocol for a multicentre nested case–control study. Front Med (Lausanne) 2023; 10:1131921. [PMID: 37081834 PMCID: PMC10110954 DOI: 10.3389/fmed.2023.1131921] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/21/2023] [Indexed: 04/07/2023] Open
Abstract
BackgroundThe widespread occurrence of syphilis remains a global public health problem. Although penicillin has been recommended as the first-line therapy for syphilis for more than 70 years, treatment failure occurs in 10–20% of patients with early syphilis. Recent studies have reported varied single-nucleotide polymorphisms (SNPs) of Treponema pallidum related to penicillin resistance. The clinical relevance of these SNPs to treatment failure in patients with early syphilis is unresolved. In this work, a protocol is developed to evaluate the association between treatment failure in patients with early syphilis and penicillin resistance-related gene mutations of T. pallidum.MethodsA multicentre nested case–control study is designed, and patients who are diagnosed with early syphilis and treated with penicillin will be recruited for the study cohort. Before the first treatment, baseline information and biological specimens will be collected from the subjects, and serological tests for syphilis will be performed. Each participant will be followed up at 1, 3, 6, 9, and 12 months after the first treatment, and the clinical manifestations and serum non-treponemal test titres will be evaluated at each follow-up. Patients who will fail treatment are defined as cases, and those who will respond to treatment are defined as controls. Tests for SNPs related to penicillin-binding proteins and Tp47 will be performed in these cases and controls. Survival analysis is used performed to identify gene mutations of T. pallidum related to penicillin resistance and their combinations associated with treatment failure.DiscussionThis protocol provides a practical clinical study design that illustrates the role of gene mutations of T. pallidum related to penicillin resistance in the treatment outcome of patients with early syphilis.
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Affiliation(s)
- Hong-Fei Mi
- Zhongshan Hospital, Fudan University (Xiamen Branch), Xiamen, China
| | - Xu Shen
- Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Xiao-Qing Chen
- Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Xiao-Luo Zhang
- Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- *Correspondence: Xiao-Luo Zhang,
| | - Wu-Jian Ke
- Dermatology Hospital, Southern Medical University, Guangzhou, China
- Wu-Jian Ke,
| | - Yao Xiao
- Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Yao Xiao,
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Yu D, Guo D, Zheng Y, Yang Y. A review of penicillin binding protein and group A Streptococcus with reduced-β-lactam susceptibility. Front Cell Infect Microbiol 2023; 13:1117160. [PMID: 37065204 PMCID: PMC10102528 DOI: 10.3389/fcimb.2023.1117160] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/21/2023] [Indexed: 04/03/2023] Open
Abstract
With the widespread use of antibiotics, antimicrobial resistance (AMR) has become a global problem that endangers public health. Despite the global high prevalence of group A Streptococcus (GAS) infections and the global widespread use of β-lactams, β-lactams remain the first-line treatment option for GAS infection. β-hemolytic streptococci maintain a persistent susceptibility to β-lactams, which is an extremely special phenomenon in the genus Streptococci, while the exact current mechanism is not known. In recent years, several studies have found that the gene encoding penicillin binding protein 2X (pbp2x) is associated with GAS with reduced-β-lactam susceptibility. The purpose of this review is to summarize the current published data on GAS penicillin binding proteins and β-lactam susceptibility, to explore the relationship between them, and to be alert to the emergence of GAS with reduced susceptibility to β-lactams.
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Affiliation(s)
- Dingle Yu
- Shenzhen Children’s Hospital, Shenzhen, China
| | - Danchun Guo
- Shenzhen Children’s Hospital, Shenzhen, China
| | - Yuejie Zheng
- Shenzhen Children’s Hospital, Shenzhen, China
- *Correspondence: Yuejie Zheng, ; Yonghong Yang,
| | - Yonghong Yang
- Shenzhen Children’s Hospital, Shenzhen, China
- Microbiology Laboratory, National Center for Children’s Health, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Beijing, China
- *Correspondence: Yuejie Zheng, ; Yonghong Yang,
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Ibraheim HK, Madhi KS, Baqer GK, Gharban HAJ. Effectiveness of raw bacteriocin produced from lactic acid bacteria on biofilm of methicillin-resistant Staphylococcus aureus. Vet World 2023; 16:491-499. [PMID: 37041833 PMCID: PMC10082751 DOI: 10.14202/vetworld.2023.491-499] [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: 12/06/2022] [Accepted: 01/18/2023] [Indexed: 04/13/2023] Open
Abstract
Background and Aim Probiotics are proven beneficial to health since they enhance immunity against dangerous pathogens and increase resistance to illness. Bacteriocin produced by lactic acid bacteria (LAB), demonstrates a broad inhibitory spectrum and therapeutic potential. This study aimed to isolate LAB-producing bacteriocin and investigate the effect of crude bacteriocin on biofilm from methicillin-resistant Staphylococcus aureus (MRSA). Materials and Methods This study used randomly collected 80 white soft local cheeses (40 each from cows and sheep) from different supermarkets in Basrah Province. The obtained samples were cultured and the bacterial suspension of S. aureus was prepared at 1.5 × 108 cells/mL. The crude bacteriocin extracted from LAB was obtained, and the tube was dried and inverted to detect the biofilm loss at the bottom. Results There were 67 (83.75%) LAB isolates. Among 40 milk samples collected directly and indirectly, there were 36 (83.33%). Staphylococcus aureus isolates based on conventional bacteriological analysis and biochemical tests. Molecular testing was conducted to identify LAB and MRSA. Depending on genotypic results, the effect of white soft local cheese (cows and sheep) and the amplification results of the 16S rRNA gene were detected in 46 LAB isolates from white soft local cheese from cows and sheep. Based on the molecular identification of the mecA, results on Staphylococcus determined that only 2 of 36 isolates of S. aureus carried the mecA. Moreover, there were 26 (86.66%) isolates (MRSA) from samples of raw milk from local markets and subclinical mastitis in cows. The ability of LAB isolates was tested. The effects of bacteriocin production on preventing biofilm growth and formation were investigated. Results demonstrated that bacteriocin has high activity. Microtiter plates applied to investigate the ability of S. aureus to produce biofilms revealed that all isolates were either weak or moderate biofilm producers, with neither non-biofilm nor strong biofilm producers found among the tested isolates. Conclusion Lactic acid bacteria demonstrate a high ability to produce bacteriocin. Crude bacteriocin from LAB has a restrictive effect on biofilms produced by MRSA; thus, it can be used to reduce the pathogenicity of this bacterium.
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Affiliation(s)
- Hanaa Khaleel Ibraheim
- Department of Microbiology, College of Veterinary Medicine, University of Basrah, Basrah, Iraq
- Corresponding author: Hanaa Khaleel Ibraheim, e-mail: Co-authors: KSM: , GKB: , HAJG:
| | - Khadeeja S. Madhi
- Department of Microbiology, College of Medicine, University of Basrah, Basrah, Iraq
| | - Gaida K. Baqer
- Department of Microbiology, College of Medicine, University of Basrah, Basrah, Iraq
| | - Hasanain A. J. Gharban
- Department of Internal and Preventive Veterinary Medicine, College of Veterinary Medicine, University of Wasit, Wasit, Iraq
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Fauzia KA, Aftab H, Tshibangu-Kabamba E, Alfaray RI, Saruuljavkhlan B, Cimuanga-Mukanya A, Matsumoto T, Subsomwong P, Akada J, Miftahussurur M, Yamaoka Y. Mutations Related to Antibiotics Resistance in Helicobacter pylori Clinical Isolates from Bangladesh. Antibiotics (Basel) 2023; 12:antibiotics12020279. [PMID: 36830189 PMCID: PMC9952455 DOI: 10.3390/antibiotics12020279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023] Open
Abstract
Current management of gastric inflammation involves the eradication of Helicobacter pylori. However, the effectiveness of commonly used antibiotics against H. pylori infection has decreased due to antibiotic resistance. Phenotypic-based diagnostics are laborious and finding the cause of resistance can be difficult. Therefore, early detection and understanding of the underlying mechanism of this resistance are necessary. This study evaluated the mutations in the genes related to the Antimicrobial Resistance (AMR) of the clinical isolates from Bangladeshi subjects. Whole-genome sequencing was performed on 56 isolates and the genes (such as pbp1a, rdxA, ribF, fur, gyrA, gyrB, 23S rRNA, and infB) were extracted. The reads were assembled, and the SNPs were extracted by the latest pipeline for antibiotic mutation analysis, ARIBA. The mutations and the association with the antibiotic phenotypes were evaluated using Fisher's exact test. In this study, the clarithromycin resistance rate was high, 39.3% (22/56), with the median MIC 24 mg/L ranging from 2 to 128 mg/L. The mutation of A2147G was significantly associated with resistance (p = 0.000018) but not in locus A2146G (p = 0.056). Levofloxacin also posed a high resistance. We observed that the mutation of D91N (but not D91Y) (p = 0.002) and N87K (p = 0.002) of gyrA was associated with levofloxacin resistance. Mutations in locus A343V (p = 0.041) of gyrB also showed a significant association. Meanwhile, in the pbp1a gene, several mutations might explain the resistance; they were G594fs (p = 0.036), K306R (p = 0.036), N562Y (p = 0.0006), and V45I (p = 0.018). The prevalence of metronidazole was exceptionally high (96.4%), and numerous mutations occurred in rdxA genes, including the truncation of genes. These results imply that the mutation in genes encoding the target protein of antibiotics remains the critical resistance mechanism in H. pylori.
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Affiliation(s)
- Kartika Afrida Fauzia
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu 879-5593, Japan
- Department of Public Health and Preventive Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya 60115, Indonesia
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Hafeza Aftab
- Department of Gastroenterology, Dhaka Medical College and Hospital, Dhaka 1000, Bangladesh
| | - Evariste Tshibangu-Kabamba
- Research Center for Infectious Sciences, Department of Parasitology, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan
| | - Ricky Indra Alfaray
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu 879-5593, Japan
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Batsaikhan Saruuljavkhlan
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu 879-5593, Japan
| | - Alain Cimuanga-Mukanya
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu 879-5593, Japan
- Department of Internal Medicine, Faculty of Medicine, Pharmacy and Public Health, University of Mbujimayi, Mbujimayi 225-80, Democratic Republic of the Congo
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu 879-5593, Japan
| | - Phawinee Subsomwong
- Department of Microbiology and Immunology, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu 879-5593, Japan
| | - Muhammad Miftahussurur
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine-Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya 60131, Indonesia
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu 879-5593, Japan
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine-Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya 60131, Indonesia
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX 77030, USA
- Research Center for Global and Local Infectious Diseases, Oita University, Yufu 879-5593, Japan
- Borneo Medical and Health Research Centre, University Malaysia Sabah, Kota Kinabalu, Sabah 88400, Malaysia
- Correspondence:
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Relationship between Penicillin-Binding Proteins Alterations and β-Lactams Non-Susceptibility of Diseased Pig-Isolated Streptococcus suis. Antibiotics (Basel) 2023; 12:antibiotics12010158. [PMID: 36671359 PMCID: PMC9854507 DOI: 10.3390/antibiotics12010158] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/03/2023] [Accepted: 01/10/2023] [Indexed: 01/14/2023] Open
Abstract
Streptococcus suis is a zoonotic pathogen causing disease in both animals and humans, and the emergence of increasingly resistant bacteria to antimicrobial agents has become a significant challenge globally. The objective of this study was to investigate the genetic basis for declining susceptibility to penicillin and other β-lactams among S. suis. Antimicrobial susceptibility testing and penicillin-binding proteins (PBP1a, PBP2a, PBP2b, and PBP2x) sequence analysis were performed on 225 S. suis isolated from diseased pigs. This study found that a growing trend of isolates displayed reduced susceptibility to β-lactams including penicillin, ampicillin, amoxicillin/clavulanic acid, and cephalosporins. A total of 342 substitutions within the transpeptidase domain of four PBPs were identified, of which 18 substitutions were most statistically associated with reduced β-lactams susceptibility. Almost all the S. suis isolates which exhibited penicillin-non-susceptible phenotype (71.9%) had single nucleotide polymorphisms, leading to alterations of PBP1a (P409T) and PBP2a (T584A and H588Y). The isolates may manifest a higher level of penicillin resistance by additional mutation of M341I in the 339STMK active site motif of PBP2x. The ampicillin-non-susceptible isolates shared the mutations in PBP1a (P409T) and PBP2a (T584A and H588Y) with additional alterations of PBP2b (T625R) and PBP2x (T467S). The substitutions, including PBP1a (M587S/T), PBP2a (M433T), PBP2b (I428L), and PBP2x (Q405E/K/L), appeared to play significant roles in mediating the reduction in amoxicillin/clavulanic acid susceptibility. Among the cephalosporins, specific mutations strongly associated with the decrease in cephalosporins susceptibility were observed for ceftiofur: PBP1a (S477D/G), PBP2a (E549Q and A568S), PBP2b (T625R), and PBP2x (Q453H). It is concluded that there was genetically widespread presence of PBPs substitutions associated with reduced susceptibility to β-lactam antibiotics.
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Genome-Wide Transposon Mutagenesis Screens Identify Group A Streptococcus Genes Affecting Susceptibility to β-Lactam Antibiotics. J Bacteriol 2022; 204:e0028722. [PMID: 36374114 PMCID: PMC9765115 DOI: 10.1128/jb.00287-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Group A streptococcus (GAS) is a Gram-positive human bacterial pathogen responsible for more than 700 million infections annually worldwide. Beta-lactam antibiotics are the primary agents used to treat GAS infections. Naturally occurring GAS clinical isolates with decreased susceptibility to beta-lactam antibiotics attributed to mutations in PBP2X have recently been documented. This prompted us to perform a genome-wide screen to identify GAS genes that alter beta-lactam susceptibility in vitro. Using saturated transposon mutagenesis, we screened for GAS gene mutations conferring altered in vitro susceptibility to penicillin G and/or ceftriaxone, two beta-lactam antibiotics commonly used to treat GAS infections. In the aggregate, we found that inactivating mutations in 150 GAS genes are associated with altered susceptibility to penicillin G and/or ceftriaxone. Many of the genes identified were previously not known to alter beta-lactam susceptibility or affect cell wall biosynthesis. Using isogenic mutant strains, we confirmed that inactivation of clpX (Clp protease ATP-binding subunit) or cppA (CppA proteinase) resulted in decreased in vitro susceptibility to penicillin G and ceftriaxone. Deletion of murA1 (UDP-N-acetylglucosamine 1-carboxyvinyltransferase) conferred increased susceptibility to ceftriaxone. Our results provide new information about the GAS genes affecting susceptibility to beta-lactam antibiotics. IMPORTANCE Beta-lactam antibiotics are the primary drugs prescribed to treat infections caused by group A streptococcus (GAS), an important human pathogen. However, the molecular mechanisms of GAS interactions with beta-lactam antibiotics are not fully understood. In this study, we performed a genome-wide mutagenesis screen to identify GAS mutations conferring altered susceptibility to beta-lactam antibiotics. In the aggregate, we discovered that mutations in 150 GAS genes were associated with altered beta-lactam susceptibility. Many identified genes were previously not known to alter beta-lactam susceptibility or affect cell wall biosynthesis. Our results provide new information about the molecular mechanisms of GAS interaction with beta-lactam antibiotics.
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Colagrossi L, Costabile V, Scutari R, Agosta M, Onori M, Mancinelli L, Lucignano B, Onetti Muda A, Del Baldo G, Mastronuzzi A, Locatelli F, Trua G, Montanari M, Alteri C, Bernaschi P, Perno CF. Evidence of pediatric sepsis caused by a drug resistant Lactococcus garvieae contaminated platelet concentrate. Emerg Microbes Infect 2022; 11:1325-1334. [PMID: 35475418 PMCID: PMC9132404 DOI: 10.1080/22221751.2022.2071174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Owing to an increasing number of infections in adults, Lactococcus (L.) garvieae has gained recognition as an emerging human pathogen, causing bacteraemia and septicaemia. In September 2020, four paediatric onco-hematologic patients received a platelet concentrate from the same adult donor at Bambino Gesù Children’s Hospital IRCCS, Rome. Three of four patients experienced L. garvieae sepsis one day after transfusion. The L. garvieae pediatric isolates and the donor’s platelet concentrates were retrospectively collected for whole-genome sequencing and shot-gun metagenomics, respectively (Illumina HiSeq). By de novo assembly of the L. garvieae genomes, we found that all three pediatric isolates shared a 99.9% identity and were characterized by 440 common SNPs. Plasmid pUC11C (conferring virulence properties) and the temperate prophage Plg-Tb25 were detected in all three strains. Core SNP genome-based maximum likelihood and Bayesian trees confirmed their phylogenetic common origin and revealed their relationship with L. garvieae strains affecting cows and humans (bootstrap values >100 and posterior probabilities = 1.00). Bacterial reads obtained by the donor’s platelet concentrate have been profiled with MetaPhlAn2 (v.2.7.5); among these, 29.9% belonged to Firmicutes, and 5.16% to Streptococcaceae (>97% identity with L. garvieae), confirming the presence of L. garvieae in the platelet concentrate transfusion. These data showed three episodes of sepsis for the first time due to a transfusion-associated transmission of L. garvieae in three pediatric hospitalized hematology patients. This highlights the importance to implement the screening of platelet components with new human-defined pathogens for ensuring the safety of blood supply, and more broadly, for the surveillance of emerging pathogens.
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Affiliation(s)
- Luna Colagrossi
- Department of Laboratories, Unit of Diagnostic Microbiology and Immunology and Multimodal Medicine Area, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Valentino Costabile
- Department of Laboratories, Unit of Diagnostic Microbiology and Immunology and Multimodal Medicine Area, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Rossana Scutari
- Department of Laboratories, Unit of Diagnostic Microbiology and Immunology and Multimodal Medicine Area, Bambino Gesù Children's Hospital IRCCS, Rome, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Marilena Agosta
- Department of Laboratories, Unit of Diagnostic Microbiology and Immunology and Multimodal Medicine Area, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Manuela Onori
- Department of Laboratories, Unit of Diagnostic Microbiology and Immunology and Multimodal Medicine Area, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Livia Mancinelli
- Department of Laboratories, Unit of Diagnostic Microbiology and Immunology and Multimodal Medicine Area, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Barbara Lucignano
- Department of Laboratories, Unit of Diagnostic Microbiology and Immunology and Multimodal Medicine Area, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Andrea Onetti Muda
- Department of Laboratories, Unit of Diagnostic Microbiology and Immunology and Multimodal Medicine Area, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Giada Del Baldo
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Angela Mastronuzzi
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Guglielmo Trua
- Department of Transfusion Medicine, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Mauro Montanari
- Department of Transfusion Medicine, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Claudia Alteri
- Department of Laboratories, Unit of Diagnostic Microbiology and Immunology and Multimodal Medicine Area, Bambino Gesù Children's Hospital IRCCS, Rome, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Paola Bernaschi
- Department of Laboratories, Unit of Diagnostic Microbiology and Immunology and Multimodal Medicine Area, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Carlo Federico Perno
- Department of Laboratories, Unit of Diagnostic Microbiology and Immunology and Multimodal Medicine Area, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
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65
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Mahjabeen F, Saha U, Mostafa MN, Siddique F, Ahsan E, Fathma S, Tasnim A, Rahman T, Faruq R, Sakibuzzaman M, Dilnaz F, Ashraf A. An Update on Treatment Options for Methicillin-Resistant Staphylococcus aureus (MRSA) Bacteremia: A Systematic Review. Cureus 2022; 14:e31486. [DOI: 10.7759/cureus.31486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2022] [Indexed: 11/16/2022] Open
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66
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Liu S, Deng S, Liu H, Tang L, Wang M, Xin B, Li F. Four Novel Leaderless Bacteriocins, Bacin A1, A2, A3, and A4 Exhibit Potent Antimicrobial and Antibiofilm Activities against Methicillin-Resistant Staphylococcus aureus. Microbiol Spectr 2022; 10:e0094522. [PMID: 36000904 PMCID: PMC9602277 DOI: 10.1128/spectrum.00945-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/26/2022] [Indexed: 12/30/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a major bacterial pathogen that causes hospital- and community-acquired infections. Owing to its multidrug resistance, it is imperative to develop new antimicrobial agents to treat MRSA infections. In this study, using genome mining analysis and a culture-based screening method to detect bacteriocin activity, we screened a strain, Bacillus sp. TL12, which harbored a putative leaderless bacteriocin gene cluster (bac gene cluster) and exhibited potent anti-MRSA activity. The antimicrobial agents, products of the bac gene cluster, were purified and identified as four novel leaderless bacteriocins: bacin A1, A2, A3, and A4. Bacin A2 was evaluated as a representative antimicrobial agent and showed remarkable antimicrobial activity against S. aureus, MRSA, and the foodborne pathogens Listeria monocytogenes and Bacillus cereus. Mechanistic experiments revealed that bacin A2 damaged cell membranes and exhibited bactericidal activity against MRSA. Bacin A2 effectively inhibited the formation of S. aureus and MRSA biofilms (>0.5× MIC) and killed the cells in their established biofilms (>4× MIC). The hemolytic and NIH/3T3 cytotoxicity assay results for bacin A2 confirmed its biosafety. Thus, bacins have potential as alternative antimicrobial agents for treating MRSA infections. IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is a major human pathogen that is difficult to treat because of its resistance to several widely used antibiotics. The present study aimed to identify novel anti-MRSA bacteriocins in a prominent producer of bacteriocins, Bacillus cereus group. Four novel leaderless bacteriocins, bacin A1, A2, A3, and A4, which show potent bactericidal effect against S. aureus and MRSA, were identified in Bacillus sp. TL12. Moreover, bacins inhibited biofilm formation and killed cells in the established biofilms of S. aureus and MRSA. These findings suggest that bacins are promising alternatives to treat MRSA infections.
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Affiliation(s)
- Shu Liu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui Province, China
| | - Shulin Deng
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui Province, China
| | - Hualin Liu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Liang Tang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui Province, China
| | - Mengqi Wang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui Province, China
| | - Bingyue Xin
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui Province, China
| | - Feng Li
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui Province, China
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67
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Li D, Yi J, Han G, Qiao L. MALDI-TOF Mass Spectrometry in Clinical Analysis and Research. ACS MEASUREMENT SCIENCE AU 2022; 2:385-404. [PMID: 36785658 PMCID: PMC9885950 DOI: 10.1021/acsmeasuresciau.2c00019] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/15/2022] [Accepted: 07/15/2022] [Indexed: 05/04/2023]
Abstract
In the decade after being awarded the Nobel Prize in Chemistry in 2002, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been widely used as an analytical chemistry tool for the detection of large and small molecules (e.g., polymers, proteins, peptides, nucleic acids, amino acids, lipids, etc.) and for clinical analysis and research (e.g., pathogen identification, genetic disorders screening, cancer diagnosis, etc.). In view of the fast development of MALDI-TOF MS in clinical usage, this review systematically summarizes the most important applications of MALDI-TOF MS in clinical analysis and research by analyzing MALDI TOF MS-related reviews collected in the Web of Science database. On the basis of the analysis of keyword co-occurrence of over 2000 review articles, four themes consisting of "pathogen identification", "disease diagnosis", "nucleic acids analysis", and "small molecules analysis" were found. For each theme, the review further outlined their application implications, analytical methods, and systems as well as limitations that need to be addressed. Overall, the review summarizes and elaborates on the clinical applications of MALDI-TOF MS, providing a comprehensive picture for researchers embarking on MALDI TOF MS-related clinical analysis and research.
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68
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Olsen RJ, Zhu L, Mangham RE, Faili A, Kayal S, Beres SB, Musser JM. A Chimeric Penicillin Binding Protein 2X Significantly Decreases in Vitro Beta-Lactam Susceptibility and Increases in Vivo Fitness of Streptococcus pyogenes. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:1397-1406. [PMID: 35843262 PMCID: PMC9552024 DOI: 10.1016/j.ajpath.2022.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
All tested strains of Streptococcus pyogenes (group A streptococcus, GAS) remain susceptible to penicillin. However, GAS strains with amino acid substitutions in penicillin-binding proteins that confer decreased susceptibility to beta-lactam antibiotics have been identified recently. This discovery raises concerns about emergence of beta-lactam antibiotic resistance in GAS. Whole genome sequencing recently identified GAS strains with a chimeric penicillin-binding protein 2X (PBP2X) containing a recombinant segment from Streptococcus dysgalactiae subspecies equisimilis (SDSE). To directly test the hypothesis that the chimeric SDSE-like PBP2X alters beta-lactam susceptibility in vitro and fitness in vivo, an isogenic mutant strain was generated and virulence assessed in a mouse model of necrotizing myositis. Compared with naturally occurring and isogenic strains with a wild-type GAS-like PBP2X, strains with the chimeric SDSE-like PBP2X had reduced susceptibility in vitro to nine beta-lactam antibiotics. In a mouse model of necrotizing myositis, the strains had identical fitness in the absence of benzylpenicillin treatment. However, mice treated intermittently with a subtherapeutic dose of benzylpenicillin had significantly more colony-forming units recovered from limbs infected with strains with the chimeric SDSE-like PBP2X. These results show that mutations such as the PBP2X chimera may result in significantly decreased beta-lactam susceptibility and increased fitness and virulence. Expanded diagnostic laboratory surveillance, genome sequencing, and molecular pathogenesis study of potentially emergent beta-lactam antibiotic resistance among GAS are needed.
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Affiliation(s)
- Randall J Olsen
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, New York.
| | - Luchang Zhu
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, New York
| | - Regan E Mangham
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Ahmad Faili
- Inserm, CIC 1414, Rennes, France; Faculty of Pharmacy, Université Rennes 1, Rennes, France; CHU de Rennes, Rennes, France
| | - Samer Kayal
- Inserm, CIC 1414, Rennes, France; CHU de Rennes, Rennes, France; Faculty of Medicine, Université Rennes 1, Rennes, France
| | - Stephen B Beres
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - James M Musser
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, New York
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69
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Emergence and spread of antibiotic-resistant foodborne pathogens from farm to table. Food Sci Biotechnol 2022; 31:1481-1499. [PMID: 36065433 PMCID: PMC9435411 DOI: 10.1007/s10068-022-01157-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/26/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Antibiotics have been overused and misused for preventive and therapeutic purposes. Specifically, antibiotics are frequently used as growth promoters for improving productivity and performance of food-producing animals such as pigs, cattle, and poultry. The increasing use of antibiotics has been of great concern worldwide due to the emergence of antibiotic resistant bacteria. Food-producing animals are considered reservoirs for antibiotic resistance genes (ARGs) and residual antibiotics that transfer from the farm through the table. The accumulation of residual antibiotics can lead to additional antibiotic resistance in bacteria. Therefore, this review evaluates the risk of carriage and spread of antibiotic resistance through food chain and the potential impact of antibiotic use in food-producing animals on food safety. This review also includes in-depth discussion of promising antibiotic alternatives such as vaccines, immune modulators, phytochemicals, antimicrobial peptides, probiotics, and bacteriophages.
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70
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Aribisala JO, Sabiu S. Cheminformatics Identification of Phenolics as Modulators of Penicillin-Binding Protein 2a of Staphylococcus aureus: A Structure–Activity-Relationship-Based Study. Pharmaceutics 2022; 14:pharmaceutics14091818. [PMID: 36145565 PMCID: PMC9503099 DOI: 10.3390/pharmaceutics14091818] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 01/16/2023] Open
Abstract
The acquisition of penicillin-binding protein (PBP) 2a in resistant strains of Staphylococcus aureus allows for the continuous production of cell walls even after the inactivation of intrinsic PBPs. Thus, the discovery of novel therapeutics with enhanced modulatory activity on PBP2a is crucial, and plant secondary metabolites, such as phenolics, have found relevance in this regard. In this study, using computational techniques, phenolics were screened against the active site of PBP2a, and the ability of the lead phenolics to modulate PBP2a’s active and allosteric sites was studied. The top-five phenolics (leads) identified through structure–activity-based screening, pharmacokinetics and synthetic feasibility evaluations were subjected to molecular dynamics simulations. Except for propan-2-one at the active site, the leads had a higher binding free energy at both the active and allosteric sites of PBP2a than amoxicillin. The leads, while promoting the thermodynamic stability of PBP2a, showed a more promising affinity at the allosteric site than the active site, with silicristin (−25.61 kcal/mol) and epicatechin gallate (−47.65 kcal/mol) having the best affinity at the active and allosteric sites, respectively. Interestingly, the modulation of Tyr446, the active site gatekeeper residue in PBP2a, was noted to correlate with the affinity of the leads at the allosteric site. Overall, these observations point to the leads’ ability to inhibit PBP2a, either directly or through allosteric modulation with conventional drugs. Further confirmatory in vitro studies on the leads are underway.
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Hemez C, Clarelli F, Palmer AC, Bleis C, Abel S, Chindelevitch L, Cohen T, Abel zur Wiesch P. Mechanisms of antibiotic action shape the fitness landscapes of resistance mutations. Comput Struct Biotechnol J 2022; 20:4688-4703. [PMID: 36147681 PMCID: PMC9463365 DOI: 10.1016/j.csbj.2022.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 11/15/2022] Open
Abstract
Antibiotic-resistant pathogens are a major public health threat. A deeper understanding of how an antibiotic's mechanism of action influences the emergence of resistance would aid in the design of new drugs and help to preserve the effectiveness of existing ones. To this end, we developed a model that links bacterial population dynamics with antibiotic-target binding kinetics. Our approach allows us to derive mechanistic insights on drug activity from population-scale experimental data and to quantify the interplay between drug mechanism and resistance selection. We find that both bacteriostatic and bactericidal agents can be equally effective at suppressing the selection of resistant mutants, but that key determinants of resistance selection are the relationships between the number of drug-inactivated targets within a cell and the rates of cellular growth and death. We also show that heterogeneous drug-target binding within a population enables resistant bacteria to evolve fitness-improving secondary mutations even when drug doses remain above the resistant strain's minimum inhibitory concentration. Our work suggests that antibiotic doses beyond this "secondary mutation selection window" could safeguard against the emergence of high-fitness resistant strains during treatment.
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Affiliation(s)
- Colin Hemez
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Graduate Program in Biophysics, Harvard University, Boston, MA 02115, USA
- Corresponding authors at: Broad Institute, 75 Ames St, Room 3035, Cambridge, MA 02412, USA (C. Hemez). Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway (P. Abel zur Wiesch).
| | - Fabrizio Clarelli
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Adam C. Palmer
- Department of Pharmacology, Computational Medicine Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christina Bleis
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Sören Abel
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Division of Infection Control, Norwegian Institute of Public Health, Oslo 0318, Norway
| | - Leonid Chindelevitch
- Department of Infectious Disease Epidemiology, Imperial College, London SW7 2AZ, UK
| | - Theodore Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA
| | - Pia Abel zur Wiesch
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Division of Infection Control, Norwegian Institute of Public Health, Oslo 0318, Norway
- Corresponding authors at: Broad Institute, 75 Ames St, Room 3035, Cambridge, MA 02412, USA (C. Hemez). Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway (P. Abel zur Wiesch).
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Chudyk EI, Beer M, Limb MAL, Jones CA, Spencer J, van der Kamp MW, Mulholland AJ. QM/MM Simulations Reveal the Determinants of Carbapenemase Activity in Class A β-Lactamases. ACS Infect Dis 2022; 8:1521-1532. [PMID: 35877936 PMCID: PMC9379904 DOI: 10.1021/acsinfecdis.2c00152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Indexed: 11/28/2022]
Abstract
β-lactam antibiotic resistance in Gram-negative bacteria, primarily caused by β-lactamase enzymes that hydrolyze the β-lactam ring, has become a serious clinical problem. Carbapenems were formerly considered "last resort" antibiotics because they escaped breakdown by most β-lactamases, due to slow deacylation of the acyl-enzyme intermediate. However, an increasing number of Gram-negative bacteria now produce β-lactamases with carbapenemase activity: these efficiently hydrolyze the carbapenem β-lactam ring, severely limiting the treatment of some bacterial infections. Here, we use quantum mechanics/molecular mechanics (QM/MM) simulations of the deacylation reactions of acyl-enzyme complexes of eight β-lactamases of class A (the most widely distributed β-lactamase group) with the carbapenem meropenem to investigate differences between those inhibited by carbapenems (TEM-1, SHV-1, BlaC, and CTX-M-16) and those that hydrolyze them (SFC-1, KPC-2, NMC-A, and SME-1). QM/MM molecular dynamics simulations confirm the two enzyme groups to differ in the preferred acyl-enzyme orientation: carbapenem-inhibited enzymes favor hydrogen bonding of the carbapenem hydroxyethyl group to deacylating water (DW). QM/MM simulations of deacylation give activation free energies in good agreement with experimental hydrolysis rates, correctly distinguishing carbapenemases. For the carbapenem-inhibited enzymes, free energies for deacylation are significantly higher than for the carbapenemases, even when the hydroxyethyl group was restrained to prevent interaction with the DW. Analysis of these simulations, and additional simulations of mutant enzymes, shows how factors including the hydroxyethyl orientation, the active site volume, and architecture (conformations of Asn170 and Asn132; organization of the oxyanion hole; and the Cys69-Cys238 disulfide bond) collectively determine catalytic efficiency toward carbapenems.
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Affiliation(s)
- Ewa I. Chudyk
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Michael Beer
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
- School
of Cellular and Molecular Medicine, University
of Bristol Medical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Michael A. L. Limb
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Charlotte A. Jones
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - James Spencer
- School
of Cellular and Molecular Medicine, University
of Bristol Medical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Marc W. van der Kamp
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
- School
of Biochemistry, University of Bristol Medical
Sciences Building, University Walk, Bristol BS8 1TD, United
Kingdom
| | - Adrian J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
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73
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Takata M, Ubukata K, Miyazaki H, Iwata S, Nakamura S. Diversity of amino acid substitutions of penicillin-binding proteins in penicillin-non-susceptible and non-vaccine type Streptococcus pneumoniae. J Infect Chemother 2022; 28:1523-1530. [PMID: 35963598 DOI: 10.1016/j.jiac.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/28/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022]
Abstract
PURPOSE In Japan, the introduction of pneumococcal conjugate vaccine (PCV) in children has decreased vaccine-type (VT) pneumococcal infections caused by penicillin (PEN)-non-susceptible Streptococcus pneumoniae. PEN-non-susceptible strains have gradually emerged among non-vaccine types (NVT). In this study, we aim to investigate the pbp gene mutations and the characteristics of PEN-binding proteins (PBPs) that mediate PEN resistance in NVT strains. MATERIALS AND METHODS Pneumococcal 41 strains of NVT isolated from patients with invasive pneumococcal infection were randomly selected. Nucleotide sequences for pbp genes encoding PBP1A, PBP2X, and PBP2B were analyzed, and amino acid (AA) substitutions that contribute to β-lactam resistance were identified. In addition, the three-dimensional (3D) structure of abnormal PBPs in the resistant strain was compared with that of a reference R6 strain via homology modeling. RESULTS In PEN-non-susceptible NVT strains, Thr to Ala or Ser substitutions in the conserved AA motif (STMK) were important in PBP1A and PBP2X. In PBP2B, substitutions from Thr to Ala, adjacent to the SSN motif, and from Glu to Gly were essential. The 3D structure modeling indicated that AA substitutions are characterized by accumulation around the enzymatic active pocket in PBPs. Many AA substitutions detected throughout the PBP domains were not associated with resistance, except for AA substitutions in or adjacent to AA motifs. Clonal complexes and sequence types showed that almost all NVT cases originated in other countries and spread to Japan via repeat mutations. CONCLUSIONS NVT with diverse AA substitutions increased gradually with pressure from both antimicrobial agents and vaccines.
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Affiliation(s)
- Misako Takata
- Department of Microbiology, Tokyo Medical University, Tokyo, Japan
| | - Kimiko Ubukata
- Department of Microbiology, Tokyo Medical University, Tokyo, Japan; Department of General Medicine, Keio University School of Medicine, Tokyo, Japan.
| | - Haruko Miyazaki
- Department of Microbiology, Tokyo Medical University, Tokyo, Japan
| | - Satoshi Iwata
- Department of Infectious Diseases, National Cancer Hospital, Tokyo, Japan; Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Shigeki Nakamura
- Department of Microbiology, Tokyo Medical University, Tokyo, Japan
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74
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Volov A, Shkodenko L, Koshel E, Drozdov AS. Bio-Inspired Surface Modification of Magnetite Nanoparticles with Dopamine Conjugates. NANOMATERIALS 2022; 12:nano12132230. [PMID: 35808066 PMCID: PMC9268593 DOI: 10.3390/nano12132230] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/24/2022] [Accepted: 06/26/2022] [Indexed: 11/25/2022]
Abstract
Organically-coated nanomaterials are intensively studied and find numerous applications in a wide range of areas from optics to biomedicine. One of the recent trends in material science is the application of bio-mimetic polydopamine coatings that can be produced on a variety of substrates in a cost-efficient way under mild conditions. Such coatings not only modify the biocompatibility of the material but also add functional amino groups to the surface that can be further modified by classic conjugation techniques. Here we show an alternative strategy for substrates modification using dopamine conjugates instead of native dopamine. Compared to the classic scheme, the proposed strategy allows separation of the “organic” and “colloidal” stages, and simplified identification and purification steps. Modification with pre-modified dopamine made it possible to achieve high loading capacities with active components up to 10.5% wt. A series of organo-inorganic hybrids were synthesized and their bioactivity was analyzed.
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Affiliation(s)
- Alexander Volov
- Department of Chemistry, Moscow State University, 119234 Moscow, Russia;
| | - Liubov Shkodenko
- SCAMT Institute, ITMO University, 191002 Saint Petersburg, Russia; (L.S.); (E.K.)
| | - Elena Koshel
- SCAMT Institute, ITMO University, 191002 Saint Petersburg, Russia; (L.S.); (E.K.)
| | - Andrey S. Drozdov
- Laboratory of Nanobiotechnologies, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Moscow Region, Russia
- Correspondence:
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75
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Shirley JD, Nauta KM, Carlson EE. Live-Cell Profiling of Penicillin-Binding Protein Inhibitors in Escherichia coli MG1655. ACS Infect Dis 2022; 8:1241-1252. [PMID: 35763562 PMCID: PMC10040144 DOI: 10.1021/acsinfecdis.2c00004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Penicillin-binding proteins (PBPs) make up an essential class of bacterial enzymes that carry out the final steps of peptidoglycan synthesis and regulate the recycling of this polymeric structure. PBPs are an excellent drug target and have been the most clinically relevant antibacterial target since the 1940s with the introduction of β-lactams. Despite this, a large gap in knowledge remains regarding the individual function and regulation of each PBP homologue in most bacteria. This can be attributed to a lack of chemical tools and methods that enable the study of individual PBPs in an activity-dependent manner and in their native environment. The development of such methods in Gram-negative bacteria has been particularly challenging due to the presence of an outer membrane and numerous resistance mechanisms. To address this, we have developed an optimized live-cell assay for screening inhibitors of the PBPs in Escherichia coli MG1655. We utilized EDTA to permeabilize Gram-negative cells, enabling increased penetration of our readout probe, Bocillin-FL, and subsequent analysis of PBP-inhibition profiles. To identify scaffolds for future development of PBP-selective activity-based probes, we screened ten β-lactams, one diazabicyclooctane, and one monobactam for their PBP-selectivity profiles in E. coli MG1655. These results demonstrate the utility of our assay for the screening of inhibitors in live, non-hypersusceptible Gram-negative organisms.
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Affiliation(s)
- Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota, 208 Harvard Street SE, Minneapolis, Minnesota 55454, United States
| | - Kelsie M Nauta
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Erin E Carlson
- Department of Medicinal Chemistry, University of Minnesota, 208 Harvard Street SE, Minneapolis, Minnesota 55454, United States.,Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55454, United States.,Department of Pharmacology, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55454, United States
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76
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Zhang Y, Chen C, Cheng B, Gao L, Qin C, Zhang L, Zhang X, Wang J, Wan Y. Discovery of Quercetin and Its Analogs as Potent OXA-48 Beta-Lactamase Inhibitors. Front Pharmacol 2022; 13:926104. [PMID: 35814247 PMCID: PMC9258905 DOI: 10.3389/fphar.2022.926104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Carbapenem resistance in Enterobacteriaceae caused by OXA-48 β-lactamase is a growing global health threat and has rapidly spread in many regions of the world. Developing inhibitors is a promising way to overcome antibiotic resistance. However, there are few options for problematic OXA-48. Here we identified quercetin, fisetin, luteolin, 3′,4′,7-trihydroxyflavone, apigenin, kaempferol, and taxifolin as potent inhibitors of OXA-48 with IC50 values ranging from 0.47 to 4.54 μM. Notably, the structure-activity relationship revealed that the substitute hydroxyl groups in the A and B rings of quercetin and its structural analogs improved the inhibitory effect against OXA-48. Mechanism studies including enzymatic kinetic assay, isothermal titration calorimetry (ITC), and surface plasmon resonance (SPR) analysis demonstrated that quercetin reversibly inhibited OXA-48 through a noncompetitive mode. Molecular docking suggested that hydroxyl groups at the 3′, 4′ and 7 positions in flavonoids formed hydrogen-bonding interactions with the side chains of Thr209, Ala194, and Gln193 in OXA-48. Quercetin, fisetin, luteolin, and 3′,4′,7-trihydroxyflavone effectively restored the antibacterial efficacy of piperacillin or imipenem against E. coli producing OXA-48, resulting in 2–8-fold reduction in MIC. Moreover, quercetin combined with piperacillin showed antimicrobial efficacy in mice infection model. These studies provide potential lead compounds for the development of β-lactamase inhibitors and in combination with β-lactams to combat OXA-48 producing pathogen.
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Affiliation(s)
- Yuejuan Zhang
- Microbiology Institute of Shaanxi, Xi’an, China
- Engineering Center of Qinling Mountains Natural Products, Shaanxi Academy of Sciences, Xi’an, China
| | - Cheng Chen
- College of Forestry, Northwest A&F University, Yangling, China
| | - Bin Cheng
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Lei Gao
- Microbiology Institute of Shaanxi, Xi’an, China
- Engineering Center of Qinling Mountains Natural Products, Shaanxi Academy of Sciences, Xi’an, China
| | - Chuan Qin
- Microbiology Institute of Shaanxi, Xi’an, China
- Engineering Center of Qinling Mountains Natural Products, Shaanxi Academy of Sciences, Xi’an, China
| | - Lixia Zhang
- Clinical Laboratory, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Xu Zhang
- Microbiology Institute of Shaanxi, Xi’an, China
- Engineering Center of Qinling Mountains Natural Products, Shaanxi Academy of Sciences, Xi’an, China
| | - Jun Wang
- Microbiology Institute of Shaanxi, Xi’an, China
- Engineering Center of Qinling Mountains Natural Products, Shaanxi Academy of Sciences, Xi’an, China
| | - Yi Wan
- Microbiology Institute of Shaanxi, Xi’an, China
- Engineering Center of Qinling Mountains Natural Products, Shaanxi Academy of Sciences, Xi’an, China
- *Correspondence: Yi Wan,
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77
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Penicillin-Binding Protein 1 (PBP1) of Staphylococcus aureus Has Multiple Essential Functions in Cell Division. mBio 2022; 13:e0066922. [PMID: 35703435 PMCID: PMC9426605 DOI: 10.1128/mbio.00669-22] [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] [Indexed: 11/28/2022] Open
Abstract
Bacterial cell division is a complex process requiring the coordination of multiple components to allow the appropriate spatial and temporal control of septum formation and cell scission. Peptidoglycan (PG) is the major structural component of the septum, and our recent studies in the human pathogen Staphylococcus aureus have revealed a complex, multistage PG architecture that develops during septation. Penicillin-binding proteins (PBPs) are essential for the final steps of PG biosynthesis; their transpeptidase activity links the peptide side chains of nascent glycan strands. PBP1 is required for cell division in S. aureus, and here, we demonstrate that it has multiple essential functions associated with its enzymatic activity and as a regulator of division. Loss of PBP1, or just its C-terminal PASTA domains, results in cessation of division at the point of septal plate formation. The PASTA domains can bind PG and thereby potentially coordinate the cell division process. The transpeptidase activity of PBP1 is also essential, but its loss leads to a strikingly different phenotype of thickened and aberrant septa, which is phenocopied by the morphological effects of adding the PBP1-specific β-lactam, meropenem. Together, these results lead to a model for septal PG synthesis where PBP1 enzyme activity is required for the characteristic architecture of the septum and PBP1 protein molecules enable the formation of the septal plate.
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78
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Apostolos AJ, Ocius KL, Koyasseril-Yehiya TM, Santamaria C, Silva JRA, Lameira J, Alves CN, Siegrist MS, Pires MM. Metabolic Processing of Selenium-Based Bioisosteres of meso-Diaminopimelic Acid in Live Bacteria. Biochemistry 2022; 61:1404-1414. [PMID: 35687722 DOI: 10.1021/acs.biochem.2c00120] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A primary component of all known bacterial cell walls is the peptidoglycan (PG) layer, which is composed of repeating units of sugars connected to short and unusual peptides. The various steps within PG biosynthesis are targets of potent antibiotics as proper assembly of the PG is essential for cellular growth and survival. Synthetic mimics of PG have proven to be indispensable tools to study the bacterial cell structure, growth, and remodeling. Yet, a common component of PG, meso-diaminopimelic acid (m-DAP) at the third position of the stem peptide, remains challenging to access synthetically and is not commercially available. Here, we describe the synthesis and metabolic processing of a selenium-based bioisostere of m-DAP (selenolanthionine) and show that it is installed within the PG of live bacteria by the native cell wall crosslinking machinery in mycobacterial species. This PG probe has an orthogonal release mechanism that could be important for downstream proteomics studies. Finally, we describe a bead-based assay that is compatible with high-throughput screening of cell wall enzymes. We envision that this probe will supplement the current methods available for investigating PG crosslinking in m-DAP-containing organisms.
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Affiliation(s)
- Alexis J Apostolos
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Karl L Ocius
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | | | - Carolina Santamaria
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts 01003-9298, United States.,Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003-9298, United States
| | - José Rogério A Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará 66075-110, Brazil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará 66075-110, Brazil
| | - Cláudio N Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará 66075-110, Brazil
| | - M Sloan Siegrist
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts 01003-9298, United States.,Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003-9298, United States
| | - Marcos M Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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79
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Malla TR, Brewitz L, Muntean DG, Aslam H, Owen CD, Salah E, Tumber A, Lukacik P, Strain-Damerell C, Mikolajek H, Walsh MA, Schofield CJ. Penicillin Derivatives Inhibit the SARS-CoV-2 Main Protease by Reaction with Its Nucleophilic Cysteine. J Med Chem 2022; 65:7682-7696. [PMID: 35549342 PMCID: PMC9115881 DOI: 10.1021/acs.jmedchem.1c02214] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Indexed: 12/05/2022]
Abstract
The SARS-CoV-2 main protease (Mpro) is a medicinal chemistry target for COVID-19 treatment. Given the clinical efficacy of β-lactams as inhibitors of bacterial nucleophilic enzymes, they are of interest as inhibitors of viral nucleophilic serine and cysteine proteases. We describe the synthesis of penicillin derivatives which are potent Mpro inhibitors and investigate their mechanism of inhibition using mass spectrometric and crystallographic analyses. The results suggest that β-lactams have considerable potential as Mpro inhibitors via a mechanism involving reaction with the nucleophilic cysteine to form a stable acyl-enzyme complex as shown by crystallographic analysis. The results highlight the potential for inhibition of viral proteases employing nucleophilic catalysis by β-lactams and related acylating agents.
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Affiliation(s)
- Tika R. Malla
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Lennart Brewitz
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Dorian-Gabriel Muntean
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Hiba Aslam
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - C. David Owen
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Eidarus Salah
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Anthony Tumber
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Petra Lukacik
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Claire Strain-Damerell
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Halina Mikolajek
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Martin A. Walsh
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
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80
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Atze H, Liang Y, Hugonnet JE, Gutierrez A, Rusconi F, Arthur M. Heavy isotope labeling and mass spectrometry reveal unexpected remodeling of bacterial cell wall expansion in response to drugs. eLife 2022; 11:72863. [PMID: 35678393 PMCID: PMC9249393 DOI: 10.7554/elife.72863] [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: 08/06/2021] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
Antibiotics of the β-lactam (penicillin) family inactivate target enzymes called D,D-transpeptidases or penicillin-binding proteins (PBPs) that catalyze the last cross-linking step of peptidoglycan synthesis. The resulting net-like macromolecule is the essential component of bacterial cell walls that sustains the osmotic pressure of the cytoplasm. In Escherichia coli, bypass of PBPs by the YcbB L,D-transpeptidase leads to resistance to these drugs. We developed a new method based on heavy isotope labeling and mass spectrometry to elucidate PBP- and YcbB-mediated peptidoglycan polymerization. PBPs and YcbB similarly participated in single-strand insertion of glycan chains into the expanding bacterial side wall. This absence of any transpeptidase-specific signature suggests that the peptidoglycan expansion mode is determined by other components of polymerization complexes. YcbB did mediate β-lactam resistance by insertion of multiple strands that were exclusively cross-linked to existing tripeptide-containing acceptors. We propose that this undocumented mode of polymerization depends upon accumulation of linear glycan chains due to PBP inactivation, formation of tripeptides due to cleavage of existing cross-links by a β-lactam-insensitive endopeptidase, and concerted cross-linking by YcbB.
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Affiliation(s)
- Heiner Atze
- INSERM, UMR-S 1138, Centre de Recherche des Cordeliers, Paris, France
| | | | | | - Arnaud Gutierrez
- INSERM, UMR-S 1138, Centre de Recherche des Cordeliers, Paris, France
| | | | - Michel Arthur
- INSERM, UMR-S 1138, Centre de Recherche des Cordeliers, Paris, France
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81
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Gupta A, Verma S, Javed R, Sudhakar S, Srivastava S, Nair NN. Exploration of high dimensional free energy landscapes by a combination of temperature-accelerated sliced sampling and parallel biasing. J Comput Chem 2022; 43:1186-1200. [PMID: 35510789 DOI: 10.1002/jcc.26882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/27/2022] [Accepted: 04/11/2022] [Indexed: 12/22/2022]
Abstract
Temperature-accelerated sliced sampling (TASS) is an enhanced sampling method for achieving accelerated and controlled exploration of high-dimensional free energy landscapes in molecular dynamics simulations. With the aid of umbrella bias potentials, the TASS method realizes a controlled exploration and divide-and-conquer strategy for computing high-dimensional free energy surfaces. In TASS, diffusion of the system in the collective variable (CV) space is enhanced with the help of metadynamics bias and elevated-temperature of the auxiliary degrees of freedom (DOF) that are coupled to the CVs. Usually, a low-dimensional metadynamics bias is applied in TASS. In order to further improve the performance of TASS, we propose here to use a highdimensional metadynamics bias, in the same form as in a parallel bias metadynamics scheme. Here, a modified reweighting scheme, in combination with artificial neural network is used for computing unbiased probability distribution of CVs and projections of high-dimensional free energy surfaces. We first validate the accuracy and efficiency of our method in computing the four-dimensional free energy landscape for alanine tripeptide in vacuo. Subsequently, we employ the approach to calculate the eight-dimensional free energy landscape of alanine pentapeptide in vacuo. Finally, the method is applied to a more realistic problem wherein we compute the broad four-dimensional free energy surface corresponding to the deacylation of a drug molecule which is covalently complexed with a β-lactamase enzyme. We demonstrate that using parallel bias in TASS improves the efficiency of exploration of high-dimensional free energy landscapes.
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Affiliation(s)
- Abhinav Gupta
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Shivani Verma
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Ramsha Javed
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Suraj Sudhakar
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Saurabh Srivastava
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India.,Department of Chemistry, Manipal University Jaipur, Jaipur, Rajasthan, India
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
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82
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Oluwole AO, Corey RA, Brown CM, Hernández-Rocamora VM, Stansfeld PJ, Vollmer W, Bolla JR, Robinson CV. Peptidoglycan biosynthesis is driven by lipid transfer along enzyme-substrate affinity gradients. Nat Commun 2022; 13:2278. [PMID: 35477938 PMCID: PMC9046198 DOI: 10.1038/s41467-022-29836-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 03/31/2022] [Indexed: 01/02/2023] Open
Abstract
Maintenance of bacterial cell shape and resistance to osmotic stress by the peptidoglycan (PG) renders PG biosynthetic enzymes and precursors attractive targets for combating bacterial infections. Here, by applying native mass spectrometry, we elucidate the effects of lipid substrates on the PG membrane enzymes MraY, MurG, and MurJ. We show that dimerization of MraY is coupled with binding of the carrier lipid substrate undecaprenyl phosphate (C55-P). Further, we demonstrate the use of native MS for biosynthetic reaction monitoring and find that the passage of substrates and products is controlled by the relative binding affinities of the different membrane enzymes. Overall, we provide a molecular view of how PG membrane enzymes convey lipid precursors through favourable binding events and highlight possible opportunities for intervention. Bacterial cell wall enzymes and their precursors are critical targets for antibiotic development. Here, the authors investigate several biosynthetic enzymes with their substrates and show that the passage of substrates and products in the pathway is controlled by their relative binding affinities.
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Affiliation(s)
- Abraham O Oluwole
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.,The Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford, OX1 3QU, UK
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Chelsea M Brown
- School of Life Sciences and Department of Chemistry, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK
| | - Victor M Hernández-Rocamora
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.,School of Life Sciences and Department of Chemistry, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Jani R Bolla
- The Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford, OX1 3QU, UK. .,Department of Plant Sciences/Biology, University of Oxford, Oxford, OX1 3RB, UK.
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK. .,The Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford, OX1 3QU, UK.
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83
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Wajima T, Hagimoto A, Tanaka E, Kawamura Y, Nakaminami H. Identification and characterization of a novel multidrug-resistant streptococcus, Streptococcus toyakuensis sp. nov., from a blood sample. J Glob Antimicrob Resist 2022; 29:316-322. [DOI: 10.1016/j.jgar.2022.04.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/06/2022] [Accepted: 04/26/2022] [Indexed: 11/28/2022] Open
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84
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Zhou M, Wang L, Wang Z, Kudinha T, Wang Y, Xu Y, Liu Z. Molecular Characterization of Penicillin-Binding Protein2x, 2b and 1a of Streptococcus pneumoniae Causing Invasive Pneumococcal Diseases in China: A Multicenter Study. Front Microbiol 2022; 13:838790. [PMID: 35300486 PMCID: PMC8921733 DOI: 10.3389/fmicb.2022.838790] [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: 12/18/2021] [Accepted: 01/19/2022] [Indexed: 11/26/2022] Open
Abstract
Streptococcus pneumoniae is a common human pathogen that can cause severe invasive pneumococcal diseases (IPDs). Penicillin-binding proteins (PBPs) are the targets for β-lactam antibiotics (BLAs), which are the common empirical drugs for treatment of pneumococcal infection. This study investigated the serotype distribution and antibiotic resistance patterns of S. pneumoniae strains causing IPD in China, including exploring the association between penicillin (PEN) susceptibility and PBPs variations. A total of 300 invasive S. pneumoniae isolates were collected from 27 teaching hospitals in China (2010-2015). Serotypes were determined by Quellung reaction. Serotypes 23F and 19F were the commonest serotypes in isolates from cerebrospinal fluid (CSF), whilst serotypes 19A and 23F were most commonly seen in non-CSF specimens. Among the 300 invasive S. pneumoniae strains, only one strain (serotype 6A, MIC = 0.25 μg/ml) with PEN MIC value ≤ 0.25 μg/ml did not have any substitutions in the PBPs active sites. All the strains with PEN MIC value ≥ 0.5 μg/ml had different substitutions within PBPs active sites. Substitutions in PBP2b and PBP2x active sites were common in low-level penicillin-resistant S. pneumoniae (PRSP) strains (MIC = 0.5 μg/ml), with or without PBP1a substitution, while all strains with PEN MIC ≥ 1 μg/ml had substitutions in PBP1a active sites, accompanied by PBP2b and PBP2x active site substitutions. Based on the three PBPs substitution combinations, a high degree of diversity was observed amongst the isolates. This study provides some new insights for understanding the serology and antibiotic resistance dynamics of S. pneumoniae causing IPD in China. However, further genomic studies are needed to facilitate a comprehensive understanding of antibiotic resistance mechanisms of S. pneumoniae.
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Affiliation(s)
- Menglan Zhou
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Lulu Wang
- Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Ziran Wang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Timothy Kudinha
- School of Biomedical Sciences, Charles Sturt University, Orange, NSW, Australia.,NSW Health Pathology, Regional and Rural, Orange Hospital, Orange, NSW, Australia
| | - Yao Wang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Zhengyin Liu
- Department of Infectious Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
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85
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Sharan D, Carlson EE. Expanded profiling of β-lactam selectivity for penicillin-binding proteins in Streptococcus pneumoniae D39. Biol Chem 2022; 403:433-443. [PMID: 35218689 DOI: 10.1515/hsz-2021-0386] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 02/10/2022] [Indexed: 12/17/2022]
Abstract
Penicillin-binding proteins (PBPs) are integral to bacterial cell division as they mediate the final steps of cell wall maturation. Selective fluorescent probes are useful for understanding the role of individual PBPs, including their localization and activity during growth and division of bacteria. For the development of new selective probes for PBP imaging, several β-lactam antibiotics were screened, as they are known to covalently bind PBP in vivo. The PBP inhibition profiles of 16 commercially available β-lactam antibiotics were evaluated in an unencapsulated derivative of the D39 strain of Streptococcus pneumoniae, IU1945. These β-lactams have not previously been characterized for their PBP inhibition profiles in S. pneumoniae and these data augment those obtained from a library of 20 compounds that we previously reported. We investigated seven penicillins, three carbapenems, and six cephalosporins. Most of these β-lactams were found to be co-selective for PBP2x and PBP3, as was noted in our previous studies. Six out of 16 antibiotics were selective for PBP3 and one molecule was co-selective for PBP1a and PBP3. Overall, this work expands the chemical space available for development of future β-lactam-based probes for specific pneumococcal PBP labeling and these methods can be used for the development of probes for PBP labelling in other bacterial species.
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Affiliation(s)
- Deepti Sharan
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA.,Department of Medicinal Chemistry, University of Minnesota, 208 Harvard Street SE, Minneapolis, MN 55454, USA.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church St SE, Minneapolis, MN 55454, USA.,Department of Pharmacology, University of Minnesota, 321 Church St SE, Minneapolis, MN 55454, USA
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86
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Granlund M, Åberg CH, Johansson A, Claesson R. Discrepancies in Antimicrobial Susceptibility between the JP2 and the Non-JP2 Genotype of Aggregatibacter actinomycetemcomitans. Antibiotics (Basel) 2022; 11:antibiotics11030317. [PMID: 35326780 PMCID: PMC8944592 DOI: 10.3390/antibiotics11030317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/17/2022] [Accepted: 02/24/2022] [Indexed: 12/04/2022] Open
Abstract
The Aggregatibacter actinomycetemcomitans JP2 genotype is associated with high leukotoxin production and severe (aggressive) periodontitis. The aim of this study was to compare the antimicrobial susceptibility of JP2 and non-JP2 genotype strains. Minimal inhibitory concentrations (MICs) of 11 antimicrobials were determined for 160 A. actinomycetemcomitans of serotype a, b, or c, mostly isolated in Sweden or Ghana. MIC distributions for benzylpenicillin and fusidic acid revealed a more susceptible subpopulation for 38 serotype b strains, including the 32 of the JP2 genotype, with a benzylpenicillin MIC range of 0.125−0.5 mg/L. In contrast, benzylpenicillin MIC ≤ 16 mg/L was the estimated 99.5% epidemiological cutoff (ECOFF) of all strains. Beta-lactamase production was not detected. The fusidic acid MIC distribution of 11 strains of Aggregatibacter aphrophilus agreed with that found in non-JP2 strains. Cefotaxime, meropenem, levofloxacin, and trimethoprim−sulfamethoxazole MICs were all ≤0.25 mg/L, while MIC90 values for amoxicillin, azithromycin and tetracycline were 1 mg/L. Metronidazole MICs varied between 0.5 and >256 mg/L. The discrepant findings indicate that A. actinomycetemcomitans may be divided into two separate wild types, with a suggested intrinsic reduced susceptibility for benzylpenicillin in the majority of non-JP2 genotype strains. Possible implications for the treatment of A. actinomycetemcomitans infections are discussed.
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Affiliation(s)
- Margareta Granlund
- Department of Clinical Microbiology, Umeå University, S-90187 Umeå, Sweden;
| | - Carola Höglund Åberg
- Division of Molecular Periodontology, Department of Odontology, Umeå University, S-90187 Umeå, Sweden; (C.H.Å.); (A.J.)
| | - Anders Johansson
- Division of Molecular Periodontology, Department of Odontology, Umeå University, S-90187 Umeå, Sweden; (C.H.Å.); (A.J.)
| | - Rolf Claesson
- Division of Oral Microbiology, Department of Odontology, Umeå University, S-90187 Umeå, Sweden
- Correspondence: ; Tel.:+76-70-3090126
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87
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Integrative Reverse Genetic Analysis Identifies Polymorphisms Contributing to Decreased Antimicrobial Agent Susceptibility in Streptococcus pyogenes. mBio 2022; 13:e0361821. [PMID: 35038921 PMCID: PMC8764543 DOI: 10.1128/mbio.03618-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Identification of genetic polymorphisms causing increased antibiotic resistance in bacterial pathogens traditionally has proceeded from observed phenotype to defined mutant genotype. The availability of large collections of microbial genome sequences that lack antibiotic susceptibility metadata provides an important resource and opportunity to obtain new information about increased antimicrobial resistance by a reverse genotype-to-phenotype bioinformatic and experimental workflow. We analyzed 26,465 genome sequences of Streptococcus pyogenes, a human pathogen causing 700 million infections annually. The population genomic data identified amino acid changes in penicillin-binding proteins 1A, 1B, 2A, and 2X with signatures of evolution under positive selection as potential candidates for causing decreased susceptibility to β-lactam antibiotics. Construction and analysis of isogenic mutant strains containing individual amino acid replacements in penicillin-binding protein 2X (PBP2X) confirmed that the identified residues produced decreased susceptibility to penicillin. We also discovered the first chimeric PBP2X in S. pyogenes and show that strains containing it have significantly decreased β-lactam susceptibility. The novel integrative reverse genotype-to-phenotype strategy presented is broadly applicable to other pathogens and likely will lead to new knowledge about antimicrobial agent resistance, a massive public health problem worldwide. IMPORTANCE The recent demonstration that naturally occurring amino acid substitutions in Streptococcus pyogenes PBP2X are sufficient to cause severalfold reduced susceptibility to multiple β-lactam antibiotics in vitro raises the concern that these therapeutic agents may become compromised. Substitutions in PBP2X are common first-step mutations that, with the incremental accumulation of additional adaptive mutations within the PBPs, can result in high-level resistance. Because β-lactam susceptibility testing is not routinely performed, the nature and extent of such substitutions within the PBPs of S. pyogenes are poorly characterized. To address this knowledge deficit, polymorphisms in the PBPs were identified among the most comprehensive cohort of S. pyogenes genome sequences investigated to date. The mutational processes and selective forces acting on the PBPs were assessed to identify specific substitutions likely to influence β-lactam susceptibility and to evaluate factors posited to be impediments to resistance emergence.
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88
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Sulaima JE, Lam H. Proteomics in antibiotic resistance and tolerance research: Mapping the resistome and the tolerome of bacterial pathogens. Proteomics 2022; 22:e2100409. [PMID: 35143120 DOI: 10.1002/pmic.202100409] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/31/2022] [Accepted: 01/31/2022] [Indexed: 11/12/2022]
Abstract
Antibiotic resistance, the ability of a microbial pathogen to evade the effects of antibiotics thereby allowing them to grow under elevated drug concentrations, is an alarming health problem worldwide and has attracted the attention of scientists for decades. On the other hand, the clinical importance of persistence and tolerance as alternative mechanisms for pathogens to survive prolonged lethal antibiotic doses has recently become increasingly appreciated. Persisters and high-tolerance populations are thought to cause the relapse of infectious diseases, and provide opportunities for the pathogens to evolve resistance during the course of antibiotic therapy. Although proteomics and other omics methodology have long been employed to study resistance, its applications in studying persistence and tolerance are still limited. However, due to the growing interest in the topic and recent progress in method developments to study them, there have been some proteomic studies that yield fresh insights into the phenomenon of persistence and tolerance. Combined with the studies on resistance, these collectively guide us to novel molecular targets for the potential drugs for the control of these dangerous pathogens. In this review, we surveyed previous proteomic studies to investigate resistance, persistence, and tolerance mechanisms, and discussed emerging experimental strategies for studying these phenotypes with a combination of adaptive laboratory evolution and high-throughput proteomics. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jordy Evan Sulaima
- Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong
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89
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Abo-Bakr AM, Alsoghier HM, Abdelmonsef AH. Molecular docking, modeling, semiempirical calculations studies and in vitro evaluation of new synthesized pyrimidin-imide derivatives. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131548] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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90
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Identification of the Extracytoplasmic Function σ Factor σ P Regulon in Bacillus thuringiensis. mSphere 2022; 7:e0096721. [PMID: 35080471 PMCID: PMC8791391 DOI: 10.1128/msphere.00967-21] [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] [Indexed: 11/22/2022] Open
Abstract
Bacillus thuringiensis and other members of the Bacillus cereus family are resistant to many β-lactams. Resistance is dependent upon the extracytoplasmic function sigma factor σP. We used label-free quantitative proteomics to identify proteins whose expression was dependent upon σP. We compared the protein profiles of strains which either lacked σP or overexpressed σP. We identified 8 members of the σP regulon which included four β-lactamases as well as three penicillin-binding proteins (PBPs). Using transcriptional reporters, we confirmed that these genes are induced by β-lactams in a σP-dependent manner. These genes were deleted individually or in various combinations to determine their role in resistance to a subset of β-lactams, including ampicillin, methicillin, cephalexin, and cephalothin. We found that different combinations of β-lactamases and PBPs are involved in resistance to different β-lactams. Our data show that B. thuringiensis utilizes a suite of enzymes to protect itself from β-lactam antibiotics. IMPORTANCE Antimicrobial resistance is major concern for public health. β-Lactams remain an important treatment option for many diseases. However, the spread of β-lactam resistance continues to rise. Many pathogens acquire antibiotic resistance from environmental bacteria. Thus, understanding β-lactam resistance in environmental strains may provide insights into additional mechanisms of antibiotic resistance. Here, we describe how a single regulatory system, σP, in B. thuringiensis controls expression of multiple genes involved in resistance to β-lactams. Our findings indicate that some of these genes are partially redundant. Our data also suggest that the large number of genes controlled by σP results in increased resistance to a wider range of β-lactam classes than any single gene could provide.
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91
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Lazzaro LM, Cassisi M, Stefani S, Campanile F. Impact of PBP4 Alterations on β-Lactam Resistance and Ceftobiprole Non-Susceptibility Among Enterococcus faecalis Clinical Isolates. Front Cell Infect Microbiol 2022; 11:816657. [PMID: 35127564 PMCID: PMC8811369 DOI: 10.3389/fcimb.2021.816657] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/23/2021] [Indexed: 12/18/2022] Open
Abstract
Penicillin-resistance among Enterococcus faecalis clinical isolates has been recently associated with overexpression or aminoacidic substitutions in low-affinity PBP4. Ceftobiprole (BPR), a new-generation cephalosporin, is a therapeutic option against E. faecalis. Here, we present evidence that pbp4 gene sequence alterations may influence the expression level of the gene and ceftobiprole binding to PBP4 in E. faecalis clinical isolates showing remarkable MDR-phenotypes, and how this could interfere with BPR in vitro antibacterial and bactericidal activity. Seven E. faecalis strains from bloodstream infections were analyzed for their antibiotic and β-lactam resistance. BPR bactericidal activity was assessed by time-kill analysis; pbp4 genes were sequenced and pbp4 relative expression levels of transcription were performed by RT-qPCR. Five penicillin-resistant ampicillin-susceptible (PRAS) isolates were detected, 4 of which were also BPR non-susceptible (BPR-NS). In the time-kill experiments, BPR exposure resulted in a potent bactericidal activity (3-5 log10 reduction) at the different concentrations tested. pbp4 gene sequence analysis revealed some mutations that may account for the changes in PBP4 affinity and MIC increase in the 4 BPR-NS strains (MICs 4-16 mg/L): the deletion of an adenine (delA) in the promoter region in all PRAS/BPR-NS strains; 12 different amino acid substitutions, 7 of which were next to the PBP catalytic-sites. The most significant were: T418A, located 6 amino acids (aa) upstream of the catalytic-serine included in the 424STFK427motif I; L475Q, 7 aa upstream of the 482SDN484motif II; V606A and the novel Y605H, 13/14 aa upstream of the 619KTGT622motif III. Taken together, our data showed that elevated BPR MICs were attributable to increased transcription of pbp4 - associated with a single upstream adenine deletion and PBP4 alterations in the catalytic-site motifs – which might interfere with the formation of the BPR/PBP4 complex. pbp4 molecular alterations may account for the changes in PBP4 affinity and MIC increase, without affecting BPR cidal activity. Indeed, our in vitro dynamic analysis by time-kill assays showed that BPR exerted a bactericidal activity against E. faecalis clinical isolates, despite their MDR phenotypes.
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92
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OUP accepted manuscript. J Antimicrob Chemother 2022; 77:1847-1850. [DOI: 10.1093/jac/dkac139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/05/2022] [Indexed: 11/15/2022] Open
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93
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Mora-Ochomogo M, Lohans CT. β-Lactam antibiotic targets and resistance mechanisms: from covalent inhibitors to substrates. RSC Med Chem 2021; 12:1623-1639. [PMID: 34778765 PMCID: PMC8528271 DOI: 10.1039/d1md00200g] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/25/2021] [Indexed: 12/24/2022] Open
Abstract
The β-lactams are the most widely used antibacterial agents worldwide. These antibiotics, a group that includes the penicillins and cephalosporins, are covalent inhibitors that target bacterial penicillin-binding proteins and disrupt peptidoglycan synthesis. Bacteria can achieve resistance to β-lactams in several ways, including the production of serine β-lactamase enzymes. While β-lactams also covalently interact with serine β-lactamases, these enzymes are capable of deacylating this complex, treating the antibiotic as a substrate. In this tutorial-style review, we provide an overview of the β-lactam antibiotics, focusing on their covalent interactions with their target proteins and resistance mechanisms. We begin by describing the structurally diverse range of β-lactam antibiotics and β-lactamase inhibitors that are currently used as therapeutics. Then, we introduce the penicillin-binding proteins, describing their functions and structures, and highlighting their interactions with β-lactam antibiotics. We next describe the classes of serine β-lactamases, exploring some of the mechanisms by which they achieve the ability to degrade β-lactams. Finally, we introduce the l,d-transpeptidases, a group of bacterial enzymes involved in peptidoglycan synthesis which are also targeted by β-lactam antibiotics. Although resistance mechanisms are now prevalent for all antibiotics in this class, past successes in antibiotic development have at least delayed this onset of resistance. The β-lactams continue to be an essential tool for the treatment of infectious disease, and recent advances (e.g., β-lactamase inhibitor development) will continue to support their future use.
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Affiliation(s)
| | - Christopher T Lohans
- Department of Biomedical and Molecular Sciences, Queen's University Kingston ON K7L 3N6 Canada
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94
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Briggs NS, Bruce KE, Naskar S, Winkler ME, Roper DI. The Pneumococcal Divisome: Dynamic Control of Streptococcus pneumoniae Cell Division. Front Microbiol 2021; 12:737396. [PMID: 34737730 PMCID: PMC8563077 DOI: 10.3389/fmicb.2021.737396] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/15/2021] [Indexed: 12/14/2022] Open
Abstract
Cell division in Streptococcus pneumoniae (pneumococcus) is performed and regulated by a protein complex consisting of at least 14 different protein elements; known as the divisome. Recent findings have advanced our understanding of the molecular events surrounding this process and have provided new understanding of the mechanisms that occur during the division of pneumococcus. This review will provide an overview of the key protein complexes and how they are involved in cell division. We will discuss the interaction of proteins in the divisome complex that underpin the control mechanisms for cell division and cell wall synthesis and remodelling that are required in S. pneumoniae, including the involvement of virulence factors and capsular polysaccharides.
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Affiliation(s)
- Nicholas S. Briggs
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Kevin E. Bruce
- Department of Biology, Indiana University Bloomington, Bloomington, IN, United States
| | - Souvik Naskar
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Malcolm E. Winkler
- Department of Biology, Indiana University Bloomington, Bloomington, IN, United States
| | - David I. Roper
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
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95
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Hsieh PY, Meng FC, Guo CW, Hu KH, Shih YL, Cheng WC. Harnessing Fluorescent Moenomycin A Antibiotics for Bacterial Cell Wall Imaging Studies. Chembiochem 2021; 22:3462-3468. [PMID: 34606179 DOI: 10.1002/cbic.202100433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/30/2021] [Indexed: 11/11/2022]
Abstract
The imaging of peptidoglycan (PGN) dynamics in living bacteria facilitates the understanding of PGN biosynthesis and wall-targeting antibiotics. The main tools for imaging bacterial PGN are fluorescent probes, such as the well-known PGN metabolic labeling probes. However, fluorescent small-molecule probes for labeling key PGN-synthesizing enzymes, especially for transglycosylases (TGases), remain to be explored. In this work, the first imaging probe for labeling TGase in bacterial cell wall studies is reported. We synthesized various fluorescent MoeA-based molecules by derivatizing the natural antibiotic moenomycin A (MoeA), and used them to label TGases in living bacteria, monitor bacterial growth and division cycles by time-lapse imaging, and study cell wall growth in the mecA-carrying methicillin-resistant Staphylococcus aureus (MRSA) strains when the β-lactam-based probes were unsuitable.
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Affiliation(s)
- Pei-Yu Hsieh
- Institute of Biological Chemistry, Academia Sinica, No. 128, Academia Road Sec. 2, Taipei, 115, Taiwan
| | - Fan-Chun Meng
- Genomics Research Center, Academia Sinica, No. 128, Academia Road Sec. 2, Taipei, 115, Taiwan
| | - Chih-Wei Guo
- Genomics Research Center, Academia Sinica, No. 128, Academia Road Sec. 2, Taipei, 115, Taiwan
| | - Kung-Hsiang Hu
- Genomics Research Center, Academia Sinica, No. 128, Academia Road Sec. 2, Taipei, 115, Taiwan
| | - Yu-Ling Shih
- Institute of Biological Chemistry, Academia Sinica, No. 128, Academia Road Sec. 2, Taipei, 115, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 106, Taiwan.,Department of Microbiology, College of Medicine, National Taiwan University, No.1, Sec 1. Jen Ai Rd., Taipei, 100, Taiwan
| | - Wei-Chieh Cheng
- Genomics Research Center, Academia Sinica, No. 128, Academia Road Sec. 2, Taipei, 115, Taiwan.,Department of Chemistry, National Cheng Kung University, No.1, University Road, Tainan, 701, Taiwan.,Department of Applied Chemistry, National Chiayi University, No. 300, Syuefu Road, Chiayi, 600, Taiwan.,Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, No.100, Shin-Chuan 1st Road, Kaohsiung, 807, Taiwan
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96
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Ozma MA, Khodadadi E, Rezaee MA, Asgharzadeh M, Aghazadeh M, Zeinalzadeh E, Ganbarov K, Kafil H. Bacterial proteomics and its application for pathogenesis studies. Curr Pharm Biotechnol 2021; 23:1245-1256. [PMID: 34503411 DOI: 10.2174/1389201022666210908153234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/12/2021] [Accepted: 06/13/2021] [Indexed: 01/09/2023]
Abstract
Bacteria build their structures by implementing several macromolecules such as proteins, polysaccharides, phospholipids, and nucleic acids, which leads to preserve their lives and play an essential role in their pathogenesis. There are two genomic and proteomic methods to study various macromolecules of bacteria, which are complementary methods and provide comprehensive information. Proteomic approaches are used to identify proteins and their cell applications. Furthermore, to study bacterial proteins, macromolecules are involved in the bacteria's structures and functions. These protein-based methods provide comprehensive information about the cells, such as the external structures, internal compositions, post-translational modifications, and mechanisms of particular actions such as biofilm formation, antibiotic resistance, and adaptation to the environment, which are helpful in promoting bacterial pathogenesis. These methods use various devices such as MALDI-TOF MS, LC-MS, and two-dimensional electrophoresis, which are valuable tools for studying different structural and functional proteins of the bacteria and their mechanisms of pathogenesis that causes rapid, easy, and accurate diagnosis of the infections.
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Affiliation(s)
- Mahdi Asghari Ozma
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Ehsaneh Khodadadi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | | | - Mohammad Asgharzadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Mohammad Aghazadeh
- Microbiome and Health Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Elham Zeinalzadeh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | | | - Hossein Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz 5166614711. Iran
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Nasal Carriage of Methicillin-Resistant Staphylococcus aureus among Healthcare Workers in a Tertiary Care Hospital, Kathmandu, Nepal. Int J Microbiol 2021; 2021:8825746. [PMID: 34422056 PMCID: PMC8373499 DOI: 10.1155/2021/8825746] [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: 09/19/2020] [Revised: 07/03/2021] [Accepted: 08/02/2021] [Indexed: 11/17/2022] Open
Abstract
Introduction Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most common causes of nosocomial infections. One of the potential risk factors for nosocomial staphylococcal infections is colonization of the anterior nares of healthcare workers (HCWs). Our study aimed to determine the rate of nasal carriage MRSA among HCWs at Manmohan Memorial Medical College and Teaching Hospital, Kathmandu. Methods Two hundred and thirty-two nasal swabs were collected from HCWs of Manmohan Memorial Medical College and Teaching Hospital, Kathmandu, Nepal, within six months (February 2018-July 2018). Nasal swabs were cultured, and S. aureus isolates were subjected to the antimicrobial susceptibility test by the modified Kirby-Bauer disc diffusion method. MRSA and iMLSB (inducible macrolide lincosamide streptogramin B) resistance was screened using the cefoxitin disc (30 μg) and D-test (clindamycin and erythromycin sensitivity pattern), respectively, following CLSI (Clinical and Laboratory Standard Institute) guidelines. Risk factors for MRSA colonization were determined using the chi-square test considering the p value ˂0.05 as significant. Results A total of 34/232 (14.7%) S. aureus were isolated, out of which 12 (35.3%) were MRSA. The overall rate of nasal carriage MRSA among HCWs was 5.2% (12/232). Colonization of MRSA was higher in males (8.7%) than in females (4.3%). MRSA colonization was found to be at peak among the doctors (11.4%). HCWs of the postoperative ward were colonized highest (18.2%). All MRSA isolates were sensitive to linezolid and tetracycline. iMLSB resistance was shown by 7(20.6%) of the isolates. MRSA strains showed higher iMLSB resistance accounting for 33.3% (4/12) in comparison to methicillin-susceptible strains with 13.6% (3/22). Smoking was found to be significantly associated with MRSA colonization (p=0.004). Conclusion Rate of nasal carriage MRSA is high among HCWs and hence needs special attention to prevent HCW-associated infections that may result due to nasal colonization.
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98
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Berni F, Kalfopoulou E, Gimeno Cardells AM, Carboni F, van der Es D, Romero-Saavedra F, Laverde D, Miklic K, Malic S, Rovis TL, Jonjic S, Ali S, Overkleeft HS, Hokke CH, van Diepen A, Adamo R, Jiménez-Barbero J, van der Marel GA, Huebner J, Codée JDC. Epitope Recognition of a Monoclonal Antibody Raised against a Synthetic Glycerol Phosphate Based Teichoic Acid. ACS Chem Biol 2021; 16:1344-1349. [PMID: 34255482 PMCID: PMC8389533 DOI: 10.1021/acschembio.1c00422] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/08/2021] [Indexed: 11/29/2022]
Abstract
Glycerol phosphate (GroP)-based teichoic acids (TAs) are antigenic cell-wall components found in both enterococcus and staphylococcus species. Their immunogenicity has been explored using both native and synthetic structures, but no details have yet been reported on the structural basis of their interaction with antibodies. This work represents the first case study in which a monoclonal antibody, generated against a synthetic TA, was developed and employed for molecular-level binding analysis using TA microarrays, ELISA, SPR-analyses, and STD-NMR spectroscopy. Our findings show that the number and the chirality of the GroP residues are crucial for interaction and that the sugar appendage contributes to the presentation of the backbone to the binding site of the antibody.
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Affiliation(s)
- Francesca Berni
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Ermioni Kalfopoulou
- Division
of Pediatric Infectious Diseases, Dr. von Hauner Children’s
Hospital, Ludwig-Maximilians-University, 80337 Munich, Germany
- Institute
for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, 81675 Munich, Germany
| | - Ana M. Gimeno Cardells
- CIC
bioGUNE, Basque Research and Technology
Alliance (BRTA), Bizkaia
Technology Park, 48160 Derio, Spain
- Ikerbasque, Basque
Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Spain
| | - Filippo Carboni
- Research
and Development Centre, GlaxoSmithKline
(GSK), 53100 Siena, Italy
| | - Daan van der Es
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Felipe Romero-Saavedra
- Division
of Pediatric Infectious Diseases, Dr. von Hauner Children’s
Hospital, Ludwig-Maximilians-University, 80337 Munich, Germany
| | - Diana Laverde
- Division
of Pediatric Infectious Diseases, Dr. von Hauner Children’s
Hospital, Ludwig-Maximilians-University, 80337 Munich, Germany
| | - Karmela Miklic
- Centre
for Proteomics, Faculty of Medicine, University
of Rijeka, 51000 Rijeka, Croatia
| | - Suzana Malic
- Centre
for Proteomics, Faculty of Medicine, University
of Rijeka, 51000 Rijeka, Croatia
| | - Tihana L. Rovis
- Centre
for Proteomics, Faculty of Medicine, University
of Rijeka, 51000 Rijeka, Croatia
| | - Stipan Jonjic
- Centre
for Proteomics, Faculty of Medicine, University
of Rijeka, 51000 Rijeka, Croatia
| | - Sara Ali
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Herman S. Overkleeft
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Cornelis H. Hokke
- Department
of Parasitology, Leiden University Medical
Center, Albinusdreef
2, 2333 ZA Leiden, The Netherlands
| | - Angela van Diepen
- Department
of Parasitology, Leiden University Medical
Center, Albinusdreef
2, 2333 ZA Leiden, The Netherlands
| | - Roberto Adamo
- Research
and Development Centre, GlaxoSmithKline
(GSK), 53100 Siena, Italy
| | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Basque Research and Technology
Alliance (BRTA), Bizkaia
Technology Park, 48160 Derio, Spain
- Ikerbasque, Basque
Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Spain
| | | | - Johannes Huebner
- Division
of Pediatric Infectious Diseases, Dr. von Hauner Children’s
Hospital, Ludwig-Maximilians-University, 80337 Munich, Germany
| | - Jeroen D. C. Codée
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
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99
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Batra A, Roemhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. High potency of sequential therapy with only β-lactam antibiotics. eLife 2021; 10:68876. [PMID: 34318749 PMCID: PMC8456660 DOI: 10.7554/elife.68876] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/22/2021] [Indexed: 12/17/2022] Open
Abstract
Evolutionary adaptation is a major source of antibiotic resistance in bacterial pathogens. Evolution-informed therapy aims to constrain resistance by accounting for bacterial evolvability. Sequential treatments with antibiotics that target different bacterial processes were previously shown to limit adaptation through genetic resistance trade-offs and negative hysteresis. Treatment with homogeneous sets of antibiotics is generally viewed to be disadvantageous as it should rapidly lead to cross-resistance. We here challenged this assumption by determining the evolutionary response of Pseudomonas aeruginosa to experimental sequential treatments involving both heterogenous and homogeneous antibiotic sets. To our surprise, we found that fast switching between only β-lactam antibiotics resulted in increased extinction of bacterial populations. We demonstrate that extinction is favored by low rates of spontaneous resistance emergence and low levels of spontaneous cross-resistance among the antibiotics in sequence. The uncovered principles may help to guide the optimized use of available antibiotics in highly potent, evolution-informed treatment designs. Overuse of antibiotic drugs is leading to the appearance of antibiotic-resistant bacteria; this is, bacteria with mutations that allow them to survive treatment with specific antibiotics. This has made some bacterial infections difficult or impossible to treat. Learning more about how bacteria evolve resistance to antibiotics could help scientists find ways to prevent it and develop more effective treatments. Changing antibiotics frequently may be one way to prevent bacteria from evolving resistance. That way if a bacterium acquires mutations that allow it to escape one antibiotic, another antibiotic will kill it, stopping it from dividing and preventing the appearance of descendants with resistance to several antibiotics. In order to use this approach, testing is needed to find the best sequences of antibiotics to apply and the optimal timings of treatment. To find out more, Batra, Roemhild et al. grew bacteria in the laboratory and exposed them to different sequences of antibiotics, switching antibiotics at different time intervals. This showed that sequential treatments with different antibiotics can limit bacterial evolution, especially when antibiotics are switched quickly. Unexpectedly, one of the most effective sequences used very similar antibiotics. This was surprising because using similar antibiotics should lead to the evolution of cross-resistance, which is when a drug causes changes that make the bacterium less sensitive to other treatments. However, in the tested case, cross-resistance did not evolve when antibiotics were switched quickly, thereby ensuring efficiency of treatment. Batra et al. show that alternating sequences of antibiotics may be an effective strategy to prevent drug resistance. Because the experiments were done in a laboratory setting it will be important to verify the results in studies in animals and humans before the approach can be used in medical or veterinary settings. If the results are confirmed, it could reduce the need to develop new antibiotics, which is expensive and time consuming.
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Affiliation(s)
- Aditi Batra
- Department of Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany.,Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Roderich Roemhild
- Department of Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany.,Max Planck Institute for Evolutionary Biology, Ploen, Germany.,Institute of Science and Technology, Klosterneuburg, Austria
| | - Emilie Rousseau
- Borstel Research Centre, National Reference Center for Mycobacteria, Borstel, Germany
| | - Sören Franzenburg
- Competence Centre for Genomic Analysis Kiel, University of Kiel, Kiel, Germany
| | - Stefan Niemann
- Borstel Research Centre, National Reference Center for Mycobacteria, Borstel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, University of Kiel, Kiel, Germany.,Max Planck Institute for Evolutionary Biology, Ploen, Germany
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100
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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