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Kollár L, Grabrijan K, Hrast Rambaher M, Bozovičar K, Imre T, Ferenczy GG, Gobec S, Keserű GM. Boronic acid inhibitors of penicillin-binding protein 1b: serine and lysine labelling agents. J Enzyme Inhib Med Chem 2024; 39:2305833. [PMID: 38410950 PMCID: PMC10901194 DOI: 10.1080/14756366.2024.2305833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/08/2024] [Indexed: 02/28/2024] Open
Abstract
Penicillin-binding proteins (PBPs) contribute to bacterial cell wall biosynthesis and are targets of antibacterial agents. Here, we investigated PBP1b inhibition by boronic acid derivatives. Chemical starting points were identified by structure-based virtual screening and aliphatic boronic acids were selected for further investigations. Structure-activity relationship studies focusing on the branching of the boron-connecting carbon and quantum mechanical/molecular mechanical simulations showed that reaction barrier free energies are compatible with fast reversible covalent binding and small or missing reaction free energies limit the inhibitory activity of the investigated boronic acid derivatives. Therefore, covalent labelling of the lysine residue of the catalytic dyad was also investigated. Compounds with a carbonyl warhead and an appropriately positioned boronic acid moiety were shown to inhibit and covalently label PBP1b. Reversible covalent labelling of the catalytic lysine by imine formation and the stabilisation of the imine by dative N-B bond is a new strategy for PBP1b inhibition.
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Affiliation(s)
- Levente Kollár
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | | | | | | | - Tímea Imre
- MS Metabolomics Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
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Kawaguchiya M, Urushibara N, Aung MS, Kudo K, Ito M, Habadera S, Kobayashi N. Genetic characterization of penicillin-binding proteins of nonencapsulated Streptococcus pneumoniae in the postpneumococcal conjugate vaccine era in Japan. Int J Infect Dis 2022; 120:174-176. [PMID: 35470022 DOI: 10.1016/j.ijid.2022.04.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/14/2022] [Accepted: 04/14/2022] [Indexed: 10/18/2022] Open
Abstract
OBJECTIVES Nonencapsulated Streptococcus pneumoniae (NESp) is emerging after the introduction of pneumococcal conjugate vaccines (PCVs). This study aimed to elucidate the genetic characteristics of penicillin-binding proteins (PBPs; PBP1a, 2b, and 2x) associated with penicillin nonsusceptibility in emergent NESp. METHODS A total of 71 NESp isolates that were identified in our previous study during the PCV era in Japan (2011-2019) were analyzed for their amino acid sequences of transpeptidase domain in PBP 1a, 2b, and 2x. RESULTS Overall, we identified 21 different PBP profiles (1a-2b-2x), all of which represent novel PBP profiles. The dominant PBP profiles were 13-16-ne1 (32.4%, n = 23), ne1-16-ne2 (14.1%, n = 10), and 13-7-ne4 (7.0%, n = 5) (novel PBP type was numbered with "ne" denoting "nonencapsulated"), accounting for 53.5% of all isolates. All isolates with the PBP profiles 13-16-ne1 and 13-7-ne4 and those having PBP1a type-13 and -131, PBP2b type-7, -ne1, and -ne2 showed nonsusceptibility to penicillin. A high degree of genetic diversity was found in PBP2x, with most of them (81.7%) being new types. CONCLUSIONS Our current study identified the 21 novel PBP profiles and remarkable mutations in the PBPs, which may be potentially associated with penicillin nonsusceptibility in NESp.
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Affiliation(s)
- Mitsuyo Kawaguchiya
- Department of Hygiene, School of Medicine, Sapporo Medical University, S-1 W-17, Chuo-ku, Sapporo 060-8556, Japan.
| | - Noriko Urushibara
- Department of Hygiene, School of Medicine, Sapporo Medical University, S-1 W-17, Chuo-ku, Sapporo 060-8556, Japan
| | - Meiji Soe Aung
- Department of Hygiene, School of Medicine, Sapporo Medical University, S-1 W-17, Chuo-ku, Sapporo 060-8556, Japan
| | - Kenji Kudo
- Sapporo Clinical Laboratory, Inc., Sapporo, Japan
| | - Masahiko Ito
- Sapporo Clinical Laboratory, Inc., Sapporo, Japan
| | | | - Nobumichi Kobayashi
- Department of Hygiene, School of Medicine, Sapporo Medical University, S-1 W-17, Chuo-ku, Sapporo 060-8556, Japan
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3
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von Specht M, García Gabarrot G, Mollerach M, Bonofiglio L, Gagetti P, Kaufman S, Vigliarolo L, Toresani I, Lopardo HA. Resistance to β-lactams in Streptococcus pneumoniae. Rev Argent Microbiol 2021:S0325-7541(21)00041-9. [PMID: 33875295 DOI: 10.1016/j.ram.2021.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 01/18/2021] [Accepted: 02/28/2021] [Indexed: 11/21/2022] Open
Abstract
Streptococcus pneumoniae is an important causal agent of pneumonia, meningitis, sepsis, bacteremia, and otitis media. Penicillin resistance rates in S. pneumoniae have remained stable in Argentina in the last years. In the late '90s more isolates with MIC of penicillin ≥2μg/ml were observed; however, their frequency has decreased in recent years. The phenotypic expression of penicillin resistance is due to a modification in penicillin-binding proteins associated with a mosaic structure in the coding genes. The expansion of successful resistant clones varies among the different regions and is influenced by the use of antibiotics, vaccines, particularly conjugated ones, as well as population density. Parenteral treatment with high doses of penicillin G continues to be effective for the treatment of pneumonia and bacteremia, oral aminopenicillins for otitis media and sinusitis and third generation cephalosporins for meningitis.
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Sharifzadeh S, Brown NW, Shirley JD, Bruce KE, Winkler ME, Carlson EE. Chemical tools for selective activity profiling of bacterial penicillin-binding proteins. Methods Enzymol 2020; 638:27-55. [PMID: 32416917 DOI: 10.1016/bs.mie.2020.02.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Penicillin-binding proteins (PBPs) are membrane-associated proteins involved in the biosynthesis of peptidoglycan (PG), the main component of bacterial cell walls. These proteins were discovered and named for their affinity to bind the β-lactam antibiotic penicillin. The importance of the PBPs has long been appreciated; however, specific roles of individual family members in each bacterial strain, as well as their protein-protein interactions, are yet to be understood. The apparent functional redundancy of the 4-18 PBPs that most eubacteria possess makes determination of their individual roles difficult. Existing techniques to study PBPs are not ideal because they do not directly visualize protein activity and can suffer from artifacts and perturbations of native PBP function. Therefore, development of new methods for studying the roles of individual PBPs in cell wall synthesis is required. We recently generated a library of fluorescent chemical probes containing a β-lactone scaffold that specifically targets the PBPs, enabling the visualization of their catalytic activity. Herein, we describe a general protocol to label and detect the activity of individual PBPs in Streptococcus pneumoniae using our fluorescent β-lactone probes.
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Affiliation(s)
- Shabnam Sharifzadeh
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Nathaniel W Brown
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Kevin E Bruce
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Malcolm E Winkler
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, United States; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States.
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5
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Abstract
Understanding the mechanisms of bacterial cell wall synthesis is essential for microbiology and medicine alike. A key step in this process is peptidoglycan crosslinking, which confers mechanical strength to the cell wall and represents a target for numerous classes of antibiotics. However, the biology of crosslinking remains poorly understood due to a lack of tools for studying the reaction in vivo. Recently, we developed a class of synthetic probes called fluorescent stem peptide mimics (FSPMs) that meet this need, allowing quantification and localization of crosslinking activity in live bacteria. We have utilized FSPMs to describe novel aspects of peptidoglycan synthesis in the human pathogen, Staphylococcus aureus. To enable wider use of our methodology, we provide detailed protocols herein for the synthesis of FSPMs, labeling of live bacteria, and evaluation of crosslinking by flow cytometry and super-resolution microscopy. We believe that FSPMs, together with complementary biosynthetic probes and traditional bacteriologic methods, will help to advance our understanding of peptidoglycan biology and accelerate the search for new antibiotics.
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Affiliation(s)
- Samir Gautam
- Yale University School of Medicine, Department of Internal Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, New Haven, CT, United States; Yale University, Department of Chemistry, New Haven, CT, United States
| | - Taehan Kim
- Yale University, Department of Chemistry, New Haven, CT, United States
| | - Rebecca Howell
- Yale University, Department of Chemistry, New Haven, CT, United States
| | - David A Spiegel
- Yale University, Department of Chemistry, New Haven, CT, United States.
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6
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Patiño-Navarrete R, Rosinski-Chupin I, Cabanel N, Gauthier L, Takissian J, Madec JY, Hamze M, Bonnin RA, Naas T, Glaser P. Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producing Escherichia coli. Genome Med 2020; 12:10. [PMID: 31955713 PMCID: PMC6970295 DOI: 10.1186/s13073-019-0699-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/21/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Carbapenem-resistant Enterobacteriaceae are considered by WHO as "critical" priority pathogens for which novel antibiotics are urgently needed. The dissemination of carbapenemase-producing Escherichia coli (CP-Ec) in the community is a major public health concern. However, the global molecular epidemiology of CP-Ec isolates remains largely unknown as well as factors contributing to the acquisition of carbapenemase genes. METHODS We first analyzed the whole-genome sequence and the evolution of the E. coli sequence type (ST) 410 and its disseminated clade expressing the carbapenemase OXA-181. We reconstructed the phylogeny of 19 E. coli ST enriched in CP-Ec and corresponding to a total of 2026 non-redundant isolates. Using the EpiCs software, we determined the significance of the association between specific mutations and the acquisition of a carbapenemase gene and the most probable order of events. The impact of the identified mutations was assessed experimentally by genetic manipulations and phenotypic testing. RESULTS In 13 of the studied STs, acquisition of carbapenemase genes occurred in multidrug-resistant lineages characterized by a combination of mutations in ftsI encoding the penicillin-binding protein 3 and in the porin genes ompC and ompF. Mutated ftsI genes and a specific ompC allele related to that from ST38 inducing reduced susceptibility to diverse β-lactams spread across the species by recombination. We showed that these mutations precede in most cases the acquisition of a carbapenemase gene. The ompC allele from ST38 might have contributed to the selection of CP-Ec disseminated lineages within this ST. On the other hand, in the pandemic ST131 lineage, CP-Ec were not associated with mutations in ompC or ftsI and show no signs of dissemination. CONCLUSIONS Lineages of CP-Ec have started to disseminate globally. However, their selection is a multistep process involving mutations, recombination, acquisition of antibiotic resistance genes, and selection by β-lactams from diverse families. This process did not yet occur in the high-risk lineage ST131.
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Affiliation(s)
- Rafael Patiño-Navarrete
- Unité EERA, Institut Pasteur, APHP, Université Paris Saclay, 28 Rue du Dr Roux, 75015, Paris, France.,UMR3525, CNRS, 28 rue du Dr Roux, 75015, Paris, France
| | - Isabelle Rosinski-Chupin
- Unité EERA, Institut Pasteur, APHP, Université Paris Saclay, 28 Rue du Dr Roux, 75015, Paris, France.,UMR3525, CNRS, 28 rue du Dr Roux, 75015, Paris, France
| | - Nicolas Cabanel
- Unité EERA, Institut Pasteur, APHP, Université Paris Saclay, 28 Rue du Dr Roux, 75015, Paris, France.,UMR3525, CNRS, 28 rue du Dr Roux, 75015, Paris, France
| | - Lauraine Gauthier
- Unité EERA, Institut Pasteur, APHP, Université Paris Saclay, 28 Rue du Dr Roux, 75015, Paris, France.,EA7361 Faculty of Medicine of University Paris-Sud, Le Kremlin-Bicêtre, France.,Department of Bacteriology-Hygiene, Bicêtre Hospital, APHP, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Julie Takissian
- Unité EERA, Institut Pasteur, APHP, Université Paris Saclay, 28 Rue du Dr Roux, 75015, Paris, France.,Associated French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Jean-Yves Madec
- Université de Lyon - Agence Nationale de Sécurité Sanitaire (ANSES), Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Remy A Bonnin
- Unité EERA, Institut Pasteur, APHP, Université Paris Saclay, 28 Rue du Dr Roux, 75015, Paris, France.,Department of Bacteriology-Hygiene, Bicêtre Hospital, APHP, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Thierry Naas
- Unité EERA, Institut Pasteur, APHP, Université Paris Saclay, 28 Rue du Dr Roux, 75015, Paris, France.,EA7361 Faculty of Medicine of University Paris-Sud, Le Kremlin-Bicêtre, France.,Department of Bacteriology-Hygiene, Bicêtre Hospital, APHP, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Philippe Glaser
- Unité EERA, Institut Pasteur, APHP, Université Paris Saclay, 28 Rue du Dr Roux, 75015, Paris, France. .,UMR3525, CNRS, 28 rue du Dr Roux, 75015, Paris, France.
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7
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Vigliotta G, Giordano D, Verdino A, Caputo I, Martucciello S, Soriente A, Marabotti A, De Rosa M. New compounds for a good old class: Synthesis of two Β-lactam bearing cephalosporins and their evaluation with a multidisciplinary approach. Bioorg Med Chem 2020; 28:115302. [PMID: 31932194 DOI: 10.1016/j.bmc.2019.115302] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/13/2019] [Accepted: 12/31/2019] [Indexed: 11/21/2022]
Abstract
Antimicrobial resistance is spreading massively in the world and is becoming one of the main health threats of the 21st century. One of the possible strategies to overcome this problem is to modify the known classes of antibiotics in a rational way, with the aim of tuning their efficacy. In this paper, we present the synthesis and the evaluation of the biological activity of a series of two β-lactam bearing cephalosporin derivatives, in which an additional isolated azetidinone ring, bearing different substituents, is joined to the classical cephalosporanic nucleus by a chain of variable length. A computational approach has been also applied in order to predict the molecular interactions between some representative derivatives and selected penicillin-binding proteins, the natural targets of β-lactam antibiotics. All these derivatives are active against Gram-positive bacteria, with MIC100 comparable or even better than that of the reference antibiotic ceftriaxone, and show no or very low cytotoxic activity on different cell lines. Overall, these molecules appear to be able to exert their activity in particular against microorganisms belonging to some of the species more involved in the development of multidrug resistance.
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8
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Bongiorno D, Mongelli G, Stefani S, Campanile F. Genotypic analysis of Italian MRSA strains exhibiting low-level ceftaroline and ceftobiprole resistance. Diagn Microbiol Infect Dis 2019; 95:114852. [PMID: 31288948 DOI: 10.1016/j.diagmicrobio.2019.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/29/2019] [Accepted: 06/06/2019] [Indexed: 11/19/2022]
Abstract
The aim of this study was to address the involvement of PBP mutations in the bactericidal activity to novel cephalosporins, alone and in combination with daptomycin, in not-related multidrug-resistant methicillin-resistant Staphylococcus aureus strains isolated during a nationwide Italian survey. MICs determination and time-killing assays were performed and mecA, pbp1, pbp2, pbp3, pbp4, and gdpP genes were sequenced. Ten strains showed low-level resistance to ceftaroline and ceftobiprole. PBP2a sequence analysis identified four different mutations (N146K; N204K; T235I; E239K) uniquely present in the non-penicillin-binding domain (nPBD). Epidemiologically, this resistance was associated with the most widespread MDR Italian clone ST228-SCCmecI-t001/t041, confirming its proclivity to accumulate mutations, and it is also associated to substitutions in the GdpP signaling protein, involved in the maintenance of di-AMP balance, recently associated with resistance to beta-lactams. Despite these mutations, both drugs retained their potent in vitro bactericidal activity and showed a synergistic effect towards difficult-to-treat isolates.
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Affiliation(s)
- Dafne Bongiorno
- Department of Biomedical and Biotechnological Sciences (BIOMETEC) - Medical Molecular Microbiology and Antibiotic Resistance laboratory (MMARLab), - University of Catania, Italy
| | - Gino Mongelli
- Department of Biomedical and Biotechnological Sciences (BIOMETEC) - Medical Molecular Microbiology and Antibiotic Resistance laboratory (MMARLab), - University of Catania, Italy
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Sciences (BIOMETEC) - Medical Molecular Microbiology and Antibiotic Resistance laboratory (MMARLab), - University of Catania, Italy
| | - Floriana Campanile
- Department of Biomedical and Biotechnological Sciences (BIOMETEC) - Medical Molecular Microbiology and Antibiotic Resistance laboratory (MMARLab), - University of Catania, Italy.
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9
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Mallick S, Das J, Verma J, Mathew S, Maiti TK, Ghosh AS. Role of Escherichia coli endopeptidases and dd-carboxypeptidases in infection and regulation of innate immune response. Microbes Infect 2019; 21:464-474. [PMID: 31085336 DOI: 10.1016/j.micinf.2019.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 04/21/2019] [Accepted: 04/23/2019] [Indexed: 01/13/2023]
Abstract
The low-molecular-mass penicillin-binding proteins, involved in peptidoglycan recycling can also produce peptidoglycan fragments capable of activating an innate immune response in host. To investigate how these proteins in Enterobacteriaceae play a role to elicit/evade innate immune responses during infections, we deleted certain endopeptidases and dd-carboxypeptidases from Escherichia coli CS109 and studied the viability of these mutants in macrophages. The ability of infected macrophages to exert oxidative killing, express surface activation markers TLR2, MHC class II and release TNFα, were assessed. Immune responses were elevated in macrophages infected with dd-carboxypeptidase mutants but reduced for endopeptidase mutants. However, the NFκB, iNOS, and TLR2 transcripts remained elevated in macrophages infected with both mutant types. Overall, we have shown, under normal conditions endopeptidases have a tendency to elicit the immune response but their effect is suppressed by the presence of dd-carboxypeptidases. Conversely, DD-carboxypeptidases, normally, tend to reduce immune responses, as their deletions enhanced the same in macrophages. Therefore, we conclude that the roles of endopeptidases and dd-carboxypeptidases are possibly counter-active in wild-type cells where either class of enzymes suppresses each other's immunogenic properties rendering overall maintenance of low immunogenicity that helps E. coli in evading the host immune responses.
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Affiliation(s)
- Sathi Mallick
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal, 721302, India
| | - Joyjyoti Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal, 721302, India
| | - Jyoti Verma
- Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, West Bengal, 721302, India
| | - Samatha Mathew
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal, 721302, India
| | - Tapas K Maiti
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal, 721302, India
| | - Anindya S Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, West Bengal, 721302, India.
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Diawara I, Nayme K, Katfy K, Barguigua A, Kettani-Halabi M, Belabbes H, Timinouni M, Zerouali K, Elmdaghri N. Analysis of amino acid motif of penicillin-binding proteins 1a, 2b, and 2x in invasive Streptococcus pneumoniae nonsusceptible to penicillin isolated from pediatric patients in Casablanca, Morocco. BMC Res Notes 2018; 11:632. [PMID: 30170603 PMCID: PMC6119257 DOI: 10.1186/s13104-018-3719-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/20/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES This study aimed to investigate the nature of the amino acid motifs found in PBPs of Streptococcus pneumoniae isolates in invasive diseases from pediatric patients at Casablanca, Morocco. Five penicillin-susceptible (PSSP), ten penicillin-intermediate (PISP), and fifteen penicillin-resistant S. pneumoniae (PRSP) were studied by PCR-RFLP and DNA sequencing of the pbp1a, - 2b, and - 2x genes. RESULTS There were no changes in the conserved motifs of PBP1a, PBP2b and PBP2x for PSSP strains. Substitution close to PBP1a conserved motifs were found in all PRSP isolates and six/five PISP. Analysis of PBP2b showed that all but one of the 10 PISP strains and all PRSP had substitutions. Substitution close to PBP2x motifs showed that all but three of the 10 PISP strains and all PRSP had substitutions in tow conserved motifs. A total of 6, 11 and 10 genotypes were found after analysis of pbp1a, pbp2b, and pbp2x, respectively. The penicillin-nonsusceptible S. pneumoniae isolated in Casablanca share most amino acid substitutions of those reported worldwide, but they occurred among pneumococci with low level resistance to b-lactams.
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Affiliation(s)
- Idrissa Diawara
- Laboratoire de Microbiologie, Faculté de Médecine et de Pharmacie, Hassan II University of Casablanca, B.P 5696, Casablanca, Morocco. .,Service de Microbiologie, CHU Ibn Rochd, B.P 2698, Casablanca, Morocco. .,Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco.
| | - Kaotar Nayme
- Molecular Bacteriology Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Khalid Katfy
- Laboratoire de Microbiologie, Faculté de Médecine et de Pharmacie, Hassan II University of Casablanca, B.P 5696, Casablanca, Morocco.,Service de Microbiologie, CHU Ibn Rochd, B.P 2698, Casablanca, Morocco
| | - Abouddihaj Barguigua
- Laboratory of Biotechnology and Sustainable Development of Natural Ressources, Polydisciplinary Faculty, Université Sultan Moulay Slimane, Beni Mellal, Morocco
| | | | - Houria Belabbes
- Laboratoire de Microbiologie, Faculté de Médecine et de Pharmacie, Hassan II University of Casablanca, B.P 5696, Casablanca, Morocco.,Service de Microbiologie, CHU Ibn Rochd, B.P 2698, Casablanca, Morocco
| | - Mohammed Timinouni
- Molecular Bacteriology Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Khalid Zerouali
- Laboratoire de Microbiologie, Faculté de Médecine et de Pharmacie, Hassan II University of Casablanca, B.P 5696, Casablanca, Morocco.,Service de Microbiologie, CHU Ibn Rochd, B.P 2698, Casablanca, Morocco
| | - Naima Elmdaghri
- Laboratoire de Microbiologie, Faculté de Médecine et de Pharmacie, Hassan II University of Casablanca, B.P 5696, Casablanca, Morocco.,Service de Microbiologie, CHU Ibn Rochd, B.P 2698, Casablanca, Morocco
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11
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Jindal HM, Ramanathan B, Le CF, Gudimella R, Razali R, Manikam R, Sekaran SD. Comparative genomic analysis of ten clinical Streptococcus pneumoniae collected from a Malaysian hospital reveal 31 new unique drug-resistant SNPs using whole genome sequencing. J Biomed Sci 2018; 25:15. [PMID: 29448938 PMCID: PMC5815235 DOI: 10.1186/s12929-018-0414-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/29/2018] [Indexed: 11/30/2022] Open
Abstract
Background Streptococcus pneumoniae or pneumococcus is a leading cause of morbidity and mortality worldwide, specifically in relation to community-acquired pneumonia. Due to the overuse of antibiotics, S. pneumoniae has developed a high degree of resistance to a wide range of antibacterial drugs. Methods In this study, whole genome sequencing (WGS) was performed for 10 clinical strains of S. pneumoniae with different levels of sensitivity to standard antibiotics. The main objective was to investigate genetic changes associated with antibiotic resistance in S. pneumoniae. Results Our results showed that resistant isolates contain a higher number of non-synonymous single nucleotide polymorphisms (SNPs) as compared to susceptible isolates. We were able to identify SNPs that alter a single amino acid in many genes involved in virulence and capsular polysaccharide synthesis. In addition, 90 SNPs were only presented in the resistant isolates, and 31 SNPs were unique and had not been previously reported, suggesting that these unique SNPs could play a key role in altering the level of resistance to different antibiotics. Conclusion Whole genome sequencing is a powerful tool for comparing the full genome of multiple isolates, especially those closely related, and for analysing the variations found within antibiotic resistance genes that lead to differences in antibiotic sensitivity. We were able to identify specific mutations within virulence genes related to resistant isolates. These findings could provide insights into understanding the role of single nucleotide mutants in conferring drug resistance. Electronic supplementary material The online version of this article (10.1186/s12929-018-0414-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hassan Mahmood Jindal
- Department of Medical Microbiology, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Babu Ramanathan
- Department of Biological Sciences, School of Science and Technology, Sunway University, 47500, Kuala Lumpur, Malaysia
| | - Cheng Foh Le
- School of Pharmacy, University of Nottingham Malaysia Campus, 43500, Semenyih, Selangor, Malaysia
| | | | - Rozaimi Razali
- Sengenics HIR, University Malaya, 50603, Kuala Lumpur, Malaysia
| | - Rishya Manikam
- Department of Trauma and Emergency, University Malaya Medical Centre, 50603, Kuala Lumpur, Malaysia
| | - Shamala Devi Sekaran
- Department of Microbiology, Faculty of Medicine, MAHSA University, 42610, Jenjarom, Malaysia.
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Diawara I, Barguigua A, Katfy K, Nayme K, Belabbes H, Timinouni M, Zerouali K, Elmdaghri N. Molecular characterization of penicillin non-susceptible Streptococcus pneumoniae isolated before and after pneumococcal conjugate vaccine implementation in Casablanca, Morocco. Ann Clin Microbiol Antimicrob 2017; 16:23. [PMID: 28376809 PMCID: PMC5381081 DOI: 10.1186/s12941-017-0200-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/30/2017] [Indexed: 11/10/2022] Open
Abstract
Background Streptococcus pneumoniae is a major cause of morbidity and mortality worldwide, especially among children and the elderly. The ability to effectively treat pneumococcal infection has been compromised due to the acquisition of antibiotic resistance, particularly to β-lactam drugs. This study aimed to describe the prevalence and molecular evolution of penicillin non-susceptible S. pneumoniae (PNSP) isolated from invasive diseases before and after pneumococcal conjugate vaccine implementation in Casablanca, Morocco. Methods Isolates were obtained from the Microbiology Laboratory of Ibn Rochd University Hospital Centre of Casablanca. Serogrouping was done by Pneumotest Kit and serotyping by the Quellung capsular swelling. Antibiotic susceptibility pattern was determined by disk diffusion and E-test methods. The PNSP were analyzed by pulsed-field gel electrophoresis (PFGE) and by genotyping of pbp1a, pbp2b, and pbp2x genes. Results A total of 361 S. pneumoniae isolates were collected from 2007 to 2014. Of these isolates, 58.7% were obtained before vaccination (2007–2010) and 41.3% after vaccination (2011–2014). Of the 361 isolates, 80 were PNSP (22.2%). Generally, the proportion of PNSP between pre- and post-vaccination periods were 31 and 13% (p = 0.009), respectively. The proportion of PNSP isolated from pediatric and adult (age > 14 years) patients decreased from 34.5 to 22.9% (p = 0.1) and from 17.7 to 10.2% (p = 0.1) before and after vaccine implementation, respectively. The leading serotypes of PNSP were 14 (33 vs. 57%) and 19A (18 vs. 14%) before and after vaccination among children. For adults, serotypes 19A (53%) and 23F (24%) were the dominant serotypes in the pre-vaccination period, while serotype 14 (22%) was the most prevalent after vaccination. There were 21 pbp genotypes in the pre-vaccination period vs. 12 for post-vaccination period. PFGE clustering showed six clusters of PNSP grouped into three clusters specific to pre-vaccination period (clusters I, II and III), two clusters specific to post-period (clusters V and VI) and a cluster (IV) that contained clones belonging to the two periods of vaccination. Conclusion Our observations demonstrate a high degree of genetic diversity among PNSP. Genetic clustering among PNSP strains showed that they spread mainly by a restricted number of PNSP clones with vaccine serotypes. PFGE clustering combined with pbp genotyping revealed that vaccination can change the population structure of PNSP.
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Affiliation(s)
- Idrissa Diawara
- Laboratoire de Microbiologie, Faculté de Médecine et de Pharmacie, Hassan II University of Casablanca, B.P 5696, Casablanca, Morocco. .,Service de Microbiologie, CHU Ibn Rochd, B.P 2698, Casablanca, Morocco.
| | - Abouddihaj Barguigua
- Laboratoire Polyvalent en Recherche et Développement, département de Biologie-Géologie, Faculté polydisciplinaire, Université Sultan Moulay Slimane, Beni Mellal, Morocco
| | - Khalid Katfy
- Laboratoire de Microbiologie, Faculté de Médecine et de Pharmacie, Hassan II University of Casablanca, B.P 5696, Casablanca, Morocco.,Service de Microbiologie, CHU Ibn Rochd, B.P 2698, Casablanca, Morocco
| | - Kaotar Nayme
- Laboratoire de Microbiologie, Faculté de Médecine et de Pharmacie, Hassan II University of Casablanca, B.P 5696, Casablanca, Morocco.,Molecular Bacteriology Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Houria Belabbes
- Laboratoire de Microbiologie, Faculté de Médecine et de Pharmacie, Hassan II University of Casablanca, B.P 5696, Casablanca, Morocco.,Service de Microbiologie, CHU Ibn Rochd, B.P 2698, Casablanca, Morocco
| | - Mohammed Timinouni
- Molecular Bacteriology Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Khalid Zerouali
- Laboratoire de Microbiologie, Faculté de Médecine et de Pharmacie, Hassan II University of Casablanca, B.P 5696, Casablanca, Morocco.,Service de Microbiologie, CHU Ibn Rochd, B.P 2698, Casablanca, Morocco
| | - Naima Elmdaghri
- Laboratoire de Microbiologie, Faculté de Médecine et de Pharmacie, Hassan II University of Casablanca, B.P 5696, Casablanca, Morocco.,Service de Microbiologie, CHU Ibn Rochd, B.P 2698, Casablanca, Morocco
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Conceição N, da Silva LEP, Darini ALDC, Pitondo-Silva A, de Oliveira AG. Penicillin-resistant, ampicillin-susceptible Enterococcus faecalis of hospital origin: pbp4 gene polymorphism and genetic diversity. Infect Genet Evol 2014; 28:289-95. [PMID: 25445645 DOI: 10.1016/j.meegid.2014.10.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 10/14/2014] [Accepted: 10/23/2014] [Indexed: 10/24/2022]
Abstract
Despite the spread of penicillin-resistant, ampicillin-susceptible Enterococcus faecalis (PRASEF) isolates in diverse countries, the mechanisms leading to this unusual resistance phenotype have not yet been investigated. The aim of this study was to evaluate whether polymorphism in the pbp4 gene is associated with penicillin resistance in PRASEF isolates and to determine their genetic diversity. E. faecalis isolates were recovered from different clinical specimens of hospitalized patients from February 2006 to June 2010. The β-lactam minimal inhibitory concentrations (MICs) were determined by E-test®. The PCR-amplified pbp4 gene was sequenced with an automated sequencer. The genetic diversities of the isolates were established by PFGE (pulsed-field gel electrophoresis) and MLST (multilocus sequencing typing). Seventeen non-producing β-lactamase PRASEF and 10 penicillin-susceptible, ampicillin-susceptible E. faecalis (PSASEF) strains were analyzed. A single-amino-acid substitution (Asp-573→Glu) in the penicillin-binding domain was significantly found in all PRASEF isolates by sequencing of the pbp4 gene but not in the penicillin-susceptible isolates. In contrast to the PSASEF isolates, a majority of the PRASEFs had similar PFGE profiles. Six representative PRASEF isolates were resolved by MLST into ST9 and ST524 and belong to the globally dispersed clonal complex 9 (CC9). In conclusion, it appears quite likely that the amino acid alteration (Asp-573→Glu) found in the PBP4 of the Brazilian PRASEF isolates may account for their reduced susceptibility to penicillin, although other resistance mechanisms remain to be investigated.
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Affiliation(s)
- Natália Conceição
- Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil; Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Ana Lúcia da Costa Darini
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - André Pitondo-Silva
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Adriana Gonçalves de Oliveira
- Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil.
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Dave K, Palzkill T, Pratt RF. Neutral β-Lactams Inactivate High Molecular Mass Penicillin-Binding Proteins of Class B1, Including PBP2a of MRSA. ACS Med Chem Lett 2014; 5:154-7. [PMID: 24900789 DOI: 10.1021/ml400408c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 12/06/2013] [Indexed: 11/28/2022] Open
Abstract
The targets of β-lactam antibiotics are bacterial DD-peptidases (penicillin-binding proteins). β-Lactam SAR studies over many years have demonstrated the importance of a specifically placed negative charge, usually carboxylate, on these molecules. We show here that neutral analogues of classical β-lactam antibiotics are of comparable activity to the originals against β-lactam-resistant high molecular mass DD-peptidases of the B1 class, a group that includes PBP2a of methicillin-resistant Staphylococcus aureus. These neutral β-lactams may direct new development of antibiotics against certain penicillin-resistant bacteria. These molecules do have antibiotic activity against Gram-positive bacteria.
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Affiliation(s)
- Kinjal Dave
- Department
of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Timothy Palzkill
- Departments of Pharmacology, and Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - R. F. Pratt
- Department
of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
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Kim BJ, Kim JG. Substitutions in penicillin-binding protein 1 in amoxicillin-resistant Helicobacter pylori strains isolated from Korean patients. Gut Liver 2013; 7:655-60. [PMID: 24312705 PMCID: PMC3848547 DOI: 10.5009/gnl.2013.7.6.655] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 02/05/2013] [Accepted: 02/05/2013] [Indexed: 12/11/2022] Open
Abstract
Background/Aims A worldwide increase in amoxicillin resistance in Helicobacter pylori is having an adverse effect on eradication therapy. In this study, we investigated the mechanism of the amoxicillin resistance of H. pylori in terms of amino acid substitutions in penicillin-binding protein 1 (PBP1). Methods In total, 150 H. pylori strains were isolated from 144 patients with chronic gastritis, peptic ulcers, or stomach cancer. The minimum inhibitory concentrations (MICs) of the strains were determined with a serial 2-fold agar dilution method. The resistance breakpoint for amoxicillin was defined as >0.5 µg/mL. Results Nine of 150 H. pylori strains showed amoxicillin resistance (6%). The MIC values of the resistant strains ranged from 1 to 4 µg/mL. A PBP1 sequence analysis of the resistant strains revealed multiple amino acid substitutions: Val16→Ile, Val45→Ile, Ser414→Arg, Asn562→Tyr, Thr593→Ala, Gly595→Ser, and Ala599→Thr. The natural transformation of these mutated genes into amoxicillin-sensitive strains was performed in two separate pbp1 gene segments. A moderate increase in the amoxicillin MIC was observed in the segment that contained the penicillin-binding motif of the C-terminal portion, the transpeptidase domain. Conclusions pbp1 mutation affects the amoxicillin resistance of H. pylori through the transfer of the penicillin-binding motif.
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Affiliation(s)
- Beom Jin Kim
- Department of Internal Medicine, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, Korea
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