1
|
Sanz-García F, Laborda P, Ochoa-Sánchez LE, Martínez JL, Hernando-Amado S. The Pseudomonas aeruginosa Resistome: Permanent and Transient Antibiotic Resistance, an Overview. Methods Mol Biol 2024; 2721:85-102. [PMID: 37819517 DOI: 10.1007/978-1-0716-3473-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
One of the most concerning characteristics of Pseudomonas aeruginosa is its low susceptibility to several antibiotics of common use in clinics, as well as its facility to acquire increased resistance levels. Consequently, the study of the antibiotic resistance mechanisms of this bacterium is of relevance for human health. For such a study, different types of resistance should be distinguished. The intrinsic resistome is composed of a set of genes, present in the core genome of P. aeruginosa, which contributes to its characteristic, species-specific, phenotype of susceptibility to antibiotics. Acquired resistance refers to those genetic events, such as the acquisition of mutations or antibiotic resistance genes that reduce antibiotic susceptibility. Finally, antibiotic resistance can be transiently acquired in the presence of specific compounds or under some growing conditions. The current article provides information on methods currently used to analyze intrinsic, mutation-driven, and transient antibiotic resistance in P. aeruginosa.
Collapse
Affiliation(s)
| | - Pablo Laborda
- Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | | | | | | |
Collapse
|
2
|
Lumbreras-Iglesias P, Rodrigo-Arrazola E, López-Amor L, Fernández-Suárez J, Rodicio MR, Fernández J. Clinical and Microbiological Risk Factors for 30-Day Mortality of Bloodstream Infections Caused by OXA-48-Producing Klebsiella pneumoniae. Pathogens 2023; 13:11. [PMID: 38276157 PMCID: PMC10819929 DOI: 10.3390/pathogens13010011] [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: 11/22/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Bloodstream infections (BSI) caused by carbapenem-resistant Klebsiella pneumoniae are associated with high morbidity and mortality, and the therapy options available for their treatment are frequently scarce. The aim of this study was to analyze risk factors for 30-day mortality in patients with BSI caused by OXA-48-producing K. pneumoniae. The clinical and treatment features of the patients, who attended a single hospital over a five-year period, were retrospectively reviewed. The microbiological features, including the sequence types (ST) and the somatic (O) and capsular (K) antigens, as well as their resistance properties, comprising phenotypes and genetic background, were also considered. To identify the risk factors for 30-day mortality, uni- and multivariate statistical analyses were performed. The univariate analysis revealed statistically significant correlations for age, male gender, lower respiratory system infection, infection by ST147 isolates, and infection by isolates expressing the K64 antigen. The multivariate analysis, applied to variables yielding p-values close to or lower than 0.05 in the univariate analysis, confirmed gender, lower respiratory system infection, and infection with ST147 isolates, but not age or infection with K64 isolates, as risk factors for 30-day mortality. Moreover, the multivariate analysis showed that patients suffering from hematological malignancies or having been treated with inappropriate therapy, both having p-values slightly higher than 0.05 in the univariate analysis, exhibited significantly poorer outcomes in the multivariant analysis. The association of the ST147 clone with an increased risk of mortality is a novel finding that deserves further attention. Studies like the one presented here can certainly benefit the management of patients with nosocomial BSI caused by carbapenemase-producing K. pneumoniae.
Collapse
Affiliation(s)
- Pilar Lumbreras-Iglesias
- Traslational Microbiology Group, Health Research Institute of the Principality of Asturias (ISPA), 33011 Oviedo, Spain; (P.L.-I.); (J.F.-S.)
- Department of Clinical Microbiology, Central University Hospital of Asturias (HUCA), 33011 Oviedo, Spain;
- Hematological Malignancies Group, Health Research Institute of the Principality of Asturias (ISPA), 33011 Oviedo, Spain
| | - Edurne Rodrigo-Arrazola
- Department of Clinical Microbiology, Central University Hospital of Asturias (HUCA), 33011 Oviedo, Spain;
| | - Lucía López-Amor
- Department of Intensive Care Medicine, San Agustín University Hospital (HUSA), 33401 Avilés, Spain;
| | - Jonathan Fernández-Suárez
- Traslational Microbiology Group, Health Research Institute of the Principality of Asturias (ISPA), 33011 Oviedo, Spain; (P.L.-I.); (J.F.-S.)
- Department of Clinical Microbiology, Central University Hospital of Asturias (HUCA), 33011 Oviedo, Spain;
| | - María Rosario Rodicio
- Traslational Microbiology Group, Health Research Institute of the Principality of Asturias (ISPA), 33011 Oviedo, Spain; (P.L.-I.); (J.F.-S.)
- Department of Functional Biology, Microbiology Area, University of Oviedo, 33006 Oviedo, Spain
| | - Javier Fernández
- Traslational Microbiology Group, Health Research Institute of the Principality of Asturias (ISPA), 33011 Oviedo, Spain; (P.L.-I.); (J.F.-S.)
- Department of Clinical Microbiology, Central University Hospital of Asturias (HUCA), 33011 Oviedo, Spain;
- Department of Functional Biology, Microbiology Area, University of Oviedo, 33006 Oviedo, Spain
- Research & Innovation, Artificial Intelligence and Statistical Department, Pragmatech AI Solutions, 33001 Oviedo, Spain
- Biomedical Research Networking Center—Respiratory Diseases, 28029 Madrid, Spain
| |
Collapse
|
3
|
Bina XR, Weng Y, Budnick J, Van Allen ME, Bina JE. Klebsiella pneumoniae TolC contributes to antimicrobial resistance, exopolysaccharide production, and virulence. Infect Immun 2023; 91:e0030323. [PMID: 37982617 PMCID: PMC10715176 DOI: 10.1128/iai.00303-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/26/2023] [Indexed: 11/21/2023] Open
Abstract
Klebsiella pneumoniae is a Gram-negative bacterium that causes a variety of human diseases, ranging from pneumonia to urinary tract infections and invasive diseases. The emergence of K. pneumoniae strains that are resistant to multiple antibiotics has made treatment more complex and led to K. pneumoniae becoming a global health threat. Addressing this threat necessitates the development of new therapeutic strategies to combat this pathogen, including strategies to overcome antimicrobial resistance and therapeutics for novel targets such as antivirulence. Here, we investigated the function of TolC, an outer membrane protein essential for the function of tripartite transporters, in K. pneumoniae. Mutation of tolC rendered K. pneumoniae hypersensitive to multiple antibiotics. Moreover, the tolC mutation impaired capsule production and affected the expression of key capsule biosynthetic genes, indicating a regulatory role for TolC in capsule biosynthesis. Additionally, TolC was essential for growth under iron-limiting conditions, suggesting its involvement in iron acquisition. The tolC mutant exhibited increased adherence to human enterocytes and enhanced serum sensitivity. In the Galleria mellonella infection model, the tolC mutant displayed reduced virulence compared to the wild type. Our findings highlight the pleiotropic role of TolC in K. pneumoniae pathobiology, influencing antimicrobial resistance, capsule production, iron homeostasis, adherence to host cells, and virulence. Understanding the multifaceted role of TolC in K. pneumoniae may guide the development of new therapeutic strategies against this pathogen. .
Collapse
Affiliation(s)
- X. Renee Bina
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yuding Weng
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - James Budnick
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mia E. Van Allen
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - James E. Bina
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| |
Collapse
|
4
|
Vitale M. Antibiotic Resistance: Do We Need Only Cutting-Edge Methods, or Can New Visions Such as One Health Be More Useful for Learning from Nature? Antibiotics (Basel) 2023; 12:1694. [PMID: 38136728 PMCID: PMC10740918 DOI: 10.3390/antibiotics12121694] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Antibiotic resistance is an increasing global problem for public health, and focusing on biofilms has provided further insights into resistance evolution in bacteria. Resistance is innate in many bacterial species, and many antibiotics are derived from natural molecules of soil microorganisms. Is it possible that nature can help control AMR diffusion? In this review, an analysis of resistance mechanisms is summarized, and an excursus of the different approaches to challenging resistance spread based on natural processes is presented as "lessons from Nature". On the "host side", immunotherapy strategies for bacterial infections have a long history before antibiotics, but continuous new inputs through biotechnology advances are enlarging their applications, efficacy, and safety. Antimicrobial peptides and monoclonal antibodies are considered for controlling antibiotic resistance. Understanding the biology of natural predators is providing new, effective, and safe ways to combat resistant bacteria. As natural enemies, bacteriophages were used to treat severe infections before the discovery of antibiotics, marginalized during the antibiotic era, and revitalized upon the diffusion of multi-resistance. Finally, sociopolitical aspects such as education, global action, and climate change are also considered as important tools for tackling antibiotic resistance from the One Health perspective.
Collapse
Affiliation(s)
- Maria Vitale
- Genetics of Microorganisms Laboratory, Molecular Biology Department, Istituto Zooprofilattico Sperimentale della Sicilia "A. Mirri", 90129 Palermo, Italy
| |
Collapse
|
5
|
Yu J, Hong C, Yin L, Ping Q, Hu G. Antimicrobial activity of phenyllactic acid against Klebsiella pneumoniae and its effect on cell wall membrane and genomic DNA. Braz J Microbiol 2023; 54:3245-3255. [PMID: 37728681 PMCID: PMC10689709 DOI: 10.1007/s42770-023-01126-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/09/2023] [Indexed: 09/21/2023] Open
Abstract
As Klebsiella pneumoniae (KP) has acquired high levels of resistance to multiple antibiotics, it is considered a worldwide pathogen of concern, and substitutes for traditional antibiotics are urgently needed. 3-Phenyllactic acid (PLA) has been reported to have antimicrobial activity against food-borne bacteria. However, there was no experiment evidence for the exact antibacterial effect and mechanism of PLA kills pathogenic KP. In this study, the Oxford cup method indicated that PLA is effective to KP with a minimum inhibitory concentration of 2.5 mg/mL. Furthermore, PLA inhibited the growth and biofilm formation of in a time- and concentration-dependent manner. In vivo, PLA could significantly increase the survival rate of infected mice and reduce the pathological tissue damage. The antibacterial mode of PLA against KP was further explored. Firstly, scanning electron microscopy illustrated the disruption of cellular ultrastructure caused by PLA. Secondly, measurement of leaked alkaline phosphatase demonstrated that PLA disrupted the cell wall integrity of KP and flow cytometry analysis with propidium iodide staining suggested that PLA damaged the cell membrane integrity. Finally, the results of fluorescence spectroscopy and agarose gel electrophoresis demonstrated that PLA bound to genomic DNA and initiated its degradation. The anti-KP mode of action of PLA was attributed to the destruction of the cell wall, membrane, and genomic DNA binding. These findings suggest that PLA has great potential applications as antibiotic substitutes in feed additives against KP infection in animals.
Collapse
Affiliation(s)
- Jianyun Yu
- College of Life Sciences, Taizhou key Laboratory of Biomass Functional Materials Development and Application, Taizhou University, Taizhou, Zhejiang, 318000, China
| | - Chunli Hong
- College of Life Sciences, Taizhou key Laboratory of Biomass Functional Materials Development and Application, Taizhou University, Taizhou, Zhejiang, 318000, China
| | - Longfei Yin
- College of Life Sciences, Taizhou key Laboratory of Biomass Functional Materials Development and Application, Taizhou University, Taizhou, Zhejiang, 318000, China
| | - Qingbo Ping
- College of Life Sciences, Taizhou key Laboratory of Biomass Functional Materials Development and Application, Taizhou University, Taizhou, Zhejiang, 318000, China
| | - Gaowei Hu
- College of Life Sciences, Taizhou key Laboratory of Biomass Functional Materials Development and Application, Taizhou University, Taizhou, Zhejiang, 318000, China.
| |
Collapse
|
6
|
de Almeida FM, de Campos TA, Pappas Jr GJ. Scalable and versatile container-based pipelines for de novo genome assembly and bacterial annotation. F1000Res 2023; 12:1205. [PMID: 37970066 PMCID: PMC10646344 DOI: 10.12688/f1000research.139488.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/16/2023] [Indexed: 11/17/2023] Open
Abstract
Background: Advancements in DNA sequencing technology have transformed the field of bacterial genomics, allowing for faster and more cost effective chromosome level assemblies compared to a decade ago. However, transforming raw reads into a complete genome model is a significant computational challenge due to the varying quality and quantity of data obtained from different sequencing instruments, as well as intrinsic characteristics of the genome and desired analyses. To address this issue, we have developed a set of container-based pipelines using Nextflow, offering both common workflows for inexperienced users and high levels of customization for experienced ones. Their processing strategies are adaptable based on the sequencing data type, and their modularity enables the incorporation of new components to address the community's evolving needs. Methods: These pipelines consist of three parts: quality control, de novo genome assembly, and bacterial genome annotation. In particular, the genome annotation pipeline provides a comprehensive overview of the genome, including standard gene prediction and functional inference, as well as predictions relevant to clinical applications such as virulence and resistance gene annotation, secondary metabolite detection, prophage and plasmid prediction, and more. Results: The annotation results are presented in reports, genome browsers, and a web-based application that enables users to explore and interact with the genome annotation results. Conclusions: Overall, our user-friendly pipelines offer a seamless integration of computational tools to facilitate routine bacterial genomics research. The effectiveness of these is illustrated by examining the sequencing data of a clinical sample of Klebsiella pneumoniae.
Collapse
Affiliation(s)
- Felipe Marques de Almeida
- Programa de Pós-graduação em Biologia Molecular, Universidade de Brasilia, Brasília, FD, 70910-900, Brazil
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Tatiana Amabile de Campos
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
- Programa de Pós-graduação em Biologia Microbiana, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Georgios Joannis Pappas Jr
- Programa de Pós-graduação em Biologia Molecular, Universidade de Brasilia, Brasília, FD, 70910-900, Brazil
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| |
Collapse
|
7
|
Li ZT, Han SX, Pu JY, Wang YY, Jiang Y, Gao MJ, Zhan XB, Xu S. In Vitro Digestion and Fecal Fermentation of Low-Gluten Rice and Its Effect on the Gut Microbiota. Foods 2023; 12:foods12040855. [PMID: 36832930 PMCID: PMC9956666 DOI: 10.3390/foods12040855] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023] Open
Abstract
Low-gluten rice is part of a special diet for chronic kidney disease patients, but its digestive mechanism in the gastrointestinal tract is unclear. In this study, low-gluten rice (LGR), common rice (CR), and rice starch (RS) were used as experimental samples, and their digestion and bacterial fermentation were simulated using an in vitro gastrointestinal reactor to investigate the mechanism of the effect of LGR on human health. The starch digestibility of CR was higher than that of LGR, with statistically significant differences. LGR has growth-promoting and metabolic effects on Akkermansia muciniphila. Among the beneficial metabolites, the concentration of short-chain fatty acids (SCFAs) from LGR reached 104.85 mmol/L, an increase of 44.94% (versus RS) and 25.33% (versus CR). Moreover, the concentration of lactic acid reached 18.19 mmol/L, an increase of 60.55% (versus RS) and 25.28% (versus CR). Among the harmful metabolites, the concentration of branched-chain fatty acids (BCFAs) in LGR was 0.29 mmol/L and the concentration of ammonia was 2.60 mmol/L, which was 79.31% and 16.15% lower than CR, respectively. A significant increase in the concentration of the beneficial intestinal bacteria Bacteroides and Bifidobacterium occurred from LGR. The 16s rDNA sequencing showed that the abundance of the Bacteroidetes and Firmicutes increased and the abundance of the Proteobacteria and Fusobacteria decreased. Thus, LGR has positive effects on digestion and gut microbiota structure and metabolism in humans.
Collapse
Affiliation(s)
- Zhi-Tao Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Shuang-Xin Han
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jia-Yang Pu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yu-Ying Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yun Jiang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Min-Jie Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiao-Bei Zhan
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Correspondence: (X.-B.Z.); (S.X.); Tel.: +86-51085918299 (X.-B.Z.); +86-51068089784 (S.X.)
| | - Song Xu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Jiangnan University, Wuxi 214122, China
- Correspondence: (X.-B.Z.); (S.X.); Tel.: +86-51085918299 (X.-B.Z.); +86-51068089784 (S.X.)
| |
Collapse
|
8
|
Emam SH, Hassan RA, Osman EO, Hamed MIA, Abdou AM, Kandil MM, Elbaz EM, Mikhail DS. Coumarin derivatives with potential anticancer and antibacterial activity: Design, synthesis, VEGFR-2 and DNA gyrase inhibition, and in silico studies. Drug Dev Res 2023; 84:433-457. [PMID: 36779381 DOI: 10.1002/ddr.22037] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 01/05/2023] [Accepted: 01/13/2023] [Indexed: 02/14/2023]
Abstract
A series of coumarin derivatives were designed, synthesized, and evaluated for their antiproliferative activity. Compound 3e exhibited significant antiproliferative activity and was further evaluated at five doses at the National Cancer Institute. It effectively inhibited vascular endothelial growth factor receptor-2 (VEGFR-2) with an IC50 value of 0.082 ± 0.004 µM compared with sorafenib. While compound 3e significantly downregulated total VEGFR-2 and its phosphorylation, it markedly reduced the HUVEC's migratory potential, resulting in a significant disruption in wound healing. Furthermore, compound 3e caused a 22.51-fold increment in total apoptotic level in leukemia cell line HL-60(TB) and a 6.91-fold increase in the caspase-3 level. Compound 3e also caused cell cycle arrest, mostly at the G1/S phase. Antibacterial activity was evaluated against Gram-positive and Gram-negative bacterial strains. Compound 3b was the most active derivative, with the same minimum inhibitory concentration and minimum bactericidal concentration value of 128 μg/mL against K. pneumonia and high stability in mammalian plasma. Moreover, compounds 3b and 3f inhibited Gram-negative DNA gyrase with IC50 = 0.73 ± 0.05 and 1.13 ± 0.07 µM, respectively, compared to novobiocin with an IC50 value of 0.17 ± 0.02 µM. The binding affinity and pattern of derivative 3e toward the VEGFR-2 active site and compounds 3a-c and 3f in the DNA gyrase active site were evaluated using molecular modeling. Overall, ADME studies of the synthesized coumarin derivatives displayed promising pharmacokinetic properties.
Collapse
Affiliation(s)
- Soha H Emam
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Rasha A Hassan
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Eman O Osman
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Mohammed I A Hamed
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, Fayoum University, Fayoum, Egypt
| | - Amr M Abdou
- Department of Microbiology and Immunology, National Research Centre, Dokki, Giza, Egypt
| | - Mai M Kandil
- Department of Microbiology and Immunology, National Research Centre, Dokki, Giza, Egypt
| | - Eman Maher Elbaz
- Department of Biochemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Demiana S Mikhail
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| |
Collapse
|
9
|
Kumar S, Anwer R, Azzi A. Molecular typing methods & resistance mechanisms of MDR Klebsiella pneumoniae. AIMS Microbiol 2023; 9:112-130. [PMID: 36891535 PMCID: PMC9988409 DOI: 10.3934/microbiol.2023008] [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: 11/20/2022] [Revised: 02/12/2023] [Accepted: 02/20/2023] [Indexed: 03/02/2023] Open
Abstract
The emergence and transmission of carbapenem-resistant Klebsiella pneumoniae (CRKP) have been recognized as a major public health concern. Here, we investigated the molecular epidemiology and its correlation with the mechanisms of resistance in CRKP isolates by compiling studies on the molecular epidemiology of CRKP strains worldwide. CRKP is increasing worldwide, with poorly characterized epidemiology in many parts of the world. Biofilm formation, high efflux pump gene expression, elevated rates of resistance, and the presence of different virulence factors in various clones of K. pneumoniae strains are important health concerns in clinical settings. A wide range of techniques has been implemented to study the global epidemiology of CRKP, such as conjugation assays, 16S-23S rDNA, string tests, capsular genotyping, multilocus sequence typing, whole-genome sequencing-based surveys, sequence-based PCR, and pulsed-field gel electrophoresis. There is an urgent need to conduct global epidemiological studies on multidrug-resistant infections of K. pneumoniae across all healthcare institutions worldwide to develop infection prevention and control strategies. In this review, we discuss different typing methods and resistance mechanisms to explore the epidemiology of K. pneumoniae pertaining to human infections.
Collapse
Affiliation(s)
- Sunil Kumar
- Department of Microbiology, Kampala International University, Western Campus, Ishaka, Uganda
| | - Razique Anwer
- Department of Pathology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Arezki Azzi
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| |
Collapse
|
10
|
Li Y, Ge X. Discovering interrelated natural mutations of efflux pump
KmrA
from
Klebsiella pneumoniae
that confer increased multidrug resistance. Protein Sci 2022; 31:e4323. [DOI: 10.1002/pro.4323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/03/2022] [Accepted: 04/11/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Ying Li
- College of Biochemical Engineering Beijing Union University Beijing China
| | - Xizhen Ge
- College of Biochemical Engineering Beijing Union University Beijing China
| |
Collapse
|
11
|
Chen H, Bai X, Gao Y, Liu W, Yao X, Wang J. Profile of Bacteria with ARGs Among Real-World Samples from ICU Admission Patients with Pulmonary Infection Revealed by Metagenomic NGS. Infect Drug Resist 2021; 14:4993-5004. [PMID: 34866919 PMCID: PMC8636693 DOI: 10.2147/idr.s335864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/16/2021] [Indexed: 12/27/2022] Open
Abstract
Background Treatment of pulmonary infections in the intensive care unit (ICU) represents a great challenge, especially infections caused by antibiotic resistance pathogens. A thorough and up-to-date knowledge of the local spectrum of antibiotic resistant bacteria can improve the antibiotic treatment efficiency. In this study, we aimed to reveal the profile of bacteria with antibiotic resistance genes (ARGs) in real-world samples from ICU admission patients with pulmonary infection in Mainland, China, by metagenomic next-generation sequencing (mNGS). Methods A total of 504 different types of clinical samples from 452 ICU admission patients with pulmonary infection were detected by mNGS analysis. Results A total of 485 samples from 434 patients got successful mNGS results. Among 434 patients, one or more bacteria with ARGs were detected in 192 patients (44.24%, 192/434), and ≥2 bacteria with ARGs were detected in 85 (19.59%, 85/434) patients. The predominant detected bacteria were Corynebacterium striatum (C. striatum) (11.76%, 51/434), Acinetobacter baumannii (A. baumannii) (11.52%, 50/434) and Enterococcus faecium (E. faecium) (8.99%, 39/434). ermX conferred resistance to MSLB and cmx to phenicol were the only two ARGs detected in C. striatum; in A. baumannii, most of ARGs were resistance-nodulation-division (RND)-type efflux pumps genes, which conferred resistance to multi-drug; ermB conferred resistance to MSLB and efmA to multi-drug were the predominant ARGs in E. faecium. Bacteria with ARGs were detected in 50% (140/280) bronchoalveolar lavage fluid (BALF) and 50.5% (48/95) sputum samples, which were significantly higher than in blood and cerebrospinal fluid (CSF) samples. Conclusion High level of bacteria with ARGs was observed in clinical samples, especially BALF and sputum samples from ICU admission patients with pulmonary infection in Mainland, China. And C. striatum resistant to MSLB and/or phenicol, multi-drug resistance A. baumannii and E. faecium were the lead bacteria.
Collapse
Affiliation(s)
- Huijuan Chen
- Department of Biomedical Engineering, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, People's Republic of China
| | - Xinhua Bai
- Department of Clinical Laboratory, Beijing Capitalbio Medlab, Beijing, People's Republic of China
| | - Yang Gao
- Department of Clinical Laboratory, Beijing Capitalbio Medlab, Beijing, People's Republic of China
| | - Wenxuan Liu
- Department of Clinical Laboratory, Beijing Capitalbio Medlab, Beijing, People's Republic of China
| | - Xuena Yao
- Department of Clinical Laboratory, Beijing Capitalbio Medlab, Beijing, People's Republic of China
| | - Jing Wang
- Department of Clinical Laboratory, Beijing Capitalbio Medlab, Beijing, People's Republic of China
| |
Collapse
|
12
|
The Association of the Phylogenetic Typing of the Klebsiella pneumoniae Isolates with Antibiotic Resistance. Emerg Med Int 2021; 2021:1316992. [PMID: 34777863 PMCID: PMC8589475 DOI: 10.1155/2021/1316992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/09/2021] [Accepted: 10/22/2021] [Indexed: 11/17/2022] Open
Abstract
Klebsiella pneumoniae complex (KPC) accounts for approximately one-third of all Gram-negative infections. Moreover, it is highly resistant and can taxonomically be distributed into KpI, KpII, and KpIII phylogroups. This study aimed to investigate the distribution of phylogenetic groups and the relationship between them and antibiotic resistance patterns. For this purpose, we collected KPC isolates from Tabriz, Iran, between 2018 and 2020. Antimicrobial susceptibility testing was performed by disk diffusion agar, and phylogenetic groups were then examined using gyrA restriction fragment length polymorphism (RFLP) and parC PCR methods. A total of 100 KPC isolates were obtained from the clinical specimens (urine, respiratory secretion, blood, wounds, and trachea). The enrolled patients included 47 men and 53 women aged from 1 to 91 years old. The highest sensitivity was found related to fosfomycin as 85%, followed by amikacin as 66%. The three phylogenetically groups by the RFLP-PCR method were found in KPC, 96% (96 isolates) as KpI, 3% (3 isolates) as KpII, and 1% (1isolate) as KpIII. The highest antibiotic resistance was observed in KpI. It was shown that a valid identification of three phylogenetic groups of KPC can be done by combining both gyrA PCR-RFLP and parC PCR. Of note, the KpI group was also observed as the dominant phylogenetic group with the highest resistance to antibiotics.
Collapse
|
13
|
Duse A, Persson-Waller K, Pedersen K. Microbial Aetiology, Antibiotic Susceptibility and Pathogen-Specific Risk Factors for Udder Pathogens from Clinical Mastitis in Dairy Cows. Animals (Basel) 2021; 11:ani11072113. [PMID: 34359241 PMCID: PMC8300163 DOI: 10.3390/ani11072113] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Mastitis is among the diseases in dairy cows that most often require antibiotic treatment. In order to maintain optimal treatment, it is important to have updated knowledge about the causative agents and their antibiotic resistance patterns. This investigation aimed to reveal the most important bacterial pathogens and their resistance patterns in Sweden, and we also identified some risk factors for infection with certain pathogens. The bacteria that were the most common causes of mastitis were, in descending order, Staphylococcus aureus, Streptococcus dysgalactiae, Escherichia coli, and Streptococcus uberis. Only a few Gram-positive bacteria were resistant to penicillin, and in general, the occurrence of antibiotic resistance was low. Therefore, the potential for antibiotic treatment of bovine mastitis in Sweden is good. Abstract Mastitis is one of the most important infectious diseases and one of the diseases that causes the greatest use of antibiotics in dairy cows. Therefore, updated information on the bacteria that cause mastitis and their antibiotic susceptibility properties is important. Here, for the first time in over 10 years, we updated the bacterial findings in clinical mastitis in Swedish dairy cows together with their antibiotic resistance patterns and risk factors for each bacterial species. During the period 2013–2018, samples from clinical mastitis were collected, together with information on the cows and herds of origin. The samples were cultured, and a total of 664 recovered bacterial isolates were subjected to susceptibility testing. Staphylococcus aureus (S. aureus) was the most common pathogen and accounted for 27.8% of diagnoses, followed by Streptococcus dysgalactiae (S. dysgalactiae) (15.8%), Escherichia coli (E. coli) (15.1%), Streptococcus uberis (S. uberis) (11.4%), Trueperella pyogenes (T. pyogenes) (7.7%), non-aureus staphylococci (NAS) (2.8%), Klebsiella spp. (2.7%), Enterococcus spp. (1.3%), and Streptococcus agalactiae (S. agalactiae) (1.2%). Various other bacteria accounted for 2.6%. Staphylococci were, in general, susceptible to most antibiotics, but 2.6% of S. aureus and 30.4% of NAS were resistant to penicillin. No methicillin-resistant staphylococci were found. All S. agalactiae were susceptible to penicillin. Bimodal and trimodal MIC distributions for penicillin in S. dysgalactiae and S. uberis, respectively, indicate acquired reduced susceptibility in some isolates. The mostly unimodal MIC distributions of T. pyogenes indicate that acquired resistance does usually not occur in this species. Among E. coli, 14.7% were resistant to at least one antibiotic, most often ampicillin (8.7%), streptomycin (7.8%), or sulphamethoxazole (6.9%). Klebsiella spp. had low resistance to tetracycline (9.1%) but is considered intrinsically resistant to ampicillin. Pathogen-specific risk factors were investigated using multivariable models. Staphylococcus aureus, S. dysgalactiae, and T. pyogenes were more common, while E. coli was less common in quarters with more than one pathogen. S. aureus and T. pyogenes were mostly seen in early lactation, while E. coli was more common in peak to mid lactation and S. dysgalactiae in early to peak lactation. Trueperella pyogenes and Klebsiella spp. were associated with a previous case of clinical mastitis in the current lactation. Staphylococcus aureus was associated with tie stalls and T. pyogenes with loose housing. All pathogens except E. coli and S. dysgalactiae had a seasonal distribution. In conclusion, the aetiological agents for clinical bovine mastitis have remained relatively stable over the last 10–15 years, S. aureus, S. dysgalactiae, E. coli and S. uberis being the most important. Resistance to penicillin among Gram-positive agents was low, and in general, antibiotic resistance to other compounds was low among both Gram-positive and Gram-negative agents.
Collapse
|
14
|
Gil-Gil T, Ochoa-Sánchez LE, Baquero F, Martínez JL. Antibiotic resistance: Time of synthesis in a post-genomic age. Comput Struct Biotechnol J 2021; 19:3110-3124. [PMID: 34141134 PMCID: PMC8181582 DOI: 10.1016/j.csbj.2021.05.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 12/20/2022] Open
Abstract
Antibiotic resistance has been highlighted by international organizations, including World Health Organization, World Bank and United Nations, as one of the most relevant global health problems. Classical approaches to study this problem have focused in infected humans, mainly at hospitals. Nevertheless, antibiotic resistance can expand through different ecosystems and geographical allocations, hence constituting a One-Health, Global-Health problem, requiring specific integrative analytic tools. Antibiotic resistance evolution and transmission are multilayer, hierarchically organized processes with several elements (from genes to the whole microbiome) involved. However, their study has been traditionally gene-centric, each element independently studied. The development of robust-economically affordable whole genome sequencing approaches, as well as other -omic techniques as transcriptomics and proteomics, is changing this panorama. These technologies allow the description of a system, either a cell or a microbiome as a whole, overcoming the problems associated with gene-centric approaches. We are currently at the time of combining the information derived from -omic studies to have a more holistic view of the evolution and spread of antibiotic resistance. This synthesis process requires the accurate integration of -omic information into computational models that serve to analyse the causes and the consequences of acquiring AR, fed by curated databases capable of identifying the elements involved in the acquisition of resistance. In this review, we analyse the capacities and drawbacks of the tools that are currently in use for the global analysis of AR, aiming to identify the more useful targets for effective corrective interventions.
Collapse
Affiliation(s)
- Teresa Gil-Gil
- Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Madrid, Spain
| | | | - Fernando Baquero
- Department of Microbiology, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain
| | | |
Collapse
|
15
|
Gil-Gil T, Corona F, Martínez JL, Bernardini A. The Inactivation of Enzymes Belonging to the Central Carbon Metabolism Is a Novel Mechanism of Developing Antibiotic Resistance. mSystems 2020; 5:e00282-20. [PMID: 32487742 PMCID: PMC8534728 DOI: 10.1128/msystems.00282-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 05/14/2020] [Indexed: 11/20/2022] Open
Abstract
Fosfomycin is a bactericidal antibiotic, analogous to phosphoenolpyruvate, that exerts its activity by inhibiting the activity of MurA. This enzyme catalyzes the first step of peptidoglycan biosynthesis, the transfer of enolpyruvate from phosphoenolpyruvate to uridine-diphosphate-N-acetylglucosamine. Fosfomycin is increasingly being used, mainly for treating infections caused by Gram-negative multidrug-resistant bacteria. The mechanisms of mutational resistance to fosfomycin in Stenotrophomonas maltophilia, an opportunistic pathogen characterized by its low susceptibility to commonly used antibiotics, were studied in the current work. None of the mechanisms reported so far for other organisms, which include the production of fosfomycin-inactivating enzymes, target modification, induction of an alternative peptidoglycan biosynthesis pathway, and the impaired entry of the antibiotic, are involved in the acquisition of such resistance by this bacterial species. Instead, the unique cause of resistance in the mutants studied is the mutational inactivation of different enzymes belonging to the Embden-Meyerhof-Parnas central metabolism pathway. The amount of intracellular fosfomycin accumulation did not change in any of these mutants, showing that neither inactivation nor transport of the antibiotic is involved. Transcriptomic analysis also showed that the mutants did not present changes in the expression level of putative alternative peptidoglycan biosynthesis pathway genes or any related enzyme. Finally, the mutants did not present an increased phosphoenolpyruvate concentration that might compete with fosfomycin for its binding to MurA. On the basis of these results, we describe a completely novel mechanism of antibiotic resistance based on mutations of genes encoding metabolic enzymes.IMPORTANCE Antibiotic resistance has been largely considered a specific bacterial response to an antibiotic challenge. Indeed, its study has been mainly concentrated on mechanisms that affect the antibiotics (mutations in transporters, efflux pumps, and antibiotic-modifying enzymes, or their regulators) or their targets (i.e., target mutations, protection, or bypass). Usually, antibiotic resistance-associated metabolic changes were considered a consequence (fitness costs) and not a cause of antibiotic resistance. Herein, we show that alterations in the central carbon bacterial metabolism can also be the cause of antibiotic resistance. In the study presented here, Stenotrophomonas maltophilia acquires fosfomycin resistance through the inactivation of glycolytic enzymes belonging to the Embden-Meyerhof-Parnas pathway. Besides resistance to fosfomycin, this inactivation also impairs the bacterial gluconeogenic pathway. Together with previous work showing that antibiotic resistance can be under metabolic control, our results provide evidence that antibiotic resistance is intertwined with the bacterial metabolism.
Collapse
|
16
|
Abstract
Klebsiella pneumoniae is a common cause of antimicrobial-resistant opportunistic infections in hospitalized patients. The species is naturally resistant to penicillins, and members of the population often carry acquired resistance to multiple antimicrobials. However, knowledge of K. pneumoniae ecology, population structure or pathogenicity is relatively limited. Over the past decade, K. pneumoniae has emerged as a major clinical and public health threat owing to increasing prevalence of healthcare-associated infections caused by multidrug-resistant strains producing extended-spectrum β-lactamases and/or carbapenemases. A parallel phenomenon of severe community-acquired infections caused by 'hypervirulent' K. pneumoniae has also emerged, associated with strains expressing acquired virulence factors. These distinct clinical concerns have stimulated renewed interest in K. pneumoniae research and particularly the application of genomics. In this Review, we discuss how genomics approaches have advanced our understanding of K. pneumoniae taxonomy, ecology and evolution as well as the diversity and distribution of clinically relevant determinants of pathogenicity and antimicrobial resistance. A deeper understanding of K. pneumoniae population structure and diversity will be important for the proper design and interpretation of experimental studies, for interpreting clinical and public health surveillance data and for the design and implementation of novel control strategies against this important pathogen.
Collapse
|