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Huynh TQ, Tran VN, Thai VC, Nguyen HA, Nguyen NTG, Tran MK, Nguyen TPT, Le CA, Ho LTN, Surian NU, Chen S, Nguyen TTH. Genomic alterations involved in fluoroquinolone resistance development in Staphylococcus aureus. PLoS One 2023; 18:e0287973. [PMID: 37494330 PMCID: PMC10370734 DOI: 10.1371/journal.pone.0287973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/19/2023] [Indexed: 07/28/2023] Open
Abstract
AIM Fluoroquinolone (FQ) is a potent antibiotic class. However, resistance to this class emerges quickly which hinders its application. In this study, mechanisms leading to the emergence of multidrug-resistant (MDR) Staphylococcus aureus (S. aureus) strains under FQ exposure were investigated. METHODOLOGY S. aureus ATCC 29213 was serially exposed to ciprofloxacin (CIP), ofloxacin (OFL), or levofloxacin (LEV) at sub-minimum inhibitory concentrations (sub-MICs) for 12 days to obtain S. aureus -1 strains and antibiotic-free cultured for another 10 days to obtain S. aureus-2 strains. The whole genome (WGS) and target sequencing were applied to analyze genomic alterations; and RT-qPCR was used to access the expressions of efflux-related genes, alternative sigma factors, and genes involved in FQ resistance. RESULTS A strong and irreversible increase of MICs was observed in all applied FQs (32 to 128 times) in all S. aureus-1 and remained 16 to 32 times in all S. aureus-2. WGS indicated 10 noticeable mutations occurring in all FQ-exposed S. aureus including 2 insdel mutations in SACOL0573 and rimI; a synonymous mutation in hslO; and 7 missense mutations located in an untranslated region. GrlA, was found mutated (R570H) in all S. aureus-1 and -2. Genes encoding for efflux pumps and their regulator (norA, norB, norC, and mgrA); alternative sigma factors (sigB and sigS); acetyltransferase (rimI); methicillin resistance (fmtB); and hypothetical protein BJI72_0645 were overexpressed in FQ-exposed strains. CONCLUSION The emergence of MDR S. aureus was associated with the mutations in the FQ-target sequences and the overexpression of efflux pump systems and their regulators.
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Affiliation(s)
- Thuc Quyen Huynh
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Research Center for Infectious Diseases, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Van Nhi Tran
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Van Chi Thai
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Hoang An Nguyen
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Ngoc Thuy Giang Nguyen
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Minh Khang Tran
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Thi Phuong Truc Nguyen
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Cat Anh Le
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Le Thanh Ngan Ho
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | | | - Swaine Chen
- Genome Institute of Singapore, Singapore, Singapore
| | - Thi Thu Hoai Nguyen
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Research Center for Infectious Diseases, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
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Zhou YY, Ma LY, Yu L, Lu X, Liang WL, Kan B, Su JR. Quinolone Resistance Genes and Their Contribution to Resistance in Vibrio cholerae Serogroup O139. Antibiotics (Basel) 2023; 12:antibiotics12020416. [PMID: 36830326 PMCID: PMC9952142 DOI: 10.3390/antibiotics12020416] [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: 12/14/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND Quinolones are commonly used for reducing the duration of diarrhea, infection severity, and limiting further transmission of disease related to Vibrio cholerae, but V. cholerae susceptibility to quinolone decreases over time. In addition to mutations in the quinolone-resistance determining regions (QRDRs), the presence of qnr and other acquired genes also contributes to quinolone resistance. RESULTS We determined the prevalence of quinolone resistance related genes among V. cholerae O139 strains isolated in China. We determined that eight strains carried qnrVC, which encodes a pentapeptide repeat protein of the Qnr subfamily, the members of which protect topoisomerases from quinolone action. Four qnrVC alleles were detected: qnrVC1, qnrVC5, qnrVC12, and qnrVC9. However, the strains carrying qnrVC1, qnrVC5, and qnrVC12 were ciprofloxacin (CIP)-sensitive. Contrastingly, the strain carrying qnrVC9 demonstrated high CIP resistance. qnrVC9 was carried by a small plasmid, which was conjugative and contributed to the high CIP resistance to the receptor V. cholerae strain. The same plasmid was also detected in V. vulnificus. The qnrVC1, qnrVC5, and qnrVC12 were cloned into expression plasmids and conferred CIP resistance on the host V. cholerae O139 strain. CONCLUSIONS Our results revealed the contribution of quinolone resistance mediated by the qnrVC9 carried on the small plasmid and its active horizontal transfer among Vibrio species. The results also suggested the different effects of qnrVC alleles in different V. cholerae strains, which is possibly due to differences in sequences of qnrVC alleles and even the genetic characteristics of the host strains.
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Affiliation(s)
- Yan-Yan Zhou
- Department of Clinical Laboratory Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Li-Yan Ma
- Department of Clinical Laboratory Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Li Yu
- Beijing Municipal Center for Disease Prevention and Control, Beijing 100013, China
| | - Xin Lu
- Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, National Institute for Communicable Disease Control and Prevention, Beijing 102206, China
| | - Wei-Li Liang
- Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, National Institute for Communicable Disease Control and Prevention, Beijing 102206, China
| | - Biao Kan
- Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, National Institute for Communicable Disease Control and Prevention, Beijing 102206, China
- Correspondence: (B.K.); (J.-R.S.); Tel.: +10-58900743 (B.K.); +10-63138545 (J.-R.S.)
| | - Jian-Rong Su
- Department of Clinical Laboratory Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- Correspondence: (B.K.); (J.-R.S.); Tel.: +10-58900743 (B.K.); +10-63138545 (J.-R.S.)
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3
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Ding Y, Hao J, Zeng Z, Jinbo Liu. Identification and genomic analysis of a Vibrio cholerae strain isolated from a patient with bloodstream infection. Heliyon 2022; 8:e11572. [PMID: 36439761 PMCID: PMC9681642 DOI: 10.1016/j.heliyon.2022.e11572] [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: 04/15/2022] [Revised: 07/25/2022] [Accepted: 11/07/2022] [Indexed: 11/18/2022] Open
Abstract
Vibrio cholerae is a bacterium ubiquitous in aquatic environments which can cause widespread infection worldwide. V. cholerae gradually became a rare species of bacteria in clinical microbiology laboratories with the control of the cholera epidemic. In this study, we isolated a V. cholerae strain, named VCHL017, from the blood of an elderly patient without gastrointestinal symptoms. The patient had a history of hookworm infection and multiple myeloma. Furthermore, she was immunocompromised, and received long-term chemotherapy and antimicrobial agents. VCHL017 was inoculated on blood agar and thiosulfate citrate bile salt sucrose plates (TCBS) to observe morphological characteristics. Then this isolate was identified by matrix-assisted laser desorption/ionization time-of-flight spectrometry (MALDI-TOF MS). The minimum inhibitory concentrations (MICs) for cefazolin, ceftazidime, cefepime, meropenem, tetracycline, ciprofloxacin, chloramphenicol, and gentamicin of VCHL017 were determined by the microbroth dilution method. PCR and serum agglutination tests were used to determine whether the serogroups of the isolate belonged to the O1/O139 and cholera toxin encoding genes. Finally, the genomic features and phylogeny of VCHL017 were analyzed by whole genome sequencing (WGS). VCHL017 was a non-O1/O139 V cholerae strain that did not carry the ctxA gene. Antimicrobial susceptibility tests revealed that VCHL017 was susceptive to chloramphenicol and tetracycline. Although it did not carry the genes encoding the cholera toxin, WGS indicated that VCHL017 carried a variety of other virulence factors. By calculating the average nucleotide identity (ANI), we precisely identified the species of VCHL017 as V. cholerae. There are also A171S and A202S missense mutations in gyrA of VCHL017. The phylogenetic analysis indicated that VCHL017 was closely related to V. cholerae strains isolated from aquatic environments. Our results suggest that continuous monitoring is necessary for non-O1/O139 V cholerae strains isolated from outside the digestive tract, which could be pathogenic through multiple virulence factors.
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Affiliation(s)
| | | | - Zhangrui Zeng
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Jinbo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
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Fuesslin V, Krautwurst S, Srivastava A, Winter D, Liedigk B, Thye T, Herrera-León S, Wohl S, May J, Fobil JN, Eibach D, Marz M, Schuldt K. Prediction of Antibiotic Susceptibility Profiles of Vibrio cholerae Isolates From Whole Genome Illumina and Nanopore Sequencing Data: CholerAegon. Front Microbiol 2022; 13:909692. [PMID: 35814690 PMCID: PMC9257098 DOI: 10.3389/fmicb.2022.909692] [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: 03/31/2022] [Accepted: 05/02/2022] [Indexed: 12/01/2022] Open
Abstract
During the last decades, antimicrobial resistance (AMR) has become a global public health concern. Nowadays multi-drug resistance is commonly observed in strains of Vibrio cholerae, the etiological agent of cholera. In order to limit the spread of pathogenic drug-resistant bacteria and to maintain treatment options the analysis of clinical samples and their AMR profiles are essential. Particularly, in low-resource settings a timely analysis of AMR profiles is often impaired due to lengthy culturing procedures for antibiotic susceptibility testing or lack of laboratory capacity. In this study, we explore the applicability of whole genome sequencing for the prediction of AMR profiles of V. cholerae. We developed the pipeline CholerAegon for the in silico prediction of AMR profiles of 82 V. cholerae genomes assembled from long and short sequencing reads. By correlating the predicted profiles with results from phenotypic antibiotic susceptibility testing we show that the prediction can replace in vitro susceptibility testing for five of seven antibiotics. Because of the relatively low costs, possibility for real-time data analyses, and portability, the Oxford Nanopore Technologies MinION sequencing platform-especially in light of an upcoming less error-prone technology for the platform-appears to be well suited for pathogen genomic analyses such as the one described here. Together with CholerAegon, it can leverage pathogen genomics to improve disease surveillance and to control further spread of antimicrobial resistance.
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Affiliation(s)
- Valeria Fuesslin
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Sebastian Krautwurst
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Akash Srivastava
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Doris Winter
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Britta Liedigk
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Thorsten Thye
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Silvia Herrera-León
- National Center of Microbiology, Institute of Health Carlos III, Madrid, Spain
| | - Shirlee Wohl
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Jürgen May
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Tropical Medicine II, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Julius N. Fobil
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, University of Ghana, Accra, Ghana
| | - Daniel Eibach
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Kathrin Schuldt
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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Xia H, Yan N, Jin J, Hou W, Wang H, Zhou M. Genomic Characterization of Ciprofloxacin Resistance in Laboratory-Derived Mutants of Vibrio parahaemolyticus. Foodborne Pathog Dis 2022; 19:543-549. [PMID: 35727114 DOI: 10.1089/fpd.2022.0015] [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: 11/13/2022] Open
Abstract
The quinolone ciprofloxacin is a broad-spectrum bactericidal antibiotic used for human medicine as well as the aquaculture industry. The emergence of ciprofloxacin-resistant Vibrio parahaemolyticus strains is currently a global public health concern. However, the mechanism of ciprofloxacin resistance in V. parahaemolyticus is not yet fully clarified. We generated mutants with decreased ciprofloxacin susceptibility using in vitro selection and investigated genes associated with ciprofloxacin resistance on a genetic level. Our selection process yielded mutants that possessed altered minimal inhibitory concentrations (MICs) for ciprofloxacin and other unrelated antibiotics. These included Ser83Ile mutations in GyrA and Val461Glu in ParE as well as mutations in the resistance nodulation cell division (RND) family transporter gene vmeD and the putative TetR family regulator gene vp0040 upstream of the vmeCD operon. Measurements of steady-state mRNA levels revealed that the ciprofloxacin-resistant mutants overexpressed vmeCD. Further, the introduction of the vp0040 mutated allele from H512 into the sensitive parental strain increased the MIC for ciprofloxacin 31.25-fold. Taken together, these results indicated that ciprofloxacin resistance in these mutants was due to the quinolone resistance determining region mutation as well as overexpression of vmeCD caused by a loss of vp0040 gene repression. This also accounted for the presence of the multidrug resistance phenotype for these mutant strains since RND efflux system can export structurally unrelated antibiotics.
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Affiliation(s)
- Hai Xia
- Department of Food Quality and Safety, School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Na Yan
- Department of Food Quality and Safety, School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Jiaqi Jin
- Department of Food Quality and Safety, School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Wenfu Hou
- Department of Food Quality and Safety, School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Hongxun Wang
- Department of Food Quality and Safety, School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Min Zhou
- Department of Food Quality and Safety, School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
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De R. Mobile Genetic Elements of Vibrio cholerae and the Evolution of Its Antimicrobial Resistance. FRONTIERS IN TROPICAL DISEASES 2021. [DOI: 10.3389/fitd.2021.691604] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Vibrio cholerae (VC) is the causative agent of the severe dehydrating diarrheal disease cholera. The primary treatment for cholera is oral rehydration therapy (ORT). However, in case of moderate to severe dehydration, antibiotics are administered to reduce morbidity. Due to the emergence of multidrug resistant (MDR) strains of VC routinely used antibiotics fail to be effective in cholera patients. Antimicrobial resistance (AMR) is encoded in the genome of bacteria and is usually acquired from other organisms cohabiting in the environment or in the gut with which it interacts in the gut or environmental niche. The antimicrobial resistance genes (ARGs) are usually borne on mobile genetic elements (MGEs) like plasmids, transposons, integrons and SXT constin. Horizontal gene transfer (HGT) helps in the exchange of ARGs among bacteria leading to dissemination of AMR. In VC the acquisition and loss of AMR to many antibiotics have been found to be a dynamic process. This review describes the different AMR determinants and mechanisms of resistance that have been discovered in VC. These ARGs borne usually on MGEs have been recovered from isolates associated with past and present epidemics worldwide. These are responsible for resistance of VC to common antibiotics and are periodically lost and gained contributing to its genetic evolution. These resistance markers can be routinely used for AMR surveillance in VC. The review also presents a precise perspective on the importance of the gut microbiome in the emergence of MDR VC and concludes that the gut microbiome is a potential source of molecular markers and networks which can be manipulated for the interception of AMR in the future.
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7
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Ekeng E, Tchatchouang S, Akenji B, Issaka BB, Akintayo I, Chukwu C, Dano ID, Melingui S, Ousmane S, Popoola MO, Nzouankeu A, Boum Y, Luquero F, Ahumibe A, Naidoo D, Azman A, Lessler J, Wohl S. Regional sequencing collaboration reveals persistence of the T12 Vibrio cholerae O1 lineage in West Africa. eLife 2021; 10:e65159. [PMID: 34143732 PMCID: PMC8213408 DOI: 10.7554/elife.65159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/05/2021] [Indexed: 11/23/2022] Open
Abstract
Background Despite recent insights into cholera transmission patterns in Africa, regional and local dynamics in West Africa-where cholera outbreaks occur every few years-are still poorly understood. Coordinated genomic surveillance of Vibrio cholerae in the areas most affected may reveal transmission patterns important for cholera control. Methods During a regional sequencing workshop in Nigeria, we sequenced 46 recent V. cholerae isolates from Cameroon, Niger, and Nigeria (37 from 2018 to 2019) to better understand the relationship between the V. cholerae bacterium circulating in these three countries. Results From these isolates, we generated 44 whole Vibrio cholerae O1 sequences and analyzed them in the context of 1280 published V. cholerae O1 genomes. All sequences belonged to the T12 V. cholerae seventh pandemic lineage. Conclusions Phylogenetic analysis of newly generated and previously published V. cholerae genomes suggested that the T12 lineage has been continuously transmitted within West Africa since it was first observed in the region in 2009, despite lack of reported cholera in the intervening years. The results from this regional sequencing effort provide a model for future regionally coordinated surveillance efforts. Funding Funding for this project was provided by Bill and Melinda Gates Foundation OPP1195157.
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Affiliation(s)
- Eme Ekeng
- Nigeria Centre for Disease ControlAbujaNigeria
| | | | | | | | - Ifeoluwa Akintayo
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | | | | | | | - Sani Ousmane
- Centre de Recherche Médicale et SanitaireNiameyNiger
| | | | | | | | | | | | | | - Andrew Azman
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Shirlee Wohl
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
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Kowalczyk A, Paneth A, Trojanowski D, Paneth P, Zakrzewska-Czerwińska J, Stączek P. Thiosemicarbazide Derivatives Decrease the ATPase Activity of Staphylococcus aureus Topoisomerase IV, Inhibit Mycobacterial Growth, and Affect Replication in Mycobacterium smegmatis. Int J Mol Sci 2021; 22:ijms22083881. [PMID: 33918623 PMCID: PMC8069432 DOI: 10.3390/ijms22083881] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 11/16/2022] Open
Abstract
Compounds targeting bacterial topoisomerases are of interest for the development of antibacterial agents. Our previous studies culminated in the synthesis and characterization of small-molecular weight thiosemicarbazides as the initial prototypes of a novel class of gyrase and topoisomerase IV inhibitors. To expand these findings with further details on the mode of action of the most potent compounds, enzymatic studies combined with a molecular docking approach were carried out, the results of which are presented herein. The biochemical assay for 1-(indol-2-oyl)-4-(4-nitrophenyl) thiosemicarbazide (4) and 4-benzoyl-1-(indol-2-oyl) thiosemicarbazide (7), showing strong inhibitory activity against Staphylococcus aureus topoisomerase IV, confirmed that these compounds reduce the ability of the ParE subunit to hydrolyze ATP rather than act by stabilizing the cleavage complex. Compound 7 showed better antibacterial activity than compound 4 against clinical strains of S. aureus and representatives of the Mycobacterium genus. In vivo studies using time-lapse microfluidic microscopy, which allowed for the monitoring of fluorescently labelled replisomes, revealed that compound 7 caused an extension of the replication process duration in Mycobacterium smegmatis, as well as the growth arrest of bacterial cells. Despite some similarities to the mechanism of action of novobiocin, these compounds show additional, unique properties, and can thus be considered a novel group of inhibitors of the ATPase activity of bacterial type IIA topoisomerases.
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Affiliation(s)
- Aleksandra Kowalczyk
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland;
| | - Agata Paneth
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland
- Correspondence: (A.P.); (P.S.)
| | - Damian Trojanowski
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland; (D.T.); (J.Z.-C.)
| | - Piotr Paneth
- Institute of Applied Radiation Chemistry, Łódź University of Technology, Żeromskiego 116, 90-924 Łódź, Poland;
- International Centre for Research on Innovative Biobased Materials (ICRI-BioM)—International Research Agenda, Łódź University of Technology, Żeromskiego 116, 90-924 Łódź, Poland
| | - Jolanta Zakrzewska-Czerwińska
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland; (D.T.); (J.Z.-C.)
| | - Paweł Stączek
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland;
- Correspondence: (A.P.); (P.S.)
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Arteaga M, Velasco J, Rodriguez S, Vidal M, Arellano C, Silva F, Carreño LJ, Vidal R, Montero DA. Genomic characterization of the non-O1/non-O139 Vibrio cholerae strain that caused a gastroenteritis outbreak in Santiago, Chile, 2018. Microb Genom 2020; 6:e000340. [PMID: 32100707 PMCID: PMC7200058 DOI: 10.1099/mgen.0.000340] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/29/2020] [Indexed: 02/06/2023] Open
Abstract
Vibrio cholerae is a human pathogen, which is transmitted by the consumption of contaminated food or water. V. cholerae strains belonging to the serogroups O1 and O139 can cause cholera outbreaks and epidemics, a severe life-threatening diarrheal disease. In contrast, serogroups other than O1 and O139, denominated as non-O1/non-O139, have been mainly associated with sporadic cases of moderate or mild diarrhea, bacteremia and wound infections. Here we investigated the virulence determinants and phylogenetic origin of a non-O1/non-O139 V. cholerae strain that caused a gastroenteritis outbreak in Santiago, Chile, 2018. We found that this outbreak strain lacks the classical virulence genes harboured by O1 and O139 strains, including the cholera toxin (CT) and the toxin-coregulated pilus (TCP). However, this strain carries genomic islands (GIs) encoding Type III and Type VI secretion systems (T3SS/T6SS) and antibiotic resistance genes. Moreover, we found these GIs are wide distributed among several lineages of non-O1/non-O139 strains. Our results suggest that the acquisition of these GIs may enhance the virulence of non-O1/non-O139 strains that lack the CT and TCP-encoding genes. Our results highlight the pathogenic potential of these V. cholerae strains.
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Affiliation(s)
- Mónica Arteaga
- Servicio de Urgencia Infantil, Hospital Clínico de la Universidad de Chile “Dr. José Joaquín Aguirre”, Santiago, Chile
| | - Juliana Velasco
- Servicio de Urgencia Infantil, Hospital Clínico de la Universidad de Chile “Dr. José Joaquín Aguirre”, Santiago, Chile
| | - Shelly Rodriguez
- Servicio de Urgencia Infantil, Hospital Clínico de la Universidad de Chile “Dr. José Joaquín Aguirre”, Santiago, Chile
| | - Maricel Vidal
- Laboratorio de Salud Pública Ambiental y Laboral, Secretaría Regional Ministerial de Salud Región Metropolitana, Santiago, Chile
| | - Carolina Arellano
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Francisco Silva
- Servicio de Laboratorio Clínico, Hospital Clínico de la Universidad de Chile “Dr. José Joaquín Aguirre”, Santiago, Chile
| | - Leandro J. Carreño
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Instituto Milenio de Inmunología e Inmunoterapia, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Roberto Vidal
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Instituto Milenio de Inmunología e Inmunoterapia, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - David A. Montero
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
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Dorman MJ, Domman D, Uddin MI, Sharmin S, Afrad MH, Begum YA, Qadri F, Thomson NR. High quality reference genomes for toxigenic and non-toxigenic Vibrio cholerae serogroup O139. Sci Rep 2019; 9:5865. [PMID: 30971707 PMCID: PMC6458141 DOI: 10.1038/s41598-019-41883-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 03/13/2019] [Indexed: 01/09/2023] Open
Abstract
Toxigenic Vibrio cholerae of the O139 serogroup have been responsible for several large cholera epidemics in South Asia, and continue to be of clinical and historical significance today. This serogroup was initially feared to represent a new, emerging V. cholerae clone that would lead to an eighth cholera pandemic. However, these concerns were ultimately unfounded. The majority of clinically relevant V. cholerae O139 isolates are closely related to serogroup O1, biotype El Tor V. cholerae, and comprise a single sublineage of the seventh pandemic El Tor lineage. Although related, these V. cholerae serogroups differ in several fundamental ways, in terms of their O-antigen, capsulation phenotype, and the genomic islands found on their chromosomes. Here, we present four complete, high-quality genomes for V. cholerae O139, obtained using long-read sequencing. Three of these sequences are from toxigenic V. cholerae, and one is from a bacterium which, although classified serologically as V. cholerae O139, lacks the CTXφ bacteriophage and the ability to produce cholera toxin. We highlight fundamental genomic differences between these isolates, the V. cholerae O1 reference strain N16961, and the prototypical O139 strain MO10. These sequences are an important resource for the scientific community, and will improve greatly our ability to perform genomic analyses of non-O1 V. cholerae in the future. These genomes also offer new insights into the biology of a V. cholerae serogroup that, from a genomic perspective, is poorly understood.
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Affiliation(s)
- Matthew J Dorman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom
| | - Daryl Domman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom
| | - Muhammad Ikhtear Uddin
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Salma Sharmin
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Mokibul Hassan Afrad
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Yasmin Ara Begum
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh.
| | - Nicholas R Thomson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom.
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom.
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Ma G, Wu G, Li X, Wang H, Zhou M. Characterization of Ciprofloxacin Resistance in Laboratory-Derived Mutants of Vibrio parahaemolyticus with qnr Gene. Foodborne Pathog Dis 2018; 15:711-717. [PMID: 30074404 DOI: 10.1089/fpd.2018.2476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Ciprofloxacin, a broad-spectrum fluoroquinolone, is a bactericidal antibiotic targeting DNA gyrase and DNA topoisomerase IV encoded by the gyrA and parC genes. Resistance to fluoroquinolones requires the accumulation of multiple mutations including those that alter target genes and increase drug efflux. To examine the development of fluoroquinolones resistance in Vibrio parahaemolyticus, ciprofloxacin induction and selection was used to obtain several resistant V. parahaemolyticus mutants, which showed decreased susceptibilities to quinolones, and increased or decreased susceptibility to other structurally unrelated antibiotics. Quinolone resistance-determining region mutations were characterized, and it was found that gyrA mutations occurred in some of the high-level resistant mutants although qnr was present in both wild-type susceptible and resistant mutant strains. The mutants showed increased qnr expression and exposure to sub-inhibitory concentrations of ciprofloxacin caused a further increase in qnr expression independently of the SOS system. Two mutants demonstrated increased expression of the VmeCD-VpoC pump gene that promotes quinolone efflux. In addition, some of the high-level resistance mutants significantly decreased bacterial fitness. These data suggested that multiple genes contributed to the enhanced ciprofloxacin resistance appeared in V. parahaemolyticus and that acquisition of ciprofloxacin resistance impaired bacterial fitness.
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Affiliation(s)
- Gengqin Ma
- School of Food Science and Engineering, Wuhan Polytechnic University , Wuhan, China
| | - Gaosheng Wu
- School of Food Science and Engineering, Wuhan Polytechnic University , Wuhan, China
| | - Xiaofang Li
- School of Food Science and Engineering, Wuhan Polytechnic University , Wuhan, China
| | - Hongxun Wang
- School of Food Science and Engineering, Wuhan Polytechnic University , Wuhan, China
| | - Min Zhou
- School of Food Science and Engineering, Wuhan Polytechnic University , Wuhan, China
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Vinothkumar K, Bhalara SR, Shah A, Ramamurthy T, Niyogi SK, Kumar GN, Bhardwaj AK. Involvement of topoisomerase mutations and qnr and aac(6′)Ib -cr genes in conferring quinolone resistance to clinical isolates of Vibrio and Shigella spp. from Kolkata, India (1998–2009). J Glob Antimicrob Resist 2018; 13:85-90. [DOI: 10.1016/j.jgar.2017.10.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 07/16/2017] [Accepted: 10/11/2017] [Indexed: 11/29/2022] Open
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Vinué L, Hooper DC, Jacoby GA. Chromosomal mutations that accompany qnr in clinical isolates of Escherichia coli. Int J Antimicrob Agents 2018; 51:479-483. [PMID: 29360506 DOI: 10.1016/j.ijantimicag.2018.01.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/10/2018] [Accepted: 01/13/2018] [Indexed: 10/18/2022]
Abstract
We examined 13 qnr-positive and 14 qnr-negative clinical isolates of Escherichia coli for mutations previously seen in a qnr-containing laboratory strain exposed to supra minimum inhibitory concentrations (MICs) of ciprofloxacin. Among the qnr-positive strains, those with ciprofloxacin MICs of ≥ 2 µg/mL had at least one mutation in gyrA. Mutations in parC were present in strains with a ciprofloxacin MIC of ≥ 128 µg/mL. The 6 most ciprofloxacin-resistant strains contained additional plasmid-mediated quinolone resistance determinants. aac(6')-Ib-cr was found in 5 of the 6 strains. Eleven of the 13 strains had alterations in MarR, 9 in SoxR, and 5 had mutations in AcrR. All had elevated expression of at least one efflux pump gene, predominantly acrA (92% of the strains), followed by mdtE (54%) and ydhE (46%). Nine had functionally silent alterations in rfa, two had mutations in gmhB, and one of these also had a mutation in surA. An E. coli with ciprofloxacin MIC of 1024 µg/mL contained 4 different plasmid-mediated quinolone resistance determinants as well as gyrA, parC, parE and pump overexpression mutations. Nine of the 14 qnr-negative strains had mutations in topoisomerase genes with a ciprofloxacin MIC of 0.25 to 256 µg/mL. The three most resistant strains also had mutations in parE. Twelve had alterations in MarR, 10 in SoxR and 5 in AcrR. Ten of the 14 strains had elevated expression of efflux pumps with acrA (71.4%), followed by ydhE (50%) and mdtE (14.3%). A diversity of resistance mechanisms occurs in clinical isolates with and without qnr genes.
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Affiliation(s)
- Laura Vinué
- Massachusetts General Hospital, Boston, Massachusetts, USA.
| | - David C Hooper
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | - George A Jacoby
- Lahey Hospital and Medical Center, Burlington, Massachusetts, USA
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Runcharoen C, Moradigaravand D, Blane B, Paksanont S, Thammachote J, Anun S, Parkhill J, Chantratita N, Peacock SJ. Whole genome sequencing reveals high-resolution epidemiological links between clinical and environmental Klebsiella pneumoniae. Genome Med 2017; 9:6. [PMID: 28118859 PMCID: PMC5264300 DOI: 10.1186/s13073-017-0397-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 01/03/2017] [Indexed: 12/22/2022] Open
Abstract
Background Klebsiella pneumoniae is a gram-negative bacterial species capable of occupying a broad range of environmental and clinical habitats. Known as an opportunistic pathogen, it has recently become a major causative agent of clinical infections worldwide. Despite growing knowledge about the highly diverse population of K. pneumoniae, the evolution and clinical significance of environmental K. pneumoniae, as well as the relationship between clinical and environmental K. pneumoniae, are poorly defined. Methods We isolated and sequenced K. pneumoniae from in-patients in a single hospital in Thailand, as well as hospital sewage, and surrounding canals and farms within a 20-km radius. Results Phylogenetic analysis of 77 K. pneumoniae (48 clinical and 29 non-clinical isolates) demonstrated that the two groups were intermixed throughout the tree and in some cases resided in the same clade, suggesting recent divergence from a common ancestor. Phylogenetic comparison of the 77 Thai genomes with 286 K. pneumoniae from a global collection showed that Thai isolates were closely related to the clinical sub-population of the global collection, indicating that Thai clinical isolates belonged to globally circulating lineages. Dating of four Thai K. pneumoniae clades indicated that they emerged between 50 and 150 years ago. Despite their phylogenetic relatedness, virulence factors and β-lactamase resistance genes were more numerous in clinical than in environmental isolates. Our results indicate that clinical and environmental K. pneumoniae are closely related, but that hospitals may select for isolates with a more resistant and virulent genotype. Conclusions These findings highlight the clinical relevance of environmental K. pneumoniae isolates. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0397-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chakkaphan Runcharoen
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Danesh Moradigaravand
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
| | - Beth Blane
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Box 157, Hills Road, Cambridge, CB2 0QQ, UK
| | - Suporn Paksanont
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Jeeranan Thammachote
- Division of Clinical Microbiology, Medical Technology Department, Buddhasothorn hospital, Chachoengsao, 24000, Thailand
| | - Suthatip Anun
- Division of Clinical Microbiology, Medical Technology Department, Buddhasothorn hospital, Chachoengsao, 24000, Thailand
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Sharon J Peacock
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK. .,Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Box 157, Hills Road, Cambridge, CB2 0QQ, UK. .,London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
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