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Jeremia L, Deprez BE, Dey D, Conn GL, Wuest WM. Ribosome-targeting antibiotics and resistance via ribosomal RNA methylation. RSC Med Chem 2023; 14:624-643. [PMID: 37122541 PMCID: PMC10131624 DOI: 10.1039/d2md00459c] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/17/2023] [Indexed: 03/05/2023] Open
Abstract
The rise of multidrug-resistant bacterial infections is a cause of global concern. There is an urgent need to both revitalize antibacterial agents that are ineffective due to resistance while concurrently developing new antibiotics with novel targets and mechanisms of action. Pathogen associated resistance-conferring ribosomal RNA (rRNA) methyltransferases are a growing threat that, as a group, collectively render a total of seven clinically-relevant ribosome-targeting antibiotic classes ineffective. Increasing frequency of identification and their growing prevalence relative to other resistance mechanisms suggests that these resistance determinants are rapidly spreading among human pathogens and could contribute significantly to the increased likelihood of a post-antibiotic era. Herein, with a view toward stimulating future studies to counter the effects of these rRNA methyltransferases, we summarize their prevalence, the fitness cost(s) to bacteria of their acquisition and expression, and current efforts toward targeting clinically relevant enzymes of this class.
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Affiliation(s)
- Learnmore Jeremia
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
| | - Benjamin E Deprez
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
| | - William M Wuest
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
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2
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Yang Y, Yang Y, Ahmed MAEGES, Qin M, He R, Wu Y, Liang X, Zhong LL, Chen P, Deng B, Hassan RM, Wen W, Xu L, Huang X, Xu L, Tian GB. Carriage of distinct bla KPC-2 and bla OXA-48 plasmids in a single ST11 hypervirulent Klebsiella pneumoniae isolate in Egypt. BMC Genomics 2022; 23:20. [PMID: 34996351 PMCID: PMC8742346 DOI: 10.1186/s12864-021-08214-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 11/25/2021] [Indexed: 11/28/2022] Open
Abstract
Background Carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) causes serious infections with significant morbidity and mortality. However, the epidemiology and transmission mechanisms of CR-hvKP and the corresponding carbapenem-resistant plasmids require further investigation. Herein, we have characterized an ST11 K. pneumoniae strain EBSI041 from the blood sample encoding both hypervirulence and carbapenem resistance phenotypes from a patient in Egypt. Results K. pneumoniae strain EBSI041 showed multidrug-resistance phenotypes, where it was highly resistant to almost all tested antibiotics including carbapenems. And hypervirulence phenotypes of EBSI041 was confirmed by the model of Galleria mellonella infection. Whole-genome sequencing analysis showed that the hybrid plasmid pEBSI041-1 carried a set of virulence factors rmpA, rmpA2, iucABCD and iutA, and six resistance genes aph(3′)-VI, armA, msr(E), mph(E), qnrS, and sul2. Besides, blaOXA-48 and blaSHV-12 were harboured in a novel conjugative IncL-type plasmid pEBSI041-2. The blaKPC-2-carrying plasmid pEBSI041-3, a non-conjugative plasmid lacking the conjugative transfer genes, could be transferred with the help of pEBSI041-2, and the two plasmids could fuse into a new plasmid during co-transfer. Moreover, the emergence of the p16HN-263_KPC-like plasmids is likely due to the integration of pEBSI041-3 and pEBSI041-4 via IS26-mediated rearrangement. Conclusion To the best of our knowledge, this is the first report on the complete genome sequence of KPC-2- and OXA-48-coproducing hypervirulent K. pneumoniae from Egypt. These results give new insights into the adaptation and evolution of K. pneumoniae during nosocomial infections. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08214-9.
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Affiliation(s)
- Yanxian Yang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China
| | - Yongqiang Yang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.,School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, 510006, China
| | - Mohamed Abd El-Gawad El-Sayed Ahmed
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.,Department of Microbiology and Immunology, Faculty of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, Cairo, 6th of October City, Egypt
| | - Mingyang Qin
- Department of Pathogen Biology, School of Basic Medical, Xinxiang Medical University, Xinxiang, 453003, China
| | - Ruowen He
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China
| | - Yiping Wu
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China
| | - Xiaoxue Liang
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, 610500, China
| | - Lan-Lan Zhong
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China
| | - Ping Chen
- Department of Pathogen Biology, School of Basic Medical, Xinxiang Medical University, Xinxiang, 453003, China
| | - Baoguo Deng
- Department of Pathogen Biology, School of Basic Medical, Xinxiang Medical University, Xinxiang, 453003, China
| | - Reem Mostafa Hassan
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Weihong Wen
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Lingqing Xu
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511518, China
| | - Xubin Huang
- Department of Pulmonary and Critical Care Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Lin Xu
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China. .,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China. .,Research Center for Clinical Laboratory Standard, Zhongshan School of Medicine, Sun Yat⁃sen University, Guangzhou, China.
| | - Guo-Bao Tian
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China. .,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China. .,School of Medicine, Xizang Minzu University, Xianyang, 712082, Shaanxi, China.
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3
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Fayez MS, Hakim TA, Agwa MM, Abdelmoteleb M, Aly RG, Montaser NN, Abdelsattar AS, Rezk N, El-Shibiny A. Topically Applied Bacteriophage to Control Multi-Drug Resistant Klebsiella pneumoniae Infected Wound in a Rat Model. Antibiotics (Basel) 2021; 10:antibiotics10091048. [PMID: 34572629 PMCID: PMC8470685 DOI: 10.3390/antibiotics10091048] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/18/2021] [Accepted: 08/24/2021] [Indexed: 12/18/2022] Open
Abstract
(Background): Multi-drug-resistant Klebsiella pneumoniae (MDR-KP) has steadily grown beyond antibiotic control. Wound infection kills many patients each year, due to the entry of multi-drug resistant (MDR) bacterial pathogens into the skin gaps. However, a bacteriophage (phage) is considered to be a potential antibiotic alternative for treating bacterial infections. This research aims at isolating and characterizing a specific phage and evaluate its topical activity against MDR-KP isolated from infected wounds. (Methods): A lytic phage ZCKP8 was isolated by using a clinical isolate KP/15 as a host strain then characterized. Additionally, phage was assessed for its in vitro host range, temperature, ultraviolet (UV), and pH sensitivity. The therapeutic efficiency of phage suspension and a phage-impeded gel vehicle were assessed in vivo against a K. pneumoniae infected wound on a rat model. (Result): The phage produced a clear plaque and was classified as Siphoviridae. The phage inhibited KP/15 growth in vitro in a dose-dependent pattern and it was found to resist high temperature (˂70 °C) and was primarily active at pH 5; moreover, it showed UV stability for 45 min. Phage-treated K. pneumoniae inoculated wounds showed the highest healing efficiency by lowering the infection. The quality of the regenerated skin was evidenced via histological examination compared to the untreated control group. (Conclusions): This research represents the evidence of effective phage therapy against MDR-KP.
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Affiliation(s)
- Mohamed S. Fayez
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza 12578, Egypt; (M.S.F.); (A.S.A.); (N.R.)
| | - Toka A. Hakim
- Faculty of Biotechnology, October University for Modern Sciences and Arts, Giza 11223, Egypt; (T.A.H.); (N.N.M.)
| | - Mona M. Agwa
- Department of Chemistry of Natural and Microbial Products, Pharmaceutical and Drug Industries Research Division, National Research Centre, Dokki, Giza 12622, Egypt;
| | - Mohamed Abdelmoteleb
- Department of Botany, Faculty of Science, Mansoura University, Mansoura 35516, Egypt;
| | - Rania G. Aly
- Department of Surgical Pathology, Faculty of Medicine, Alexandria University, Alexandria 21131, Egypt;
| | - Nada N. Montaser
- Faculty of Biotechnology, October University for Modern Sciences and Arts, Giza 11223, Egypt; (T.A.H.); (N.N.M.)
| | - Abdallah S. Abdelsattar
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza 12578, Egypt; (M.S.F.); (A.S.A.); (N.R.)
- Center for X-ray and Determination of Structure of Matter, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Nouran Rezk
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza 12578, Egypt; (M.S.F.); (A.S.A.); (N.R.)
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, Giza 12578, Egypt; (M.S.F.); (A.S.A.); (N.R.)
- Faculty of Environmental Agricultural Sciences, Arish University, Arish 45511, Egypt
- Correspondence:
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Kiani A, Nami Y, Hedayati S, Jaymand M, Samadian H, Haghshenas B. Tarkhineh as a new microencapsulation matrix improves the quality and sensory characteristics of probiotic Lactococcus lactis KUMS-T18 enriched potato chips. Sci Rep 2021; 11:12599. [PMID: 34131254 PMCID: PMC8206370 DOI: 10.1038/s41598-021-92095-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 06/03/2021] [Indexed: 12/12/2022] Open
Abstract
In the present study, probiotic potato chips containing a newly isolated probiotic Lactococcus lactis KUMS-T18 strain were produced by using a simple spraying method and then enhancing the stability, survival rate, and sensory characteristics of product during storage at 4 °C and 25 °C was examined for four months. Based on the results, Lactococcus lactis KUMS-T18 isolated from traditional Tarkhineh as a safe strain had high tolerance to low pH and high bile salt, anti-pathogenic activity, hydrophobicity, adhesion to human epithelial cells, auto- and co-aggregation, cholesterol assimilation and antibiotic susceptibility. Meanwhile, by micro-coating the probiotic cells in Tarkhineh formulations, elliptical to spherical shape (460-740 µm) probiotic drops were produced. The results revealed that potato chips produced with turmeric and plain Tarkhineh during storage at 4 °C, had excellent protection abilities for probiotic cells with about 4.52 and 3.46 log decreases in CFU/g respectively. On the other hand, probiotic potato chips, compared to non-probiotic and commercial potato chips, showed the criteria of probiotic products such as excellent quality and superior sensory characteristics. In summary, this study proved that probiotic Lactococcus lactis KUMS-T18 strain covered by Tarkhineh formulations as protective matrix has high potential to be used in the production of probiotic potato chips.
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Affiliation(s)
- Amir Kiani
- Regenerative Medicine Research Center (RMRC), Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, 67146, Iran
| | - Yousef Nami
- Department of Food Biotechnology, Branch for Northwest and West Region, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran.
| | - Shahab Hedayati
- Students Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mehdi Jaymand
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hadi Samadian
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Babak Haghshenas
- Regenerative Medicine Research Center (RMRC), Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, 67146, Iran.
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5
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Abstract
A putative type II toxin-antitoxin (TA) module almost exclusively associated with conjugative IncC plasmids is homologous to the higBA family of TA systems found in chromosomes and plasmids of several species of bacteria. Despite the clinical significance and strong association with high-profile antimicrobial resistance (AMR) genes, the TA system of IncC plasmids remains largely uncharacterized. In this study, we present evidence that IncC plasmids encode a bona fide HigB-like toxin that strongly inhibits bacterial growth and results in cell elongation in Escherichia coli. IncC HigB toxin acts as a ribosome-dependent endoribonuclease that significantly reduces the transcript abundance of a subset of adenine-rich mRNA transcripts. A glycine residue at amino acid position 64 is highly conserved in HigB toxins from different bacterial species, and its replacement with valine (G64V) abolishes the toxicity and the mRNA cleavage activity of the IncC HigB toxin. The IncC plasmid higBA TA system functions as an effective addiction module that maintains plasmid stability in an antibiotic-free environment. This higBA addiction module is the only TA system that we identified in the IncC backbone and appears essential for the stable maintenance of IncC plasmids. We also observed that exposure to subinhibitory concentrations of ciprofloxacin, a DNA-damaging fluoroquinolone antibiotic, results in elevated higBA expression, which raises interesting questions about its regulatory mechanisms. A better understanding of this higBA-type TA module potentially allows for its subversion as part of an AMR eradication strategy. IMPORTANCE Toxin-antitoxin (TA) systems play vital roles in maintaining plasmids in bacteria. Plasmids with incompatibility group C are large plasmids that disseminate via conjugation and carry high-profile antibiotic resistance genes. We present experimental evidence that IncC plasmids carry a TA system that functions as an effective addiction module and maintains plasmid stability in an antibiotic-free environment. The toxin of IncC plasmids acts as an endoribonuclease that targets a subset of mRNA transcripts. Overexpressing the IncC toxin gene strongly inhibits bacterial growth and results in cell elongation in Escherichia coli hosts. We also identify a conserved amino acid residue in the toxin protein that is essential for its toxicity and show that the expression of this TA system is activated by a DNA-damaging antibiotic, ciprofloxacin. This mobile TA system may contribute to managing bacterial stress associated with DNA-damaging antibiotics.
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6
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Kiani A, Nami Y, Hedayati S, Elieh Ali Komi D, Goudarzi F, Haghshenas B. Application of Tarkhineh Fermented Product to Produce Potato Chips With Strong Probiotic Properties, High Shelf-Life, and Desirable Sensory Characteristics. Front Microbiol 2021; 12:657579. [PMID: 34054754 PMCID: PMC8153181 DOI: 10.3389/fmicb.2021.657579] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/20/2021] [Indexed: 11/17/2022] Open
Abstract
The application of Tarkhineh texture to protect probiotics in potato chips has been investigated as the main goal in this paper. In this study, the probiotic assessments, morphological characteristics, sensory evaluation, and survival rates of the covered probiotic cells with Tarkhineh in potato chips during storage time were assessed. Based on results, T34 isolated from traditional Tarkhineh as a safe strain had a high tolerance to low pH and bile salt conditions, displayed acceptable anti-pathogenic activities, and also showed desirable antibiotic susceptibility. Two types of Tarkhineh formulations (plain Tarkhineh and turmeric Tarkhineh) were applied using a simple spraying method for covering T34 cells in potato chips. All formulations showed elliptical to spherical (480-770 μm) shape probiotic drops. Storage stability results revealed that T34 cells mixed with turmeric and plain Tarkhineh during 4 months of storage at 4°C displayed excellent protection abilities with about 3.70 and 2.85 log decreases in CFU/g respectively. Additionally, probiotic potato chips compared to non-probiotic and commercial potato chips, exhibited probiotic product criteria such as excellent quality and superior sensory properties during storage time. In conclusion, Tarkhineh showed high potential as a protective matrix for probiotic cells in potato chips.
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Affiliation(s)
- Amir Kiani
- Regenerative Medicine Research Center (RMRC), Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Yousef Nami
- Department of Food Biotechnology, Branch for Northwest & West Region, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran
| | - Shahab Hedayati
- Students Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Daniel Elieh Ali Komi
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Farjam Goudarzi
- Regenerative Medicine Research Center (RMRC), Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Babak Haghshenas
- Regenerative Medicine Research Center (RMRC), Kermanshah University of Medical Sciences, Kermanshah, Iran
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7
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Zhang Y, Lei CW, Chen X, Yao TG, Yu JW, Hu WL, Mao X, Wang HN. Characterization of IncC Plasmids in Enterobacterales of Food-Producing Animals Originating From China. Front Microbiol 2020; 11:580960. [PMID: 33193210 PMCID: PMC7652850 DOI: 10.3389/fmicb.2020.580960] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/07/2020] [Indexed: 01/13/2023] Open
Abstract
Incompatibility group C (IncC) plasmids have received attention due to their broad host range and because they harbor key antibiotic resistance genes. Because these resistance genes can spread from food-producing animals to human, the proliferation of these plasmids represents a public health risk. In this study, a total of 20 IncC plasmids were collected from food-producing animals in China, and characterized by Oxford Nanopore Technologies long-read sequencing. Based on four key differences of the IncC backbone, 4 IncC plasmids were classified as type 1, 15 were classified as type 1/2 hybrid, and one was classified as type 2. The 15 type 1/2 hybrids were further divided into 13 type 1/2a and 2 type 1/2b, based on sequence differences arising from different homologous recombination events between type 1 and type 2 IncC backbones. Genome comparison of accessory resistance modules showed that different IncC plasmids exhibited various phenotypes via loss and gain of diverse modules, mainly within the blaCMY-carrying region, and two antibiotic resistance islands designated ARI-A and ARI-B. Interestingly, in addition to insertion and deletion events, IS26 or IS1294-mediated large sequence inversions were found in the IncC genome of the 4 type1/2a plasmids, suggesting that insertion sequence-mediated rearrangements also promote the diversity of the IncC genome. This study provides insight into the structural diversification and multidrug resistance of IncC plasmids identified from food-producing animals in China.
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Affiliation(s)
- Yu Zhang
- College of Life Sciences, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, Chengdu, China
| | - Chang-Wei Lei
- College of Life Sciences, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, Chengdu, China
| | - Xuan Chen
- College of Life Sciences, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, Chengdu, China
| | - Tian-Ge Yao
- College of Life Sciences, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, Chengdu, China
| | - Jing-Wen Yu
- College of Life Sciences, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, Chengdu, China
| | - Wan-Long Hu
- College of Life Sciences, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, Chengdu, China
| | - Xuan Mao
- College of Life Sciences, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, Chengdu, China
| | - Hong-Ning Wang
- College of Life Sciences, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, Chengdu, China
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8
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Emerging Antimicrobial-Resistant High-Risk Klebsiella pneumoniae Clones ST307 and ST147. Antimicrob Agents Chemother 2020; 64:AAC.01148-20. [PMID: 32747358 DOI: 10.1128/aac.01148-20] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
There is an enormous global public health burden due to antimicrobial-resistant (AMR) Klebsiella pneumoniae high-risk clones. K. pneumoniae ST307 and ST147 are recent additions to the family of successful clones in the species. Both clones likely emerged in Europe during the early to mid-1990s and, in a relatively short time, became prominent global pathogens, spreading to all continents (with the exception of Antarctica). ST307 and ST147 consist of multiple clades/clusters and are associated with various carbapenemases (i.e., KPCs, NDMs, OXA-48-like, and VIMs). ST307 is endemic in Italy, Colombia, the United States (Texas), and South Africa, while ST147 is endemic in India, Italy, Greece, and certain North African countries. Both clones have been introduced into regions of nonendemicity, leading to worldwide nosocomial outbreaks. Genomic studies showed ST307 and ST147 contain identical gyrA and parC mutations and likely obtained plasmids with bla CTX-M-15 during the early to mid-2000s, which aided in their global distribution. ST307 and ST147 then acquired plasmids with various carbapenemases during the late 2000s, establishing themselves as important AMR pathogens in certain regions. Both clones are likely underreported due to restricted detection methodologies. ST307 and ST147 have the ability to become major threats to public health due to their worldwide distribution, ability to cause serious infections, and association with AMR, including panresistance. The medical community at large, especially those concerned with antimicrobial resistance, should be aware of the looming threat posed by emerging AMR high-risk clones such as K. pneumoniae ST307 and ST147.
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9
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Venturini C, Ben Zakour NL, Bowring B, Morales S, Cole R, Kovach Z, Branston S, Kettle E, Thomson N, Iredell JR. Fine capsule variation affects bacteriophage susceptibility in Klebsiella pneumoniae ST258. FASEB J 2020; 34:10801-10817. [PMID: 32598522 DOI: 10.1096/fj.201902735r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 05/27/2020] [Accepted: 06/04/2020] [Indexed: 12/22/2022]
Abstract
Multidrug resistant (MDR) carbapenemase-producing (CP) Klebsiella pneumoniae, belonging to clonal group CG258, is capable of causing severe disease in humans and is classified as an urgent threat by health agencies worldwide. Bacteriophages are being actively explored as therapeutic alternatives to antibiotics. In an effort to define a robust experimental approach for effective selection of lytic viruses for therapy, we have fully characterized the genomes of 18 Kumoniae target strains and tested them against novel lytic bacteriophages (n = 65). The genomes of K pneumoniae carrying blaNDM and blaKPC were sequenced and CG258 isolates selected for bacteriophage susceptibility testing. The local K pneumoniae CG258 population was dominated by sequence type ST258 clade 1 (86%) with variations in capsular locus (cps) and prophage content. CG258-specific bacteriophages primarily targeted the capsule, but successful infection is also likely blocked in some by immunity conferred by existing prophages. Five tailed bacteriophages against K pneumoniae ST258 clade 1 were selected for further characterization. Our findings show that effective control of K pneumoniae CG258 with bacteriophage will require mixes of diverse lytic viruses targeting relevant cps variants and allowing for variable prophage content. These insights will facilitate identification and selection of therapeutic bacteriophage candidates against this serious pathogen.
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Affiliation(s)
- Carola Venturini
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research (WIMR), Westmead, NSW, Australia.,School of Medicine, Sydney Medical School, University of Sydney, NSW, Australia
| | - Nouri L Ben Zakour
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research (WIMR), Westmead, NSW, Australia.,School of Medicine, Sydney Medical School, University of Sydney, NSW, Australia
| | - Bethany Bowring
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research (WIMR), Westmead, NSW, Australia
| | | | - Robert Cole
- AmpliPhi Australia Pty Ltd, Brookvale, NSW, Australia
| | | | | | - Emma Kettle
- Westmead Research Hub Electron Microscope Core Facility, The Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Nicholas Thomson
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,The London School of Hygiene and Tropical Medicine, London, UK
| | - Jonathan R Iredell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research (WIMR), Westmead, NSW, Australia.,School of Medicine, Sydney Medical School, University of Sydney, NSW, Australia.,Westmead Hospital, Western Sydney Local Health District (WSLHD), Sydney, NSW, Australia
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10
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Sękowska A, Bogiel T, Kaczmarek A. Evaluation of the usefulness of selected methods for the detection of carbapenemases in Klebsiella strains. J Med Microbiol 2020; 69:792-796. [PMID: 32459618 DOI: 10.1099/jmm.0.001202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Klebsiella rods, belonging to the family Enterobacteriaceae, are generally opportunistic pathogens commonly associated with nosocomial infections, especially in intensive care units. Interestingly, strains of this genus also show multi-drug resistance. In recent years, multiple studies have indicated that the prevalence of carbapenem resistance has increased rapidly among Klebsiella representatives.Aim. The aim of this study was to assess the usefulness of selected phenotypic and genotypic methods for the detection of the most important carbapenemases in Klebsiella strains.Methodology. The study involved 51 Klebsiella strains. The ability to produce carbapenemases was determined by phenotypic methods (double disc synergy test, test with four discs and three inhibitors, CarbaNP test, culture on chromogenic medium, panels of automatic method - Phoenix, CIM test and modified Hodge test). The potential for carbapenemase synthesis was also evaluated using real-time PCR, detecting bla VIM/IMP, bla KPC, bla NDM and bla OXA-48 genes.Results. Using the phenotypic methods, positive results were obtained for all of the analysed strains. Using PCR, carbapenemase synthesis potential was confirmed on the molecular level; the bla VIM gene was detected in 23 strains, the bla NDM gene in 26 strains and the bla OXA-48 gene in two strains.Conclusion. There was complete agreement between the carbapenemases detected by the genetic method and the results obtained with phenotypic methods.
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Affiliation(s)
- Alicja Sękowska
- Department of Microbiology, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 9 M. Sklodowska-Curie Street, 85-094 Bydgoszcz, Poland
| | - Tomasz Bogiel
- Department of Microbiology, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 9 M. Sklodowska-Curie Street, 85-094 Bydgoszcz, Poland
| | - Agnieszka Kaczmarek
- Department of Microbiology, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 9 M. Sklodowska-Curie Street, 85-094 Bydgoszcz, Poland
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11
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Nishida S, Ono Y. Genomic analysis of a pan-resistant Klebsiella pneumoniae sequence type 11 identified in Japan in 2016. Int J Antimicrob Agents 2020; 55:105854. [DOI: 10.1016/j.ijantimicag.2019.11.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 11/01/2019] [Accepted: 11/13/2019] [Indexed: 10/25/2022]
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12
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Wang J, Ning Y, Li S, Wang Y, Liang J, Jin C, Yan H, Huang Y. Multidrug-resistant Acinetobacter baumannii strains with NDM-1: Molecular characterization and in vitro efficacy of meropenem-based combinations. Exp Ther Med 2019; 18:2924-2932. [PMID: 31572535 PMCID: PMC6755477 DOI: 10.3892/etm.2019.7927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/31/2018] [Indexed: 11/24/2022] Open
Abstract
Acinetobacter baumannii is an important cause of hospital-acquired, multidrug-resistant (MDR) infections occurring worldwide. Anti-microbial combination regimens may be the only feasible treatment option for affected patients. In the present study, the efficacy of the combined therapy of meropenem with colistin, ampicillin-sulbactam, tazobactam and vancomycin against clinical strains of MDR A. baumannii was determined. Anti-microbial susceptibility testing was performed and resistance genes were characterized by a multiplex polymerase chain reaction (PCR)-reverse line blot assay. The genetic background of New Delhi metallo-β-lactamase 1 (NDM-1) was analysed by primer walking. The presence of NDM-1 was detected using the modified Hodge test and the EDTA-combined disk test. To screen for synergistic drug effects, the fractional inhibitory concentration index was calculated using a checkerboard assay. The results of the PCR as well as the sequence analyses suggested that NDM-1 was located downstream of the ISAba125 element. In addition, a synergistic effect was determined for meropenem + vancomycin, meropenem + tazobactam and meropenem + ampicillin + sulbactam in two strains each, and in four strains for meropenem + colistin. A total of five A. baumannii strains with resistance to numerous antibiotics and carrying numerous resistance genes were identified. In the strains of A. baumannii, the NDM-1 gene was integrated in a transposon structure with a copy of the ISAba125 insertion sequence. However, the genetic background was not identical among the different species and strains. The genetic variability of NDM-1 may facilitate the rapid dissemination of this gene. In conclusion, meropenem may enhance the efficacy of antibiotics in A. baumannii strains with NDM-1-associated MDR.
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Affiliation(s)
- Jingjing Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Henan University of Science and Technology, Luoyang, Henan 471000, P.R. China
| | - Yongzhong Ning
- Department of Laboratory Medicine, Beijing ChuiYangLiu Hospital Affiliated to Tsinghua University, Beijing 100022, P.R. China
| | - Shu Li
- Department of Laboratory Medicine, Hongqi Hospital Affiliated to Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
| | - Yun Wang
- Department of Laboratory Medicine, Hongqi Hospital Affiliated to Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
| | - Jinhua Liang
- Department of Laboratory Medicine, Hongqi Hospital Affiliated to Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
| | - Chunming Jin
- Department of Laboratory Medicine, Hongqi Hospital Affiliated to Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
| | - Hairun Yan
- Department of Laboratory Medicine, Hongqi Hospital Affiliated to Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, P.R. China
| | - Yongcun Huang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Mudanjiang Medical College, Mudanjiang, Heilongjiang 157001, P.R. China
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13
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Ko KS. Antibiotic-resistant clones in Gram-negative pathogens: presence of global clones in Korea. J Microbiol 2018; 57:195-202. [PMID: 30552629 DOI: 10.1007/s12275-019-8491-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 12/26/2022]
Abstract
Antibiotic resistance is a global concern in public health. Antibiotic-resistant clones can spread nationally, internationally, and globally. This review considers representative antibiotic-resistant Gram-negative bacterial clones-CTX-M- 15-producing ST131 in Escherichia coli, extended-spectrum ß-lactamase-producing ST11 and KPC-producing ST258 in Klebsiella pneumoniae, IMP-6-producing, carbapenem-resistant ST235 in Pseudomonas aeruginosa, and OXA-23-producing global clone 2 in Acinetobacter baumannii-that have disseminated worldwide, including in Korea. The findings highlight the urgency for systematic monitoring and international cooperation to suppress the emergence and propagation of antibiotic resistance.
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Affiliation(s)
- Kwan Soo Ko
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea.
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14
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Ambrose SJ, Harmer CJ, Hall RM. Evolution and typing of IncC plasmids contributing to antibiotic resistance in Gram-negative bacteria. Plasmid 2018; 99:40-55. [PMID: 30081066 DOI: 10.1016/j.plasmid.2018.08.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/12/2018] [Accepted: 08/02/2018] [Indexed: 01/14/2023]
Abstract
The large, broad host range IncC plasmids are important contributors to the spread of key antibiotic resistance genes and over 200 complete sequences of IncC plasmids have been reported. To track the spread of these plasmids accurate typing to identify the closest relatives is needed. However, typing can be complicated by the high variability in resistance gene content and various typing methods that rely on features of the conserved backbone have been developed. Plasmids can be broadly typed into two groups, type 1 and type 2, using four features that differentiate the otherwise closely related backbones. These types are found in many different countries in bacteria from humans and animals. However, hybrids of type 1 and type 2 are also occasionally seen, and two further types, each represented by a single plasmid, were distinguished. Generally, the antibiotic resistance genes are located within a small number of resistance islands, only one of which, ARI-B, is found in both type 1 and type 2. The introduction of each resistance island generates a new lineage and, though they are continuously evolving via the loss of resistance genes or introduction of new ones, the island positions serve as valuable lineage-specific markers. A current type 2 lineage of plasmids is derived from an early type 2 plasmid but the sequences of early type 1 plasmids include features not seen in more recent type 1 plasmids, indicating a shared ancestor rather than a direct lineal relationship. Some features, including ones essential for maintenance or for conjugation, have been examined experimentally.
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Affiliation(s)
- Stephanie J Ambrose
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Christopher J Harmer
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia.
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
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15
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Yoon EJ, Yang JW, Kim JO, Lee H, Lee KJ, Jeong SH. Carbapenemase-producing Enterobacteriaceae in South Korea: a report from the National Laboratory Surveillance System. Future Microbiol 2018; 13:771-783. [PMID: 29478336 DOI: 10.2217/fmb-2018-0022] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To assess the epidemiology of carbapenemase-producing Enterobacteriaceae (CPE) in South Korea. MATERIALS & METHODS From 2011 to 2015, 2487 carbapenem-nonsusceptible Enterobacteriaceae were collected through the Korean National Laboratory Surveillance System. Disk-diffusion for antimicrobial susceptibility, PCR/sequencing to detect carbapenemase genes and multilocus sequence typing for molecular epidemiology were carried out. RESULTS The number of carbapenem-nonsusceptible Enterobacteriaceae was increasing approximately 1.5-fold per year and the proportion of CPEs was exponentially confirmed from 2014. KPC was the most dominant, mostly associated with Klebsiella pneumoniae ST11 and ST307, NDM was the second and OXA-48-like was the third dominant carbapenemases. The IMP, VIM and GES-5 CPEs were identified sporadically. CONCLUSION The nation-wide spreads of KPC, NDM and OXA-48-like CPEs were in an alarming epidemiological stage.
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Affiliation(s)
- Eun-Jeong Yoon
- Department of Laboratory Medicine & Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Ji Woo Yang
- Division of Antimicrobial Resistance, National Institute of Health, Centers for Disease Control & Prevention, Cheongju, South Korea
| | - Jung Ok Kim
- Department of Laboratory Medicine & Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Hyukmin Lee
- Department of Laboratory Medicine & Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Kwang Jun Lee
- Division of Antimicrobial Resistance, National Institute of Health, Centers for Disease Control & Prevention, Cheongju, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine & Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
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16
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Abderrahim A, Djahmi N, Pujol C, Nedjai S, Bentakouk MC, Kirane-Gacemi D, Dekhil M, Sotto A, Lavigne JP, Pantel A. First Case of NDM-1-ProducingKlebsiella pneumoniaein Annaba University Hospital, Algeria. Microb Drug Resist 2017; 23:895-900. [DOI: 10.1089/mdr.2016.0213] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Amel Abderrahim
- Institut National de la Santé et de la Recherche Médicale, U1047, Université de Montpellier, UFR de Médecine, Nîmes, France
- Laboratoire d'Amélioration Génétique des Plantes, Equipe Microorganismes et Environnement, Université Badji Mokhtar, Annaba, Algérie
| | - Nassima Djahmi
- Laboratoire de Microbiologie, CHU Ibn Rochd, Annaba, Algérie
| | | | - Sabina Nedjai
- Laboratoire de Microbiologie, CHU Ibn Rochd, Annaba, Algérie
| | - Mohamed Cherif Bentakouk
- Centre de Réanimation et de Traitement des Brûlés, Hôpital Ibn-Sina, CHU Annaba, Annaba, Algérie
| | - Djamila Kirane-Gacemi
- Laboratoire d'Amélioration Génétique des Plantes, Equipe Microorganismes et Environnement, Université Badji Mokhtar, Annaba, Algérie
| | - Mazouz Dekhil
- Laboratoire de Microbiologie, CHU Ibn Rochd, Annaba, Algérie
| | - Albert Sotto
- Institut National de la Santé et de la Recherche Médicale, U1047, Université de Montpellier, UFR de Médecine, Nîmes, France
- Service des Maladies Infectieuses et Tropicales, CHU Carémeau, Nîmes, France
| | - Jean-Philippe Lavigne
- Institut National de la Santé et de la Recherche Médicale, U1047, Université de Montpellier, UFR de Médecine, Nîmes, France
- Service de Microbiologie, CHU Carémeau, Nîmes, France
| | - Alix Pantel
- Institut National de la Santé et de la Recherche Médicale, U1047, Université de Montpellier, UFR de Médecine, Nîmes, France
- Service de Microbiologie, CHU Carémeau, Nîmes, France
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17
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Ko JH, Baek JY, Peck KR, Cho SY, Ha YE, Kim SH, Huh HJ, Lee NY, Kang CI, Chung DR, Song JH. Discrepant susceptibility to gentamicin despite amikacin resistance in Klebsiella pneumoniae by VITEK 2 represents false susceptibility associated with the armA 16S rRNA methylase gene. J Med Microbiol 2017; 66:1448-1450. [PMID: 28893358 DOI: 10.1099/jmm.0.000583] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Because we experienced gentamicin failure in Klebsiella pneumoniae bacteraemia that was susceptible to gentamicin despite amikacin resistance, as determined by VITEK 2, we evaluated the true susceptibility and mechanism of resistance. We screened 2818 K. pneumoniae isolates during a 1-year period at a university hospital and reviewed anti-microbial susceptibility reports using the VITEK 2 system. The minimum inhibitory concentration was substantiated by broth microdilution (BMD), and the presence of 16S rRNA methylase genes and aminoglycoside-modifying enzymes was also investigated. A total of 131 amikacin-resistant isolates from 19 patients were gentamicin non-resistant according to the VITEK 2 system. Among these, we were able to collect isolates from 12 patients (63.2 %), and a single isolate from each patient was tested. Eleven of the gentamicin non-resistant isolates (91.7 %) showed high-level resistance to both amikacin and gentamicin by BMD in association with the armA gene. Gentamicin is not an adequate treatment option for amikacin-resistant K. pneumoniae, even if VITEK 2 reports susceptibility.
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Affiliation(s)
- Jae-Hoon Ko
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Republic of Korea.,Present address: Division of Infectious Diseases, Department of Internal Medicine, Armed Forces Capital Hospital, Seongnam, Republic of Korea
| | - Jin Yang Baek
- Asia Pacific Foundation for Infectious Diseases (APFID), Seoul, Republic of Korea
| | - Kyong Ran Peck
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Republic of Korea
| | - Sun Young Cho
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Republic of Korea
| | - Young Eun Ha
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Republic of Korea
| | - So Hyun Kim
- Asia Pacific Foundation for Infectious Diseases (APFID), Seoul, Republic of Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Cheol-In Kang
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Republic of Korea
| | - Doo Ryeon Chung
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Republic of Korea
| | - Jae-Hoon Song
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Republic of Korea
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18
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Williams MR, Stedtfeld RD, Waseem H, Stedtfeld T, Upham B, Khalife W, Etchebarne B, Hughes M, Tiedje JM, Hashsham SA. Implications of direct amplification for measuring antimicrobial resistance using point-of-care devices. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2017; 9:1229-1241. [PMID: 29657581 PMCID: PMC5898395 DOI: 10.1039/c6ay03405e] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Antimicrobial resistance (AMR) is recognized as a global threat to human health. Rapid detection and characterization of AMR is a critical component of most antibiotic stewardship programs. Methods based on amplification of nucleic acids for detection of AMR are generally faster than culture-based approaches but they still require several hours to more than a day due to the need for transporting the sample to a centralized laboratory, processing of sample, and sometimes DNA purification and concentration. Nucleic acids-based point-of-care (POC) devices are capable of rapidly diagnosing antibiotic-resistant infections which may help in making timely and correct treatment decisions. However, for most POC platforms, sample processing for nucleic acids extraction and purification is also generally required prior to amplification. Direct amplification, an emerging possibility for a number of polymerases, has the potential to eliminate these steps without significantly impacting diagnostic performance. This review summarizes direct amplification methods and their implication for rapid measurement of AMR. Future research directions that may further strengthen the possibility of integrating direct amplification methods with POC devices are also summarized.
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Affiliation(s)
- M R Williams
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - R D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - H Waseem
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - T Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - B Upham
- Pediatrics and Human Development, Michigan State University, East Lansing, MI 48824, USA
| | - W Khalife
- Department of Microbiology, Sparrow Laboratories, Sparrow Health System, Lansing, MI 48912, USA
| | - B Etchebarne
- Osteopathic Medical Specialties, Section of Emergency Medicine, Michigan State University, East Lansing, MI 4882, USA
| | - M Hughes
- Osteopathic Medical Specialties, Section of Emergency Medicine, Michigan State University, East Lansing, MI 4882, USA
| | - J M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - S A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
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19
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Subramanian GK, Soundari PG, Ramanathan V, Krishnan P. Endemic Indian clones of Klebsiella pneumoniae-harbouring New Delhi metallo-beta-lactamase-1 on a hybrid plasmid replicon type: A case of changing New Delhi metallo-beta-lactamase plasmid landscapes in India? Indian J Med Microbiol 2017; 34:286-92. [PMID: 27514948 DOI: 10.4103/0255-0857.188314] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
PURPOSE blaNDM genes are MBL genes that confer resistance to carbapenems. Globally, they are associated with diverse clones and plasmids. In this study, we characterised three isolates of Klebsiella pneumoniae-harbouring blaNDM1 from patients undergoing chronic haemodialysis and renal transplantation. MATERIALS AND METHODS 3 blaNDM1 -producing K. pneumoniae were isolated from end-stage renal disease patients undergoing haemodialysis and renal transplantation from a nephrology unit. All the three isolates were screened for clinically relevant resistant genes. Plasmid replicon content was analysed by polymerase chain reaction based replicon typing. Conjugation assays were done using azide-resistant Escherichia coli J53 as the recipient strain. Multilocus sequence typing and variable number tandem repeat typing were done to find the clonality. Replicon sequence based typing was attempted to find the diversity of replicon-associated sequences in IncHI3 plasmids. RESULTS All the 3 blaNDM positive isolates possessed the New Delhi metallo-beta-lactamase-1 (NDM-1) allele with an IncHI3 plasmid which was not transferable in one isolate. The isolates were found to be sequence type 14 (ST14; 2 nos) and ST38 both of which were previously reported to be the NDM-producing K. pneumoniae STs prevalent in India. Replicon sequence analysis revealed limited sequence diversity within the repHI3 and repFIB locus. CONCLUSION To the best of our knowledge, this is the first report of IncHI3, a newly assigned enterobacterial plasmid incompatibility group from India. This could either be a case of importation or a widely circulating NDM plasmid type in India.
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Affiliation(s)
- G K Subramanian
- Department of Microbiology, Dr. ALM PGIBMS, University of Madras, Chennai, Tamil Nadu, India
| | - P G Soundari
- Department of Microbiology, Dr. ALM PGIBMS, University of Madras, Chennai, Tamil Nadu, India
| | - V Ramanathan
- Nephrology Unit, Billroth Hospitals, Chennai - 600 028, Tamil Nadu, India
| | - P Krishnan
- Department of Microbiology, Dr. ALM PGIBMS, University of Madras, Chennai, Tamil Nadu, India
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20
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Park EA, Kim YT, Cho JH, Ryu S, Lee JH. Characterization and genome analysis of novel bacteriophages infecting the opportunistic human pathogens Klebsiella oxytoca and K. pneumoniae. Arch Virol 2016; 162:1129-1139. [PMID: 28028618 DOI: 10.1007/s00705-016-3202-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 12/11/2016] [Indexed: 11/27/2022]
Abstract
Klebsiella is a genus of well-known opportunistic human pathogens that are associated with diabetes mellitus and chronic pulmonary obstruction; however, this pathogen is often resistant to multiple drugs. To control this pathogen, two Klebsiella-infecting phages, K. oxytoca phage PKO111 and K. pneumoniae phage PKP126, were isolated from a sewage sample. Analysis of their host range revealed that they infect K. pneumoniae and K. oxytoca, suggesting host specificity for members of the genus Klebsiella. Stability tests confirmed that the phages are stable under various temperature (4 to 60 °C) and pH (3 to 11) conditions. A challenge assay showed that PKO111 and PKP126 inhibit growth of their host strains by 2 log and 4 log, respectively. Complete genome sequencing of the phages revealed that their genome sizes are quite different (168,758 bp for PKO111 and 50,934 bp for PKP126). Their genome annotation results showed that they have no human virulence-related genes, an important safety consideration. In addition, no lysogen-formation gene cluster was detected in either phage genome, suggesting that they are both virulent phages in their bacterial hosts. Based on these results, PKO111 and PKP126 may be good candidates for development of biocontrol agents against members of the genus Klebsiella for therapeutic purposes. A comparative analysis of tail-associated gene clusters of PKO111 and PKP126 revealed relatively low homology, suggesting that they might differ in the way they recognize and infect their specific hosts.
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Affiliation(s)
- Eun-Ah Park
- Department of Food Science and Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin, 446-701, Korea
| | - You-Tae Kim
- Department of Food Science and Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin, 446-701, Korea
| | - Jae-Hyun Cho
- Department of Food Science and Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin, 446-701, Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Department of Agriculture Biotechnology, Research Institute of Agriculture and Life Sciences, and Center for Food and Bioconvergence, Seoul National University, Seoul, 151-921, Korea
| | - Ju-Hoon Lee
- Department of Food Science and Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin, 446-701, Korea.
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21
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Li JJ, Munoz-Price LS, Spychala CN, DePascale D, Doi Y. New Delhi Metallo-β-Lactamase-1-Producing Klebsiella pneumoniae, Florida, USA(1). Emerg Infect Dis 2016; 22:744-6. [PMID: 26983001 PMCID: PMC4806972 DOI: 10.3201/eid2204.151176] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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22
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Lee CR, Lee JH, Park KS, Kim YB, Jeong BC, Lee SH. Global Dissemination of Carbapenemase-Producing Klebsiella pneumoniae: Epidemiology, Genetic Context, Treatment Options, and Detection Methods. Front Microbiol 2016; 7:895. [PMID: 27379038 PMCID: PMC4904035 DOI: 10.3389/fmicb.2016.00895] [Citation(s) in RCA: 446] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 05/26/2016] [Indexed: 01/08/2023] Open
Abstract
The emergence of carbapenem-resistant Gram-negative pathogens poses a serious threat to public health worldwide. In particular, the increasing prevalence of carbapenem-resistant Klebsiella pneumoniae is a major source of concern. K. pneumoniae carbapenemases (KPCs) and carbapenemases of the oxacillinase-48 (OXA-48) type have been reported worldwide. New Delhi metallo-β-lactamase (NDM) carbapenemases were originally identified in Sweden in 2008 and have spread worldwide rapidly. In this review, we summarize the epidemiology of K. pneumoniae producing three carbapenemases (KPCs, NDMs, and OXA-48-like). Although the prevalence of each resistant strain varies geographically, K. pneumoniae producing KPCs, NDMs, and OXA-48-like carbapenemases have become rapidly disseminated. In addition, we used recently published molecular and genetic studies to analyze the mechanisms by which these three carbapenemases, and major K. pneumoniae clones, such as ST258 and ST11, have become globally prevalent. Because carbapenemase-producing K. pneumoniae are often resistant to most β-lactam antibiotics and many other non-β-lactam molecules, the therapeutic options available to treat infection with these strains are limited to colistin, polymyxin B, fosfomycin, tigecycline, and selected aminoglycosides. Although, combination therapy has been recommended for the treatment of severe carbapenemase-producing K. pneumoniae infections, the clinical evidence for this strategy is currently limited, and more accurate randomized controlled trials will be required to establish the most effective treatment regimen. Moreover, because rapid and accurate identification of the carbapenemase type found in K. pneumoniae may be difficult to achieve through phenotypic antibiotic susceptibility tests, novel molecular detection techniques are currently being developed.
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Affiliation(s)
- Chang-Ro Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Kwang Seung Park
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Young Bae Kim
- Division of STEM, North Shore Community College, Danvers MA, USA
| | - Byeong Chul Jeong
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
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Haghshenas B, Haghshenas M, Nami Y, Yari Khosroushahi A, Abdullah N, Barzegari A, Rosli R, Hejazi MS. Probiotic Assessment of Lactobacillus plantarum 15HN and Enterococcus mundtii 50H Isolated from Traditional Dairies Microbiota. Adv Pharm Bull 2016; 6:37-47. [PMID: 27123416 DOI: 10.15171/apb.2016.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 11/01/2015] [Accepted: 01/07/2016] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Probiotics are microorganisms, which show beneficial health effects on hosts once consumed in sufficient amounts. Among probiotic bacteria, the bioactive compounds from lactic acid bacteria (LAB) group can be utilized as preservative agents. LAB group can be isolated and characterized from traditional dairy sources. This study aimed to isolate, identify, and biologically characterize probiotic LAB strains from Iranian traditional dairy products. METHODS A total of 19 LAB strains were identified by sequencing of their 16S rRNA genes. They were examined for adherence to human intestinal Caco-2 cells and tolerance to low pH/high bile salts and simulated in vitro digestion conditions. Moreover, they were evaluated further to assess their ability to prevent the adhesion of Escherichia coli 026 to the intestinal mucosa, inhibitory functions against pathogens, and sensitivity to conventional antibiotics. RESULTS L. plantarum 15HN and E. mundtii 50H strains displayed ≥ 71% survival rates at low pH/high bile salts and ≥ 40% survival rates in digestive conditions. Their adherences to Caco-2 cells were 3.2×105 and 2.6×105 CFU mL-1 respectively and high values of anti-adhesion capability were observed (≥36%). They inhibited the growth of 13 and 11 indicator pathogens respectively. Moreover, they were sensitive or semi-sensitive to seven and three out of eight antibiotics respectively. CONCLUSION L. plantarum 15HN and E. mundtii 50H, which were isolated from shiraz product, displayed above-average results for all of the criteria. Therefore, they can be introduced as novel candidate probiotics that could be used in the food industry.
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Affiliation(s)
- Babak Haghshenas
- Institute of Biosciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Minoo Haghshenas
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Yousef Nami
- Institute of Biosciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | | | - Norhafizah Abdullah
- Chemical and Environmental Engineering Department, Faculty of Engineering, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Abolfazl Barzegari
- Tabriz University of Medical Sciences, Molecular Medicine and Therapy Lab, Research Center for Pharmaceutical Nanotechnology, Tabriz, Iran
| | - Rozita Rosli
- Institute of Biosciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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High-level carbapenem-resistant OXA-48-producing Klebsiella pneumoniae with a novel OmpK36 variant and low-level, carbapenem-resistant, non-porin-deficient, OXA-181-producing Escherichia coli from Thailand. Diagn Microbiol Infect Dis 2016; 85:221-6. [PMID: 27041106 DOI: 10.1016/j.diagmicrobio.2016.03.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 03/03/2016] [Accepted: 03/05/2016] [Indexed: 11/21/2022]
Abstract
Five blaOXA-48-like-carrying Enterobacteriaceae isolates collected from two Thai patients in December 2012 were characterized. Three Klebsiella pneumoniae isolates giving two different pulsed-field gel electrophoresis patterns and sequence types (ST11 and ST37) from patient 1 harbored blaOXA-48 locating on Tn1999.2, whereas two Escherichia coli isolates with the same pulsotype and ST5 from Patient 2 carried ISEcp1-associated blaOXA-181. One K. pneumoniae strain had blaSHV-12, blaDHA-1, qnrB, and qnrS, while another strain harbored blaCTX-M-15, qnrS and aac(6')-Ib-cr. The E. coli strain contained blaCTX-M-15, blaCMY-2, qnrS, and aac(6')-Ib-cr. Interestingly, the OXA-48 producers with a novel OmpK36 variant by a substitution of Gly to Asp in the L3 loop-borne PEFXG motif exhibited high-level resistance to ertapenem, imipenem, and meropenem. In contrast, the OXA-181 producer with non-porin-deficient background showed low-level resistance to ertapenem only. Both patients died because of either septic shock or pneumonia. This study showed the impact of OXA-48-like carbapenemases in porin-defective clinical isolate background, which may lead to serious therapeutic problems in the near future.
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Haghshenas B, Haghshenas M, Nami Y, Yari Khosroushahi A, Abdullah N, Barzegari A, Rosli R, Hejazi MS. Probiotic Assessment of Lactobacillus plantarum 15HN and Enterococcus mundtii 50H Isolated from Traditional Dairies Microbiota. Adv Pharm Bull 2016; 6:37-47. [PMID: 27123416 PMCID: PMC4845554 DOI: 10.15171/apb.2016.07] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 11/01/2015] [Accepted: 01/07/2016] [Indexed: 08/05/2023] Open
Abstract
PURPOSE Probiotics are microorganisms, which show beneficial health effects on hosts once consumed in sufficient amounts. Among probiotic bacteria, the bioactive compounds from lactic acid bacteria (LAB) group can be utilized as preservative agents. LAB group can be isolated and characterized from traditional dairy sources. This study aimed to isolate, identify, and biologically characterize probiotic LAB strains from Iranian traditional dairy products. METHODS A total of 19 LAB strains were identified by sequencing of their 16S rRNA genes. They were examined for adherence to human intestinal Caco-2 cells and tolerance to low pH/high bile salts and simulated in vitro digestion conditions. Moreover, they were evaluated further to assess their ability to prevent the adhesion of Escherichia coli 026 to the intestinal mucosa, inhibitory functions against pathogens, and sensitivity to conventional antibiotics. RESULTS L. plantarum 15HN and E. mundtii 50H strains displayed ≥ 71% survival rates at low pH/high bile salts and ≥ 40% survival rates in digestive conditions. Their adherences to Caco-2 cells were 3.2×105 and 2.6×105 CFU mL-1 respectively and high values of anti-adhesion capability were observed (≥36%). They inhibited the growth of 13 and 11 indicator pathogens respectively. Moreover, they were sensitive or semi-sensitive to seven and three out of eight antibiotics respectively. CONCLUSION L. plantarum 15HN and E. mundtii 50H, which were isolated from shiraz product, displayed above-average results for all of the criteria. Therefore, they can be introduced as novel candidate probiotics that could be used in the food industry.
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Affiliation(s)
- Babak Haghshenas
- Institute of Biosciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Minoo Haghshenas
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Yousef Nami
- Institute of Biosciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | | | - Norhafizah Abdullah
- Chemical and Environmental Engineering Department, Faculty of Engineering, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Abolfazl Barzegari
- Tabriz University of Medical Sciences, Molecular Medicine and Therapy Lab, Research Center for Pharmaceutical Nanotechnology, Tabriz, Iran
| | - Rozita Rosli
- Institute of Biosciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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Abstract
Enterobacteriaceae are responsible for a large proportion of serious, life-threatening infections and resistance to multiple antibiotics in these organisms is an increasing global public health problem. Mutations in chromosomal genes contribute to antibiotic resistance, but Enterobacteriaceae are adapted to sharing genetic material and much important resistance is due to 'mobile' resistance genes. Different mobile genetic elements, which have different characteristics, are responsible for capturing these genes from the chromosomes of a variety of bacterial species and moving them between DNA molecules. If transferred to plasmids, these resistance genes are then able to be transferred 'horizontally' between different bacterial cells, including different species, and well as being transferred 'vertically' during cell division. Carriage of several resistance genes on the same plasmid enables a bacterial cell to acquire multi-resistance in a single step and means that spread of one resistance gene may be co-selected for by use of antibiotics other than those to which it confers resistance. Many different mobile genes conferring resistance to each class of antibiotic have been identified, complicating detection of the factors responsible for a particular resistance phenotype, especially when changes in chromosomal genes may also confer or contribute to resistance. Understanding the mechanisms of antibiotic resistance, and the means by which these mechanisms can evolve and disseminate, is important for developing ways to efficiently track the spread of resistance and to optimise treatment.
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Genomic Characteristics of NDM-Producing Enterobacteriaceae Isolates in Australia and Their blaNDM Genetic Contexts. Antimicrob Agents Chemother 2015; 60:136-41. [PMID: 26482302 DOI: 10.1128/aac.01243-15] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 10/03/2015] [Indexed: 11/20/2022] Open
Abstract
blaNDM has been reported in different Enterobacteriaceae species and on numerous plasmid replicon types (Inc). Plasmid replicon typing, in combination with genomic characteristics of the bacterial host (e.g., sequence typing), is used to infer the spread of antimicrobial resistance determinants between genetically unrelated bacterial hosts. The genetic context of blaNDM is heterogeneous. In this study, we genomically characterized 12 NDM-producing Enterobacteriaceae isolated in Australia between 2012 and 2014: Escherichia coli (n = 6), Klebsiella pneumoniae (n = 3), Enterobacter cloacae (n = 2) and Providencia rettgeri (n = 1). We describe their blaNDM genetic contexts within Tn125, providing insights into the acquisition of blaNDM into Enterobacteriaceae. IncFII-type (n = 7) and IncX3 (n = 4) plasmids were the most common plasmid types found. The IncHI1B (n = 1) plasmid was also identified. Five different blaNDM genetic contexts were identified, indicating four particular plasmids with specific blaNDM genetic contexts (NGCs), three of which were IncFII plasmids (FII-A to -C). Of note, the blaNDM genetic context of P. rettgeri was not conjugative. Epidemiological links between our NDM-producing Enterobacteriaceae were established by their acquisition of these five particular plasmid types. The combination of different molecular and genetic characterization methods allowed us to provide insight into the spread of plasmids transmitting blaNDM.
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Garneau-Tsodikova S, Labby KJ. Mechanisms of Resistance to Aminoglycoside Antibiotics: Overview and Perspectives. MEDCHEMCOMM 2015; 7:11-27. [PMID: 26877861 DOI: 10.1039/c5md00344j] [Citation(s) in RCA: 267] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Aminoglycoside (AG) antibiotics are used to treat many Gram-negative and some Gram-positive infections and, importantly, multidrug-resistant tuberculosis. Among various bacterial species, resistance to AGs arises through a variety of intrinsic and acquired mechanisms. The bacterial cell wall serves as a natural barrier for small molecules such as AGs and may be further fortified via acquired mutations. Efflux pumps work to expel AGs from bacterial cells, and modifications here too may cause further resistance to AGs. Mutations in the ribosomal target of AGs, while rare, also contribute to resistance. Of growing clinical prominence is resistance caused by ribosome methyltransferases. By far the most widespread mechanism of resistance to AGs is the inactivation of these antibiotics by AG-modifying enzymes. We provide here an overview of these mechanisms by which bacteria become resistant to AGs and discuss their prevalence and potential for clinical relevance.
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Affiliation(s)
- Sylvie Garneau-Tsodikova
- University of Kentucky, Department of Pharmaceutical Sciences, 789 South Limestone Street, Lexington, KY, USA. ; Tel: 859-218-1686
| | - Kristin J Labby
- Beloit College, Department of Chemistry, 700 College Street, Beloit, WI, USA. ; Tel: 608-363-2273
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Baraniak A, Izdebski R, Fiett J, Gawryszewska I, Bojarska K, Herda M, Literacka E, Żabicka D, Tomczak H, Pewińska N, Szarata M, Ozorowski T, Milner A, Hryniewicz W, Gniadkowski M. NDM-producing Enterobacteriaceae in Poland, 2012–14: inter-regional outbreak ofKlebsiella pneumoniaeST11 and sporadic cases. J Antimicrob Chemother 2015; 71:85-91. [DOI: 10.1093/jac/dkv282] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 08/11/2015] [Indexed: 11/13/2022] Open
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Carbapenemase-Producing Klebsiella pneumoniae, a Key Pathogen Set for Global Nosocomial Dominance. Antimicrob Agents Chemother 2015; 59:5873-84. [PMID: 26169401 DOI: 10.1128/aac.01019-15] [Citation(s) in RCA: 545] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The management of infections due to Klebsiella pneumoniae has been complicated by the emergence of antimicrobial resistance, especially to carbapenems. Resistance to carbapenems in K. pneumoniae involves multiple mechanisms, including the production of carbapenemases (e.g., KPC, NDM, VIM, OXA-48-like), as well as alterations in outer membrane permeability mediated by the loss of porins and the upregulation of efflux systems. The latter two mechanisms are often combined with high levels of other types of β-lactamases (e.g., AmpC). K. pneumoniae sequence type 258 (ST258) emerged during the early to mid-2000s as an important human pathogen and has spread extensively throughout the world. ST258 comprises two distinct lineages, namely, clades I and II, and it seems that ST258 is a hybrid clone that was created by a large recombination event between ST11 and ST442. Incompatibility group F plasmids with blaKPC have contributed significantly to the success of ST258. The optimal treatment of infections due to carbapenemase-producing K. pneumoniae remains unknown. Some newer agents show promise for treating infections due to KPC producers; however, effective options for the treatment of NDM producers remain elusive.
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Espedido BA, Dimitrijovski B, van Hal SJ, Jensen SO. The use of whole-genome sequencing for molecular epidemiology and antimicrobial surveillance: identifying the role of IncX3 plasmids and the spread of blaNDM-4-like genes in the Enterobacteriaceae. J Clin Pathol 2015; 68:835-8. [PMID: 26056157 DOI: 10.1136/jclinpath-2015-203044] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/20/2015] [Indexed: 11/04/2022]
Abstract
AIMS To characterise the resistome of a multi-drug resistant Klebsiella pneumoniae (Kp0003) isolated from an Australian traveller who was repatriated to a Sydney Metropolitan Hospital from Myanmar with possible prosthetic aortic valve infective endocarditis. METHODS Kp0003 was recovered from a blood culture of the patient and whole genome sequencing was performed. Read mapping and de novo assembly of reads facilitated in silico multi-locus sequence and plasmid replicon typing as well as the characterisation of antibiotic resistance genes and their genetic context. Conjugation experiments were also performed to assess the plasmid (and resistance gene) transferability and the effect on the antibiotic resistance phenotype. RESULTS Importantly, and of particular concern, the carbapenem-hydrolysing β-lactamase gene blaNDM-4 was identified on a conjugative IncX3 plasmid (pJEG027). In this respect, the blaNDM-4 genetic context is similar (at least to some extent) to what has previously been identified for blaNDM-1 and blaNDM-4-like variants. CONCLUSIONS This study highlights the potential role that IncX3 plasmids have played in the emergence and dissemination of blaNDM-4-like variants worldwide and emphasises the importance of resistance gene surveillance.
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Affiliation(s)
- Björn A Espedido
- Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney, New South Wales, Australia Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Borce Dimitrijovski
- Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney, New South Wales, Australia Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Sebastiaan J van Hal
- Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Slade O Jensen
- Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney, New South Wales, Australia Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia South Western Sydney Clinical School, University of New South Wales, Sydney, New South Wales, Australia
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Dominance of IMP-4-producing enterobacter cloacae among carbapenemase-producing Enterobacteriaceae in Australia. Antimicrob Agents Chemother 2015; 59:4059-66. [PMID: 25918153 DOI: 10.1128/aac.04378-14] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 04/19/2015] [Indexed: 12/16/2022] Open
Abstract
The prevalence of carbapenemase-producing Enterobacteriaceae (CPE) has been increasing worldwide. blaIMP has been reported to be the predominant carbapenemase-encoding gene within Enterobacteriaceae in Australia. However, there are limited data currently available on CPE from Queensland, Australia. A total of 58 CPE isolates were isolated between July 2009 and March 2014 from Queensland hospitals. The clonality of isolates was determined by Diversilab repetitive sequence-based PCR. The isolates were investigated for the resistance mechanisms carbapenemase, extended-spectrum β-lactamase, and AmpC β-lactamase and for aminoglycoside resistance and plasmid-mediated quinolone resistance genes by PCR. The plasmid types associated with carbapenemase-encoding genes were characterized. The majority of the CPE were Enterobacter cloacae (n = 29). The majority of Queensland CPE isolates were IMP producers and comprised 11 species (n = 48). Nine NDM-producing Enterobacteriaceae were identified. One NDM-producing Klebsiella pneumoniae isolate coproduced OXA-48. One K. pneumoniae isolate was an OXA-181 producer. The incidence of IMP producers increased significantly in 2013. blaIMP-4 was found in all IMP-producing isolates. blaTEM, qnrB, and aacA4 were common among IMP-4 producers. The HI2 (67%) and L/M (21%) replicons were associated with blaIMP-4. All HI2 plasmids were of sequence type 1 (ST1). All but one of the NDM producers possessed blaCTX-M-15. The 16S rRNA methylase genes found among NDM producers were armA, rmtB, rmtC, and rmtF. The substantial increase in the prevalence of CPE in Queensland has been associated mainly with the emergence E. cloacae strains possessing HI2 plasmids carrying blaIMP-4 over the past 2 years. The importation of NDM producers and/or OXA-48-like producers in patients also contributed to the increased emergence of CPE.
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Evaluation of the efficacy of a bacteriophage in the treatment of pneumonia induced by multidrug resistance Klebsiella pneumoniae in mice. BIOMED RESEARCH INTERNATIONAL 2015; 2015:752930. [PMID: 25879036 PMCID: PMC4387947 DOI: 10.1155/2015/752930] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/19/2015] [Accepted: 03/04/2015] [Indexed: 12/25/2022]
Abstract
Multidrug-resistant Klebsiella pneumoniae (MRKP) has steadily grown beyond antibiotic control. However, a bacteriophage is considered to be a potential antibiotic alternative for treating bacterial infections. In this study, a lytic bacteriophage, phage 1513, was isolated using a clinical MRKP isolate KP 1513 as the host and was characterized. It produced a clear plaque with a halo and was classified as Siphoviridae. It had a short latent period of 30 min, a burst size of 264 and could inhibit KP 1513 growth in vitro with a dose-dependent pattern. Intranasal administration of a single dose of 2 × 109 PFU/mouse 2 h after KP 1513 inoculation was able to protect mice against lethal pneumonia. In a sublethal pneumonia model, phage-treated mice exhibited a lower level of K. pneumoniae burden in the lungs as compared to the untreated control. These mice lost less body weight and exhibited lower levels of inflammatory cytokines in their lungs. Lung lesion conditions were obviously improved by phage therapy. Therefore, phage 1513 has a great effect in vitro and in vivo, which has potential to be used as an alternative to an antibiotic treatment of pneumonia that is caused by the multidrug-resistant K. pneumoniae.
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Abstract
Antimicrobial resistance, including multidrug resistance (MDR), is an increasing problem globally. MDR bacteria are frequently detected in humans and animals from both more- and less-developed countries and pose a serious concern for human health. Infections caused by MDR microbes may increase morbidity and mortality and require use of expensive drugs and prolonged hospitalization. Humans may be exposed to MDR pathogens through exposure to environments at health-care facilities and farms, livestock and companion animals, human food, and exposure to other individuals carrying MDR microbes. The Centers for Disease Control and Prevention classifies drug-resistant foodborne bacteria, including Campylobacter, Salmonella Typhi, nontyphoidal salmonellae, and Shigella, as serious threats. MDR bacteria have been detected in both meat and fresh produce. Salmonellae carrying genes coding for resistance to multiple antibiotics have caused numerous foodborne MDR outbreaks. While there is some level of resistance to antimicrobials in environmental bacteria, the widespread use of antibiotics in medicine and agriculture has driven the selection of a great variety of microbes with resistance to multiple antimicrobials. MDR bacteria on meat may have originated in veterinary health-care settings or on farms where animals are given antibiotics in feed or to treat infections. Fresh produce may be contaminated by irrigation or wash water containing MDR bacteria. Livestock, fruits, and vegetables may also be contaminated by food handlers, farmers, and animal caretakers who carry MDR bacteria. All potential sources of MDR bacteria should be considered and strategies devised to reduce their presence in foods. Surveillance studies have documented increasing trends in MDR in many pathogens, although there are a few reports of the decline of certain multidrug pathogens. Better coordination of surveillance programs and strategies for controlling use of antimicrobials need to be implemented in both human and animal medicine and agriculture and in countries around the world.
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Affiliation(s)
- Marjorie E Doyle
- Food Research Institute, University of Wisconsin , Madison, Wisconsin
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35
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Haghshenas B, Nami Y, Abdullah N, Radiah D, Rosli R, Barzegari A, Yari Khosroushahi A. Potentially probiotic acetic acid bacteria isolation and identification from traditional dairies microbiota. Int J Food Sci Technol 2014. [DOI: 10.1111/ijfs.12718] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Babak Haghshenas
- Institute of Biosciences; University Putra Malaysia; 43400 UPM Serdang Selangor Malaysia
| | - Yousef Nami
- Institute of Biosciences; University Putra Malaysia; 43400 UPM Serdang Selangor Malaysia
| | - Norhafizah Abdullah
- Chemical and Environmental Engineering Department; Faculty of Engineering; University Putra Malaysia; 43400 UPM Serdang Selangor Malaysia
| | - Dayang Radiah
- Chemical and Environmental Engineering Department; Faculty of Engineering; University Putra Malaysia; 43400 UPM Serdang Selangor Malaysia
| | - Rozita Rosli
- Institute of Biosciences; University Putra Malaysia; 43400 UPM Serdang Selangor Malaysia
| | - Abolfazl Barzegari
- Drug Applied Research Center; Tabriz University of Medical Sciences; Tabriz Iran
| | - Ahmad Yari Khosroushahi
- Drug Applied Research Center; Tabriz University of Medical Sciences; Tabriz Iran
- Department of Pharmacognosy; Faculty of Pharmacy; Tabriz University of Medical Sciences; Tabriz Iran
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36
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Quiles MG, Rocchetti TT, Fehlberg LC, Kusano EJU, Chebabo A, Pereira RMG, Gales AC, Pignatari ACC. Unusual association of NDM-1 with KPC-2 and armA among Brazilian Enterobacteriaceae isolates. ACTA ACUST UNITED AC 2014; 48:174-7. [PMID: 25466163 PMCID: PMC4321224 DOI: 10.1590/1414-431x20144154] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 10/13/2014] [Indexed: 05/28/2023]
Abstract
We report the microbiological characterization of four New Delhi
metallo-β-lactamase-1 (blaNDM-1)-producing Enterobacteriaceae isolated in Rio de
Janeiro, Brazil. blaNDM-1 was located on a conjugative plasmid and was associated with
Klebsiella pneumoniae carbapenemase-2 (blaKPC-2) or aminoglycoside-resistance methylase (armA), a
16S rRNA methylase not previously reported in Brazil, in two distinct strains of
Enterobacter cloacae. Our results suggested that the introduction
of blaNDM-1 in Brazil has been accompanied by rapid spread, since our isolates
showed no genetic relationship.
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Affiliation(s)
- M G Quiles
- Laboratório Especial de Microbiologia Clínica, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brasil
| | - T T Rocchetti
- Laboratório Especial de Microbiologia Clínica, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brasil
| | - L C Fehlberg
- Laboratório Especial de Microbiologia Clínica, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brasil
| | - E J U Kusano
- Laboratório Diagnósticos da América, DASA, São Paulo, SP, Brasil
| | - A Chebabo
- Laboratório Diagnósticos da América, DASA, São Paulo, SP, Brasil
| | - R M G Pereira
- Laboratório Diagnósticos da América, DASA, São Paulo, SP, Brasil
| | - A C Gales
- Laboratório Especial de Microbiologia Clínica, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brasil
| | - A C C Pignatari
- Laboratório Especial de Microbiologia Clínica, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brasil
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Dissemination of NDM metallo-β-lactamase genes among clinical isolates of Enterobacteriaceae collected during the SMART global surveillance study from 2008 to 2012. Antimicrob Agents Chemother 2014; 59:826-30. [PMID: 25403666 DOI: 10.1128/aac.03938-14] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The prevalence of carbapenemase enzymes continues to increase. Among the Ambler class B enzymes is the New Delhi metallo-β-lactamase (NDM). This particular enzyme is capable of hydrolyzing nearly all β-lactam antimicrobial agents and has spread rapidly, becoming a global problem. Therapeutic treatment options for patients infected with isolates which produce this enzyme are difficult to manage, as cross-resistance to other antimicrobial classes is common. The Study for Monitoring Antimicrobial Resistance Trends (SMART) is a global surveillance study evaluating the antimicrobial susceptibilities of numerous Gram-negative bacterial species recovered from people with intra-abdominal and urinary tract infections. The Clinical and Laboratory Standards Institute methods and a molecular analysis identified 134 isolates of Enterobacteriaceae (nine species) and one Acinetobacter sp. with blaNDM genes. These isolates were collected in nine countries, and >95% of the isolates possessed the NDM-1 variant. The MIC90 values were >4 mg/liter and >8 mg/liter for ertapenem and imipenem, respectively. No tested β-lactam or β-lactamase inhibitor combination had activity against these isolates. Resistance to amikacin (79.9%) and levofloxacin (82.8%) was common. Nearly all the isolates encoded additional enzymes, including AmpC cephalosporinases and extended-spectrum β-lactamases. There is an urgent need for infection control and continued global monitoring of isolates which harbor the NDM enzyme, as evidenced by recent outbreaks.
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Haghshenas B, Nami Y, Abdullah N, Radiah D, Rosli R, Khosroushahi AY. Anti-proliferative effects of Enterococcus strains isolated from fermented dairy products on different cancer cell lines. J Funct Foods 2014. [DOI: 10.1016/j.jff.2014.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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Hazelton B, Thomas LC, Olma T, Kok J, O'Sullivan M, Chen SCA, Iredell JR. Rapid and accurate direct antibiotic susceptibility testing of blood culture broths using MALDI Sepsityper combined with the BD Phoenix automated system. J Med Microbiol 2014; 63:1590-1594. [PMID: 25212759 DOI: 10.1099/jmm.0.075580-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Antibiotic susceptibility testing with the BD Phoenix system on bacterial cell pellets generated from blood culture broths using the Bruker MALDI Sepsityper kit was evaluated. Seventy-six Gram-negative isolates, including 12 with defined multi-resistant phenotypes, had antibiotic susceptibility testing (AST) performed by Phoenix on the cell pellet in parallel with conventional methods. In total, 1414/1444 (97.9 %) of susceptibility tests were concordant, with only 1 (0.07 %) very major error. This novel method has the potential to reduce the turnaround time for AST results by up to a day for Gram-negative bacteraemias.
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Affiliation(s)
- Briony Hazelton
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales 2145, Australia
| | - Lee C Thomas
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales 2145, Australia
| | - Thomas Olma
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales 2145, Australia
| | - Jen Kok
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Westmead Hospital, Westmead, New South Wales 2145, Australia.,Centre for Research Excellence in Critical Infection, Westmead Millennium Institute, Westmead Hospital, Westmead, New South Wales 2145, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales 2145, Australia
| | - Matthew O'Sullivan
- Centre for Research Excellence in Critical Infection, Westmead Millennium Institute, Westmead Hospital, Westmead, New South Wales 2145, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales 2145, Australia
| | - Sharon C-A Chen
- Centre for Research Excellence in Critical Infection, Westmead Millennium Institute, Westmead Hospital, Westmead, New South Wales 2145, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales 2145, Australia
| | - Jonathan R Iredell
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Westmead Hospital, Westmead, New South Wales 2145, Australia.,Centre for Research Excellence in Critical Infection, Westmead Millennium Institute, Westmead Hospital, Westmead, New South Wales 2145, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales 2145, Australia
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40
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Nagasawa M, Kaku M, Kamachi K, Shibayama K, Arakawa Y, Yamaguchi K, Ishii Y. Loop-mediated isothermal amplification assay for 16S rRNA methylase genes in Gram-negative bacteria. J Infect Chemother 2014; 20:635-8. [PMID: 25179393 DOI: 10.1016/j.jiac.2014.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/01/2014] [Accepted: 08/09/2014] [Indexed: 11/27/2022]
Abstract
Using the loop-mediated isothermal amplification (LAMP) method, we developed a rapid assay for detection of 16S rRNA methylase genes (rmtA, rmtB, and armA), and investigated 16S rRNA methylase-producing strains among clinical isolates. Primer Explorer V3 software was used to design the LAMP primers. LAMP primers were prepared for each gene, including two outer primers (F3 and B3), two inner primers (FIP and BIP), and two loop primers (LF and LB). Detection was performed with the Loopamp DNA amplification kit. For all three genes (rmtA, rmtB, and armA), 10(2) copies/tube could be detected with a reaction time of 60 min. When nine bacterial species (65 strains saved in National Institute of Infectious Diseases) were tested, which had been confirmed to possess rmtA, rmtB, or armA by PCR and DNA sequencing, the genes were detected correctly in these bacteria with no false negative or false positive results. Among 8447 clinical isolates isolated at 36 medical institutions, the LAMP method was conducted for 191 strains that were resistant to aminoglycosides based on the results of antimicrobial susceptibility tests. Eight strains were found to produce 16S rRNA methylase (0.09%), with rmtB being identified in three strains (0.06%) of 4929 isolates of Enterobacteriaceae, rmtA in three strains (0.10%) of 3284 isolates of Pseudomonas aeruginosa, and armA in two strains (0.85%) of 234 isolates of Acinetobacter spp. At present, the incidence of strains possessing 16S rRNA methylase genes is very low in Japan. However, when Gram-negative bacteria showing high resistance to aminoglycosides are isolated by clinical laboratories, it seems very important to investigate the status of 16S rRNA methylase gene-harboring bacilli and monitor their trends among Japanese clinical settings.
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Affiliation(s)
- Mitsuaki Nagasawa
- Department of Microbiology and Infectious Disease, Toho University School of Medicine, Tokyo, Japan; Department of Laboratory Medicine, Tohoku University Hospital, Miyagi, Japan; Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan.
| | - Mitsuo Kaku
- Department of Infection Control and Laboratory Diagnostics, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Kazunari Kamachi
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshichika Arakawa
- Department of Bacteriology/Drug Resistance and Pathogenesis, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keizo Yamaguchi
- Department of Microbiology and Infectious Disease, Toho University School of Medicine, Tokyo, Japan
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Disease, Toho University School of Medicine, Tokyo, Japan
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Gharout-Sait A, Alsharapy SA, Brasme L, Touati A, Kermas R, Bakour S, Guillard T, de Champs C. Enterobacteriaceae isolates carrying the New Delhi metallo-β-lactamase gene in Yemen. J Med Microbiol 2014; 63:1316-1323. [PMID: 25009193 DOI: 10.1099/jmm.0.073767-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Ten carbapenem-resistant Enterobacteriaceae (eight Klebsiella pneumoniae isolates and two Enterobacter cloacae) isolates from Yemen were investigated using in vitro antimicrobial susceptibility testing, phenotypic carbapenemase detection, multilocus sequence typing (MLST) and replicon typing. Carbapenemase, extended-spectrum β-lactamase (ESBL) and plasmid-mediated quinolone resistance determinant genes were identified using PCR and sequencing. All of the 10 carbapenem-resistant Enterobacteriaceae were resistant to β-lactams, tobramycin, ciprofloxacin and cotrimoxazole. Imipenem, doripenem and meropenem MICs ranged from 2 to >32 mg l(-1) and ertapenem MICs ranged from 6 to >32 mg l(-1). All of the K. pneumoniae isolates showed ESBL activity in phenotypic tests. Genes encoding blaNDM were detected in all strains. All K. pneumoniae strains produced CTX-M-15 ESBL and SHV β-lactamases. TEM-1 β-lactamase was detected in seven isolates. Nine isolates were qnr positive including QnrB1, QnrA1 and QnrS1, and six isolates produced AAC-6'-Ib-cr. MLST identified five different sequence types (STs): ST1399, ST147, ST29, ST405 and ST340. Replicon typing showed the presence of IncFII1K plasmids in four transformants. To the best of our knowledge, this is the first report of NDM-1-producing Enterobacteriaceae isolates in Yemen.
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Affiliation(s)
- Alima Gharout-Sait
- Laboratoire de Microbiologie Appliquée, FSNV, Université de Bejaia 06000, Algeria
| | | | - Lucien Brasme
- Laboratoire de Bactériologie-Virologie-Hygiène Hospitalière, CHU Reims, Hôpital Robert Debré, Avenue du Général Koenig, 51092 Reims Cedex, France
| | - Abdelaziz Touati
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia 06000, Algeria
| | - Rachida Kermas
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia 06000, Algeria
| | - Sofiane Bakour
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia 06000, Algeria
| | - Thomas Guillard
- EA4687 UFR Médecine SFR CAP-Santé (FED 4231), Université de Reims-Champagne-Ardenne, Reims, France.,Laboratoire de Bactériologie-Virologie-Hygiène Hospitalière, CHU Reims, Hôpital Robert Debré, Avenue du Général Koenig, 51092 Reims Cedex, France
| | - Christophe de Champs
- EA4687 UFR Médecine SFR CAP-Santé (FED 4231), Université de Reims-Champagne-Ardenne, Reims, France.,Laboratoire de Bactériologie-Virologie-Hygiène Hospitalière, CHU Reims, Hôpital Robert Debré, Avenue du Général Koenig, 51092 Reims Cedex, France
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Simple multiplex real-time PCR for rapid detection of common 16S rRNA methyltransferase genes. Diagn Microbiol Infect Dis 2014; 80:29-31. [PMID: 25012151 DOI: 10.1016/j.diagmicrobio.2014.05.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 05/16/2014] [Accepted: 05/26/2014] [Indexed: 11/20/2022]
Abstract
We have developed a real-time multiplex PCR assay to detect the three most common 16S rRNA methyltransferase genes (armA, rmtB and rmtC), which encode problematic high-level resistance to all clinically-relevant aminoglycoside antibiotics. All results were consistent with published conventional PCR assays and these genes still appear rare in Australia.
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