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Wight J, Byrne AS, Tahlan K, Lang AS. Anthropogenic contamination sources drive differences in antimicrobial-resistant Escherichia coli in three urban lakes. Appl Environ Microbiol 2024; 90:e0180923. [PMID: 38349150 PMCID: PMC10952509 DOI: 10.1128/aem.01809-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/12/2024] [Indexed: 03/21/2024] Open
Abstract
Antimicrobial resistance (AMR) is an ever-present threat to the treatment of infectious diseases. However, the potential relevance of this phenomenon in environmental reservoirs still raises many questions. Detection of antimicrobial-resistant bacteria in the environment is a critical aspect for understanding the prevalence of resistance outside of clinical settings, as detection in the environment indicates that resistance is likely already widespread. We isolated antimicrobial-resistant Escherichia coli from three urban waterbodies over a 15-month time series, determined their antimicrobial susceptibilities, investigated their population structure, and identified genetic determinants of resistance. We found that E. coli populations at each site were composed of different dominant phylotypes and showed distinct patterns of antimicrobial and multidrug resistance, despite close geographic proximity. Many strains that were genome-sequenced belonged to sequence types of international concern, particularly the ST131 clonal complex. We found widespread resistance to clinically important antimicrobials such as amoxicillin, cefotaxime, and ciprofloxacin, but found that all strains were susceptible to amikacin and the last-line antimicrobials meropenem and fosfomycin. Resistance was most often due to acquirable antimicrobial resistance genes, while chromosomal mutations in gyrA, parC, and parE conferred resistance to quinolones. Whole-genome analysis of a subset of strains further revealed the diversity of the population of E. coli present, with a wide array of AMR and virulence genes identified, many of which were present on the chromosome, including blaCTX-M. Finally, we determined that environmental persistence, transmission between sites, most likely mediated by wild birds, and transfer of mobile genetic elements likely contributed significantly to the patterns observed.IMPORTANCEA One Health perspective is crucial to understand the extent of antimicrobial resistance (AMR) globally, and investigation of AMR in the environment has been increasing in recent years. However, most studies have focused on waterways that are directly polluted by sewage, industrial manufacturing, or agricultural activities. Therefore, there remains a lack of knowledge about more natural, less overtly impacted environments. Through phenotypic and genotypic investigation of AMR in Escherichia coli, this study adds to our understanding of the extent and patterns of resistance in these types of environments, including over a time series, and showed that complex biotic and abiotic factors contribute to the patterns observed. Our study further emphasizes the importance of incorporating the surveillance of microbes in freshwater environments in order to better comprehend potential risks for both human and animal health and how the environment may serve as a sentinel for potential future clinical infections.
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Affiliation(s)
- Jordan Wight
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Alexander S. Byrne
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
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Swedan S, Alabdallah EA, Ababneh Q. Resistance to aminoglycoside and quinolone drugs among Klebsiella pneumoniae clinical isolates from northern Jordan. Heliyon 2024; 10:e23368. [PMID: 38163217 PMCID: PMC10757003 DOI: 10.1016/j.heliyon.2023.e23368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 11/09/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024] Open
Abstract
This study aimed to identify phenotypic and genotypic aminoglycoside and quinolone non-susceptibility and the prevalence of aminoglycoside-modifying enzymes and plasmid-mediated quinolone resistance genes among K. pneumoniae clinical isolates from northern Jordan. K. pneumoniae isolates (n = 183) were tested for antimicrobial susceptibility using the Kirby-Bauer disk diffusion method. The double-disk synergy test was used for the detection of the extended-spectrum beta-lactamase phenotype. Polymerase chain reaction was used to detect genes encoding aminoglycoside-modifying enzyme (aac (3')-II, aac (6')-II, aac (6')-Ib, ant (3″)-I, aph (3')-VI, armA, and rmtB), and plasmid-mediated quinolone resistance (qnrA, qnrB, qnrC, qnrD, qnrS, acc(6')-Ib-cr, qepA, and oqxAB) genes. Multi-locus sequence typing was used to elucidate the genetic diversity of selected isolates. The non-susceptibility percentages to aminoglycosides and quinolones were 65.0 % and 61.7 %, respectively. The most frequent aminoglycoside-modifying enzyme gene was ant (3″)-I at 73.8 %, followed by aac (6')-Ib at 25.1 %, aac (3')-II at 17.5 %, aph (3')-VI at 12.0 %, armA at 9.8 %, and rmtB at 0.5 %. Aac (6')-II was not detected among the isolates. The most frequent plasmid-mediated quinolone resistance gene was oqxAB at 31.7 %, followed by qnrS at 26.2 %, qnrB at 25.7 %, and aac(6')-Ib-cr at 25.7 %. QnrA, qnrD, qebA, and qnrC were not detected among the isolates. Aac (3')-II, aac (6')-Ib, aph (3')-VI, armA, qnrB, qnrS, and acc(6')-Ib-cr were significantly associated with non-susceptibility to aminoglycosides, quinolones, and beta-lactams. Among 27 randomly selected K. pneumoniae isolates, the most common sequence type was ST2096, followed by ST348 and ST1207. Overall, 19 sequence types were observed, confirming a high level of genetic diversity among the isolates. High percentages of non-susceptibility to the studied antimicrobials were found and were associated with the presence of several resistance genes. Similar studies should be periodically carried out to monitor changes in the prevalence of resistance phenotypes and genotypes of isolates.
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Affiliation(s)
- Samer Swedan
- Faculty of Applied Medical Sciences, Dept. of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Emad Addin Alabdallah
- Faculty of Applied Medical Sciences, Dept. of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Qutaiba Ababneh
- Faculty of Science and Arts, Dept. of Biotechnology & Genetic Engineering, Jordan University of Science and Technology, Irbid, 22110, Jordan
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Tsai CH, Lee NY, Chao CM, Chen CC, Lai CC, Ho CH, Chen YC, Chen PY, Tang HJ, Chen HJ, Su BA, Lai HY, Chow JC, Chang TH. Emergence and dissemination of multidrug-resistant Escherichia coli ST8346 coharboring bla NDM-5 and bla OXA-181 in Southern Taiwan, 2017-2021. J Infect Public Health 2023; 16:1675-1681. [PMID: 37633229 DOI: 10.1016/j.jiph.2023.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/28/2023] [Accepted: 08/08/2023] [Indexed: 08/28/2023] Open
Abstract
BACKGROUND Enterobacterales carrying blaNDM represent an emerging challenge in treating infectious diseases. In this study, we aimed to investigate the characteristics of blaNDM-producing Enterobacterales from three hospitals in southern Taiwan. METHODS Enterobacterales strains that were nonsusceptible to more than one carbapenem (ertapenem, meropenem, imipenem, or doripenem) were collected from hospitalized patients. Molecular typing for New Delhi metallo-β-lactamase (NDM) and antibiotic susceptibility tests were performed, followed by multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and plasmid analysis by PCR-based replicon typing. RESULTS A total of 1311 carbapenem-nonsusceptible Enterobacterales were isolated from 2017 to 2021. blaNDM-encoding genes were detected in 108 isolates, with 53 (49.1%) harboring blaNDM-1 and 55 (50.9%) harboring blaNDM-5. The rate of blaNDM-1 detection among isolates decreased to 2% in 2021. However, the rate of E. coli harboring blaNDM-5 increased from 1% to 12% of total isolates during the study period. Of 47 NDM-5-positive E. coli isolates, 44 (93.6%) were ST8346 with high genetic relatedness. E. coli ST8346 isolates showed high-level resistance to both carbapenems and aminoglycosides. Most (38 out of 47, 80.9%) blaNDM-5-harboring E. coli isolates co-harbored blaOXA-181. We analyzed the regions harboring blaNDM-5 in E. coli ST8346 via PCR amplification. blaNDM-5 and blaOXA-181 were located on two separate plasmids, IncF and IncX3, respectively. CONCLUSION The dissemination of E. coli ST8346 caused an increase in blaNDM-5 and blaOXA-181 co-harboring Enterobacterales in southern Taiwan, which show high-level resistance to both carbapenems and aminoglycosides. We identified a distinct IncF plasmid encoding blaNDM-5 that has the potential for rapid spread and needs further surveillance.
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Affiliation(s)
- Chia-Hung Tsai
- Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Nan-Yao Lee
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chien-Ming Chao
- Department of Intensive Care Medicine, Chi Mei Medical Center, Liouying, Tainan, Taiwan
| | - Chi-Chung Chen
- Department of Medical Research, Chi Mei Medical Center, Tainan, Taiwan; Department of Food Science, National Chiayi University, Chiayi, Taiwan
| | - Chih-Cheng Lai
- Division of Hospital Medicine, Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan; School of Medicine, College of Medicine, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Chung-Han Ho
- Department of Medical Research, Chi Mei Medical Center, Tainan, Taiwan; Department of Information Management, Southern Taiwan University of Science and Technology, Tainan, Taiwan
| | - Yu-Chin Chen
- Department of Pediatrics, Chi Mei Medical Center, Chiali, Tainan, Taiwan
| | - Po-Yu Chen
- Department of Nursing, Min-Hwei College of Health Care Management, Tainan, Taiwan
| | - Hung-Jen Tang
- Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Hung-Jui Chen
- Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Bo-An Su
- Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Hsin-Yu Lai
- Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Julie Chi Chow
- Department of Pediatrics, Chi Mei Medical Center, Tainan, Taiwan
| | - Tu-Hsuan Chang
- Department of Pediatrics, Chi Mei Medical Center, Tainan, Taiwan.
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Barbu IC, Gheorghe-Barbu I, Grigore GA, Vrancianu CO, Chifiriuc MC. Antimicrobial Resistance in Romania: Updates on Gram-Negative ESCAPE Pathogens in the Clinical, Veterinary, and Aquatic Sectors. Int J Mol Sci 2023; 24:7892. [PMID: 37175597 PMCID: PMC10178704 DOI: 10.3390/ijms24097892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Multidrug-resistant Gram-negative bacteria such as Acinetobacter baumannii, Pseudomonas aeruginosa, and members of the Enterobacterales order are a challenging multi-sectorial and global threat, being listed by the WHO in the priority list of pathogens requiring the urgent discovery and development of therapeutic strategies. We present here an overview of the antibiotic resistance profiles and epidemiology of Gram-negative pathogens listed in the ESCAPE group circulating in Romania. The review starts with a discussion of the mechanisms and clinical significance of Gram-negative bacteria, the most frequent genetic determinants of resistance, and then summarizes and discusses the epidemiological studies reported for A. baumannii, P. aeruginosa, and Enterobacterales-resistant strains circulating in Romania, both in hospital and veterinary settings and mirrored in the aquatic environment. The Romanian landscape of Gram-negative pathogens included in the ESCAPE list reveals that all significant, clinically relevant, globally spread antibiotic resistance genes and carrying platforms are well established in different geographical areas of Romania and have already been disseminated beyond clinical settings.
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Affiliation(s)
- Ilda Czobor Barbu
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
| | - Irina Gheorghe-Barbu
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
| | - Georgiana Alexandra Grigore
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
- National Institute of Research and Development for Biological Sciences, 060031 Bucharest, Romania
| | - Corneliu Ovidiu Vrancianu
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
- Academy of Romanian Scientists, 050044 Bucharest, Romania
- Romanian Academy, 010071 Bucharest, Romania
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Alajmi RZ, Alfouzan WA, Mustafa AS. The Prevalence of Multidrug-Resistant Enterobacteriaceae among Neonates in Kuwait. Diagnostics (Basel) 2023; 13:diagnostics13081505. [PMID: 37189605 DOI: 10.3390/diagnostics13081505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/06/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Increasing numbers of neonates with serious bacterial infections, due to resistant bacteria, are associated with considerable morbidity and mortality rates. The aim of this study was to evaluate the prevalence of drug-resistant Enterobacteriaceae in the neonatal population and their mothers in Farwaniya Hospital in Kuwait and to determine the basis of resistance. Rectal screening swabs were taken from 242 mothers and 242 neonates in labor rooms and wards. Identification and sensitivity testing were performed using the VITEK® 2 system. Each isolate flagged with any resistance was subjected to the E-test susceptibility method. The detection of resistance genes was performed by PCR, and the Sanger sequencing method was used to identify mutations. Among 168 samples tested by the E-test method, no MDR Enterobacteriaceae were detected among the neonates, while 12 (13.6%) isolates from the mothers' samples were MDR. ESBL, aminoglycosides, fluoroquinolones, and folate pathway inhibitor resistance genes were detected, while beta-lactam-beta-lactamase inhibitor combinations, carbapenems, and tigecycline resistance genes were not. Our results showed that the prevalence of antibiotic resistance in Enterobacteriaceae obtained from neonates in Kuwait is low, and this is encouraging. Furthermore, it is possible to conclude that neonates are acquiring resistance mostly from the environment and after birth but not from their mothers.
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Affiliation(s)
- Rehab Zafer Alajmi
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City 13110, Kuwait
| | - Wadha Ahmed Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City 13110, Kuwait
- Microbiology Unit, Department of Laboratory Medicine, Farwaniya Hospital, Ministry of Health, Farwaniya 80000, Kuwait
| | - Abu Salim Mustafa
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City 13110, Kuwait
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Gong WT, Zhao XJ, Wang GM, Ma XL, Huang JA. Efficacy of Zidovudine-Amikacin Combination Therapy In Vitro and in a Rat Tissue Cage Infection Model against Amikacin-Resistant, Multidrug-Resistant Enterobacteriales. Microbiol Spectr 2023; 11:e0484322. [PMID: 36946744 PMCID: PMC10101109 DOI: 10.1128/spectrum.04843-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/02/2023] [Indexed: 03/23/2023] Open
Abstract
Multidrug-resistant (MDR) Enterobacteriales infections have become an urgent global threat to public health. The aim of this study was to evaluate the efficacy of zidovudine-amikacin combination therapy in vitro and in vivo. Molecular characteristics and antibiotic resistance profiles of 53 amikacin-resistant MDR, extensively drug-resistant (XDR), or pan-drug-resistant (PDR) clinical isolates were examined via PCR and susceptibility testing. Checkerboard assays were performed for these 53 isolates to assess in vitro synergistic effects of the zidovudine-amikacin combination, and static time-kill experiments were performed for four XDR or PDR Enterobacteriales isolates. A Galleria mellonella model and a rat tissue cage infection model were established to assess in vivo synergistic effects. The aac(6')-Ib gene was detected in 25 (47.2%) isolates, followed by armA in 5 (9.4%) isolates, rmtB in 27 (50.9%) isolates, and rmtC in 3 (5.8%) isolates. Checkerboard assays showed the synergy of this combination against 38 (71.7%) isolates. The time-kill assays further confirmed that zidovudine strongly synergized with amikacin against four XDR or PDR Enterobacteriales isolates. The Galleria mellonella model study showed that the survival benefit of zidovudine-amikacin combination therapy was significantly better than that of monotherapy for those four Enterobacteriales isolates. Furthermore, the rat tissue cage infection model study showed that zidovudine-amikacin combination therapy displayed more potent bactericidal activity than monotherapy after 3 and 7 days of treatment for the above four isolates. Our data support the idea that the zidovudine-amikacin combination could be a plausible alternative therapy against infections with amikacin-resistant MDR Enterobacteriales, especially with XDR and PDR Enterobacteriales. IMPORTANCE Our study revealed for the first time that the zidovudine-amikacin combination shows a significant bactericidal effect against amikacin-resistant MDR, XDR, and PDR Enterobacteriales. Second, using in vitro and in vivo approaches, our study showed that zidovudine strongly synergized with amikacin against amikacin-resistant MDR Enterobacteriales isolates. Most importantly, with regard to survival benefit, pharmacokinetics, and bactericidal effects, our in vivo experiment demonstrated the effectiveness of zidovudine-amikacin.
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Affiliation(s)
- Wei-Tao Gong
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Pulmonary and Critical Care Medicine, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xiao-Jie Zhao
- Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Gao-Ming Wang
- Department of Thoracic Surgery, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xiao-Lin Ma
- Department of Neurology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jian-An Huang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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Mohamed HS, Houmed Aboubaker M, Dumont Y, Didelot MN, Michon AL, Galal L, Jean-Pierre H, Godreuil S. Multidrug-Resistant Enterobacterales in Community-Acquired Urinary Tract Infections in Djibouti, Republic of Djibouti. Antibiotics (Basel) 2022; 11:antibiotics11121740. [PMID: 36551396 PMCID: PMC9774282 DOI: 10.3390/antibiotics11121740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
The emergence and spread of multidrug resistant Enterobacterales (MDR-E) are a global public health issue. This problem also concerns urinary tract infections (UTI), which are the second most frequent infections after respiratory infections. The objective of this study was to determine MDR-E frequency and to characterize MDR-E isolates from patients with community-acquired UTIs in Djibouti, Republic of Djibouti. From 800 clinical urinary samples collected at the Mer Rouge Laboratory, Djibouti, from January to July 2019, 142 were identified as Enterobacterales (age range of the 142 patients mean age is 42 years.) Mass spectrometry analysis of these isolates identified 117 Escherichia coli, 14 Klebsiella pneumoniae, 2 Proteus mirabilis, 4 Enterobacter spp., 4 Providencia stuartii and 1 Franconibacter helveticus. Antibiotic susceptibility testing (disk diffusion method) of these 142 isolates detected 68 MDR-E (68/142 = 48%): 65 extended-spectrum bêta lactamase- (ESBL), 2 carbapenemase- (one also ESBL), and 1 cephalosporinase-producer. Multiplex PCR and sequencing showed that the 65 ESBL-producing isolates carried genes encoding CTX-M enzymes (CTX-M-15 in 97% and CTX-M-9 in 3% of isolates). Two isolates harboured a gene encoding the OXA-48-like carbapenemase, and one the gene encoding the AmpC CMY-2 cephalosporinase. Genes implicated in resistance to quinolones (qnrB, aac (6')-Ib-cr, qnrD, oqxA and B) also were detected. Among the E. coli phylogroups, B2 was the most common phylogenetic group (21% of MDR-E isolates and 26% of non-MDR-E isolates), followed by A (14% and 12%), B1 (9% and 7%), D (3% and 3%), F (3% and 3%) and E (2% and 2%). This study highlights the high frequency of ESBL producers and the emergence of carbapenemase-producers among Enterobacterales causing community-acquired UTIs in Djibouti.
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Affiliation(s)
- Hasna Said Mohamed
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, 34295 Montpellier, France
- MIVEGEC, IRD, CNRS, Université de Montpellier, 34394 Montpellier, France
- Hospital General Peltier de Djibouti, Djibouti City 2123, Djibouti
- Laboratoire de Biologie Médicale de la Mer Rouge, Djibouti City 1119, Djibouti
- Correspondence: ; Tel.: +253-77-818-524
| | - Mohamed Houmed Aboubaker
- Laboratoire de Biologie Médicale de la Mer Rouge, Djibouti City 1119, Djibouti
- Laboratoire de la Caisse Nationale de Sécurité Sociale, Djibouti City 696, Djibouti
| | - Yann Dumont
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, 34295 Montpellier, France
- MIVEGEC, IRD, CNRS, Université de Montpellier, 34394 Montpellier, France
| | - Marie-Noëlle Didelot
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, 34295 Montpellier, France
- MIVEGEC, IRD, CNRS, Université de Montpellier, 34394 Montpellier, France
| | - Anne-Laure Michon
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, 34295 Montpellier, France
- MIVEGEC, IRD, CNRS, Université de Montpellier, 34394 Montpellier, France
| | - Lokman Galal
- MIVEGEC, IRD, CNRS, Université de Montpellier, 34394 Montpellier, France
| | - Hélène Jean-Pierre
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, 34295 Montpellier, France
- MIVEGEC, IRD, CNRS, Université de Montpellier, 34394 Montpellier, France
| | - Sylvain Godreuil
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, 34295 Montpellier, France
- MIVEGEC, IRD, CNRS, Université de Montpellier, 34394 Montpellier, France
- Jeune Equipe Associée à IRD (JEAI), FASORAM, 34394 Montpellier, France
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Prevalence and characterisation of antimicrobial resistance genes and class 1 and 2 integrons in multiresistant Escherichia coli isolated from poultry production. Sci Rep 2022; 12:6062. [PMID: 35410349 PMCID: PMC9001716 DOI: 10.1038/s41598-022-09996-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/29/2022] [Indexed: 12/29/2022] Open
Abstract
A global increase in the populations of drug resistant bacteria exerts negative effects on animal production and human health. Our study has been focused on the assessment of resistance determinants in relation to phenotypic resistance of the 74 commensal E. coli isolates present in different ecological environments. The samples were collected from poultry litter, feces, and neck skin. Among the microorganisms isolated from the poultry litter (group A), the highest resistance was noted against AMP and DOX (100%). In the E. coli extracts from the cloacal swabs (group B), the highest resistance was observed against AMP (100%) and CIP (92%). The meat samples (group C) were characterized by resistance to AMP (100%) and STX (94.7%). Genes encoding resistance to β-lactams (blaTEM, blaCTX-M), fluoroquinolones (qnrA, qnrB, qnrS), aminoglycosides (strA-strB, aphA1, aac(3)-II), sulfonamides (sul1, sul2, sul3), trimethoprim (dfr1, dfr5, dfr7/17) and tetracyclines (tetA, tetB) were detected in the studied bacterial isolates. The presence of class 1 and 2 integrons was confirmed in 75% of the MDR E. coli isolates (plasmid DNA), of which 60% contained class 1 integrons, 15% contained class 2 integrons, and 11.7% carried integrons of both classes. Thus, it may be concluded that integrons are the common mediators of antimicrobial resistance among commensal multidrug resistant Escherichia coli at important stages of poultry production.
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Characterization of Aminoglycoside Modifying Enzymes Producing E. coli and Klebsiella pneumoniae Clinical Isolates. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.4.68] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial resistance gene profile characterization and dissemination offer useful detail on the possible challenge in treating bacteria. The development of aminoglycoside modifying enzymes (AMEs) is considered as the primary mechanism of resistance to aminoglycosides, in addition to the 16S rRNA methylases. This study aimed at isolation and characterization of aminoglycosides resistant clinical isolates of enterobacteriaceae family from different clinical samples. Over a period of 24 months, thirty samples were collected and 49 clinical isolates of E. coli [n=25], Klebsiella [n=13], Enterobacter species (n=7) and Proteus species (n=4) were isolated from Egyptian clinical laboratories. The identities of the cultures were confirmed following standard microbiological procedures. Resistance of the isolates to aminoglycosides was determined by the disc diffusion method and isolates with highest resistance (n=9) were selected and investigated for 16S rRNA methylase and AMES encoding genes by polymerase chain reaction (PCR) and sequencing. In general, aminoglycoside resistance was found in 95% of the isolates; the isolates displayed the highest rate of resistance to netilmicin (75%) and kanamycin (55%), while resistance to gentamycin (18%) and tobramycin (16%) was low. A total of 9 isolates have the highest aminoglycoside resistant rate, showed the highest appearance for aac(6′)-Ib as well as ant (3″)-Ia resistant genes, with aac (3)-II (44%) and ant (4′)-IIb (34%) following closely. The high prevalence of AMEs observed among resistant isolates in this study suggests the urgent need for more efficient treatment designs to mitigate the selection burden as well as improved care of patients who have been infected with these drug-resistant organisms.
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Ahmadi M, Ranjbar R, Behzadi P, Mohammadian T. Virulence factors, antibiotic resistance patterns, and molecular types of clinical isolates of Klebsiella Pneumoniae. Expert Rev Anti Infect Ther 2021; 20:463-472. [PMID: 34612762 DOI: 10.1080/14787210.2022.1990040] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Klebsiella pneumoniae is armed with a wide range of antibiotic resistance mechanisms that mostly challenge effective treatment. The aims of the current study were to identify the clinical strains of K. pneumoniaealso to determine their phenotypes and molecular characterization related to antimicrobial resistance and virulence genes. RESEARCH DESIGN AND METHODS In this investigation, clinical specimens from different hospitals located in Tehran, Iran, were collected during a nine-month period (December 2018 to August 2019). The K. pneumoniae strains were isolated and identified through standard microbial and biochemical assays. Additionally, disk diffusion, combined disk, Modified Hodge Test (MHT) and PCR were performed for antibiotic resistance and virulence gene analysis, respectively. RESULTS Eighty-four isolates of K. pneumoniae were subjected to the study. According to the combined disk and modified Hodge test results, 27 (52%) and 15 pathotypes (62.5%) out of resistant strains of isolated K. pneumoniae were detected as ESBL and KPC producers. The virulence genes of mrkD (94%) and magA (11%) were the highest and lowest among isolates, respectively. CONCLUSIONS The high prevalence of antibiotic resistance and virulence genes in conjunction with a significant relationship between the strains revealed a high pathogenic capacity of the isolated pathotypes of K. pneumoniae.
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Affiliation(s)
- Mitra Ahmadi
- Department of Microbiology, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Payam Behzadi
- Department of Microbiology, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Taher Mohammadian
- Department of Microbiology, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
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11
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Majlander J, Anttila VJ, Nurmi W, Seppälä A, Tiedje J, Muziasari W. Routine wastewater-based monitoring of antibiotic resistance in two Finnish hospitals: focus on carbapenem resistance genes and genes associated with bacteria causing hospital-acquired infections. J Hosp Infect 2021; 117:157-164. [PMID: 34537275 DOI: 10.1016/j.jhin.2021.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/16/2021] [Accepted: 09/10/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Wastewater-based monitoring represents a useful tool for antibiotic resistance surveillance. AIM To investigate the prevalence and abundance of antibiotic resistance genes (ARGs) in hospital wastewater over time. METHODS Wastewater from two hospitals in Finland (HUS1 and HUS2) was monitored weekly for nine weeks (weeks 25-33) in summer 2020. A high-throughput real-time polymerization chain reaction (HT-qPCR) system was used to detect and quantify 216 ARGs and genes associated with mobile genetic elements (MGEs), integrons, and bacteria causing hospital-acquired infections (HAIs), as well as the 16S rRNA gene. Data from HT-qPCR were analysed and visualized using a novel digital platform, ResistApp. Eight carbapenem resistance genes (blaGES, blaKPC, blaVIM, blaNDM, blaCMY, blaMOX, blaOXA48, and blaOXA51) and three genes associated with bacteria causing HAIs (Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa) were studied. FINDINGS There was a significantly higher number of ARGs at both hospitals in weeks 27-30 (174-191 genes) compared to other sampling weeks (151-171 genes). Our analyses also indicated that the two hospitals, which used different amounts of antibiotics, had significantly different resistance gene profiles. Carbapenem resistance genes were more prevalent and abundant in HUS1 than HUS2. Across both hospitals, blaGES and blaVIM were the most prevalent and abundant. There was also a strong positive association between blaKPC and K. pneumoniae in HUS1 wastewater. CONCLUSION Routine wastewater-based monitoring using ResistApp can provide valuable information on the prevalence and abundance of ARGs in hospitals. This helps hospitals understand the spread of antibiotic resistance in hospitals and identify potential areas for intervention.
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Affiliation(s)
| | - V-J Anttila
- Helsinki University Hospital and University of Helsinki, Meilahti, Helsinki, Finland
| | - W Nurmi
- Resistomap Oy, Helsinki, Finland
| | | | - J Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, USA
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12
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Nowaczek A, Dec M, Stępień-Pyśniak D, Urban-Chmiel R, Marek A, Różański P. Antibiotic Resistance and Virulence Profiles of Escherichia coli Strains Isolated from Wild Birds in Poland. Pathogens 2021; 10:1059. [PMID: 34451523 PMCID: PMC8400592 DOI: 10.3390/pathogens10081059] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022] Open
Abstract
Wild animals are increasingly reported as carriers of antibiotic-resistant and pathogenic bacteria including Enterobacteriaceae. However, the role of free-living birds as reservoirs for potentially dangerous microbes is not yet thoroughly understood. In our work, we examined Escherichia coli strains from wild birds in Poland in relation to their antimicrobial agents susceptibility, virulence and phylogenetic affiliation. Identification of E. coli was performed using MALDI-TOF mass spectrometry. The antibiotic susceptibility of the isolates was determined by the broth microdilution method, and resistance and virulence genes were detected by PCR. E. coli bacteria were isolated from 32 of 34 samples. The strains were most often classified into phylogenetic groups B1 (50%) and A (25%). Resistance to tetracycline (50%), ciprofloxacin (46.8%), gentamicin (34.3%) and ampicillin (28.1%) was most frequently reported, and as many as 31.2% of E. coli isolates exhibited a multidrug resistance phenotype. Among resistance genes, sul2 (31.2% of isolates) and blaTEM (28.1%) were identified most frequently, while irp-2 (31.2%) and ompT (28.1%) were the most common virulence-associated genes. Five strains were included in the APEC group. The study indicates that wild birds can be carriers of potentially dangerous E. coli strains and vectors for the spread of resistant bacteria and resistance determinants in the environment.
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Affiliation(s)
- Anna Nowaczek
- Department of Veterinary Prevention and Avian Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-033 Lublin, Poland; (A.N.); (D.S.-P.); (R.U.-C.); (A.M.)
| | - Marta Dec
- Department of Veterinary Prevention and Avian Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-033 Lublin, Poland; (A.N.); (D.S.-P.); (R.U.-C.); (A.M.)
| | - Dagmara Stępień-Pyśniak
- Department of Veterinary Prevention and Avian Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-033 Lublin, Poland; (A.N.); (D.S.-P.); (R.U.-C.); (A.M.)
| | - Renata Urban-Chmiel
- Department of Veterinary Prevention and Avian Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-033 Lublin, Poland; (A.N.); (D.S.-P.); (R.U.-C.); (A.M.)
| | - Agnieszka Marek
- Department of Veterinary Prevention and Avian Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-033 Lublin, Poland; (A.N.); (D.S.-P.); (R.U.-C.); (A.M.)
| | - Paweł Różański
- Department of Animal Hygiene and Environmental Hazards, Faculty of Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland;
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Rapid and Accurate Detection of Aminoglycoside-Modifying Enzymes and 16S rRNA Methyltransferases by Targeted Liquid Chromatography-Tandem Mass Spectrometry. J Clin Microbiol 2021; 59:e0046421. [PMID: 33910961 DOI: 10.1128/jcm.00464-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
New and rapid diagnostic methods are needed for the detection of antimicrobial resistance to aid in curbing drug-resistant infections. Targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a method that could serve this purpose, as it can detect specific peptides of antimicrobial resistance mechanisms with high accuracy. In the current study, we developed an accurate and rapid targeted LC-MS/MS assay based on parallel reaction monitoring for detection of the most prevalent aminoglycoside-modifying enzymes and 16S rRNA methyltransferases in Escherichia coli and Klebsiella pneumoniae that confer resistance to aminoglycosides. Specific tryptic peptides needed for detection were selected and validated for AAC(3)-Ia, AAC(3)-II, AAC(3)-IV, AAC(3)-VI, AAC(6')-Ib, AAC(6')-Ib-cr, ANT(2″)-I, APH(3')-VI, ArmA, RmtB, RmtC, and RmtF. In total, 205 isolates containing different aminoglycoside resistance mechanisms that consisted mostly of E. coli and K. pneumoniae were selected for assay development and evaluation. Mass spectrometry results were automatically analyzed and were compared to whole-genome sequencing results. Of the 2,460 isolate and resistance mechanism combinations tested, 2,416 combinations matched. Discrepancies were further analyzed by repeating LC-MS/MS analysis and performing additional PCRs. Mass spectrometry results were also used to predict resistance and susceptibility to gentamicin, tobramycin, and amikacin in only the E. coli and K. pneumoniae isolates (n = 191). The category interpretations were correctly predicted for gentamicin in 97.4% of the isolates, for tobramycin in 97.4% of the isolates, and for amikacin in 82.7% of the isolates. Targeted LC-MS/MS can be applied for accurate and rapid detection of aminoglycoside resistance mechanisms.
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Sadeghi M, Sedigh Ebrahim-Saraie H, Mojtahedi A, Nikokar I, Atrkar Roushan Z. Genetic diversity and prevalence of aminoglycoside modifying enzymes among Escherichia coli strains isolated from inpatients with urinary tract infections. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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15
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Lalitha Aishwarya KV, Venkataramana Geetha P, Eswaran S, Mariappan S, Sekar U. Spectrum of Aminoglycoside Modifying Enzymes in Gram-Negative Bacteria Causing Human Infections. J Lab Physicians 2020; 12:27-31. [PMID: 32792790 PMCID: PMC7419166 DOI: 10.1055/s-0040-1713687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Introduction
Aminoglycosides are formidable broad-spectrum antibiotics used in clinical settings; woefully their usage has been reduced by the emergence and distribution of resistance mainly due to aminoglycoside modifying enzymes (AME).
Purpose
This study was performed to determine the diverse prevalence of AME and their pattern of occurrence in the clinical isolates of gram-negative bacteria. This study also aimed to detect the presence of AMEs that are prevalent in gram-positive bacteria, among gram negatives.
Materials and Methods
A total number of 386 clinical isolates were included in this study. Polymerase chain reaction revealed the prevalence rate of AMEs screened [aac(6′)-lb, aac(3′)-I, aac(3′)-II, aac(3′)-VI, ant(2′)-I, ant(4′)-IIb, aac(3′)-III, aac(3′)-IV, aph(2′)-Ib, aph(2′)-Ic, aph(2′)-Id, aac (6′)-Ie- aph(2′)-Ia, and aph(3′)-IIIa]. Conjugation experiment was performed for the clinical isolates which harbored any one of the AME which was prevalent in gram-positive bacteria [aph(3′)-IIIa, aac(6′)-Ie-aph(2′)-Ia].
Results
aac(6′)-lb is the most prevalent AME, followed by aac(3′)-I, aph(3′)-VI, aac(3′)-VI, and aac(3′)-II. The AMEs such as ant (2′)-I, ant(4′)-IIb, aac(3′)-III, aac(3′)-IV, aph(2′)-Ib, aph(2′)-Ic, and aph(2′)-Id were not established in our study isolates. The rate of prevalence of aph(3′)-IIIa, aac(6′)-Ie-aph(2′)-Ia—the AMEs encountered in gram-positive and their co-existence was 19.68% and the conjugation experiment revealed their transfer via plasmids.
Conclusion
This is the first report from India revealing the presence and prevalence of AMEs which are often encountered among gram-positive bacteria in gram negatives and their presence on conjugative plasmids.
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Affiliation(s)
| | - Pacha Venkataramana Geetha
- Department of Microbiology, Sri Ramachandra Institute for Higher Education and Research, Chennai, Tamil Nadu, India
| | - Sudalai Eswaran
- Department of Microbiology, Sri Ramachandra Institute for Higher Education and Research, Chennai, Tamil Nadu, India
| | - Shanthi Mariappan
- Department of Microbiology, Sri Ramachandra Institute for Higher Education and Research, Chennai, Tamil Nadu, India
| | - Uma Sekar
- Department of Microbiology, Sri Ramachandra Institute for Higher Education and Research, Chennai, Tamil Nadu, India
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Cheng P, Li F, Liu R, Yang Y, Xiao T, Ishfaq M, Xu G, Zhang X. Prevalence and molecular epidemiology characteristics of carbapenem-resistant Escherichia coli in Heilongjiang Province, China. Infect Drug Resist 2019; 12:2505-2518. [PMID: 31496764 PMCID: PMC6697665 DOI: 10.2147/idr.s208122] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 07/23/2019] [Indexed: 11/30/2022] Open
Abstract
Objective This retrospective study was conducted to determine the prevalence and molecular epidemiology characteristics of carbapenem-resistant Escherichia coli (CRE). Methods A total of 593 Escherichia coli (E. coli) isolates were recovered from pigs and urban river from 2009 to 2014 in Heilongjiang Province of China. Forty CRE including 22 strains isolated from fecal samples of pigs and 18 strains isolated from water samples were selected. PCR detection of resistance determinants, multi-locus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and phylogenetic groups were performed to characterize CRE isolates. Conjugation experiments, plasmid stability testing, PCR-based replicon typing (PBRT), and PCR mapping were conducted to analyze blaNDM-carrying plasmids. In vitro time–growth studies and competition experiments were carried out to assess the fitness impact of NDM carriage. Results Five NDM-1-positive E. coli isolates were identified from water samples. Genetic environment analysis revealed that a cluster of genes (ISAba125-blaNDM-1-bleMBL-ΔtrpF) was detected in all of the NDM-1-positive isolates. Conjugation assays showed that blaNDM-1 could be successfully transferred to E. coli J53 from 5 donor strains at frequencies of 4.6×10−5 to 2.6×10−2. The plasmids from all transconjugants belonged to different plasmid replicon types including IncA/C (n=2), IncFII (n=1) and IncX3 (n=2). In vitro time–growth studies revealed that blaNDM-1 did not have a significant impact on cell proliferation. Meanwhile, competition experiments showed that the acquisition of blaNDM-1 can place an energy burden on the bacterial host and incur fitness cost. However, plasmid stability testing showed that blaNDM-1-carrying plasmid remained stable in the hosts after seven passages without antimicrobial selection. Conclusion The study revealed the early molecular epidemiology and dissemination characteristics of CRE. In addition, the overall antimicrobial resistance in E. coli recovered from water samples is higher than the strains isolated from fecal samples of pigs. Furthermore, we isolated and identified five NDM-1-producing E. coli strains from water samples.
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Affiliation(s)
- Ping Cheng
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Fulei Li
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Ruimeng Liu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Yuqi Yang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Tianshi Xiao
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Muhammad Ishfaq
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Guofeng Xu
- First Department of Respiratory Disease, Inflammation and Allergic Diseases Research Unit, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, People's Republic of China
| | - Xiuying Zhang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
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Cooccurrence of NDM-1, ESBL, RmtC, AAC(6')-Ib, and QnrB in Clonally Related Klebsiella pneumoniae Isolates Together with Coexistence of CMY-4 and AAC(6')-Ib in Enterobacter cloacae Isolates from Saudi Arabia. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6736897. [PMID: 31467906 PMCID: PMC6699326 DOI: 10.1155/2019/6736897] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 06/18/2019] [Accepted: 07/09/2019] [Indexed: 01/07/2023]
Abstract
The aim of this study was to investigate the mechanisms responsible for resistance to antimicrobials in a collection of enterobacterial isolates recovered from two hospitals in Saudi Arabia. A total of six strains isolated from different patients showing high resistance to carbapenems was recovered in 2015 from two different hospitals, with four being Klebsiella pneumoniae and two Enterobacter cloacae. All isolates except one K. pneumoniae were resistant to tigecycline, but only one K. pneumoniae was resistant to colistin. All produced a carbapenemase according to the Carba NP test, and all were positive for the EDTA-disk synergy test for detection of MBL. Using PCR followed by sequencing, the four K. pneumoniae isolates produced the carbapenemase NDM-1, while the two E. cloacae isolates produced the carbapenemase VIM-1. Genotyping analysis by Multilocus Sequence Typing (MLST) showed that three out of the four K. pneumoniae isolates were clonally related. They had been recovered from the same hospital and belonged to Sequence Type (ST) ST152. In contrast, the fourth K. pneumoniae isolate belonged to ST572. Noticeably, the NDM-1-producing K. pneumoniae additionally produced an extended-spectrum ß-lactamase (ESBL) of the CTX-M type, together with OXA-1 and TEM-1. Surprisingly, the three clonally related isolates produced different CTX-M variants, namely, CTX-M-3, CTX-M-57, and CTX-M-82, and coproduced QnrB, which confers quinolone resistance, and the 16S rRNA methylase RmtC, which confers high resistance to all aminoglycosides. The AAC(6')-Ib acetyltransferase was detected in both K. pneumoniae and E. cloacae. Mating-out assays using Escherichia coli as recipient were successful for all isolates. The bla NDM-1 gene was always identified on a 70-kb plasmid, whereas the bla VIM-1 gene was located on either a 60-kb or a 150-kb plasmid the two E. cloacae isolates, respectively. To the best of our knowledge, this is the first report of the coexistence of an MBL (NDM-1), an ESBL (CTX-M), a 16S rRNA methylase (RmtC), an acetyltransferase (AAC[6']-Ib), and a quinolone resistance enzyme (QnrB) in K. pneumoniae isolates recovered from different patients during an outbreak in a Saudi Arabian hospital.
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Ullmann IF, Tunsjø HS, Andreassen M, Nielsen KM, Lund V, Charnock C. Detection of Aminoglycoside Resistant Bacteria in Sludge Samples From Norwegian Drinking Water Treatment Plants. Front Microbiol 2019; 10:487. [PMID: 30918503 PMCID: PMC6424899 DOI: 10.3389/fmicb.2019.00487] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 02/25/2019] [Indexed: 02/01/2023] Open
Abstract
Through a culture-based approach using sludge from drinking water treatment plants, this study reports on the presence of aminoglycoside resistant bacteria at 23 different geographical locations in Norway. Sludge samples are derived from a large environmental area including drinking water sources and their surrounding catchment areas. Aminoglycoside resistant bacteria were detected at 18 of the sample sites. Only five samples did not show any growth of isolates resistant to the selected aminoglycosides, kanamycin and gentamycin. There was a statistically significant correlation between the numbers of kanamycin and gentamycin resistant bacteria isolated from the 23 samples, perhaps suggesting common determinants of resistance. Based on 16S rRNA sequencing of 223 aminoglycoside resistant isolates, three different genera of Bacteroidetes were found to dominate across samples. These were Flavobacterium, Mucilaginibacter and Pedobacter. Further phenotypic and genotypic analyses showed that efflux pumps, reduced membrane permeability and four assayed genes coding for aminoglycoside modifying enzymes AAC(6′)-Ib, AAC(3′)-II, APH(3′)-II, APH(3′)-III, could only explain the resistance of a few of the isolates selected for testing. aph(3′)-II was detected in 1.6% of total isolates, aac(6′)-Ib and aph(3′)-III in 0.8%, while aac(3′)-II was not detected in any of the isolates. The isolates, for which potential resistance mechanisms were found, represented 13 different genera suggesting that aminoglycoside resistance is widespread in bacterial genera indigenous to sludge. The present study suggests that aminoglycoside resistant bacteria are present in Norwegian environments with limited anthropogenic exposures. However, the resistance mechanisms remain largely unknown, and further analyses, including culture-independent methods, could be performed to investigate other potential resistance mechanisms. This is, to our knowledge, the first large scale nationwide investigation of aminoglycoside resistance in the Norwegian environment.
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Affiliation(s)
- Ingvild F Ullmann
- Department of Life Sciences and Health, OsloMet - Oslo Metropolitan University, Oslo, Norway
| | - Hege S Tunsjø
- Department of Life Sciences and Health, OsloMet - Oslo Metropolitan University, Oslo, Norway
| | - Monica Andreassen
- Department of Zoonotic, Food- and Waterborne Infections, Norwegian Institute of Public Health, Oslo, Norway
| | - Kaare Magne Nielsen
- Department of Life Sciences and Health, OsloMet - Oslo Metropolitan University, Oslo, Norway
| | - Vidar Lund
- Department of Zoonotic, Food- and Waterborne Infections, Norwegian Institute of Public Health, Oslo, Norway
| | - Colin Charnock
- Department of Life Sciences and Health, OsloMet - Oslo Metropolitan University, Oslo, Norway
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Alcántar-Curiel MD, Fernández-Vázquez JL, Toledano-Tableros JE, Gayosso-Vázquez C, Jarillo-Quijada MD, López-Álvarez MDR, Giono-Cerezo S, Santos-Preciado JI. Emergence of IncFIA Plasmid-Carrying blaNDM-1 Among Klebsiella pneumoniae and Enterobacter cloacae Isolates in a Tertiary Referral Hospital in Mexico. Microb Drug Resist 2019; 25:830-838. [PMID: 30835632 DOI: 10.1089/mdr.2018.0306] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The emergence of New Delhi metallo-β-lactamase 1 on carbapenemase-producing bacteria has raised a major worldwide public health concern. This study reports the dissemination of blaNDM-1 in carbapenem-resistant isolates that caused nosocomial infections in a tertiary hospital in Mexico City. Seven Enterobacter cloacae and three Klebsiella pneumoniae nosocomial isolates from the same time period harbored the blaNDM-1 gene. The resistance phenotype and the blaNDM-1 gene were transferred through conjugative plasmids belonging to the incompatibility group IncFIA of 85, 101, and 195 kb in E. cloacae and 95 and 101 kb in K. pneumoniae isolates. Restriction fragment length polymorphism analysis showed that blaNDM-1 was carried in similar plasmids with molecular sizes of 101 and 85 kb, each one in three isolates of E. cloacae and one of 101 kb on two isolates of K. pneumoniae. During a 9-month period, six of the seven isolates of E. cloacae analyzed harbored blaNDM-1 and belonged to clone E1. Similarly, over a 5-month period, two of the three K. pneumoniae isolates that harbored blaNDM-1 belonged to clone K1. These results demonstrate the horizontal transfer of blaNDM-1 between different bacterial species, dissemination of clones with high levels of resistance to carbapenems, and underscore the need for heightened measures to control their further spread.
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Affiliation(s)
- María Dolores Alcántar-Curiel
- 1 Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - José Luis Fernández-Vázquez
- 1 Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - José Eduardo Toledano-Tableros
- 2 Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Catalina Gayosso-Vázquez
- 1 Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ma Dolores Jarillo-Quijada
- 1 Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Silvia Giono-Cerezo
- 2 Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - José Ignacio Santos-Preciado
- 1 Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
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Shen J, Zhu X, Jin K, Li Y, Gu Y, Huang J, Qu Y, Li X. A laboratory exercise for detecting microbial contaminants. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 46:279-284. [PMID: 29473287 DOI: 10.1002/bmb.21118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 01/16/2018] [Accepted: 01/28/2018] [Indexed: 06/08/2023]
Abstract
The development and evaluation of a 6-hours laboratory class, based on capillary electrophoresis (CE) and the detection of microbial contaminants, is described. It can be easily scaled up or down, to suit class sizes up to 188 and completed in a shorter time scale. CE uses narrow-bore fused-silica capillaries to separate a complex array of large and small molecules. A laboratory exercise has been devised to illustrate how CE-based genetic analysis system processes DNA fragment analysis to detect three microbial contaminants. The protocol is relatively inexpensive and uses standard molecular biology reagents and equipment. © 2018 by The International Union of Biochemistry and Molecular Biology, 46(3):279-284, 2018.
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Affiliation(s)
- Jie Shen
- College of Life Information Science & Instrument Engineering, Hangzhou Dianzi University, Hangzhou, China
| | - Xiang Zhu
- College of Life Information Science & Instrument Engineering, Hangzhou Dianzi University, Hangzhou, China
| | - Kai Jin
- College of Life Information Science & Instrument Engineering, Hangzhou Dianzi University, Hangzhou, China
| | - Ya Li
- College of Life Information Science & Instrument Engineering, Hangzhou Dianzi University, Hangzhou, China
| | - YiTian Gu
- College of Life Information Science & Instrument Engineering, Hangzhou Dianzi University, Hangzhou, China
| | - Jiahong Huang
- College of Life Information Science & Instrument Engineering, Hangzhou Dianzi University, Hangzhou, China
| | - Yulan Qu
- College of Life Information Science & Instrument Engineering, Hangzhou Dianzi University, Hangzhou, China
| | - Xiaoyu Li
- College of Life Information Science & Instrument Engineering, Hangzhou Dianzi University, Hangzhou, China
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Han Z, Sun J, Lv A, Sung Y, Sun X, Shi H, Hu X, Wang A, Xing K. A modified method for genomic DNA extraction from the fish intestinal microflora. AMB Express 2018; 8:52. [PMID: 29610998 PMCID: PMC5880796 DOI: 10.1186/s13568-018-0578-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/25/2018] [Indexed: 01/23/2023] Open
Abstract
A modified genomic DNA extraction method named the combination of lysozyme and ultrasonic lysis (CLU) method was used to analyze the fish intestinal microflora. In this method, the physical disruption and chemical lysis steps were combined, and some parameters in the key steps were adjusted. In addition, the results obtained by this method were compared with the results obtained by the Zirmil-beating cell disruption method and the QIAamp Fast DNA Stool Mini Kit. The OD260/OD280 ratio and concentration of the DNA extracted using the CLU method were 2.02 and 282.8 µg/µL, respectively; when the incubation temperatures for lysozyme and RNase were adjusted to 37 °C, those values were 2.08 and 309.8 µg/µL, respectively. On the agarose gel, a major high-intensity, discrete band of more than 10 kb was found for the CLU method. However, the smearing intensity of degraded DNA was lower when the incubation temperatures were 60 °C for lysozyme and 30 °C for RNase than when incubation temperatures of 37 °C for lysozyme and 37 °C for RNase were used. The V3 variable region of the prokaryotic 16S rDNA was amplified, and an approximately 600-bp fragment was observed when the DNA extracted using the CLU method was used as a template. The CLU method is simple and cost effective, and it yields high-quality, unsheared, high-molecular-weight DNA, which is comparable to that obtained with a commercially available kit. The extracted DNA has potential for applications in critical molecular biology techniques.
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Wang Z, Kong LC, Jia BY, Liu SM, Jiang XY, Ma HX. Aminoglycoside susceptibility of Pasteurella multocida isolates from bovine respiratory infections in China and mutations in ribosomal protein S5 associated with high-level induced spectinomycin resistance. J Vet Med Sci 2017; 79:1678-1681. [PMID: 28867688 PMCID: PMC5658559 DOI: 10.1292/jvms.17-0219] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Twenty-three isolates of Pasteurella multocida were tested for
susceptibility to six aminoglycoside agents and screened by polymerase chain reaction for
the presence of aminoglycoside resistance genes. In addition, mutations in the
resistance-determining region of strains showing a high level of induced resistance to
spectinomycin strains were examined. Susceptibility testing showed that all of the
isolates were resistant to at least two types of aminoglycosides, and that the most
effective antimicrobial was spectinomycin. The resistance genes aphA1,
strB and aacA4 were present in all 23 isolates. In the
three induced spectinomycin-resistant strains, a 9-bp deletion in rpsE
that encodes ribosomal protein S5 was detected.
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Affiliation(s)
- Zi Wang
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, P.R. China
| | - Ling-Cong Kong
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, P.R. China
| | - Bo-Yan Jia
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, P.R. China
| | - Shu-Ming Liu
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, P.R. China
| | - Xiu-Yun Jiang
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, P.R. China
| | - Hong-Xia Ma
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street No. 2888, Changchun 130118, P.R. China
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Molecular Identification of Aminoglycoside-Modifying Enzymes and Plasmid-Mediated Quinolone Resistance Genes among Klebsiella pneumoniae Clinical Isolates Recovered from Egyptian Patients. Int J Microbiol 2017. [PMID: 28638412 PMCID: PMC5468591 DOI: 10.1155/2017/8050432] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Inappropriate use of antibiotics in clinical settings is thought to have led to the global emergence and spread of multidrug-resistant pathogens. The goal of this study was to investigate the prevalence of genes encoding aminoglycoside resistance and plasmid-mediated quinolone resistance among clinical isolates of Klebsiella pneumoniae. All K. pneumoniae isolates were phenotypically identified using API 20E and then confirmed genotypically through amplification of the specific K. pneumoniae phoE gene. All isolates were genotyped by the enterobacterial repetitive intergenic consensus polymerase chain reaction technique (ERIC-PCR). Antibiotic susceptibility testing was done by a modified Kirby-Bauer method and broth microdilution. All resistant or intermediate-resistant isolates to either gentamicin or amikacin were screened for 7 different genes encoding aminoglycoside-modifying enzymes (AMEs). In addition, all resistant or intermediate-resistant isolates to either ciprofloxacin or levofloxacin were screened for 5 genes encoding the quinolone resistance protein (Qnr), 1 gene encoding quinolone-modifying enzyme, and 3 genes encoding quinolone efflux pumps. Biotyping using API 20E revealed 13 different biotypes. Genotyping demonstrated that all isolates were related to 2 main phylogenetic groups. Susceptibility testing revealed that carbapenems and tigecycline were the most effective agents. Investigation of genes encoding AMEs revealed that acc(6′)-Ib was the most prevalent, followed by acc(3′)-II, aph(3′)-IV, and ant(3′′)-I. Examination of genes encoding Qnr proteins demonstrated that qnrB was the most prevalent, followed by qnrS, qnrD, and qnrC. It was found that 61%, 26%, and 12% of quinolone-resistant K. pneumoniae isolates harbored acc(6′)-Ib-cr, oqxAB, and qebA, respectively. The current study demonstrated a high prevalence of aminoglycoside and quinolone resistance genes among clinical isolates of K. pneumoniae.
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A Programmable Digital Microfluidic Assay for the Simultaneous Detection of Multiple Anti-Microbial Resistance Genes. MICROMACHINES 2017. [PMCID: PMC6189955 DOI: 10.3390/mi8040111] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The rapid emergence of antimicrobial resistant bacteria requires the development of new diagnostic tests. Nucleic acid-based assays determine antimicrobial susceptibility by detecting genes that encode for the resistance. In this study, we demonstrate rapid and simultaneous detection of three genes that confer resistance in bacteria to extended spectrum β-lactam and carbapenem antibiotics; CTX-M-15, KPC and NDM-1. The assay uses isothermal DNA amplification (recombinase polymerase amplification, RPA) implemented on a programmable digital microfluidics (DMF) platform. Automated dispensing protocols are used to simultaneously manipulate 45 droplets of nL volume containing sample DNA, reagents, and controls. The droplets are processed and mixed under electronic control on the DMF devices with positive amplification measured by fluorescence. The assay on these devices is significantly improved with a Time to Positivity (TTP) half that of the benchtop assay.
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Ghotaslou R, Yeganeh Sefidan F, Akhi MT, Asgharzadeh M, Mohammadzadeh Asl Y. Dissemination of Genes Encoding Aminoglycoside-Modifying Enzymes and armA Among Enterobacteriaceae Isolates in Northwest Iran. Microb Drug Resist 2017; 23:826-832. [PMID: 28151044 DOI: 10.1089/mdr.2016.0224] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
INTRODUCTION Enzymatic inactivation is one of the most important mechanisms of resistance to aminoglycosides. The aim of this study was to investigate the prevalence of armA and diversity of the genes encoding aminoglycoside-modifying enzymes (AMEs) and their associations with resistance phenotypes in Enterobacteriaceae isolates. METHODS Three hundred and seven Enterobacteriaceae isolates were collected from five hospitals in northwest Iran. The disk diffusion method for amikacin, gentamicin, tobramycin, kanamycin, and streptomycin, as well as the minimum inhibitory concentration for amikacin, gentamicin, tobramycin, and kanamycin were done for susceptibility testing. Thirteen AME genes and armA methylase were screened using the PCR and sequencing assays. RESULTS Two hundred and twenty (71.7%) of isolates were resistant to aminoglycosides and 155 (70.5%) of them were positive for aminoglycoside resistance genes. The most prevalent AME genes were ant(3″)-Ia and aph(3″)-Ib with the frequency 35.9% and 30.5%, respectively. Also, 21 (9.5%) of resistant isolates were positive for armA methylase gene. CONCLUSIONS The prevalence of resistance to aminoglycoside is high and AME genes frequently are disseminated in Enterobacteriaceae isolates. There is an association between phenotypic resistance and the presence of some aminoglycoside genes.
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Affiliation(s)
- Reza Ghotaslou
- 1 Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences , Tabriz, Iran .,2 Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences , Tabriz, Iran
| | - Fatemeh Yeganeh Sefidan
- 1 Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences , Tabriz, Iran .,2 Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences , Tabriz, Iran
| | - Mohammad Taghi Akhi
- 2 Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences , Tabriz, Iran
| | - Mohammad Asgharzadeh
- 3 Department of Laboratory Sciences, Paramedical Faculty and Biotechnology Research Center, Tabriz University of Medical Sciences , Tabriz, Iran
| | - Yalda Mohammadzadeh Asl
- 2 Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences , Tabriz, Iran
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Hu L, Lin X, Nie F, ZexiaoYang, Yao X, Li G, Wu X, Ren M, Wang Y. Simultaneous typing of seven porcine pathogens by multiplex PCR with a GeXP analyser. J Virol Methods 2015; 232:21-8. [PMID: 26706731 DOI: 10.1016/j.jviromet.2015.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 12/09/2015] [Accepted: 12/10/2015] [Indexed: 12/31/2022]
Abstract
A novel high-throughput method was developed for simultaneous detection and differentiation of seven porcine pathogens by multiplex PCR based on a GenomeLab Gene Expression Profiler (GeXP) analyser. The pathogens included in this study were pseudorabies virus (PRV), classical swine fever virus (CSFV), African swine fever virus (ASFV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine parvovirus (PPV), porcine circovirus type 2 (PCV-2) and Japanese encephalitis virus (JEV). Seven pairs of chimeric primers, consisting of a pathogen-specific sequence fused to a universal sequence at the 5' end, were used to initiate the PCR, after which a set of universal primers was used for the subsequent cycles of the PCR. Amplification products were separated by capillary electrophoresis and identified using fluorescence spectrophotometry. The specificity of the GeXP assay was examined with single and mixed pathogen cDNA/DNA templates. The specific DNA product amplification peaks of seven pathogens were observed on the GeXP analyser. Negative controls did not produce DNA products. The sensitivity was evaluated by performing the assay on serial 10-fold dilutions of the plasmids containing the target sequence. Under optimised conditions this assay achieved a sensitivity of 100-1000 copies/μL for a single virus and 1000 copies/μL when all of the seven pre-mixed viral targets were present. Furthermore, the GeXP-PCR assay was 100% specific when 58 clinical samples were tested in comparison with the conventional PCR method. In conclusion, the GeXP assay is a rapid, cost-effective, sensitive, specific and high throughput method for simultaneously detecting seven pathogens that infect swine.
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Affiliation(s)
- Ling Hu
- Animal Quarantine Laboratory, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Zigong Center for Animal Disease Control and Prevention, Zigong 643000, Sichuan, China
| | - Xingyu Lin
- Animal Quarantine Laboratory, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Fuping Nie
- Chongqing Entry-Exit Inspection and Quarantine Bureau of China, Chongqing 400020, China; Chongqing Import and Export Food Safety Engineering Center, Chongqing 400020, China
| | - ZexiaoYang
- Animal Quarantine Laboratory, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xueping Yao
- Animal Quarantine Laboratory, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Guili Li
- Animal Quarantine Laboratory, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xulong Wu
- Animal Quarantine Laboratory, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Meishen Ren
- Animal Quarantine Laboratory, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yin Wang
- Animal Quarantine Laboratory, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu 611100, Sichuan, China.
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Zhang YF, Xie ZX, Xie LJ, Deng XW, Xie ZQ, Luo SS, Huang L, Huang JL, Zeng TT. GeXP analyzer-based multiplex reverse-transcription PCR assay for the simultaneous detection and differentiation of eleven duck viruses. BMC Microbiol 2015; 15:247. [PMID: 26518004 PMCID: PMC4628294 DOI: 10.1186/s12866-015-0590-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 10/23/2015] [Indexed: 01/21/2023] Open
Abstract
Background Duck viral pathogens primarily include the avian influenza virus (AIV) subtypes H5, H7, and H9; duck hepatitis virus (DHV); duck tembusu virus (DTMUV); egg drop syndrome virus (EDSV); duck enteritis virus (DEV); Newcastle disease virus (NDV); duck circovirus (DuCV); muscovy duck reovirus (MDRV); and muscovy duck parvovirus (MDPV). These pathogens cause great economic losses to China’s duck breeding industry. Result A rapid, specific, sensitive and high-throughput GeXP-based multiplex PCR assay consisting of chimeric primer-based PCR amplification with fluorescent labeling and capillary electrophoresis separation was developed and optimized to simultaneously detect these eleven viral pathogens. Single and mixed pathogen cDNA/DNA templates were used to evaluate the specificity of the GeXP-multiplex assay. Corresponding specific DNA products were amplified from each pathogen. Other pathogens, including duck Escherichia coli, duck Salmonella, duck Staphylococcus aureus, Pasteurella multocida, infectious bronchitis virus, and Mycoplasma gallisepticum, did not result in amplification products. The detection limit of GeXP was 103copies when all twelve pre-mixed plasmids containing the target genes of eleven types of duck viruses were present. To further evaluate the reliability of GeXP, 150 clinical field samples were evaluated. Comparison with the results of conventional PCR methods for the field samples, the GeXP-multiplex PCR method was more sensitive and accurate. Conclusion This GeXP-based multiplex PCR method can be utilized for the rapid differential diagnosis of clinical samples as an effective tool to prevent and control duck viruses with similar clinical symptoms.
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Affiliation(s)
- Yan-Fang Zhang
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, Nanning, 530001, China.
| | - Zhi-Xun Xie
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, Nanning, 530001, China.
| | - Li-Ji Xie
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, Nanning, 530001, China.
| | - Xian-Wen Deng
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, Nanning, 530001, China.
| | - Zhi-Qin Xie
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, Nanning, 530001, China.
| | - Si-Si Luo
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, Nanning, 530001, China.
| | - Li Huang
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, Nanning, 530001, China.
| | - Jiao-Ling Huang
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, Nanning, 530001, China.
| | - Ting-Ting Zeng
- Department of Biotechnology, Guangxi Key Laboratory of Animal Vaccines and Diagnostics, Guangxi Veterinary Research Institute, 51 Youai North Road, Nanning, 530001, China.
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Tyson GH, McDermott PF, Li C, Chen Y, Tadesse DA, Mukherjee S, Bodeis-Jones S, Kabera C, Gaines SA, Loneragan GH, Edrington TS, Torrence M, Harhay DM, Zhao S. WGS accurately predicts antimicrobial resistance in Escherichia coli. J Antimicrob Chemother 2015; 70:2763-9. [PMID: 26142410 DOI: 10.1093/jac/dkv186] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/10/2015] [Indexed: 01/22/2023] Open
Abstract
OBJECTIVES The objective of this study was to determine the effectiveness of WGS in identifying resistance genotypes of MDR Escherichia coli and whether these correlate with observed phenotypes. METHODS Seventy-six E. coli strains were isolated from farm cattle and measured for phenotypic resistance to 15 antimicrobials with the Sensititre(®) system. Isolates with resistance to at least four antimicrobials in three classes were selected for WGS using an Illumina MiSeq. Genotypic analysis was conducted with in-house Perl scripts using BLAST analysis to identify known genes and mutations associated with clinical resistance. RESULTS Over 30 resistance genes and a number of resistance mutations were identified among the E. coli isolates. Resistance genotypes correlated with 97.8% specificity and 99.6% sensitivity to the identified phenotypes. The majority of discordant results were attributable to the aminoglycoside streptomycin, whereas there was a perfect genotype-phenotype correlation for most antibiotic classes such as tetracyclines, quinolones and phenicols. WGS also revealed information about rare resistance mechanisms, such as structural mutations in chromosomal copies of ampC conferring third-generation cephalosporin resistance. CONCLUSIONS WGS can provide comprehensive resistance genotypes and is capable of accurately predicting resistance phenotypes, making it a valuable tool for surveillance. Moreover, the data presented here showing the ability to accurately predict resistance suggest that WGS may be used as a screening tool in selecting anti-infective therapy, especially as costs drop and methods improve.
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Affiliation(s)
- Gregory H Tyson
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD, USA
| | - Patrick F McDermott
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD, USA
| | - Cong Li
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD, USA
| | - Yuansha Chen
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD, USA
| | - Daniel A Tadesse
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD, USA
| | - Sampa Mukherjee
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD, USA
| | - Sonya Bodeis-Jones
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD, USA
| | - Claudine Kabera
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD, USA
| | - Stuart A Gaines
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD, USA
| | - Guy H Loneragan
- International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX, USA
| | - Tom S Edrington
- Food and Feed Safety Research Unit, Agricultural Research Service, US Department of Agriculture, College Station, TX, USA
| | - Mary Torrence
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | - Dayna M Harhay
- US Meat Animal Research Center, Agricultural Research Service, US Department of Agriculture, Clay Center, NE, USA
| | - Shaohua Zhao
- Division of Animal and Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food and Drug Administration, Laurel, MD, USA
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Chen H, Zhu Z, Lu JJ, Liu S. Charging YOYO-1 on capillary wall for online DNA intercalation and integrating this approach with multiplex PCR and bare narrow capillary-hydrodynamic chromatography for online DNA analysis. Anal Chem 2015; 87:1518-22. [PMID: 25555111 PMCID: PMC4318619 DOI: 10.1021/ac504257b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Multiplex polymerase chain reaction
(PCR) has been widely utilized
for high-throughput pathogen identification. Often, a dye is used
to intercalate the amplified DNA fragments, and identifications of
the pathogens are carried out by DNA melting curve analysis or gel
electrophoresis. Integrating DNA amplification and identification
is a logic path toward maximizing the benefit of multiplex PCR. Although
PCR and gel electrophoresis have been integrated, replenishing the
gels after each run is tedious and time-consuming. In this technical
note, we develop an approach to address this issue. We perform multiplex
PCR inside a capillary, transfer the amplified fragments to a bare
narrow capillary, and measure their lengths online using bare narrow
capillary–hydrodynamic chromatography (BaNC-HDC), a new technique
recently developed in our laboratory for free-solution DNA separation.
To intercalate the DNA with YOYO-1 (a fluorescent dye) for BaNC-HDC,
we flush the capillary column with a YOYO-1 solution; positively charged
YOYO-1 is adsorbed (or charged) onto the negatively charged capillary
wall. As DNA molecules are driven down the column for separation,
they react with the YOYO-1 stored on the capillary wall and are online-intercalated
with the dye. With a single YOYO-1 charging, the column can be used
for more than 40 runs, although the fluorescence signal intensities
of the DNA peaks decrease gradually. Although the dye-DNA intercalation
occurs during the separation, it does not affect the retention times,
separation efficiencies, or resolutions.
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Affiliation(s)
- Huang Chen
- Department of Chemistry and Biochemistry, University of Oklahoma , 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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Highly sensitive and rapid bacteria detection using molecular beacon–Au nanoparticles hybrid nanoprobes. Biosens Bioelectron 2014; 57:133-8. [DOI: 10.1016/j.bios.2014.02.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 01/30/2014] [Accepted: 02/10/2014] [Indexed: 01/31/2023]
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Çıçek AÇ, Düzgün AÖ, Saral A, Kayman T, Çızmecı Z, Balcı PÖ, Dal T, Fırat M, Tosun İ, Alıtntop YA, Çalışkan A, Yazıcı Y, Sandallı C. Detection of class 1 integron in Acinetobacter baumannii isolates collected from nine hospitals in Turkey. Asian Pac J Trop Biomed 2014; 3:743-7. [PMID: 23998017 DOI: 10.1016/s2221-1691(13)60149-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 08/23/2013] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE To investigate the antibiotic resistance genes inserted into class 1 and class 2 integrons in Acinetobacter baumannii (A. baumannii) isolates obtained from nine different cities in Turkey. METHODS A collection of 281 A. baumannii clinical isolates were collected from nine diferent state hospitals in Turkey and were confirmed as A. baumannii by conventional biochemical, API testing and bla-OXA-51 specific PCR. The isolates were examined by PCR for existence of class 1 and 2 integron gene cassettes. RESULTS They were characterized by antimicrobial susceptibility testing and the highest resistance rates were determined for piperacillin (90.03%), ciprofloxacin (87.54%), cefepime and trimethoprim/sulfamethoxazole (81.13%). The lowest resistance rates was for cefotaxime (3.55%). class I integrons were detected in 6.4% (18/281) of A. baumannii strains and no class 2 integron was detected. The gene cassettes of class 1 integrons AacC1-AAC(3)I-aadA1, AacC1-aadA1, AAC(3)-I, AAC(3)-I -AAC(3)-I -aadA1, TEM-1, AAC(3)-I-aadA1 - AAC(3)-I -AAC(3)-I, AAC(3)-I -AAC(3)-I -AAC(3)-I -aadA1, AAC(3)-I - aadA1, AAC(3)-I-AAC(3)-I, AAC(3)-I-aadA1- AAC(3)-I-aadA1, AAC(3)-I- AAC(3)-I- aadA1-AAC(3)-I-aadA1 were detected in eighteen strains. The aac genes family were most frequently found integrated into the class 1 integrons and it was followed by aadA genes and TEM-1 genes. CONCLUSIONS This is an extensive study on the distribution of class 1 integron among A. baumannii in Turkey. In addition to these, two new alleles were observed. Their percentage rates of similarity to other cassettes are 95% aadA1 ( TKA18) and 89% aadA1 (ANKA3).
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Affiliation(s)
- Ayşegül Çopur Çıçek
- Department of Medical Microbiology, Faculty of Medicine, Recep Tayyip Erdogan University, Rize, Turkey
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Tsukamoto N, Ohkoshi Y, Okubo T, Sato T, Kuwahara O, Fujii N, Tamura Y, Yokota SI. High prevalence of cross-resistance to aminoglycosides in fluoroquinolone-resistant Escherichia coli clinical isolates. Chemotherapy 2014; 59:379-84. [PMID: 24852043 DOI: 10.1159/000361011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 03/03/2014] [Indexed: 11/19/2022]
Abstract
BACKGROUND Multidrug-resistant Escherichia coli, especially a lineage of O25b:H4-ST131, has increased and spread worldwide. The surveillance of cross-resistance of E. coli is necessary. METHODS Cross-resistance to fluoroquinolones (FQs) and aminoglycosides (AGs) was examined in E. coli isolated in Hokkaido Prefecture, Japan, between 2008 and 2009. RESULTS Gentamicin (GEN) resistance was more common in FQ-resistant isolates (30/112 strains; 26.8%) than in FQ-susceptible isolates (2/100 strains; 2%). The frequency of GEN resistance was similar in two groups of FQ-resistant strains, O25b:H4-ST131 genotype (22/87 strains; 25.3%) and a group of other FQ-resistant genotypes (8/25 strains; 32.0%). The main AG resistance gene was aac(3)-II (87.5% of GEN-resistant strains). The only amikacin-resistant strain which was FQ resistant carried the aac(6')-Ib-cr gene. CTX-M type extended-spectrum β-lactamase (ESBL) genes were also found in FQ-resistant strains at a high frequency. However, the number of strains with both ESBL and AG-modifying enzyme genes was relatively low (8 strains). CONCLUSION All FQ-resistant strains, not only O25b:H4-ST131, appeared to preferentially acquire ESBL genes and/or genes encoding AG-modifying enzymes; however, the acquisitions of these genes seemed to occur independently.
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Affiliation(s)
- Naoyuki Tsukamoto
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan
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