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Li XH, Huang YY, Lu LM, Zhao LJ, Luo XK, Li RJ, Dai YY, Qin C, Huang YQ, Chen H. Early genetic diagnosis of clarithromycin resistance in Helicobacter pylori. World J Gastroenterol 2021; 27:3595-3608. [PMID: 34239272 PMCID: PMC8240046 DOI: 10.3748/wjg.v27.i24.3595] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/13/2021] [Accepted: 05/21/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The drug resistance rate of clinical Helicobacter pylori (H. pylori) isolates has increased. However, the mechanism of drug resistance remains unclear. In this study, drug-resistant H. pylori strains were isolated from different areas and different populations of Chinese for genomic analysis.
AIM To investigate drug-resistant genes in H. pylori and find the genes for the early diagnosis of clarithromycin resistance.
METHODS Three drug-resistant H. pylori strains were isolated from patients with gastritis in Bama County, China. Minimal inhibitory concentrations of clarithromycin, metronidazole, and levofloxacin were determined and complete genome sequencing was performed with annotation. Hp1181 and hp1184 genes were found in these strains and then detected by reverse transcription polymerase chain reaction. The relationships between hp1181 or hp1184 and clarithromycin resistance were ascertained with gene mutant and drug-resistant strains. The homology of the strains with hp26695 was assessed through complete genome detection and identification. Differences in genome sequences, gene quantity, and gene characteristics were detected amongst the three strains. Prediction and analysis of the function of drug-resistant genes indicated that the RNA expression of hp1181 and hp1184 increased in the three strains, which was the same in the artificially induced clarithromycin-resistant bacteria. After gene knockout, the drug sensitivity of the strains was assessed.
RESULTS The strains showing a high degree of homology with hp26695, hp1181, and hp1184 genes were found in these strains; the expression of the genes hp1184 and hp1181 was associated with clarithromycin resistance.
CONCLUSION Hp1181 and hp1184 mutations may be the earliest and most persistent response to clarithromycin resistance, and they may be the potential target genes for the diagnosis, prevention, and treatment of clarithromycin resistance.
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Affiliation(s)
- Xiao-Hua Li
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infection, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Yong-Yi Huang
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infection, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Lin-Ming Lu
- Department of Pathology, Wannan Medical College, Wuhu 241002, Anhui Province, China
| | - Li-Juan Zhao
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infection, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Xian-Ke Luo
- Department of Gastroenterology, National Hospital of Guangxi Zhuang Autonomous Region, Nanning Guangxi Zhuang Autonomous Region, 530001, China
| | - Ru-Jia Li
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infection, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Yuan-Yuan Dai
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infection, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Chun Qin
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infection, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Yan-Qiang Huang
- Research Center for the Prevention and Treatment of Drug Resistant Microbial Infection, Youjiang Medical University for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Hao Chen
- Department of Pathology, Wannan Medical College, Wuhu 241002, Anhui Province, China
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Prezioso SM, Brown NE, Goldberg JB. Elfamycins: inhibitors of elongation factor-Tu. Mol Microbiol 2017; 106:22-34. [PMID: 28710887 DOI: 10.1111/mmi.13750] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2017] [Indexed: 01/26/2023]
Abstract
Elfamycins are a relatively understudied group of antibiotics that target the essential process of translation through impairment of EF-Tu function. For the most part, the utility of these compounds has been as laboratory tools for the study of EF-Tu and the ribosome, as their poor pharmacokinetic profile and solubility has prevented implementation as therapeutic agents. However, due to the slowing of the antibiotic pipeline and the rapid emergence of resistance to approved antibiotics, this group is being reconsidered. Some researchers are using screens for novel naturally produced variants, while others are making directed, systematic chemical improvements on publically disclosed compounds. As an example of the latter approach, a GE2270 A derivative, LFF571, has completed phase 2 clinical trials, thus demonstrating the potential for elfamycins to become more prominent antibiotics in the future.
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Affiliation(s)
- Samantha M Prezioso
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Emory University School of Medicine, Atlanta, GA 30322, USA.,Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nicole E Brown
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Joanna B Goldberg
- Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.,Emory+Children's Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, GA 30322, USA
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Vélez JR, Cameron M, Rodríguez-Lecompte JC, Xia F, Heider LC, Saab M, McClure JT, Sánchez J. Whole-Genome Sequence Analysis of Antimicrobial Resistance Genes in Streptococcus uberis and Streptococcus dysgalactiae Isolates from Canadian Dairy Herds. Front Vet Sci 2017; 4:63. [PMID: 28589129 PMCID: PMC5438997 DOI: 10.3389/fvets.2017.00063] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/19/2017] [Indexed: 11/20/2022] Open
Abstract
The objectives of this study are to determine the occurrence of antimicrobial resistance (AMR) genes using whole-genome sequence (WGS) of Streptococcus uberis (S. uberis) and Streptococcus dysgalactiae (S. dysgalactiae) isolates, recovered from dairy cows in the Canadian Maritime Provinces. A secondary objective included the exploration of the association between phenotypic AMR and the genomic characteristics (genome size, guanine–cytosine content, and occurrence of unique gene sequences). Initially, 91 isolates were sequenced, and of these isolates, 89 were assembled. Furthermore, 16 isolates were excluded due to larger than expected genomic sizes (>2.3 bp × 1,000 bp). In the final analysis, 73 were used with complete WGS and minimum inhibitory concentration records, which were part of the previous phenotypic AMR study, representing 18 dairy herds from the Maritime region of Canada (1). A total of 23 unique AMR gene sequences were found in the bacterial genomes, with a mean number of 8.1 (minimum: 5; maximum: 13) per genome. Overall, there were 10 AMR genes [ANT(6), TEM-127, TEM-163, TEM-89, TEM-95, Linb, Lnub, Ermb, Ermc, and TetS] present only in S. uberis genomes and 2 genes unique (EF-TU and TEM-71) to the S. dysgalactiae genomes; 11 AMR genes [APH(3′), TEM-1, TEM-136, TEM-157, TEM-47, TetM, bl2b, gyrA, parE, phoP, and rpoB] were found in both bacterial species. Two-way tabulations showed association between the phenotypic susceptibility to lincosamides and the presence of linB (P = 0.002) and lnuB (P < 0.001) genes and the between the presence of tetM (P = 0.015) and tetS (P = 0.064) genes and phenotypic resistance to tetracyclines only for the S. uberis isolates. The logistic model showed that the odds of resistance (to any of the phenotypically tested antimicrobials) was 4.35 times higher when there were >11 AMR genes present in the genome, compared with <7 AMR genes (P < 0.001). The odds of resistance was lower for S. dysgalactiae than S. uberis (P = 0.031). When the within-herd somatic cell count was >250,000 cells/mL, a trend toward higher odds of resistance compared with the baseline category of <150,000 cells/mL was observed. When the isolate corresponded to a post-mastitis sample, there were lower odds of resistance when compared with non-clinical isolates (P = 0.01). The results of this study showed the strength of associations between phenotypic AMR resistance of both mastitis pathogens and their genotypic resistome and other epidemiological characteristics.
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Affiliation(s)
- Julián Reyes Vélez
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Marguerite Cameron
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Juan Carlos Rodríguez-Lecompte
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Fangfang Xia
- Mathematics and Computer Science Division, Argonne National Laboratory, Chicago, IL, USA
| | - Luke C Heider
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Matthew Saab
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada.,Diagnostic Services, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - J Trenton McClure
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Javier Sánchez
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
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Choi SH, Lee SO, Kim TH, Chung JW, Choo EJ, Kwak YG, Kim MN, Kim YS, Woo JH, Ryu J, Kim NJ. Clinical features and outcomes of bacteremia caused by Enterococcus casseliflavus and Enterococcus gallinarum: analysis of 56 cases. Clin Infect Dis 2003; 38:53-61. [PMID: 14679448 DOI: 10.1086/380452] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2003] [Accepted: 08/21/2003] [Indexed: 11/03/2022] Open
Abstract
The clinical significance and virulence potential of Enterococcus casseliflavus/flavescens and Enterococcus gallinarum are still uncertain. We retrospectively analyzed 56 cases of significant bacteremia caused by E. casseliflavus or E. gallinarum. Of these cases, 25 (44.6%) were associated with polymicrobial bacteremia, and 43 (76.8%) were associated with entry via the biliary tract. Resistance to vancomycin was observed in 17 (30.4%) of these 56 patients, and this resistance was significantly associated with E. gallinarum bacteremia (adjusted odds ratio [AOR], 10.56; 95% confidence interval [CI], 2.41-46.27) and bacteremia without biliary tract origin (AOR, 6.74; 95% CI, 1.44-31.67). The crude mortality rate was 13%, and the bacteremia-related mortality rate was 1.9%. In conclusion, bacteremia due to E. casseliflavus and E. gallinarum is commonly associated with biliary tract disease and may be associated with a low risk of mortality.
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Affiliation(s)
- Sang-Ho Choi
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
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Butaye P, Devriese LA, Haesebrouck F. Antimicrobial growth promoters used in animal feed: effects of less well known antibiotics on gram-positive bacteria. Clin Microbiol Rev 2003; 16:175-88. [PMID: 12692092 PMCID: PMC153145 DOI: 10.1128/cmr.16.2.175-188.2003] [Citation(s) in RCA: 406] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There are not many data available on antibiotics used solely in animals and almost exclusively for growth promotion. These products include bambermycin, avilamycin, efrotomycin, and the ionophore antibiotics (monensin, salinomycin, narasin, and lasalocid). Information is also scarce for bacitracin used only marginally in human and veterinary medicine and for streptogramin antibiotics. The mechanisms of action of and resistance mechanisms against these antibiotics are described. Special emphasis is given to the prevalence of resistance among gram-positive bacteria isolated from animals and humans. Since no susceptibility breakpoints are available for most of the antibiotics discussed, an alternative approach to the interpretation of MICs is presented. Also, some pharmacokinetic data and information on the influence of these products on the intestinal flora are presented.
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Affiliation(s)
- Patrick Butaye
- Laboratory of Veterinary Bacteriology and Mycology, Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, University of Ghent, 9820 Merelbeke, Belgium.
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Carvalho MG, Teixeira LM, Facklam RR. Use of tests for acidification of methyl-alpha-D-glucopyranoside and susceptibility to efrotomycin for differentiation of strains of Enterococcus and some related genera. J Clin Microbiol 1998; 36:1584-7. [PMID: 9620381 PMCID: PMC104881 DOI: 10.1128/jcm.36.6.1584-1587.1998] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A total of 107 Enterococcus strains, 10 Vagococcus fluvialis strains, and 8 Lactococcus garvieae strains were tested for acidification of methyl-alpha-D-glucopyranoside (MGP) and susceptibility to 100-microg efrotomycin (EFRO) disks. All 26 strains of Enterococcus casseliflavus, including 3 nonmotile and 2 nonpigmented strains, acidified MGP and were resistant to EFRO. All 22 strains of Enterococcus gallinarum, including 5 nonmotile strains, also acidified MGP and were resistant to EFRO. None of the 26 strains of Enterococcus faecium acidified MGP, and all were susceptible to EFRO. Although all 12 Enterococcus faecalis strains were also negative in the MGP test, they were resistant to EFRO. Other enterococcal strains gave variable results. All 10 strains of V. fluvialis and all 8 strains of L. garvieae gave positive and negative results, respectively, in the MGP test and were, respectively, resistant and susceptible to EFRO. These results indicate that tests of the production of acid from MGP and susceptibility to EFRO can be used as adjunct tests in the identification of typical and atypical strains of enterococci in the clinical microbiology laboratory.
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Affiliation(s)
- M G Carvalho
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Brazil
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