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Jiang X, Yan Y, Feng L, Wang F, Guo Y, Zhang X, Zhang Z. Bisphenol A alters volatile fatty acids accumulation during sludge anaerobic fermentation by affecting amino acid metabolism, material transport and carbohydrate-active enzymes. BIORESOURCE TECHNOLOGY 2021; 323:124588. [PMID: 33383358 DOI: 10.1016/j.biortech.2020.124588] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
Bisphenol A (BPA), a typical persistent organic pollutant in waste activated sludge, was chosen to explore its influence on the accumulation of volatile fatty acids (VFAs), which is an important raw material, during anaerobic fermentation. BPA in the range of 0-200 mg/kg dry sludge was beneficial to VFAs production, from 1564 mg chemical oxygen demand (COD)/L in the control to 2095 mg COD/L with 50 mg/kg BPA; the acetic acid yield was 563 and 1010 mg COD/L with 0 and 50 mg/kg BPA, respectively. The abundance of microorganisms that can consume VFAs was reduced and those responsible for producing VFAs was increased by BPA. Homologous genes of related enzymes in the pathways for amino acid metabolism, fatty acid biosynthesis, ABC transporters and quorum sensing were enhanced in the presence of BPA. The abundance of carbohydrate-active enzymes increased with BPA when compared with the control, benefitting VFAs production.
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Affiliation(s)
- Xiupeng Jiang
- School of Environmental & Safety Engineering, Changzhou University, Changzhou, Jiangsu Province 213164, China; College of Chemistry and Environment Engineering, Yancheng Teachers University, Yancheng, Jiangsu Province 224002, China
| | - Yuanyuan Yan
- College of Chemistry and Environment Engineering, Yancheng Teachers University, Yancheng, Jiangsu Province 224002, China.
| | - Leiyu Feng
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Feng Wang
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yingqing Guo
- School of Environmental & Safety Engineering, Changzhou University, Changzhou, Jiangsu Province 213164, China
| | - Xianzhong Zhang
- Shanghai Urban Construction Design & Research Institute (Group) Co., Ltd., 3447 Dongfang Road, Shanghai 200125, China
| | - Zhenguang Zhang
- Shanghai Road and Bridge Group Co., Ltd., 36 Guoke Road, Shanghai 200433, China
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Park E, Ha J, Oh H, Kim S, Choi Y, Lee Y, Kim Y, Seo Y, Kang J, Yoon Y. High Prevalence of Listeria monocytogenes in Smoked Duck: Antibiotic and Heat Resistance, Virulence, and Genetics of the Isolates. Food Sci Anim Resour 2021; 41:324-334. [PMID: 33987552 PMCID: PMC8115007 DOI: 10.5851/kosfa.2021.e2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/24/2020] [Accepted: 01/18/2021] [Indexed: 11/21/2022] Open
Abstract
This study aimed at determining the genetic and virulence characteristics of the
Listeria monocytogenes from smoked ducks. L.
monocytogenes was isolated by plating, and the isolated colonies
were identified by PCR. All the obtained seven L. monocytogenes
isolates possessed the virulence genes (inlA,
inlB, plcB, and hlyA) and
a 385 bp actA amplicon. The L. monocytogenes
isolates (SMFM2018 SD 1-1, SMFM 2018 SD 4-1, SMFM 2018 SD 4-2, SMFM 2018 SD 5-2,
SMFM 2018 SD 5-3, SMFM 2018 SD 6-2, and SMFM 2018 SD 7-1) were inoculated in
tryptic soy broth (TSB) containing 0.6% yeast extract at 60°C,
followed by cell counting on tryptic soy agar (TSA) containing 0.6% yeast
extract at 0, 2, 5, 8, and 10 min. We identified five heat resistant isolates
compared to the standard strain (L. monocytogenes ATCC13932),
among which three exhibited the serotype 1/2b and D-values of 5.41, 6.48, and
6.71, respectively at 60°C. The optical densities of the cultures were
regulated to a 0.5 McFarland standard to assess resistance against nine
antibiotics after an incubation at 30°C for 24 h. All isolates were
penicillin G resistant, possessing the virulence genes (inlA,
inlB, plcB, and hlyA) and
the 385-bp actA amplicon, moreover, three isolates showed
clindamycin resistance. In conclusion, this study allowed us to characterize
L. monocytogenes isolates from smoked ducks, exhibiting
clindamycin and penicillin G resistance, along with the 385-bp
actA amplicon, representing higher invasion efficiency than
the 268-bp actA, and the higher heat resistance serotype
1/2b.
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Affiliation(s)
- Eunyoung Park
- Department of Food and Nutrition, Sookmyung Women's University, Seoul 04310, Korea
| | - Jimyeong Ha
- Risk Analysis Research Center, Sookmyung Women's University, Seoul 04310, Korea
| | - Hyemin Oh
- Department of Food and Nutrition, Sookmyung Women's University, Seoul 04310, Korea
| | - Sejeong Kim
- Risk Analysis Research Center, Sookmyung Women's University, Seoul 04310, Korea
| | - Yukyung Choi
- Risk Analysis Research Center, Sookmyung Women's University, Seoul 04310, Korea
| | - Yewon Lee
- Department of Food and Nutrition, Sookmyung Women's University, Seoul 04310, Korea
| | - Yujin Kim
- Department of Food and Nutrition, Sookmyung Women's University, Seoul 04310, Korea
| | - Yeongeun Seo
- Department of Food and Nutrition, Sookmyung Women's University, Seoul 04310, Korea
| | - Joohyun Kang
- Department of Food and Nutrition, Sookmyung Women's University, Seoul 04310, Korea
| | - Yohan Yoon
- Department of Food and Nutrition, Sookmyung Women's University, Seoul 04310, Korea
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Artificial Intelligence to Get Insights of Multi-Drug Resistance Risk Factors during the First 48 Hours from ICU Admission. Antibiotics (Basel) 2021; 10:antibiotics10030239. [PMID: 33673564 PMCID: PMC7997208 DOI: 10.3390/antibiotics10030239] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/13/2021] [Accepted: 02/23/2021] [Indexed: 11/17/2022] Open
Abstract
Multi-drug resistance (MDR) is one of the most current and greatest threats to the global health system nowadays. This situation is especially relevant in Intensive Care Units (ICUs), where the critical health status of these patients makes them more vulnerable. Since MDR confirmation by the microbiology laboratory usually takes 48 h, we propose several artificial intelligence approaches to get insights of MDR risk factors during the first 48 h from the ICU admission. We considered clinical and demographic features, mechanical ventilation and the antibiotics taken by the patients during this time interval. Three feature selection strategies were applied to identify statistically significant differences between MDR and non-MDR patient episodes, ending up in 24 selected features. Among them, SAPS III and Apache II scores, the age and the department of origin were identified. Considering these features, we analyzed the potential of machine learning methods for predicting whether a patient will develop a MDR germ during the first 48 h from the ICU admission. Though the results presented here are just a first incursion into this problem, artificial intelligence approaches have a great impact in this scenario, especially when enriching the set of features from the electronic health records.
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Xue MY, Xie YY, Zhong YF, Liu JX, Guan LL, Sun HZ. Ruminal resistome of dairy cattle is individualized and the resistotypes are associated with milking traits. Anim Microbiome 2021; 3:18. [PMID: 33568223 PMCID: PMC7877042 DOI: 10.1186/s42523-021-00081-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 01/27/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Antimicrobial resistance is one of the most urgent threat to global public health, as it can lead to high morbidity, mortality, and medical costs for humans and livestock animals. In ruminants, the rumen microbiome carries a large number of antimicrobial resistance genes (ARGs), which could disseminate to the environment through saliva, or through the flow of rumen microbial biomass to the hindgut and released through feces. The occurrence and distribution of ARGs in rumen microbes has been reported, revealing the effects of external stimuli (e.g., antimicrobial administrations and diet ingredients) on the antimicrobial resistance in the rumen. However, the host effect on the ruminal resistome and their interactions remain largely unknown. Here, we investigated the ruminal resistome and its relationship with host feed intake and milk protein yield using metagenomic sequencing. RESULTS The ruminal resistome conferred resistance to 26 classes of antimicrobials, with genes encoding resistance to tetracycline being the most predominant. The ARG-containing contigs were assigned to bacterial taxonomy, and the majority of highly abundant bacterial genera were resistant to at least one antimicrobial, while the abundances of ARG-containing bacterial genera showed distinct variations. Although the ruminal resistome is not co-varied with host feed intake, it could be potentially linked to milk protein yield in dairy cows. Results showed that host feed intake did not affect the alpha or beta diversity of the ruminal resistome or the abundances of ARGs, while the Shannon index (R2 = 0.63, P < 0.01) and richness (R2 = 0.67, P < 0.01) of the ruminal resistome were highly correlated with milk protein yield. A total of 128 significantly different ARGs (FDR < 0.05) were identified in the high- and low-milk protein yield dairy cows. We found four ruminal resistotypes that are driven by specific ARGs and associated with milk protein yield. Particularly, cows with low milk protein yield are classified into the same ruminal resistotype and featured by high-abundance ARGs, including mfd and sav1866. CONCLUSIONS The current study uncovered the prevalence of ARGs in the rumen of a cohort of lactating dairy cows. The ruminal resistome is not co-varied with host feed intake, while it could be potentially linked to milk protein yield in dairy cows. Our results provide fundamental knowledge on the prevalence, mechanisms and impact factors of antimicrobial resistance in dairy cattle and are important for both the dairy industry and other food animal antimicrobial resistance control strategies.
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Affiliation(s)
- Ming-Yuan Xue
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yun-Yi Xie
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yi-Fan Zhong
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jian-Xin Liu
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Hui-Zeng Sun
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
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Sagmeister KJ, Schinagl CW, Kapelari S, Vrabl P. Students' Experiences of Working With a Socio-Scientific Issues-Based Curriculum Unit Using Role-Playing to Negotiate Antibiotic Resistance. Front Microbiol 2021; 11:577501. [PMID: 33552005 PMCID: PMC7855855 DOI: 10.3389/fmicb.2020.577501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/28/2020] [Indexed: 12/24/2022] Open
Abstract
The emergence and widespread of antibiotic-resistant pathogenic microorganisms are of great individual and societal relevance. Due to the complex and multilayered nature of the topic, antibiotic resistance (ABR) is the object of concern for several scientific fields, such as microbiology or medicine, and encompasses a broad range of political, economic, and social aspects. Thus, the issue related to antibiotic-resistant bacterial diseases offers an excellent platform for designing and implementing the teaching and learning of socio-scientific issues (SSI). We created a SSI-based curriculum unit for use in secondary science classrooms by developing a collaborative partnership between education researchers and microbiologists. This classroom environment allows students to explore and negotiate ABR as a societal and scientific phenomenon. For this purpose, we leveraged role-playing within the SSI-based unit as a productive context for engaging students in learning opportunities that provide multiple perspectives on ABR and the complex interplay of its accelerators. This case-based paper describes Austrian school students' experiences from their participation in a SSI-embedded role-playing classroom environment and subsequent activities that included a mini congress with a poster presentation and a panel discussion. An open-ended questionnaire-based assessment tool was used to examine the situational characteristics of the students' work. To assess students' contributions, we applied a qualitative content analysis design and identified cognitive and affective outcomes. The students' learning experiences demonstrate that they considered the content - the social complexities of antibiotic-resistant bacteria and associated diseases - exciting and very topical. The students perceived that learning about ABR is relevant for their future and involves both individual and societal responsibility for action. Although the curriculum unit and its assignments were described as labor-intensive, it became apparent that the role-playing setting has the potential to inform students about multiple stakeholder positions concerning ABR. Concerning the promotion of science practices, almost all students claimed that they learned to organize, analyze, evaluate, and present relevant information. Moreover, the students affirmed that they learned to argue from the perspective of their assigned roles. However, the students did not clarify whether they learned more through this SSI-based classroom instruction than through conventional science teaching approaches.
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Affiliation(s)
| | | | - Suzanne Kapelari
- Department of Subject-Specific Education, University of Innsbruck, Innsbruck, Austria
| | - Pamela Vrabl
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
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Mohapatra SS, Dwibedy SK, Padhy I. Polymyxins, the last-resort antibiotics: Mode of action, resistance emergence, and potential solutions. J Biosci 2021; 46:85. [PMID: 34475315 PMCID: PMC8387214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/03/2021] [Indexed: 04/04/2024]
Abstract
Infections caused by multi-drug resistant (MDR) bacterial pathogens are a leading cause of mortality and morbidity across the world. Indiscriminate use of broad-spectrum antibiotics has seriously affected this situation. With the diminishing discovery of novel antibiotics, new treatment methods are urgently required to combat MDR pathogens. Polymyxins, the cationic lipopeptide antibiotics, discovered more than half a century ago, are considered to be the last-line of antibiotics available at the moment. This antibiotic shows a great bactericidal effect against Gram-negative bacteria. Polymyxins primarily target the bacterial membrane and disrupt them, causing lethality. Because of their membrane interacting mode of action, polymyxins cause nephrotoxicity and neurotoxicity in humans, limiting their usability. However, recent modifications in their chemical structure have been able to reduce the toxic effects. The development of better dosing regimens has also helped in getting better clinical outcomes in the infections caused by MDR pathogens. Since the mid1990s the use of polymyxins has increased manifold in clinical settings, resulting in the emergence of polymyxin-resistant strains. The risk posed by the polymyxin-resistant nosocomial pathogens such as the Enterobacteriaceae group, Pseudomonas aeruginosa, and Acinetobacter baumannii, etc. is very serious considering these pathogens are resistant to almost all available antibacterial drugs. In this review article, the mode of action of the polymyxins and the genetic regulatory mechanism responsible for the emergence of resistance are discussed. Specifically, this review aims to update our current understanding in the field and suggest possible solutions that can be pursued for future antibiotic development. As polymyxins primarily target the bacterial membranes, resistance to polymyxins arises primarily by the modification of the lipopolysaccharides (LPS) in the outer membrane (OM). The LPS modification pathways are largely regulated by the bacterial two-component signal transduction (TCS) systems. Therefore, targeting or modulating the TCS signalling mechanisms can be pursued as an alternative to treat the infections caused by polymyxin-resistant MDR pathogens. In this review article, this aspect is also highlighted.
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Affiliation(s)
- Saswat S Mohapatra
- Molecular Microbiology Lab, Department of Bioscience and Bioinformatics, Khallikote University, Konisi, Berhampur, 761 008 Odisha India
| | - Sambit K Dwibedy
- Molecular Microbiology Lab, Department of Bioscience and Bioinformatics, Khallikote University, Konisi, Berhampur, 761 008 Odisha India
| | - Indira Padhy
- Molecular Microbiology Lab, Department of Bioscience and Bioinformatics, Khallikote University, Konisi, Berhampur, 761 008 Odisha India
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Fostier CR, Monlezun L, Ousalem F, Singh S, Hunt JF, Boël G. ABC-F translation factors: from antibiotic resistance to immune response. FEBS Lett 2020; 595:675-706. [PMID: 33135152 DOI: 10.1002/1873-3468.13984] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022]
Abstract
Energy-dependent translational throttle A (EttA) from Escherichia coli is a paradigmatic ABC-F protein that controls the first step in polypeptide elongation on the ribosome according to the cellular energy status. Biochemical and structural studies have established that ABC-F proteins generally function as translation factors that modulate the conformation of the peptidyl transferase center upon binding to the ribosomal tRNA exit site. These factors, present in both prokaryotes and eukaryotes but not in archaea, use related molecular mechanisms to modulate protein synthesis for heterogenous purposes, ranging from antibiotic resistance and rescue of stalled ribosomes to modulation of the mammalian immune response. Here, we review the canonical studies characterizing the phylogeny, regulation, ribosome interactions, and mechanisms of action of the bacterial ABC-F proteins, and discuss the implications of these studies for the molecular function of eukaryotic ABC-F proteins, including the three human family members.
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Affiliation(s)
- Corentin R Fostier
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Laura Monlezun
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Farès Ousalem
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Shikha Singh
- Department of Biological Sciences, 702A Sherman Fairchild Center, Columbia University, New York, NY, USA
| | - John F Hunt
- Department of Biological Sciences, 702A Sherman Fairchild Center, Columbia University, New York, NY, USA
| | - Grégory Boël
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
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Amino Acid k-mer Feature Extraction for Quantitative Antimicrobial Resistance (AMR) Prediction by Machine Learning and Model Interpretation for Biological Insights. BIOLOGY 2020; 9:biology9110365. [PMID: 33126516 PMCID: PMC7694136 DOI: 10.3390/biology9110365] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 12/31/2022]
Abstract
Machine learning algorithms can learn mechanisms of antimicrobial resistance from the data of DNA sequence without any a priori information. Interpreting a trained machine learning algorithm can be exploited for validating the model and obtaining new information about resistance mechanisms. Different feature extraction methods, such as SNP calling and counting nucleotide k-mers have been proposed for presenting DNA sequences to the model. However, there are trade-offs between interpretability, computational complexity and accuracy for different feature extraction methods. In this study, we have proposed a new feature extraction method, counting amino acid k-mers or oligopeptides, which provides easier model interpretation compared to counting nucleotide k-mers and reaches the same or even better accuracy in comparison with different methods. Additionally, we have trained machine learning algorithms using different feature extraction methods and compared the results in terms of accuracy, model interpretability and computational complexity. We have built a new feature selection pipeline for extraction of important features so that new AMR determinants can be discovered by analyzing these features. This pipeline allows the construction of models that only use a small number of features and can predict resistance accurately.
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Carvalho GG, Calarga AP, Teodoro JR, Queiroz MM, Astudillo-Trujillo CA, Levy CE, Brocchi M, Kabuki DY. Isolation, comparison of identification methods and antibiotic resistance of Cronobacter spp. in infant foods. Food Res Int 2020; 137:109643. [PMID: 33233222 DOI: 10.1016/j.foodres.2020.109643] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/25/2020] [Accepted: 08/21/2020] [Indexed: 01/10/2023]
Abstract
Cronobacter spp. are opportunistic pathogens that cause serious infections, especially in infants, elderly, and immunocompromised people. Dehydrated infant foods are the main vehicle associated with infections caused by these bacteria. Thus, this study aims to investigate the occurrence of Cronobacter spp. in 152 commercial samples of dehydrated infant formulas (77 samples) and dehydrated infant cereals (75 samples), as well as characterize the isolates. Polymerase Chain Reaction (PCR) and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF/MS) methods for isolate identification were used, and their results compared. Furthermore, the susceptibility to 11 antibiotics was tested, and DNA sequencing of one isolate with multi-drug resistance was analyzed. No contamination in the infant formula samples was found, whereas 17.33% (13/75) of the infant cereal samples presented contamination with Cronobacter sakazakii. The identification results by PCR and MALDI-TOF/MS were divergent for some isolates. The antimicrobial resistance results showed a high incidence of resistance to cefazolin (94.4%) besides resistance to amoxicillin (9.45%), cefpodoxime (5.55%), streptomycin (1.35%), and trimethoprim/sulfamethoxazole (1.35%). Whole genome sequencing of one multi-drug resistant isolate showed six genes associated with antimicrobial resistance and an 82% possibility of being a human pathogen based on the presence of virulence factors. The presence of Cronobacter spp. in infant foods represents a risk for the infant's health. Moreover, the presence of a pathogenic multi-drug resistant isolate in infant's food reinforces the necessity of improving food safety policies to protect young children.
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Affiliation(s)
- Gabriela Guimarães Carvalho
- Department of Food Science, School of Food Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil.
| | - Aline Parolin Calarga
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Josie Roberta Teodoro
- Department of Food Science, School of Food Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Murilo Mariz Queiroz
- Department of Food Science, School of Food Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Carlos Emilio Levy
- Department of Clinical Pathology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Marcelo Brocchi
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Dirce Yorika Kabuki
- Department of Food Science, School of Food Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil.
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Urmi UL, Nahar S, Rana M, Sultana F, Jahan N, Hossain B, Alam MS, Mosaddek ASM, McKimm J, Rahman NAA, Islam S, Haque M. Genotypic to Phenotypic Resistance Discrepancies Identified Involving β-Lactamase Genes, blaKPC, blaIMP, blaNDM-1, and blaVIM in Uropathogenic Klebsiella pneumoniae. Infect Drug Resist 2020; 13:2863-2875. [PMID: 32903880 PMCID: PMC7445497 DOI: 10.2147/idr.s262493] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/16/2020] [Indexed: 12/13/2022] Open
Abstract
Introduction Klebsiella pneumoniae carbapenemase (KPC) belongs to the Group-A β-lactamases that incorporate serine at their active site and hydrolyze various penicillins, cephalosporins, and carbapenems. Metallo-beta-lactamases (MBLs) are group-B enzymes that contain one or two essential zinc ions in the active sites and hydrolyze almost all clinically available β-lactam antibiotics. Klebsiella pneumoniae remains the pathogen with the most antimicrobial resistance to KPC and MBLs. Methods This research investigated the blaKPC, and MBL genes, namely, blaIMP, blaVIM, and blaNDM-1 and their phenotypic resistance to K. pneumoniae isolated from urinary tract infections (UTI) in Bangladesh. Isolated UTI K. pneumoniae were identified by API-20E and 16s rDNA gene analysis. Their phenotypic antimicrobial resistance was examined by the Kirby-Bauer disc diffusion method, followed by minimal inhibitory concentration (MIC) determination. blaKPC, blaIMP, blaNDM-1, and blaVIM genes were evaluated by polymerase chain reactions (PCR) and confirmed by sequencing. Results Fifty-eight K. pneumoniae were identified from 142 acute UTI cases. Their phenotypic resistance to amoxycillin-clavulanic acid, cephalexin, cefuroxime, ceftriaxone, and imipenem were 98.3%, 100%, 96.5%, 91.4%, 75.1%, respectively. Over half (31/58) of the isolates contained either blaKPC or one of the MBL genes. Individual prevalence of blaKPC, blaIMP, blaNDM-1, and blaVIM were 15.5% (9), 10.3% (6), 22.4% (13), and 19% (11), respectively. Of these, eight isolates (25.8%, 8/31) were found to have two genes in four different combinations. The co-existence of the ESBL genes generated more resistance than each one individually. Some isolates appeared phenotypically susceptible to imipenem in the presence of blaKPC, blaIMP, blaVIM, and blaNDM-1 genes, singly or in combination. Conclusion The discrepancy of genotype and phenotype resistance has significant consequences for clinical bacteriology, precision in diagnosis, the prudent selection of antimicrobials, and rational prescribing. Heterogeneous phenotypes of antimicrobial susceptibility testing should be taken seriously to avoid inappropriate diagnostic and therapeutic decisions.
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Affiliation(s)
- Umme Laila Urmi
- Department of Microbiology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Shamsun Nahar
- Department of Microbiology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Masud Rana
- Department of Microbiology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Fahmida Sultana
- Department of Microbiology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Nusrat Jahan
- Department of Microbiology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Billal Hossain
- Department of Microbiology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Mohammed Shah Alam
- Department of Microbiology, Gono Bishwabidyalay, Savar, Dhaka 1342, Bangladesh
| | - Abu Syed Md Mosaddek
- Department of Pharmacology, Uttara Adhunik Medical College, Uttara, Dhaka, Bangladesh
| | - Judy McKimm
- Medical Education, Strategic Educational Development, Leadership for the Health Professions, Swansea University Medical School, Swansea University, Swansea, Wales SA2 8PP, UK
| | - Nor Azlina A Rahman
- Department of Physical Rehabilitation Sciences, Kulliyyah of Allied Health Sciences, International Islamic University Malaysia, Kuantan 25200, Malaysia
| | - Salequl Islam
- Department of Microbiology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Mainul Haque
- Faculty of Medicine and Defence Health, Universiti Pertahanan Nasional Malaysia (National Defence University of Malaysia), Kuala Lumpur 57000, Malaysia
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Riccardi N, Monticelli J, Antonello RM, Di Lallo G, Frezza D, Luzzati R, Di Bella S. Therapeutic Options for Infections due to vanB Genotype Vancomycin-Resistant Enterococci. Microb Drug Resist 2020; 27:536-545. [PMID: 32799629 DOI: 10.1089/mdr.2020.0171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Enterococci are ubiquitous, facultative, anaerobic Gram-positive bacteria that mainly reside, as part of the normal microbiota, in the gastrointestinal tracts of several animal species, including humans. These bacteria have the capability to turn from a normal gut commensal organism to an invasive pathogen in patients debilitated by prolonged hospitalization, concurrent illnesses, and/or exposed to broad-spectrum antibiotics. The majority of vancomycin-resistant enterococcus (VRE) infections are linked to the vanA genotype; however, outbreaks caused by vanB-type VREs have been increasingly reported, representing a new challenge for effective antimicrobial treatment. Teicoplanin, daptomycin, fosfomycin, and linezolid are useful antimicrobials for infections due to vanB enterococci. In addition, new drugs have been developed (e.g., dalbavancin, telavancin, and tedizolid), new molecules will soon be available (e.g., eravacycline, omadacycline, and oritavancin), and new treatment strategies are progressively being used in clinical practice (e.g., combination therapies and bacteriophages). The aim of this article is to discuss the pathogenesis of infections due to enterococci harboring the vanB operon (vanBVRE) and their therapeutic, state-of-the-art, and future treatment options and provide a comprehensive and easy to use review for clinical purposes.
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Affiliation(s)
- Niccolò Riccardi
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy
| | - Jacopo Monticelli
- Hospital Direction, AULSS6 Euganea Ospedali Riuniti Padova Sud, Monselice, Italy
| | | | - Gustavo Di Lallo
- Department of Biology, University of Rome "Tor Vergata," Rome, Italy
| | - Domenico Frezza
- Department of Biology, University of Rome "Tor Vergata," Rome, Italy
| | - Roberto Luzzati
- Infectious Diseases Department, Azienda Sanitaria Universitaria Integrata di Trieste, Trieste, Italy
| | - Stefano Di Bella
- Infectious Diseases Department, Azienda Sanitaria Universitaria Integrata di Trieste, Trieste, Italy
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Guérin F, Lachaal S, Auzou M, Le Brun C, Barraud O, Decousser JW, Lienhard R, Baraduc R, Dubreuil L, Cattoir V. Molecular basis of macrolide-lincosamide-streptogramin (MLS) resistance in Finegoldia magna clinical isolates. Anaerobe 2020; 64:102220. [PMID: 32531434 DOI: 10.1016/j.anaerobe.2020.102220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 12/21/2022]
Affiliation(s)
- François Guérin
- CHU de Caen, Service de Microbiologie, Caen, F-14033, France; Université de Caen Normandie, EA4655 (équipe "Antibio-résistance"), Caen, F-14032, France
| | - Sabrine Lachaal
- CHU de Caen, Service de Microbiologie, Caen, F-14033, France
| | - Michel Auzou
- CHU de Caen, Service de Microbiologie, Caen, F-14033, France; Université de Caen Normandie, EA4655 (équipe "Antibio-résistance"), Caen, F-14032, France
| | - Cécile Le Brun
- CHRU de Tours, Service de Bactériologie-Virologie, Hôpital Bretonneau, F-37044, Tours, France
| | - Olivier Barraud
- CHU Limoges, Laboratoire de Bactériologie-Virologie-Hygiène, Limoges, F-87042, France
| | - Jean-Winoc Decousser
- CHU Henri Mondor, Assistance Publique-Hôpitaux de Paris, Laboratoire de Microbiologie, Créteil, F-94010, France
| | - Reto Lienhard
- ADMED Microbiologie, La-Chaux-de-Fonds, CH-2303, Switzerland
| | - Régine Baraduc
- CHU de Clermont-Ferrand, Laboratoire de Microbiologie, Clermont-Ferrand, F-63003, France
| | - Luc Dubreuil
- CHRU de Lille, Laboratoire de Bactériologie-Hygiène et de Virologie, Lille, F-59 037, France
| | - Vincent Cattoir
- CHU Rennes, Service de Bactériologie et Hygiène Hospitalière, Rennes, F-35033, France; CNR de la Résistance aux Antibiotiques, Rennes, F-35033, France.
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63
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Acquired Genetic Elements that Contribute to Antimicrobial Resistance in Frequent Gram-Negative Causative Agents of Healthcare-Associated Infections. Am J Med Sci 2020; 360:631-640. [PMID: 32747008 DOI: 10.1016/j.amjms.2020.06.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/26/2020] [Accepted: 06/29/2020] [Indexed: 12/12/2022]
Abstract
Antimicrobial resistance (AMR) is a worldwide public health problem that reduces therapeutic options and increases the risk of death. The causative agents of healthcare-associated infections (HAIs) are drug-resistant microorganisms of the nosocomial environment, which have developed different mechanisms of AMR. The hospital-associated microbiota has been proposed to be a reservoir of genes associated with AMR and an environment where the transfer of genetic material among organisms may occur. The ESKAPE group (Enterococcus faecalis and Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter aerogenes and Escherichia coli) is a frequent causative agents of HAIs. In this review, we address the issue of acquired genetic elements that contribute to AMR in the most frequent Gram-negative of ESKAPE, with a focus on last resort antimicrobial agents and the role of transference of genetic elements for the development of AMR.
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64
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Yushchuk O, Binda E, Marinelli F. Glycopeptide Antibiotic Resistance Genes: Distribution and Function in the Producer Actinomycetes. Front Microbiol 2020; 11:1173. [PMID: 32655512 PMCID: PMC7325946 DOI: 10.3389/fmicb.2020.01173] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/07/2020] [Indexed: 12/22/2022] Open
Abstract
Glycopeptide antibiotics (GPAs) are considered drugs of "last resort" for the treatment of life-threatening infections caused by relevant Gram-positive pathogens (enterococci, staphylococci, and clostridia). Driven by the issue of the never-stopping evolution of bacterial antibiotic resistance, research on GPA biosynthesis and resistance is developing fast in modern "post-genomic" era. It is today widely accepted that resistance mechanisms emerging in pathogens have been acquired from the soil-dwelling antibiotic-producing actinomycetes, which use them to avoid suicide during production, rather than being orchestrated de novo by pathogen bacteria upon continued treatment. Actually, more and more genomes of GPA producers are being unraveled, carrying a broad collection of differently arranged GPA resistance (named van) genes. In the producer actinomycetes, van genes are generally associated with the antibiotic biosynthetic gene clusters (BGCs) deputed to GPA biosynthesis, being probably transferred/arranged together, favoring a possible co-regulation between antibiotic production and self-resistance. GPA BGC-associated van genes have been also found mining public databases of bacterial genomic and metagenomic sequences. Interestingly, some BGCs for antibiotics, seemingly unrelated to GPAs (e.g., feglymycin), carry van gene homologues. Herein, we would like to cover the recent advances on the distribution of GPA resistance genes in genomic and metagenomics datasets related to GPA potential/proved producer microorganisms. A thorough understanding of GPA resistance in the producing microorganisms may prove useful in the future surveillance of emerging mechanisms of resistance to this clinically relevant antibiotic class.
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Affiliation(s)
- Oleksandr Yushchuk
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Elisa Binda
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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65
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De Oliveira DMP, Forde BM, Kidd TJ, Harris PNA, Schembri MA, Beatson SA, Paterson DL, Walker MJ. Antimicrobial Resistance in ESKAPE Pathogens. Clin Microbiol Rev 2020; 23:788-99. [PMID: 32404435 DOI: 10.1111/imb.12124] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
Antimicrobial-resistant ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new antimicrobial therapies, has demanded the need for better patient care, and has facilitated heightened governance over stewardship practices.
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Affiliation(s)
- David M P De Oliveira
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Brian M Forde
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Timothy J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Patrick N A Harris
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
- UQ Centre for Clinical Research, The University of Queensland, QLD, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - David L Paterson
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
- UQ Centre for Clinical Research, The University of Queensland, QLD, Australia
| | - Mark J Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
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66
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De Oliveira DMP, Forde BM, Kidd TJ, Harris PNA, Schembri MA, Beatson SA, Paterson DL, Walker MJ. Antimicrobial Resistance in ESKAPE Pathogens. Clin Microbiol Rev 2020; 33:e00181-19. [PMID: 32404435 PMCID: PMC7227449 DOI: 10.1128/cmr.00181-19] [Citation(s) in RCA: 877] [Impact Index Per Article: 219.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Antimicrobial-resistant ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new antimicrobial therapies, has demanded the need for better patient care, and has facilitated heightened governance over stewardship practices.
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Affiliation(s)
- David M P De Oliveira
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Brian M Forde
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Timothy J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Patrick N A Harris
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
- UQ Centre for Clinical Research, The University of Queensland, QLD, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - David L Paterson
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
- UQ Centre for Clinical Research, The University of Queensland, QLD, Australia
| | - Mark J Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
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67
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Merrikh H, Kohli RM. Targeting evolution to inhibit antibiotic resistance. FEBS J 2020; 287:4341-4353. [PMID: 32434280 DOI: 10.1111/febs.15370] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 03/31/2020] [Accepted: 05/15/2020] [Indexed: 12/21/2022]
Abstract
Drug-resistant bacterial infections have led to a global health crisis. Although much effort is placed on the development of new antibiotics or variants that are less subject to existing resistance mechanisms, history shows that this strategy by itself is unlikely to solve the problem of drug resistance. Here, we discuss inhibiting evolution as a strategy that, in combination with antibiotics, may resolve the problem. Although mutagenesis is the main driver of drug resistance development, attacking the drivers of genetic diversification in pathogens has not been well explored. Bacteria possess active mechanisms that increase the rate of mutagenesis, especially at times of stress, such as during replication within eukaryotic host cells, or exposure to antibiotics. We highlight how the existence of these promutagenic proteins (evolvability factors) presents an opportunity that can be capitalized upon for the effective inhibition of drug resistance development. To help move this idea from concept to execution, we first describe a set of criteria that an 'optimal' evolvability factor would likely have to meet to be a viable therapeutic target. We then discuss the intricacies of some of the known mutagenic mechanisms and evaluate their potential as drug targets to inhibit evolution. In principle, and as suggested by recent studies, we argue that the inhibition of these and other evolvability factors should reduce resistance development. Finally, we discuss the challenges of transitioning anti-evolution drugs from the laboratory to the clinic.
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Affiliation(s)
- Houra Merrikh
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rahul M Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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68
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Meng L, Liu H, Lan T, Dong L, Hu H, Zhao S, Zhang Y, Zheng N, Wang J. Antibiotic Resistance Patterns of Pseudomonas spp. Isolated From Raw Milk Revealed by Whole Genome Sequencing. Front Microbiol 2020; 11:1005. [PMID: 32655503 PMCID: PMC7326020 DOI: 10.3389/fmicb.2020.01005] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/24/2020] [Indexed: 12/11/2022] Open
Abstract
Psychrotrophic bacteria in raw milk are most well known for their spoilage potential and the economic losses they cause to the dairy industry. Food-related psychrotrophic bacteria are increasingly reported to have antibiotic resistance features. The aim of this study was to evaluate the resistance patterns of Pseudomonas spp. isolated from bulk-tank milk. In total, we investigated the antibiotic susceptibility profiles of 86 Pseudomonas spp. isolates from raw milk. All strains were tested against 15 antimicrobial agents. Pseudomonas isolates were most highly resistant to imipenem (95.3%), followed by trimethoprim-sulfamethoxazole (69.8%), aztreonam (60.5%), chloramphenicol (45.3%), and meropenem (27.9%). Their multiple antibiotic resistance (MAR) index values ranged from 0.0 to 0.8. Whole-genome sequencing revealed the presence of intrinsic resistance determinants, such as BcI, ampC-09, blaCTX-M, oprD, sul1, dfrE, catA1, catB3, catI, floR, and cmlV. Moreover, resistance-nodulation-cell division (RND) and ATP-binding cassette (ABC) antibiotic efflux pumps were also found. This study provides further knowledge of the antibiotic resistance patterns of Pseudomonas spp. in milk, which may advance our understanding of resistance in Pseudomonas and suggests that antibiotic resistance of Pseudomonas spp. in raw milk should be a concern.
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Affiliation(s)
- Lu Meng
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huimin Liu
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tu Lan
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Dong
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haiyan Hu
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Shengguo Zhao
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yangdong Zhang
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nan Zheng
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiaqi Wang
- Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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69
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Hayes K, O'Halloran F, Cotter L. A review of antibiotic resistance in Group B Streptococcus: the story so far. Crit Rev Microbiol 2020; 46:253-269. [PMID: 32363979 DOI: 10.1080/1040841x.2020.1758626] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Group B Streptococcus (GBS) is the leading cause of neonatal disease worldwide, and invasive disease in adults is becoming more prevalent. Currently, some countries adopt an intrapartum antibiotic prophylaxis regime to help prevent the transmission of GBS from mother to neonate during delivery. This precaution has reduced the incidence of GBS-associated early-onset disease; however, rates of late-onset disease and stillbirths associated with GBS infections remain unchanged. GBS is still recognized as being universally susceptible to beta-lactam antibiotics; however, there have been reports of reduced susceptibility to beta-lactams, including penicillin, in some countries. Resistance to second-line antibiotics, such as erythromycin and clindamycin, remains high amongst GBS, with several countries noting increased resistance rates in recent years. Moreover, resistance to other antibiotic classes, such as fluoroquinolones and aminoglycosides, also continues to rise. In instances where patients are allergic to penicillin and second-line antibiotics are ineffective, vancomycin is administered. While vancomycin, a last resort antibiotic, still remains largely effective, there have been two documented cases of vancomycin resistance in GBS. This review provides a comprehensive analysis of the prevalence of antibiotic resistance in GBS and outlines the specific resistance mechanisms identified in GBS isolates to date.
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70
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Zhang L, Forst CV, Gordon A, Gussin G, Geber AB, Fernandez PJ, Ding T, Lashua L, Wang M, Balmaseda A, Bonneau R, Zhang B, Ghedin E. Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection. MICROBIOME 2020; 8:39. [PMID: 32178738 PMCID: PMC7076942 DOI: 10.1186/s40168-020-00803-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 02/10/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND The abundance and diversity of antibiotic resistance genes (ARGs) in the human respiratory microbiome remain poorly characterized. In the context of influenza virus infection, interactions between the virus, the host, and resident bacteria with pathogenic potential are known to complicate and worsen disease, resulting in coinfection and increased morbidity and mortality of infected individuals. When pathogenic bacteria acquire antibiotic resistance, they are more difficult to treat and of global health concern. Characterization of ARG expression in the upper respiratory tract could help better understand the role antibiotic resistance plays in the pathogenesis of influenza-associated bacterial secondary infection. RESULTS Thirty-seven individuals participating in the Household Influenza Transmission Study (HITS) in Managua, Nicaragua, were selected for this study. We performed metatranscriptomics and 16S rRNA gene sequencing analyses on nasal and throat swab samples, and host transcriptome profiling on blood samples. Individuals clustered into two groups based on their microbial gene expression profiles, with several microbial pathways enriched with genes differentially expressed between groups. We also analyzed antibiotic resistance gene expression and determined that approximately 25% of the sequence reads that corresponded to antibiotic resistance genes mapped to Streptococcus pneumoniae and Staphylococcus aureus. Following construction of an integrated network of ARG expression with host gene co-expression, we identified several host key regulators involved in the host response to influenza virus and bacterial infections, and host gene pathways associated with specific antibiotic resistance genes. CONCLUSIONS This study indicates the host response to influenza infection could indirectly affect antibiotic resistance gene expression in the respiratory tract by impacting the microbial community structure and overall microbial gene expression. Interactions between the host systemic responses to influenza infection and antibiotic resistance gene expression highlight the importance of viral-bacterial co-infection in acute respiratory infections like influenza. Video abstract.
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Affiliation(s)
- Lingdi Zhang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA
| | - Christian V Forst
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aubree Gordon
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Gabrielle Gussin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA
| | - Adam B Geber
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA
| | - Porfirio J Fernandez
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA
| | - Tao Ding
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA
| | - Lauren Lashua
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Angel Balmaseda
- National Virology Laboratory, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Richard Bonneau
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Elodie Ghedin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA.
- Department of Epidemiology, School of Global Public Health, New York University, New York, NY, 10003, USA.
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71
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van den Honert MS, Gouws PA, Hoffman LC. A Preliminary Study: Antibiotic Resistance Patterns of Escherichia coli and Enterococcus Species from Wildlife Species Subjected to Supplementary Feeding on Various South African Farms. Animals (Basel) 2020; 10:ani10030396. [PMID: 32121124 PMCID: PMC7142571 DOI: 10.3390/ani10030396] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Supplementary feeding of wildlife allows more opportunity for disease and antibiotic resistant genes to be transferred directly between species due to increased herd density, more frequent direct contact at feeding and water points and increased human contact. The feed itself can also be a direct source of antibiotic compounds and of antibiotic resistant bacteria. This study aimed to determine whether the practice of wildlife supplementary feeding could have an influence on the antibiotic resistance of the bacteria harboured by the supplementary fed wildlife, and thus play a potential role in the dissemination of antibiotic resistance throughout nature. Overall, the E. coli and Enterococcus isolates from the supplementary fed wildlife were found to be more frequently resistant to the selection of antibiotics than from those which were not supplementary fed. Game farmers should be knowledgeable of the ingredients that are used in the game feed that is used to feed both their livestock and wildlife, as certain feed ingredients, such as antibiotics or bone meal, can have a detrimental effect on health and safety. Game farmers should also be aware that farm history can have an impact on the animals which graze on the pastures with regards to antibiotic resistance transfer. Abstract Studies have shown that antibiotic resistance among wild animals is becoming a public health concern, owing to increased contact and co-habitation with domestic animals that, in turn, results in increased human contact, indirectly and directly. This type of farming practice intensifies the likelihood of antibiotic resistant traits in microorganisms transferring between ecosystems which are linked via various transfer vectors, such as rivers and birds. This study aimed to determine whether the practice of wildlife supplementary feeding could have an influence on the antibiotic resistance of the bacteria harboured by the supplementary fed wildlife, and thus play a potential role in the dissemination of antibiotic resistance throughout nature. Escherichia coli and Enterococcus were isolated from the faeces of various wildlife species from seven different farms across South Africa. The Kirby-Bauer disk diffusion method was used according to the Clinical and Laboratory Standards Institute 2018 guidelines. The E. coli (F: 57%; N = 75% susceptible) and Enterococcus (F: 67%; N = 78% susceptible) isolates from the supplementary fed (F) wildlife were in general, found to be more frequently resistant to the selection of antibiotics than from those which were not supplementary fed (N), particularly towards tetracycline (E. coli F: 56%; N: 71%/Enterococcus F: 53%; N: 89% susceptible), ampicillin (F: 82%; N = 95% susceptible) and sulphafurazole (F: 68%; N = 98% susceptible). Interestingly, high resistance towards streptomycin was observed in the bacteria from both the supplementary fed (7% susceptible) and non-supplementary fed (6% susceptible) wildlife isolates. No resistance was found towards chloramphenicol and ceftazidime.
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Affiliation(s)
- Michaela Sannettha van den Honert
- Centre for Food Safety, Department of Food Science, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
- Department of Animal Sciences, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa;
| | - Pieter Andries Gouws
- Centre for Food Safety, Department of Food Science, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
- Correspondence:
| | - Louwrens Christiaan Hoffman
- Department of Animal Sciences, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa;
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Coopers Plains, QLD 4108, Australia
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72
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Antibiotic Resistance and Epigenetics: More to It than Meets the Eye. Antimicrob Agents Chemother 2020; 64:AAC.02225-19. [PMID: 31740560 DOI: 10.1128/aac.02225-19] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The discovery of antibiotics in the last century is considered one of the most important achievements in the history of medicine. Antibiotic usage has significantly reduced morbidity and mortality associated with bacterial infections. However, inappropriate use of antibiotics has led to emergence of antibiotic resistance at an alarming rate. Antibiotic resistance is regarded as a major health care challenge of this century. Despite extensive research, well-documented biochemical mechanisms and genetic changes fail to fully explain mechanisms underlying antibiotic resistance. Several recent reports suggest a key role for epigenetics in the development of antibiotic resistance in bacteria. The intrinsic heterogeneity as well as transient nature of epigenetic inheritance provides a plausible backdrop for high-paced emergence of drug resistance in bacteria. The methylation of adenines and cytosines can influence mutation rates in bacterial genomes, thus modulating antibiotic susceptibility. In this review, we discuss a plethora of recently discovered epigenetic mechanisms and their emerging roles in antibiotic resistance. We also highlight specific epigenetic mechanisms that merit further investigation for their role in antibiotic resistance.
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73
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Liu X, Wang C, Yan B, Lyu L, Takiff HE, Gao Q. The potassium transporter KdpA affects persister formation by regulating ATP levels in Mycobacterium marinum. Emerg Microbes Infect 2020; 9:129-139. [PMID: 31913766 PMCID: PMC6968386 DOI: 10.1080/22221751.2019.1710090] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Mycobacterial persistence mechanisms remain to be fully characterized. Screening a transposon insertion library of Mycobacterium marinum identified kdpA, whose inactivation reduced the fraction of persisters after exposure to rifampicin. kdpA encodes a transmembrane protein that is part of the Kdp-ATPase, an ATP-dependent high-affinity potassium (K+) transport system. We found that kdpA is induced under low K+ conditions and is required for pH homeostasis and growth in media with low concentrations of K+. The inactivation of the Kdp system in a kdpA insertion mutant caused hyperpolarization of the cross-membrane potential, increased proton motive force (PMF) and elevated levels of intracellular ATP. The KdpA mutant phenotype could be complemented with a functional kdpA gene or supplementation with high K+ concentrations. Taken together, our results suggest that the Kdp system is required for ATP homeostasis and persister formation. The results also confirm that ATP-mediated regulation of persister formation is a general mechanism in bacteria, and suggest that K+ transporters could play a role in the regulation of ATP levels and persistence. These findings could have implications for the development of new drugs that could either target persisters or reduce their presence.
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Affiliation(s)
- Xiaofan Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, People's Republic of China
| | - Chuan Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, People's Republic of China
| | - Bo Yan
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, People's Republic of China
| | - Liangdong Lyu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, People's Republic of China
| | - Howard E Takiff
- Integrated Mycobacterial Pathogenomics Unit, Institut Pasteur, Paris, France
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, People's Republic of China
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74
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Yuan QB, Zhai YF, Mao BY, Schwarz C, Hu N. Fates of antibiotic resistance genes in a distributed swine wastewater treatment plant. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2019; 91:1565-1575. [PMID: 31004530 DOI: 10.1002/wer.1125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/04/2019] [Accepted: 04/13/2019] [Indexed: 06/09/2023]
Abstract
This study explores the prevalence, emission, and reduction of five ARGs (sulI, tetA, mphB, qnrD, and mcr-1) and integron (intI) through a distributed swine wastewater purification facility and the effluent-receiving environment. Typical metal resistance genes (MRGs), pathogenic bacterial indicators, the bacterial community, and wastewater properties were also explored to determine their effects on the fates of ARGs. Results indicated that the purification process could hardly effectively remove ARGs' prevalence. 3.1 × 104 -7.1 × 108 copies/L were present after purification, and 4%-57% of them persisted in the subsequent creek and adjacent soil. 16S rRNA sequencing suggested that the discharge of wastewater significantly changed the bacterial community in receiving creek and soil. Molecular ecological networks analysis detected the wide co-occurrence among ARGs, MRGs, and PBGs, which could further facilitate the propagation of antibiotic resistance. ARG incidence and specific bacterial genera were closely correlated, suggesting an extensive hosting relationship. Redundancy analyses showed wastewater organics and nutrients showed positive correlation to most ARGs' abundance, but negatively correlated to their relative abundance. PRACTITIONER POINTS: Fate of five ARGs and intI was studied in a swine wastewater treatment system. The treatment process could not effectively reduce ARGs' abundance. ARGs and pathogens in wastewater were transferred to the receiving creek and soil. The network analysis found wide co-occurrence among ARGs, metal resistance genes, and pathogens. Wastewater nutrients positively correlated to ARG's abundance but negatively correlated to their relative abundance.
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Affiliation(s)
- Qing-Bin Yuan
- College of Environment Science and Engineering, Nanjing Tech University, Nanjing, China
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, USA
| | - Yi-Fan Zhai
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Bu-Yun Mao
- College of Environment Science and Engineering, Nanjing Tech University, Nanjing, China
| | - Cory Schwarz
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, USA
| | - Nan Hu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
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75
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Tan F, She P, Zhou L, Liu Y, Chen L, Luo Z, Wu Y. Bactericidal and Anti-biofilm Activity of the Retinoid Compound CD437 Against Enterococcus faecalis. Front Microbiol 2019; 10:2301. [PMID: 31649642 PMCID: PMC6794434 DOI: 10.3389/fmicb.2019.02301] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 09/20/2019] [Indexed: 01/24/2023] Open
Abstract
Enterococcus faecalis (E. faecalis), a biofilm-forming pathogen, causes nosocomial infections. In recent years, drug resistance by enterococci has become increasingly severe due to widespread antibiotic abuse. Therefore, novel antibacterial agents are urgently needed. In this study, the synthetic retinoid compound CD437 was found to have potent bactericidal effect on E. faecalis. In addition, CD437 exhibited synergistic effects when administered in combination with gentamicin and additive effects when combined with ceftriaxone sodium. CD437 also inhibited biofilm formation by E. faecalis and exerted bactericidal effect on mature biofilm. Moreover, CD437 exhibited antibacterial and anti-biofilm effects against Staphylococcus. No bactericidal action of CD437 was observed against the gram-negative bacillus, but Pseudomonas aeruginosa biofilm extracellular polymeric substances (EPS) matrix formation was reduced. Overall, these findings indicate that CD437 has the potential to be developed as a novel antibacterial drug.
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Affiliation(s)
- Fang Tan
- Department of Medicine Clinical Laboratory, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Pengfei She
- Department of Medicine Clinical Laboratory, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Linying Zhou
- Department of Medicine Clinical Laboratory, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yiqing Liu
- Department of Medicine Clinical Laboratory, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Lihua Chen
- Department of Medicine Clinical Laboratory, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Zhen Luo
- Department of Medicine Clinical Laboratory, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yong Wu
- Department of Medicine Clinical Laboratory, The Third Xiangya Hospital of Central South University, Changsha, China
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76
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Hayward JL, Huang Y, Yost CK, Hansen LT, Lake C, Tong A, Jamieson RC. Lateral flow sand filters are effective for removal of antibiotic resistance genes from domestic wastewater. WATER RESEARCH 2019; 162:482-491. [PMID: 31306951 DOI: 10.1016/j.watres.2019.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/28/2019] [Accepted: 07/03/2019] [Indexed: 06/10/2023]
Abstract
The ability of lateral flow sand filters, used as on-site wastewater treatment systems (OWTS), to remove antibiotic resistance genes (ARGs), antibiotic resistant bacteria (ARB), and other relevant genetic markers (HF183, 16S rRNA, and int1) was assessed. Municipal wastewater was settled in a septic tank prior to loading into six pilot-scale lateral flow sand filters comprised of three different sand media types, at 5 and 30% slopes. The sand filters were sampled bi-weekly for: 9 ARGs and 3 other complimentary gene markers (sul1, sul2, qnrS, tetO, ermB, blaTEM, blaCTX-M, mecA, vanA, int1, HF183, 16S rRNA), and conventional microbial and water quality indicators, from July to November in 2017, and four times in the summer of 2018. The sand filters were observed to attenuate 7 of the ARGs to mostly below 2 log gene copies per mL. Log reductions ranging from 2.9 to 5.4 log were observed for the removal of absolute abundances of ARGs from septic tank effluent in 5 of the 6 sand filters. The fine-grained filter on the 5% slope did not perform as well for ARG attenuation due to hydraulic failure. The apportionment of cell-associated versus cell-free DNA was determined for the gene markers and this indicated that the genes were primarily carried intracellularly. Average log reductions of ARB with resistance to either sulfamethoxazole, erythromycin, or tetracycline were approximately 2.3 log CFU per mL within the filters compared to the septic tank effluent. This field study provides in-depth insights into the attenuation of ARB, ARGs, and their genetic compartmentalization in variably saturated sand OWTS. Overall, this type of OWTS was found to pose little risk of antimicrobial resistance contamination spread into surrounding environments when proper hydraulic function was maintained.
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Affiliation(s)
- Jennifer L Hayward
- Centre for Water Resources Studies, Department of Civil & Resource Engineering, Dalhousie University, 1360 Barrington Street, Halifax, Nova Scotia, B3H 4R2, Canada.
| | - Yannan Huang
- Centre for Water Resources Studies, Department of Civil & Resource Engineering, Dalhousie University, 1360 Barrington Street, Halifax, Nova Scotia, B3H 4R2, Canada.
| | - Christopher K Yost
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, Saskatchewan, S4S 0A2, Canada.
| | | | - Craig Lake
- Centre for Water Resources Studies, Department of Civil & Resource Engineering, Dalhousie University, 1360 Barrington Street, Halifax, Nova Scotia, B3H 4R2, Canada.
| | - Anthony Tong
- Department of Chemistry, Acadia University, 6 University Avenue, Wolfville, Nova Scotia, B4P 2R6, Canada.
| | - Rob C Jamieson
- Centre for Water Resources Studies, Department of Civil & Resource Engineering, Dalhousie University, 1360 Barrington Street, Halifax, Nova Scotia, B3H 4R2, Canada.
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77
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Lebreton F, Valentino MD, Schaufler K, Earl AM, Cattoir V, Gilmore MS. Transferable vancomycin resistance in clade B commensal-type Enterococcus faecium. J Antimicrob Chemother 2019; 73:1479-1486. [PMID: 29462403 DOI: 10.1093/jac/dky039] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 01/18/2018] [Indexed: 12/24/2022] Open
Abstract
Objectives Vancomycin-resistant Enterococcus faecium is a leading cause of MDR hospital infection. Two genetically definable populations of E. faecium have been identified: hospital-adapted MDR isolates (clade A) and vancomycin-susceptible commensal strains (clade B). VanN-type vancomycin resistance was identified in two isolates of E. faecium recovered from blood and faeces of an immunocompromised patient. To understand the genomic context in which VanN occurred in the hospitalized patient, the risk it posed for transmission in the hospital and its origins, it was of interest to determine where these strains placed within the E. faecium population structure. Methods We obtained the genome sequence of the VanN isolates and performed comparative and functional genomics of the chromosome and plasmid content. Results We show that, in these strains, VanN occurs in a genetic background that clusters with clade B E. faecium, which is highly unusual. We characterized the chromosome and the conjugative plasmid that carries VanN resistance in these strains, pUV24. This plasmid exhibits signatures of in-host selection on the vanN operon regulatory system, which are associated with a constitutive expression of vancomycin resistance. VanN resistance in clade B strains may go undetected by current methods. Conclusions We report a case of vancomycin resistance in a commensal lineage of E. faecium responsible for an atypical bacteraemia in an immunocompromised patient. A reservoir of transferable glycopeptide resistance in the community could pose a concern for public health.
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Affiliation(s)
- François Lebreton
- Departments of Ophthalmology, Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.,Infectious Disease & Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Michael D Valentino
- Departments of Ophthalmology, Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.,Infectious Disease & Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Katharina Schaufler
- Departments of Ophthalmology, Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.,Infectious Disease & Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Ashlee M Earl
- Infectious Disease & Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Vincent Cattoir
- Université de Caen Basse-Normandie, EA4655 U2RM (équipe 'Antibio-résistance'), Caen, France.,CHU de Caen, Service de Microbiologie, Caen, France
| | - Michael S Gilmore
- Departments of Ophthalmology, Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.,Infectious Disease & Microbiome Program, The Broad Institute, Cambridge, MA, USA
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78
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Morley VJ, Woods RJ, Read AF. Bystander Selection for Antimicrobial Resistance: Implications for Patient Health. Trends Microbiol 2019; 27:864-877. [PMID: 31288975 PMCID: PMC7079199 DOI: 10.1016/j.tim.2019.06.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/29/2019] [Accepted: 06/13/2019] [Indexed: 12/15/2022]
Abstract
Antimicrobial therapy promotes resistance emergence in target infections and in off-target microbiota. Off-target resistance emergence threatens patient health when off-target populations are a source of future infections, as they are for many important drug-resistant pathogens. However, the health risks of antimicrobial exposure in off-target populations remain largely unquantified, making rational antibiotic stewardship challenging. Here, we discuss the contribution of bystander antimicrobial exposure to the resistance crisis, the implications for antimicrobial stewardship, and some novel opportunities to limit resistance evolution while treating target pathogens.
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Affiliation(s)
- Valerie J Morley
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, The Pennsylvania State University, University Park, PA, USA.
| | - Robert J Woods
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Andrew F Read
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, The Pennsylvania State University, University Park, PA, USA; Huck Institutes for the Life Sciences, The Pennsylvania State University, University Park, PA, USA
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79
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Palmer AC, Chait R, Kishony R. Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance. Mol Biol Evol 2019; 35:2669-2684. [PMID: 30169679 PMCID: PMC6231494 DOI: 10.1093/molbev/msy163] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Bacteria regulate genes to survive antibiotic stress, but regulation can be far from perfect. When regulation is not optimal, mutations that change gene expression can contribute to antibiotic resistance. It is not systematically understood to what extent natural gene regulation is or is not optimal for distinct antibiotics, and how changes in expression of specific genes quantitatively affect antibiotic resistance. Here we discover a simple quantitative relation between fitness, gene expression, and antibiotic potency, which rationalizes our observation that a multitude of genes and even innate antibiotic defense mechanisms have expression that is critically nonoptimal under antibiotic treatment. First, we developed a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression and knockout libraries, finding that resistance to a range of 31 antibiotics could result from changing expression of a large and functionally diverse set of genes, in a primarily but not exclusively drug-specific manner. Second, by synthetically controlling the expression of single-drug and multidrug resistance genes, we observed that their fitness–expression functions changed dramatically under antibiotic treatment in accordance with a log-sensitivity relation. Thus, because many genes are nonoptimally expressed under antibiotic treatment, many regulatory mutations can contribute to resistance by altering expression and by activating latent defenses.
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Affiliation(s)
- Adam C Palmer
- Department of Systems Biology, Harvard Medical School, Boston, MA.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA
| | - Remy Chait
- Department of Systems Biology, Harvard Medical School, Boston, MA.,Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Roy Kishony
- Department of Systems Biology, Harvard Medical School, Boston, MA.,Departments of Biology and Computer Science, Technion-Israel Institute of Technology, Haifa, Israel
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80
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Martínez-Agüero S, Mora-Jiménez I, Lérida-García J, Álvarez-Rodríguez J, Soguero-Ruiz C. Machine Learning Techniques to Identify Antimicrobial Resistance in the Intensive Care Unit. ENTROPY 2019; 21:e21060603. [PMID: 33267317 PMCID: PMC7515087 DOI: 10.3390/e21060603] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/04/2019] [Accepted: 06/13/2019] [Indexed: 12/21/2022]
Abstract
The presence of bacteria with resistance to specific antibiotics is one of the greatest threats to the global health system. According to the World Health Organization, antimicrobial resistance has already reached alarming levels in many parts of the world, involving a social and economic burden for the patient, for the system, and for society in general. Because of the critical health status of patients in the intensive care unit (ICU), time is critical to identify bacteria and their resistance to antibiotics. Since common antibiotics resistance tests require between 24 and 48 h after the culture is collected, we propose to apply machine learning (ML) techniques to determine whether a bacterium will be resistant to different families of antimicrobials. For this purpose, clinical and demographic features from the patient, as well as data from cultures and antibiograms are considered. From a population point of view, we also show graphically the relationship between different bacteria and families of antimicrobials by performing correspondence analysis. Results of the ML techniques evidence non-linear relationships helping to identify antimicrobial resistance at the ICU, with performance dependent on the family of antimicrobials. A change in the trend of antimicrobial resistance is also evidenced.
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Affiliation(s)
- Sergio Martínez-Agüero
- Department of Signal Theory and Communications, Telematics and Computing Systems, Rey Juan Carlos University, Madrid 28943, Spain
| | - Inmaculada Mora-Jiménez
- Department of Signal Theory and Communications, Telematics and Computing Systems, Rey Juan Carlos University, Madrid 28943, Spain
| | - Jon Lérida-García
- Department of Signal Theory and Communications, Telematics and Computing Systems, Rey Juan Carlos University, Madrid 28943, Spain
| | | | - Cristina Soguero-Ruiz
- Department of Signal Theory and Communications, Telematics and Computing Systems, Rey Juan Carlos University, Madrid 28943, Spain
- Correspondence: ; Tel.: +34-91-488-87-41
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81
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Boolchandani M, D'Souza AW, Dantas G. Sequencing-based methods and resources to study antimicrobial resistance. Nat Rev Genet 2019; 20:356-370. [PMID: 30886350 PMCID: PMC6525649 DOI: 10.1038/s41576-019-0108-4] [Citation(s) in RCA: 176] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Antimicrobial resistance extracts high morbidity, mortality and economic costs yearly by rendering bacteria immune to antibiotics. Identifying and understanding antimicrobial resistance are imperative for clinical practice to treat resistant infections and for public health efforts to limit the spread of resistance. Technologies such as next-generation sequencing are expanding our abilities to detect and study antimicrobial resistance. This Review provides a detailed overview of antimicrobial resistance identification and characterization methods, from traditional antimicrobial susceptibility testing to recent deep-learning methods. We focus on sequencing-based resistance discovery and discuss tools and databases used in antimicrobial resistance studies.
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Affiliation(s)
- Manish Boolchandani
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Alaric W D'Souza
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
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82
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Sassi M, Guérin F, Lesec L, Isnard C, Fines-Guyon M, Cattoir V, Giard JC. Genetic characterization of a VanG-type vancomycin-resistant Enterococcus faecium clinical isolate. J Antimicrob Chemother 2019; 73:852-855. [PMID: 29346643 DOI: 10.1093/jac/dkx510] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 12/08/2017] [Indexed: 01/03/2023] Open
Abstract
Objectives To characterize, phenotypically and genotypically, the first Enterococcus faecium clinical isolate harbouring a vanG operon. Methods The antibiotic resistance profile of E. faecium 16-346 was determined and its whole genome sequenced using PacBio technology. Attempts to transfer vancomycin resistance by filter mating were performed and the inducibility of expression of the vanG operon was studied by reverse-transcription quantitative PCR (RT-qPCR) in the presence or absence of subinhibitory concentrations of vancomycin. Results E. faecium 16-346 was resistant to rifampicin (MIC >4 mg/L), erythromycin (MIC >4 mg/L), tetracycline (MIC >16 mg/L) and vancomycin (MIC 8 mg/L), but susceptible to teicoplanin (MIC 0.5 mg/L). The strain harboured the vanG operon in its chromosome, integrated in a 45.5 kb putative mobile genetic element, similar to that of Enterococcus faecalis BM4518. We were unable to transfer vancomycin resistance from E. faecium 16-346 to E. faecium BM4107 and E. faecalis JH2-2. Lastly, transcription of the vanG gene was inducible by vancomycin. Conclusions This is, to the best of our knowledge, the first report of a VanG-type vancomycin-resistant strain of E. faecium. Despite the alarm pulled because of the therapeutic problems caused by VRE, our work shows that new resistant loci can still be found in E. faecium.
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Affiliation(s)
- Mohamed Sassi
- Université Rennes 1, Laboratoire de Biochimie Pharmaceutique, Inserm U1230 - UPRES EA 2311, Rennes, France
| | - François Guérin
- Université de Caen Normandie, EA4655 U2RM (équipe 'Antibio-résistance'), Caen, France.,CHU de Caen, Service de Microbiologie, Caen, France
| | - Léonie Lesec
- Université de Caen Normandie, EA4655 U2RM (équipe 'Antibio-résistance'), Caen, France
| | - Christophe Isnard
- Université de Caen Normandie, EA4655 U2RM (équipe 'Antibio-résistance'), Caen, France.,CHU de Caen, Service de Microbiologie, Caen, France
| | - Marguerite Fines-Guyon
- Université de Caen Normandie, EA4655 U2RM (équipe 'Antibio-résistance'), Caen, France.,CHU de Caen, Service de Microbiologie, Caen, France
| | - Vincent Cattoir
- CHU de Rennes - Hôpital Ponchaillou, Service de Bactériologie-Hygiène hospitalière, Rennes, France.,CNR de la Résistance aux Antibiotiques (laboratoire associé 'Entérocoques'), Rennes, France
| | - Jean-Christophe Giard
- Université de Caen Normandie, EA4655 U2RM (équipe 'Antibio-résistance'), Caen, France
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83
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Ma Y, Lan G, Li C, Cambaza EM, Liu D, Ye X, Chen S, Ding T. Stress tolerance of Staphylococcus aureus with different antibiotic resistance profiles. Microb Pathog 2019; 133:103549. [PMID: 31112770 DOI: 10.1016/j.micpath.2019.103549] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 05/17/2019] [Accepted: 05/17/2019] [Indexed: 01/19/2023]
Abstract
Staphylococcus aureus (S. aureus) is a zoonotic bacterium and is among the most important pathogens causing bacterial foodborne diseases. In recent years, disease caused by antibiotic-resistant S. aureus is a serious clinical problem that poses a great threat to public health. In this study, we examined the drug-resistance phenotypes and genotypes of 9 S. aureus strains. One strain was obtained from the China Center for Type Culture Collection (CCTCC), and the remaining eight strains were isolated from food. Two common methods (the Kirby-Bauer disk diffusion and broth microdilution methods) were used to detect bacterial drug resistance. Then, we analysed the relationship between the bacterial drug resistance phenotypes and genotypes. We found that some S. aureus strains isolated from food were drug-resistant or even multi-drug resistant and that there was not a perfect match between resistance phenotypes and genotypes. The viabilities of the drug-sensitive (DS), drug-resistant (DR), and multi-drug resistant (MDR) S. aureus strains were also compared when they were exposed to conditions of acid (HCl, pH = 1.5), heat (63 °C), and osmotic pressure (30% NaCl). The results showed that the DR and MDR bacterial strains had survival rates similar to or higher than those of the DS strains under environmental stress.
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Affiliation(s)
- Yanna Ma
- Department of Food Science and Nutrition, National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Hangzhou, Zhejiang, 310058, China
| | - Guang Lan
- 230 Gansu Province CDC, Donggang West Road, Lanzhou, Gansu, 730000, China
| | - Charlie Li
- Department of Environmental Toxicology, University of California, Davis, Ca, 95616, USA
| | - Edgar Manuel Cambaza
- Department of Biological Sciences, Faculty of Sciences, Eduardo Mondlane University, Av. Julius Nyerere, Nr. Maputo, 3453, Mozambique
| | - Donghong Liu
- Department of Food Science and Nutrition, National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Hangzhou, Zhejiang, 310058, China
| | - Xingqian Ye
- Department of Food Science and Nutrition, National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Hangzhou, Zhejiang, 310058, China
| | - Shiguo Chen
- Department of Food Science and Nutrition, National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Hangzhou, Zhejiang, 310058, China
| | - Tian Ding
- Department of Food Science and Nutrition, National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Key Laboratory for Agro-Products Postharvest Handling of Ministry of Agriculture, Zhejiang Key Laboratory for Agro-Food Processing, Hangzhou, Zhejiang, 310058, China.
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Abstract
The study of the genetics of enterococci has focused heavily on mobile genetic elements present in these organisms, the complex regulatory circuits used to control their mobility, and the antibiotic resistance genes they frequently carry. Recently, more focus has been placed on the regulation of genes involved in the virulence of the opportunistic pathogenic species Enterococcus faecalis and Enterococcus faecium. Little information is available concerning fundamental aspects of DNA replication, partition, and division; this article begins with a brief overview of what little is known about these issues, primarily by comparison with better-studied model organisms. A variety of transcriptional and posttranscriptional mechanisms of regulation of gene expression are then discussed, including a section on the genetics and regulation of vancomycin resistance in enterococci. The article then provides extensive coverage of the pheromone-responsive conjugation plasmids, including sections on regulation of the pheromone response, the conjugative apparatus, and replication and stable inheritance. The article then focuses on conjugative transposons, now referred to as integrated, conjugative elements, or ICEs, and concludes with several smaller sections covering emerging areas of interest concerning the enterococcal mobilome, including nonpheromone plasmids of particular interest, toxin-antitoxin systems, pathogenicity islands, bacteriophages, and genome defense.
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Hashimoto Y, Kurushima J, Nomura T, Tanimoto K, Tamai K, Yanagisawa H, Shirabe K, Ike Y, Tomita H. Dissemination and genetic analysis of the stealthy vanB gene clusters of Enterococcus faecium clinical isolates in Japan. BMC Microbiol 2018; 18:213. [PMID: 30545294 PMCID: PMC6293572 DOI: 10.1186/s12866-018-1342-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 11/14/2018] [Indexed: 12/18/2022] Open
Abstract
Background VanB-type vancomycin (VAN) resistance gene clusters confer VAN resistances on Enterococcus spp. over a wide range of MIC levels (MIC = 4–1000 mg/L). However, the epidemiology and the molecular characteristics of the VAN susceptible VanB-type Enterococcus still remain unclear. Results We characterized 19 isolates of VanB-type Enterococcus faecium that might colonize in the gut and were not phenotypically resistant to VAN (MIC = 3 mg/L). They were obtained from two hospitals in Japan between 2009 and 2010. These isolates had the identical vanB gene cluster and showed same multilocus sequence typing (MLST) (ST78) and the highly related profiles in pulsed-field gel electrophoresis (PFGE). The vanB gene cluster was located on a plasmid, and was transferable to E. faecium and E. faecalis. Notably, from these VanB-type VREs, VAN resistant (MIC≥16 mg/L) mutants could appear at a frequency of 10− 6–10− 7/parent cell in vitro. Most of these revertants acquired mutations in the vanSB gene, while the remainder of the revertants might have other mutations outside of the vanB gene cluster. All of the revertants we tested showed increases in the VAN-dependent expression of the vanB gene cluster, suggesting that the mutations affected the transcriptional activity and increased the VAN resistance. Targeted mutagenesis revealed that three unique nucleotide substitutions in the vanB gene cluster of these strains attenuated VAN resistance. Conclusions In summary, this study indicated that stealthy VanB-type E. faecium strains that have the potential ability to become resistance to VAN could exist in clinical settings. Electronic supplementary material The online version of this article (10.1186/s12866-018-1342-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yusuke Hashimoto
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Jun Kurushima
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Takahiro Nomura
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Koichi Tanimoto
- Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Kiyoko Tamai
- MIROKU Medical Laboratory Inc, 659-2 Innai, Saku, Nagano, 384-2201, Japan
| | - Hideji Yanagisawa
- MIROKU Medical Laboratory Inc, 659-2 Innai, Saku, Nagano, 384-2201, Japan
| | - Komei Shirabe
- Yamaguchi Prefectural Institute of Public Health and Environment, 2-5-67 Aoi, Yamaguchi, Yamaguchi, 753-0821, Japan
| | - Yasuyoshi Ike
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Haruyoshi Tomita
- Department of Bacteriology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan. .,Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan.
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86
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Lari AR, Ardebili A, Hashemi A. AdeR-AdeS mutations & overexpression of the AdeABC efflux system in ciprofloxacin-resistant Acinetobacter baumannii clinical isolates. Indian J Med Res 2018; 147:413-421. [PMID: 29998878 PMCID: PMC6057251 DOI: 10.4103/ijmr.ijmr_644_16] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background & objectives: Overexpression of efflux pumps is a cause of acquired resistance to fluoroquinolones in Acinetobacter baumannii. The present study was done to investigate the presence and overexpression of AdeABC efflux system and to analyze the sequences of AdeR-AdeS regulatory system in ciprofloxacin-resistant A. baumannii isolates. Methods: Susceptibility of 50 clinical A. baumannii isolates to ciprofloxacin, imipenem, ceftazidime, cefepime and gentamicin antimicrobials was evaluated by agar dilution method. Isolates were screened for the evidence of active efflux pump. Isolates were also examined for adeR-adeS and adeB efflux genes by polymerase chain reaction (PCR). The adeR and adeS regulatory genes were sequenced to detect amino acid substitutions. Expression of adeB was evaluated by quantitative reverse-transcriptase PCR. Results: There were high rates of resistance to ciprofloxacin (88%), ceftazidime (88%), cefepime (74%) and imipenem (72%) and less resistance rate to gentamicin (64%). Phenotypic assay showed involvement of active efflux in decreased susceptibility to ciprofloxacin among 16 isolates. The 12.27-fold increase and 4.25-fold increase were found in adeB expression in ciprofloxacin-full-resistant and ciprofloxacin-intermediate-resistant isolates, respectively. Several effective mutations, including A91V, A136V, L192R, A94V, G103D and G186V, were detected in some domains of AdeR-AdeS regulators in the overexpressed ciprofloxacin-resistant isolates. Interpretation & conclusions: The results of this study indicated that overexpression of the AdeABC efflux pump was important to reduce susceptibility to ciprofloxacin and cefepime in A. baumannii that, in turn, could be triggered by alterations in the AdeR-AdeS two-component system. However, gene expression alone does not seem adequate to explain multidrug resistance phenomenon. These results could help plan improved active efflux pump inhibitors.
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Affiliation(s)
- Abdolaziz Rastegar Lari
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Abdollah Ardebili
- Laboratory Sciences Research Center; Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ali Hashemi
- Department of Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Khoshnood S, Heidary M, Asadi A, Soleimani S, Motahar M, Savari M, Saki M, Abdi M. A review on mechanism of action, resistance, synergism, and clinical implications of mupirocin against Staphylococcus aureus. Biomed Pharmacother 2018; 109:1809-1818. [PMID: 30551435 DOI: 10.1016/j.biopha.2018.10.131] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/18/2018] [Accepted: 10/21/2018] [Indexed: 12/20/2022] Open
Abstract
Mupirocin (MUP), bactroban, or pseudomonic acid is a natural crotonic acid derivative drug extracted from Pseudomonas fluorescens which is produced by modular polyketide synthases. This antibiotic has a unique chemical structure and mechanism of action. It is a mixture of A-D pseudomonic acids and inhibits protein synthesis through binding to bacterial isoleucyl-tRNA synthetase. MUP is often prescribed to prevent skin and soft tissue infections caused by S. aureus isolates and where the MRSA isolates are epidemic, MUP may be used as a choice drug for nasal decolonization. It is also used for prevention of recurring infections and control the outbreaks. The emergence of MUP resistance has been increasing particularly among methicillin-resistant Staphylococcus aureus (MRSA) isolates in many parts of the world and such resistance is often related with MUP widespread uses. Although both low-level and high-level MUP resistance were reported among MRSA isolates, the rate of resistance is different in various geographic areas. In this review, we will report the global prevalence of MUP resistance, discuss synergism and mechanism of action of MUP, and provide new insights into the clinical use of this antibiotic.
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Affiliation(s)
- Saeed Khoshnood
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohsen Heidary
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Arezoo Asadi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Saleh Soleimani
- Department of Biology, Payame Noor University, Isfahan, Iran
| | - Moloudsadat Motahar
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Savari
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Cellular and Molecular Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Morteza Saki
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mahtab Abdi
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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88
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Santona A, Taviani E, Hoang HM, Fiamma M, Deligios M, Ngo TVQ, Van Le A, Cappuccinelli P, Rubino S, Paglietti B. Emergence of unusual vanA/vanB genotype in a highly mutated vanB-vancomycin-resistant hospital-associated E. faecium background in Vietnam. Int J Antimicrob Agents 2018; 52:586-592. [DOI: 10.1016/j.ijantimicag.2018.07.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/02/2018] [Accepted: 07/07/2018] [Indexed: 11/25/2022]
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89
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Sultan I, Rahman S, Jan AT, Siddiqui MT, Mondal AH, Haq QMR. Antibiotics, Resistome and Resistance Mechanisms: A Bacterial Perspective. Front Microbiol 2018; 9:2066. [PMID: 30298054 PMCID: PMC6160567 DOI: 10.3389/fmicb.2018.02066] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/13/2018] [Indexed: 12/28/2022] Open
Abstract
History of mankind is regarded as struggle against infectious diseases. Rather than observing the withering away of bacterial diseases, antibiotic resistance has emerged as a serious global health concern. Medium of antibiotic resistance in bacteria varies greatly and comprises of target protection, target substitution, antibiotic detoxification and block of intracellular antibiotic accumulation. Further aggravation to prevailing situation arose on observing bacteria gradually becoming resistant to different classes of antibiotics through acquisition of resistance genes from same and different genera of bacteria. Attributing bacteria with feature of better adaptability, dispersal of antibiotic resistance genes to minimize effects of antibiotics by various means including horizontal gene transfer (conjugation, transformation, and transduction), Mobile genetic elements (plasmids, transposons, insertion sequences, integrons, and integrative-conjugative elements) and bacterial toxin-antitoxin system led to speedy bloom of antibiotic resistance amongst bacteria. Proficiency of bacteria to obtain resistance genes generated an unpleasant situation; a grave, but a lot unacknowledged, feature of resistance gene transfer.
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Affiliation(s)
- Insha Sultan
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Safikur Rahman
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Arif Tasleem Jan
- School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
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90
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Vázquez-Laslop N, Mankin AS. How Macrolide Antibiotics Work. Trends Biochem Sci 2018; 43:668-684. [PMID: 30054232 PMCID: PMC6108949 DOI: 10.1016/j.tibs.2018.06.011] [Citation(s) in RCA: 177] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/17/2018] [Accepted: 06/29/2018] [Indexed: 01/24/2023]
Abstract
Macrolide antibiotics inhibit protein synthesis by targeting the bacterial ribosome. They bind at the nascent peptide exit tunnel and partially occlude it. Thus, macrolides have been viewed as 'tunnel plugs' that stop the synthesis of every protein. More recent evidence, however, demonstrates that macrolides selectively inhibit the translation of a subset of cellular proteins, and that their action crucially depends on the nascent protein sequence and on the antibiotic structure. Therefore, macrolides emerge as modulators of translation rather than as global inhibitors of protein synthesis. The context-specific action of macrolides is the basis for regulating the expression of resistance genes. Understanding the details of the mechanism of macrolide action may inform rational design of new drugs and unveil important principles of translation regulation.
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Affiliation(s)
- Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
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91
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Ling N, Li C, Zhang J, Wu Q, Zeng H, He W, Ye Y, Wang J, Ding Y, Chen M, Xue L, Ye Q, Guo W. Prevalence and Molecular and Antimicrobial Characteristics of Cronobacter spp. Isolated From Raw Vegetables in China. Front Microbiol 2018; 9:1149. [PMID: 29922254 PMCID: PMC5996200 DOI: 10.3389/fmicb.2018.01149] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 05/14/2018] [Indexed: 01/17/2023] Open
Abstract
Cronobacter spp. is a foodborne pathogen that causes life-threatening and invasive diseases, such as necrotizing enterocolitis, meningitis, and sepsis. In this study, we aimed to investigate the prevalence, molecular characteristics and antimicrobial resistance of Cronobacter spp. in raw vegetables marketed in China. Based on dietary habits in China, 403 raw vegetables that could be eaten without additional cooking were collected. Of the 403 samples tested, 122 (30.27%) were positive for Cronobacter spp., and the contamination levels exceeded 110 most probable number (MPN)/g for 16.39% (20/122) of the samples. Coriander samples had the highest contamination rate of 52.81%, and the MPN values of 19.15% of positive coriander samples exceeded 100 MPN/g. Eleven serotypes were identified among 171 isolates, with Cronobacter sakazakii serogroup O1 (41 isolates) being the dominant serotype. Molecular characterization indicated that there was quite high genetic diversity in Cronobacter spp., and multilocus sequence typing analyses yielded 106 sequence types (STs), 55 of which were newly identified. Notably, the most prevalent ST (eight isolates) was C. malonaticus ST60, which appeared in a recent clinical infectious disease study in China. Five C. sakazakii ST4, seven C. malonaticus ST7, and three C. sakazakii ST8 confirmed as pathogenic STs in other countries were also detected in this study. Furthermore, all isolates were susceptible to amikacin, amoxicillin-clavulanic, cefepime, ciprofloxacin, and imipenem, but some isolates exhibited a high ratio of resistance to cephalothin (59.65%). In this study, the high contamination rate and the detection of pathogenic and new STs in raw vegetables indicated potential hazards to customers. To the best of our knowledge, this is the first report to provide valuable information on the contamination status of Cronobacter spp. in vegetables that can be eaten raw in China.
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Affiliation(s)
- Na Ling
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
- State Key Laboratory of Applied Microbiology, South China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Chengsi Li
- State Key Laboratory of Applied Microbiology, South China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Jumei Zhang
- State Key Laboratory of Applied Microbiology, South China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology, South China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Haiyan Zeng
- State Key Laboratory of Applied Microbiology, South China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Wenjing He
- State Key Laboratory of Applied Microbiology, South China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Yingwang Ye
- State Key Laboratory of Applied Microbiology, South China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Yu Ding
- Department of Food Science & Technology, Jinan University, Guangzhou, China
| | - Moutong Chen
- State Key Laboratory of Applied Microbiology, South China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Liang Xue
- State Key Laboratory of Applied Microbiology, South China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Qinghua Ye
- State Key Laboratory of Applied Microbiology, South China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Weipeng Guo
- State Key Laboratory of Applied Microbiology, South China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
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Amman F, D'Halluin A, Antoine R, Huot L, Bibova I, Keidel K, Slupek S, Bouquet P, Coutte L, Caboche S, Locht C, Vecerek B, Hot D. Primary transcriptome analysis reveals importance of IS elements for the shaping of the transcriptional landscape of Bordetella pertussis. RNA Biol 2018; 15:967-975. [PMID: 29683387 PMCID: PMC6161684 DOI: 10.1080/15476286.2018.1462655] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 04/03/2018] [Indexed: 12/25/2022] Open
Abstract
Bordetella pertussis is the causative agent of whooping cough, a respiratory disease still considered as a major public health threat and for which recent re-emergence has been observed. Constant reshuffling of Bordetella pertussis genome organization was observed during evolution. These rearrangements are essentially mediated by Insertion Sequences (IS), a mobile genetic elements present in more than 230 copies in the genome, which are supposed to be one of the driving forces enabling the pathogen to escape from vaccine-induced immunity. Here we use high-throughput sequencing approaches (RNA-seq and differential RNA-seq), to decipher Bordetella pertussis transcriptome characteristics and to evaluate the impact of IS elements on transcriptome architecture. Transcriptional organization was determined by identification of transcription start sites and revealed also a large variety of non-coding RNAs including sRNAs, leaderless mRNAs or long 3' and 5'UTR including seven riboswitches. Unusual topological organizations, such as overlapping 5'- or 3'-extremities between oppositely orientated mRNA were also unveiled. The pivotal role of IS elements in the transcriptome architecture and their effect on the transcription of neighboring genes was examined. This effect is mediated by the introduction of IS harbored promoters or by emergence of hybrid promoters. This study revealed that in addition to their impact on genome rearrangements, most of the IS also impact on the expression of their flanking genes. Furthermore, the transcripts produced by IS are strain-specific due to the strain to strain variation in IS copy number and genomic context.
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Affiliation(s)
- Fabian Amman
- University of Vienna, Theoretical Biochemistry Group, Institute for Theoretical Chemistry, Vienna, Austria
| | - Alexandre D'Halluin
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Rudy Antoine
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Ludovic Huot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Ilona Bibova
- Institute of Microbiology of the ASCR; Laboratory of post-transcriptional control of gene expression, Prague, Czech Republic
| | - Kristina Keidel
- Institute of Microbiology of the ASCR; Laboratory of post-transcriptional control of gene expression, Prague, Czech Republic
| | - Stéphanie Slupek
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Peggy Bouquet
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Loïc Coutte
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Ségolène Caboche
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Camille Locht
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Branislav Vecerek
- Institute of Microbiology of the ASCR; Laboratory of post-transcriptional control of gene expression, Prague, Czech Republic
| | - David Hot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, Lille, France
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Streling AP, Barbosa PP, Marcondes MF, Nicoletti AG, Picão RC, Pinto EC, Marques EA, Oliveira V, Gales AC. Genetic and biochemical characterization of GES-16, a new GES-type β-lactamase with carbapenemase activity in Serratia marcescens. Diagn Microbiol Infect Dis 2018; 92:147-151. [PMID: 29861147 DOI: 10.1016/j.diagmicrobio.2018.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 04/08/2018] [Accepted: 05/04/2018] [Indexed: 10/16/2022]
Abstract
We evaluated the genetic environment of blaGES-16 found in 2 carbapenem-resistant Serratia marcescens clinical isolates recovered from patients hospitalized at a tertiary hospital located in Rio de Janeiro, Brazil. We also compared the kinetics constants for GES-16 and GES-5 against several β-lactams. Both S. marcescens isolates showed identical PFGE pattern and carried the carbapenemase-encoding gene blaGES-16 and the extended-spectrum β-lactamase encoding gene blaOXA-10. The blaGES-16 was inserted at the first position of a defective class 1 integron, composed by a fragmented integrase gene that lacked its attI1 recombination site, followed by dfr22, aac(6')-IIc, and aadA1 genes. This integron was located on a 30-kb nonconjugative plasmid. The GES-16 showed 2 amino acid substitutions (Gln38Glu and Gly170Ser) compared to GES-1. Kinetic analysis showed that GES-16 presented hydrolytic activity against all β-lactams tested, except for aztreonam. Imipenem was the carbapenem more efficiently hydrolyzed (highest kcat/Km) by GES-16. The kinetic parameters of GES-16 were similar to those of GES-5. In conclusion, we identified a new GES-type enzyme with carbapenemase activity in S. marcescens. The increasing diversity of such resistance determinants confirms the ongoing evolution of these β-lactamases towards a broader spectrum of activity.
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Affiliation(s)
- Ana Paula Streling
- Universidade Federal de São Paulo-UNIFESP, Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine. Escola Paulista de Medicina-EPM, São Paulo, Brazil.
| | - Paula P Barbosa
- Universidade Federal de São Paulo-UNIFESP, Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine. Escola Paulista de Medicina-EPM, São Paulo, Brazil
| | - Marcelo F Marcondes
- Department of Biophysics, Federal University of São Paulo-UNIFESP, São Paulo-SP, Brazil
| | - Adriana G Nicoletti
- Universidade Federal de São Paulo-UNIFESP, Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine. Escola Paulista de Medicina-EPM, São Paulo, Brazil
| | - Renata C Picão
- Universidade Federal de São Paulo-UNIFESP, Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine. Escola Paulista de Medicina-EPM, São Paulo, Brazil; Laboratório de Investigação em Microbiologia Médica-LIMM, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, Brazil
| | - Elisa C Pinto
- Hospital Universitário Pedro Ernesto, Universidade do Estado do Rio de Janeiro-UERJ, Rio de Janeiro, Brazil
| | - Elizabeth A Marques
- Hospital Universitário Pedro Ernesto, Universidade do Estado do Rio de Janeiro-UERJ, Rio de Janeiro, Brazil
| | - Vitor Oliveira
- Department of Biophysics, Federal University of São Paulo-UNIFESP, São Paulo-SP, Brazil
| | - Ana C Gales
- Universidade Federal de São Paulo-UNIFESP, Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine. Escola Paulista de Medicina-EPM, São Paulo, Brazil
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Binda E, Cappelletti P, Marinelli F, Marcone GL. Specificity of Induction of Glycopeptide Antibiotic Resistance in the Producing Actinomycetes. Antibiotics (Basel) 2018; 7:antibiotics7020036. [PMID: 29693566 PMCID: PMC6022977 DOI: 10.3390/antibiotics7020036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 12/21/2022] Open
Abstract
Glycopeptide antibiotics are drugs of last resort for treating severe infections caused by Gram-positive pathogens. It is widely believed that glycopeptide-resistance determinants (van genes) are ultimately derived from the producing actinomycetes. We hereby investigated the relationship between the antimicrobial activity of vancomycin and teicoplanins and their differential ability to induce van gene expression in Actinoplanes teichomyceticus—the producer of teicoplanin—and Nonomuraea gerenzanensis—the producer of the teicoplanin-like A40926. As a control, we used the well-characterized resistance model Streptomyces coelicolor. The enzyme activities of a cytoplasmic-soluble d,d-dipeptidase and of a membrane-associated d,d-carboxypeptidase (corresponding to VanX and VanY respectively) involved in resistant cell wall remodeling were measured in the actinomycetes grown in the presence or absence of subinhibitory concentrations of vancomycin, teicoplanin, and A40926. Results indicated that actinomycetes possess diverse self-resistance mechanisms, and that each of them responds differently to glycopeptide induction. Gene swapping among teicoplanins-producing actinomycetes indicated that cross-talking is possible and provides useful information for predicting the evolution of future resistance gene combinations emerging in pathogens.
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Affiliation(s)
- Elisa Binda
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy.
- The Protein Factory Research Center, Politecnico di Milano and University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy.
| | - Pamela Cappelletti
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy.
- The Protein Factory Research Center, Politecnico di Milano and University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy.
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy.
- The Protein Factory Research Center, Politecnico di Milano and University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy.
| | - Giorgia Letizia Marcone
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy.
- The Protein Factory Research Center, Politecnico di Milano and University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy.
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95
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Li H, Yang XL, Song HL, Zhang S, Long XZ. Effects ofdirect current on Klebsiella spp. viability and corresponding resistance gene expression in simulative bio-electrochemical reactors. CHEMOSPHERE 2018; 196:251-259. [PMID: 29306197 DOI: 10.1016/j.chemosphere.2017.12.176] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 12/02/2017] [Accepted: 12/27/2017] [Indexed: 06/07/2023]
Abstract
The fate of antibiotic-resistant bacteria (ARB) and associated antibiotic-resistant gene (ARG) expression under electrolytic stimulation in bio-electrochemical reactors (BERs) was unknown. In this study, sulfadiazine resistant bacteria (Klebsiella spp.), which were isolated from a BER, were subjected to constant direct current (DC) stimulation in a simulated BER. With an increase of the current from 7 to 28 mA, it was found that lactic dehydrogenase (LDH) showed a 1.03-, 1.21-, 1.34-, and 1.46-fold value compared with the control at 48 h, indicating that the cell membrane permeability had increased. Since the adenosine triphosphate (ATP) concentration increased with the current, the specific growth rate of Klebsiella spp. increased (R = 0.98). The viable count of Klebsiella spp. reached a maximum at 19 mA and then decreased. The percentage of ARB lethality, which was reflected by flow cytometry analysis, increased from 18% (7 mA) to 37.8% (28 mA) at 48 h. Reactive oxygen species (ROS) produced from the electrolysis of water were greater with the increasing current (R = 0.94), which may be responsible for the high lethality rate of Klebsiella spp.. Scanning electronic microscope results showed that electrolytic stimulation changed the cell surface morphology with some cell disruption. An upregulation of sulII and int1 expression was observed. A significant correlation between int1 and the current (R = 0.97) were observed. Taken together, BERs possess potential risks in accelerating ARB multiplication and promoting ARG expression.
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Affiliation(s)
- Hua Li
- School of Energy and Environment, Southeast University, Nanjing 210096, China.
| | - Xiao-Li Yang
- School of Civil Engineering, Southeast University, Nanjing 210096, China.
| | - Hai-Liang Song
- School of Environment, Nanjing Normal University, Jiangsu Engineering Lab of Water and Soil Eco-remediation, Wenyuan Road 1, Nanjing 210023, China.
| | - Shuai Zhang
- School of Energy and Environment, Southeast University, Nanjing 210096, China.
| | - Xi-Zi Long
- School of Energy and Environment, Southeast University, Nanjing 210096, China.
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96
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Phillips-Jones MK, Harding SE. Antimicrobial resistance (AMR) nanomachines-mechanisms for fluoroquinolone and glycopeptide recognition, efflux and/or deactivation. Biophys Rev 2018; 10:347-362. [PMID: 29525835 PMCID: PMC5899746 DOI: 10.1007/s12551-018-0404-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 02/05/2018] [Indexed: 12/11/2022] Open
Abstract
In this review, we discuss mechanisms of resistance identified in bacterial agents Staphylococcus aureus and the enterococci towards two priority classes of antibiotics-the fluoroquinolones and the glycopeptides. Members of both classes interact with a number of components in the cells of these bacteria, so the cellular targets are also considered. Fluoroquinolone resistance mechanisms include efflux pumps (MepA, NorA, NorB, NorC, MdeA, LmrS or SdrM in S. aureus and EfmA or EfrAB in the enterococci) for removal of fluoroquinolone from the intracellular environment of bacterial cells and/or protection of the gyrase and topoisomerase IV target sites in Enterococcus faecalis by Qnr-like proteins. Expression of efflux systems is regulated by GntR-like (S. aureus NorG), MarR-like (MgrA, MepR) regulators or a two-component signal transduction system (TCS) (S. aureus ArlSR). Resistance to the glycopeptide antibiotic teicoplanin occurs via efflux regulated by the TcaR regulator in S. aureus. Resistance to vancomycin occurs through modification of the D-Ala-D-Ala target in the cell wall peptidoglycan and removal of high affinity precursors, or by target protection via cell wall thickening. Of the six Van resistance types (VanA-E, VanG), the VanA resistance type is considered in this review, including its regulation by the VanSR TCS. We describe the recent application of biophysical approaches such as the hydrodynamic technique of analytical ultracentrifugation and circular dichroism spectroscopy to identify the possible molecular effector of the VanS receptor that activates expression of the Van resistance genes; both approaches demonstrated that vancomycin interacts with VanS, suggesting that vancomycin itself (or vancomycin with an accessory factor) may be an effector of vancomycin resistance. With 16 and 19 proteins or protein complexes involved in fluoroquinolone and glycopeptide resistances, respectively, and the complexities of bacterial sensing mechanisms that trigger and regulate a wide variety of possible resistance mechanisms, we propose that these antimicrobial resistance mechanisms might be considered complex 'nanomachines' that drive survival of bacterial cells in antibiotic environments.
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Affiliation(s)
- Mary K Phillips-Jones
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, Loughborough, Leicestershire, UK.
| | - Stephen E Harding
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, Loughborough, Leicestershire, UK
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97
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Fei P, Jiang Y, Gong S, Li R, Jiang Y, Yuan X, Wang Z, Kang H, Ali MA. Occurrence, Genotyping, and Antibiotic Susceptibility of Cronobacter spp. in Drinking Water and Food Samples from Northeast China. J Food Prot 2018; 81:456-460. [PMID: 29474142 DOI: 10.4315/0362-028x.jfp-17-326] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 10/20/2017] [Indexed: 11/11/2022]
Abstract
Cronobacter species (formerly Enterobacter sakazakii) are emerging opportunistic bacterial pathogens that can infect both infants and adults. This study was conducted to isolate and genotype diverse Cronobacter species from drinking water, chilled fresh pork, powdered infant formula, instant noodles, cookies, fruits, vegetables, and dishes in Northeast China and to evaluate the antibiotic resistance and susceptibility of the isolates. Thirty-four Cronobacter strains were isolated and identified: 21 C. sakazakii isolates (61.8%), 10 C. malonaticus isolates (29.4%), 2 C. dublinensis isolates (5.9%), and 1 C. turicensis isolate (2.9%). These isolates were further divided into 15 sequence types (STs) by multilocus sequence typing. C. sakazakii ST4 (10 isolates, 29.4%), ST1 (3 isolates, 8.8%), and ST8 (3 isolates, 8.8%) and C. malonaticus ST7 (four isolates, 11.8%) were dominant. Antibiotic susceptibility testing indicated that all 34 Cronobacter isolates were susceptible to ampicillin-sulbactam, cefotaxime, ciprofloxacin, gentamicin, meropenem, tetracycline, piperacillin-tazobactam, and trimethoprim-sulfamethoxazole, 88.2% were susceptible to chloramphenicol, and 67.6% were resistant to cephalothin. The results of this study enhance knowledge about genotyping and antibiotic resistance of these Cronobacter species and could be used to prevent potential hazards caused by these strains in drinking water and various food products.
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Affiliation(s)
- Peng Fei
- College of Food and Biological Engineering, Henan University of Science and Technology, Luoyang 471023, People's Republic of China
| | - Yichao Jiang
- Changbai Mountains Food and Drug Inspection Testing Center, Baishan 134511, People's Republic of China
| | - Shaoying Gong
- Key Laboratory of Dairy Science, Ministry of Education, Department of Food Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Ran Li
- Mars Food (China) Co. Ltd., Beijing 101407, People's Republic of China
| | - Yan Jiang
- MuLing Food Inspection Testing Center, Department of Market Supervision and Management, Mudanjiang 157500, People's Republic of China
| | - Xiujuan Yuan
- Anda Department of Animal Husbandry and Veterinary, Anda 151400, People's Republic of China
| | - Ziyuan Wang
- College of Food and Biological Engineering, Henan University of Science and Technology, Luoyang 471023, People's Republic of China
| | - Huaibin Kang
- College of Food and Biological Engineering, Henan University of Science and Technology, Luoyang 471023, People's Republic of China
| | - Md Aslam Ali
- Department of Agro-Processing, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur-1706, Bangladesh
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98
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Zhu Y, Gasilova N, Jović M, Qiao L, Liu B, Lovey LT, Pick H, Girault HH. Detection of antimicrobial resistance-associated proteins by titanium dioxide-facilitated intact bacteria mass spectrometry. Chem Sci 2018; 9:2212-2221. [PMID: 29719694 PMCID: PMC5897883 DOI: 10.1039/c7sc04089j] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/18/2018] [Indexed: 01/05/2023] Open
Abstract
Titanium dioxide-modified target plates were developed to enhance intact bacteria analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The plates were designed to photocatalytically destroy the bacterial envelope structure and improve the ionization efficiency of intracellular components, thereby promoting the measurable mass range and the achievable detection sensitivity. Accordingly, a method for rapid detection of antimicrobial resistance-associated proteins, conferring bacterial resistance against antimicrobial drugs, was established by mass spectrometric fingerprinting of intact bacteria without the need for any sample pre-treatment. With this method, the variations in resistance proteins' expression levels within bacteria were quickly measured from the relative peak intensities. This approach of resistance protein detection directly from intact bacteria by mass spectrometry is useful for fast discrimination of antimicrobial-resistant bacteria from their non-resistant counterparts whilst performing species identification. Also, it could be used as a rapid and convenient way for initial determination of the underlying resistance mechanisms.
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Affiliation(s)
- Yingdi Zhu
- Laboratoire d'Electrochimie Physique et Analytique , École Polytechnique Fédérale de Lausanne , Rue de l'industrie 17 , CH-1951 Sion , Switzerland .
| | - Natalia Gasilova
- Laboratoire d'Electrochimie Physique et Analytique , École Polytechnique Fédérale de Lausanne , Rue de l'industrie 17 , CH-1951 Sion , Switzerland . .,ISIC-GE-VS , École Polytechnique Fédérale de Lausanne , Rue de l'industrie 17 , CH-1951 Sion , Switzerland
| | - Milica Jović
- Laboratoire d'Electrochimie Physique et Analytique , École Polytechnique Fédérale de Lausanne , Rue de l'industrie 17 , CH-1951 Sion , Switzerland .
| | - Liang Qiao
- Department of Chemistry , Fudan University , Handan Road 220 , 200433 Shanghai , China
| | - Baohong Liu
- Department of Chemistry , Fudan University , Handan Road 220 , 200433 Shanghai , China
| | | | - Horst Pick
- Laboratoire de Chimie Biophysique des Macromolécules , École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne , Switzerland
| | - Hubert H Girault
- Laboratoire d'Electrochimie Physique et Analytique , École Polytechnique Fédérale de Lausanne , Rue de l'industrie 17 , CH-1951 Sion , Switzerland .
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99
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Hughes D, Andersson DI. Environmental and genetic modulation of the phenotypic expression of antibiotic resistance. FEMS Microbiol Rev 2018; 41:374-391. [PMID: 28333270 PMCID: PMC5435765 DOI: 10.1093/femsre/fux004] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 02/01/2017] [Indexed: 12/22/2022] Open
Abstract
Antibiotic resistance can be acquired by mutation or horizontal transfer of a resistance gene, and generally an acquired mechanism results in a predictable increase in phenotypic resistance. However, recent findings suggest that the environment and/or the genetic context can modify the phenotypic expression of specific resistance genes/mutations. An important implication from these findings is that a given genotype does not always result in the expected phenotype. This dissociation of genotype and phenotype has important consequences for clinical bacteriology and for our ability to predict resistance phenotypes from genetics and DNA sequences. A related problem concerns the degree to which the genes/mutations currently identified in vitro can fully explain the in vivo resistance phenotype, or whether there is a significant additional amount of presently unknown mutations/genes (genetic ‘dark matter’) that could contribute to resistance in clinical isolates. Finally, a very important question is whether/how we can identify the genetic features that contribute to making a successful pathogen, and predict why some resistant clones are very successful and spread globally? In this review, we describe different environmental and genetic factors that influence phenotypic expression of antibiotic resistance genes/mutations and how this information is needed to understand why particular resistant clones spread worldwide and to what extent we can use DNA sequences to predict evolutionary success.
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Affiliation(s)
- Diarmaid Hughes
- Corresponding author: Department of Medical Biochemistry and Microbiology, Biomedical Center (Box 582), Uppsala University, S-751 23 Uppsala, Sweden. Tel: +46 18 4714507; E-mail:
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100
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Schultz D, Palmer AC, Kishony R. Regulatory Dynamics Determine Cell Fate following Abrupt Antibiotic Exposure. Cell Syst 2017; 5:509-517.e3. [PMID: 29102611 DOI: 10.1016/j.cels.2017.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 06/26/2017] [Accepted: 09/29/2017] [Indexed: 02/06/2023]
Abstract
Bacterial resistance mechanisms must cope with transient fast-changing conditions. These systems are often repressed in the absence of the drug, and it is unclear how their regulation can provide a quick response when challenged. Here, we focus on the tet operon, which provides resistance to tetracycline through efflux pump TetA. We show that, somewhat counterintuitively, prompt expression of the TetA repressor TetR is key for cellular survival upon abrupt drug exposure. Tracking individual cells upon exposure, we find that differences in the rate of TetR elevation result in three distinct cell fates: recovery (high rate), death due to excess TetA (intermediate rate), and death from the drug (low rate). A surge of TetR expression optimizes the response by allowing sensitive detection of both the initial rise and the later decline of intracellular drug, avoiding an undesirable overshoot in TetA expression. These results show how regulatory circuits of resistance genes have evolved for optimized dynamics.
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Affiliation(s)
- Daniel Schultz
- Department of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Adam C Palmer
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Roy Kishony
- Department of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Computer Science, Technion - Israel Institute of Technology, Haifa 3200003, Israel.
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